Query         gi|254780331|ref|YP_003064744.1| 50S ribosomal protein L9 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 179
No_of_seqs    119 out of 1863
Neff          6.4 
Searched_HMMs 33803
Date          Wed Jun  1 12:14:43 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780331.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1nkw_F 50S ribosomal protein  100.0 9.8E-45       0  302.2  14.3  145   14-160     1-145 (146)
  2 >3i1n_H 50S ribosomal protein  100.0   1E-42       0  289.5 -11.8  147   14-160     1-149 (149)
  3 >1div_A Ribosomal protein L9;   99.9 3.6E-25 1.1E-29  178.9  11.6  109   53-161     1-110 (110)
  4 >2j01_I 50S ribosomal protein   99.9 1.6E-23 4.7E-28  168.5   4.6  104   54-158     1-105 (106)
  5 >3bbo_J Ribosomal protein L9;   99.7 3.7E-18 1.1E-22  134.6  -0.2   72   88-160     4-76  (76)
  6 >2j01_I 50S ribosomal protein   99.6 4.6E-17 1.4E-21  127.8   1.5   40   14-53      1-40  (40)
  7 >1div_A Ribosomal protein L9;   99.6 8.5E-17 2.5E-21  126.1   1.9   39   14-52      1-39  (39)
  8 >2hba_A BL17, 50S ribosomal pr  99.6 9.3E-17 2.7E-21  125.9   1.4   39   14-52      1-39  (39)
  9 >3f6k_A Sortilin; protein sort  66.8       4 0.00012   21.0   2.4   30   14-44     15-44  (51)
 10 >2zy9_A Mg2+ transporter MGTE;  51.0     4.6 0.00014   20.6   0.5   31   95-125    29-60  (68)
 11 >3fhm_A Uncharacterized protei  50.8     7.3 0.00022   19.4   1.5   27   96-122    28-54  (62)
 12 >2yzi_A Hypothetical protein P  48.2      14 0.00041   17.6   2.6   44   80-123    15-58  (60)
 13 >1yav_A Hypothetical protein B  44.6      13 0.00038   17.8   1.9   28   96-123    33-60  (71)
 14 >3fbi_A Mediator of RNA polyme  42.9      20 0.00061   16.5   2.8   59   48-106    20-83  (84)
 15 >3kpb_A Uncharacterized protei  42.3      15 0.00046   17.3   2.1   34   89-122    21-54  (59)
 16 >1y5h_A Hypothetical protein R  36.1      16 0.00048   17.2   1.4   39   83-121    14-52  (56)
 17 >2p9m_A Hypothetical protein M  30.8      28 0.00084   15.7   1.9   22   96-117    40-61  (63)
 18 >2p9m_A Hypothetical protein M  30.7      31  0.0009   15.4   2.0   28   96-123    45-72  (75)
 19 >3ddj_A CBS domain-containing   30.4      37  0.0011   14.9   3.0   36   82-117    18-53  (64)
 20 >2o16_A Acetoin utilization pr  30.4      32 0.00093   15.4   2.1   40   81-120    27-66  (80)
 21 >3fv6_A YQZB protein; CBS doma  30.2      37  0.0011   14.9   3.0   39   82-120    18-56  (75)
 22 >3fio_A A cystathionine beta-s  29.3      18 0.00054   16.8   0.7   28   95-122    27-54  (70)
 23 >2ef7_A Hypothetical protein S  29.3      31 0.00091   15.4   1.9   27   96-122    27-53  (56)
 24 >1zvd_A SMAD ubiquitination re  27.6      27 0.00078   15.8   1.3   41   23-63     23-64  (72)
 25 >3gby_A Uncharacterized protei  27.3      34 0.00099   15.2   1.8   36   82-117    91-126 (128)
 26 >2rc3_A CBS domain; in SITU pr  25.8      31 0.00093   15.4   1.4   27   96-122    28-54  (57)
 27 >1kzy_C Tumor suppressor P53-b  25.8      16 0.00046   17.3  -0.2   11   40-50      1-11  (49)
 28 >2ahq_A Sigma-54, RNA polymera  24.8      47  0.0014   14.3   2.4   23  105-127    37-59  (76)
 29 >3ddj_A CBS domain-containing   24.8      19 0.00056   16.8   0.1   23   96-118    27-49  (51)
 30 >1pbj_A Hypothetical protein;   24.3      29 0.00084   15.6   1.0   24   95-118    33-56  (58)
 31 >3kxr_A Magnesium transporter,  23.5      45  0.0013   14.4   1.8   23   96-118    42-64  (94)
 32 >2nyc_A Nuclear protein SNF4;   23.4      50  0.0015   14.1   3.1   38   82-119    19-56  (74)
 33 >2uv4_A 5'-AMP-activated prote  22.9      43  0.0013   14.5   1.6   37   80-116    23-59  (61)
 34 >2d4z_A Chloride channel prote  22.8      37  0.0011   14.9   1.3   24   95-118    29-52  (55)
 35 >1zfj_A Inosine monophosphate   22.4      52  0.0015   14.0   2.1   23   96-118    31-53  (58)
 36 >1nd7_A WW domain-containing p  22.2      33 0.00098   15.2   1.0   23   41-63     43-65  (74)
 37 >2yzq_A Putative uncharacteriz  21.0      56  0.0016   13.8   2.2   43   76-118    77-119 (126)
 38 >2d4z_A Chloride channel prote  20.7      56  0.0017   13.8   1.9   22   97-118    53-74  (81)
 39 >2oux_A Magnesium transporter;  20.6      57  0.0017   13.7   1.9   38   81-118    21-58  (84)
 40 >3h1d_A E3 ubiquitin-protein l  20.4      51  0.0015   14.1   1.6   22   42-63     44-65  (73)
 41 >3euj_A Chromosome partition p  20.3      57  0.0017   13.7   2.4   23   39-64      9-31  (202)
 42 >2j9l_A Chloride channel prote  20.2      52  0.0015   14.0   1.6   24   95-118    29-52  (71)

No 1  
>>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY structure, peptidyl-transferase, peptide bond formation; 3.10A {Deinococcus radiodurans} (F:)
Probab=100.00  E-value=9.8e-45  Score=302.16  Aligned_cols=145  Identities=37%  Similarity=0.579  Sum_probs=141.1

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             33465201117587783888277632110143787301220146888778999998422346789999887654321000
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLI   93 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~   93 (179)
                      |+|||++|+ +||++||+|+|++|||||||||+|+|+|||++|+++++..++..+++..+..+.|+.++.+|++..+++.
T Consensus         1 M~viL~~~~-~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~~~~~   79 (146)
T 1nkw_F            1 MQVILLEPS-RLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRSIEKRQAQEKAVAEDLASRLNGVAVELS   79 (146)
T ss_pred             CEEEEEECC-CCCCCCCEEEECCHHHHHHCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             979997447-7898899899876103354065681566699999999999999999999989999999998530244332


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEC
Q ss_conf             2556543100341078999999860887686663026564320549999996397299999999725
Q gi|254780331|r   94 RAAGDTGYLYGSVSSRDIADLLIEEGFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARS  160 (179)
Q Consensus        94 ~k~~e~gkLfGsVt~~dI~~~L~~~gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~  160 (179)
                      ++++ +|+||||||+.||+++|.+.|++|++++|.||+||+++|+|+|+|+||++|+++++|+|+++
T Consensus        80 ~~~~-~g~lfGsVt~~~I~~~l~~~gi~I~k~~I~l~~~Ik~~G~~~V~i~l~~~V~~~i~i~V~a~  145 (146)
T 1nkw_F           80 VRAG-EGKIYGAVTHQDVANSLDQLGFDVDRRKIDMPKTVKEVGEYDIAYRAHPEVTIPMKLVVHAA  145 (146)
T ss_pred             HCCC-CCCCCCCCCHHHHHHHHHHCCCCCCHHHEECCCHHHCCEEEEEEEEECCCEEEEEEEEEEEC
T ss_conf             0145-78655767889999999985994477566078702223888999994298799999999978


No 2  
>>3i1n_H 50S ribosomal protein L9; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_F 1p86_F 1vs8_H 2aw4_H 2awb_H 2gya_F 2gyc_F 1vs6_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H* 2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H 2qox_H ... (H:)
Probab=100.00  E-value=1e-42  Score=289.47  Aligned_cols=147  Identities=37%  Similarity=0.635  Sum_probs=139.6

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH
Q ss_conf             334652011175877838882776321101437873012201468887789999984223467899998876543-2100
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLAKK-NFSL   92 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~-~l~i   92 (179)
                      |+|||++||+|||++||+|+|+||||||||||+|+|+|||++|+++++..+...++......++|+.++.+|+.+ .+.|
T Consensus         1 mkVIL~~dV~~lGk~GdiV~V~~GyaRN~Lip~~~A~~at~~nl~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~~l~i   80 (149)
T 3i1n_H            1 MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTI   80 (149)
T ss_dssp             CCCEESSCCTTTCCSSCBCCCCHHHHTTTSSSSSSEECCCSSHHHHTTSTTTTTTTTTTTTTTTSTTSCSSCTTCCCCSS
T ss_pred             CEEEEECCCCCCCCCCCEEEECCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEE
T ss_conf             97999044103798899999873355564112676233067789999988999988777777789988765400047987


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHCC-CCCCCCEEEEEEEEEECCCEEEEEEEEEEEC
Q ss_conf             0255654310034107899999986088768666302-6564320549999996397299999999725
Q gi|254780331|r   93 IRAAGDTGYLYGSVSSRDIADLLIEEGFDVNRGQINL-KSPIKSVGIHNIMISLHADVSTTITLNVARS  160 (179)
Q Consensus        93 ~~k~~e~gkLfGsVt~~dI~~~L~~~gi~I~k~~I~l-~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~  160 (179)
                      .++++++|+||||||+.+|+++|+++|..+.++.+.+ ++||+++|+|.|+|+||++|+++++|+|+++
T Consensus        81 ~~k~~~~g~l~gsVt~~~I~~~l~~~~~~~~~~~i~~~~~~Ik~~G~~~v~v~l~~~v~~~i~v~V~~e  149 (149)
T 3i1n_H           81 ASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE  149 (149)
T ss_dssp             CSCCCGGGSCCCCCCTTCSTTTTCSSSCCCCCCCCCCCSCCCCSSSCCCCCCCSSSSCCCCCCCCCCCC
T ss_pred             EECCCCCCCCCCCEEHHHHHHHHHHCCCCCCHHHEECCCCCCCCCEEEEEEEEECCCEEEEEEEEEEEC
T ss_conf             630278984357240899999998749821688800788541164878999996599099999999979


No 3  
>>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Bacillus stearothermophilus} (A:40-149)
Probab=99.93  E-value=3.6e-25  Score=178.86  Aligned_cols=109  Identities=26%  Similarity=0.472  Sum_probs=105.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH-CCCCCCHHHHCCCC
Q ss_conf             20146888778999998422346789999887654321000255654310034107899999986-08876866630265
Q gi|254780331|r   53 NKENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIE-EGFDVNRGQINLKS  131 (179)
Q Consensus        53 T~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~-~gi~I~k~~I~l~~  131 (179)
                      |++|+++++.+++.++++..+.+++|+.+++.|++..|+|.+++|++|+||||||+.||+++|.+ .|++||+++|.+++
T Consensus         1 T~~n~~~~~~~~~~~~~~~~~~~~~a~~la~~L~~~~l~i~~k~g~~gklfGSVt~~~Ia~~l~~~~g~~idk~~I~l~~   80 (110)
T 1div_A            1 TPANLKALEAQKQKEQRQAAEELANAKKLKEQLEKLTVTIPAKAGEGGRLFGSITSKQIAESLQAQHGLKLDKRKIELAD   80 (110)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEECBCGGGEEEEEECHHHHHHHHHHHHCCCCCGGGBCCCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEEECHHHHHHHHHHHCCCCCCHHHHHCCC
T ss_conf             58899999998899988754234577889887433348999950689870576169999999986318766844540334


Q ss_pred             CCCCEEEEEEEEEECCCEEEEEEEEEEECH
Q ss_conf             643205499999963972999999997251
Q gi|254780331|r  132 PIKSVGIHNIMISLHADVSTTITLNVARST  161 (179)
Q Consensus       132 pIk~~G~y~V~I~L~~~V~a~i~V~V~~~~  161 (179)
                      |||++|+|.|+|+||++|+|+|+|+|++++
T Consensus        81 ~Ik~~G~~~v~i~Lh~~V~a~i~v~V~~ee  110 (110)
T 1div_A           81 AIRALGYTNVPVKLHPEVTATLKVHVTEQK  110 (110)
T ss_dssp             CEEESEEEEEEEEEETTEEEEEEEEEEECC
T ss_pred             CCCCCEEEEEEEEECCCEEEEEEEEEEECC
T ss_conf             622257789999953986999999999578


No 4  
>>2j01_I 50S ribosomal protein L9; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (I:41-148)
Probab=99.88  E-value=1.6e-23  Score=168.49  Aligned_cols=104  Identities=25%  Similarity=0.398  Sum_probs=100.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCHHHHCCCCC
Q ss_conf             01468887789999984223467899998876543210002556543100341078999999860-88768666302656
Q gi|254780331|r   54 KENKILFESQRSVLEAANLEKKAKYEGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEE-GFDVNRGQINLKSP  132 (179)
Q Consensus        54 ~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~-gi~I~k~~I~l~~p  132 (179)
                      .+|++.++.++..++++.++.+++|+.++..|++..++|.+++| +|+||||||++||+++|.++ |++||+++|.||+|
T Consensus         1 k~nl~~~~~~k~~~~~~~~~~~~~a~~~a~~L~~~~i~i~~k~g-eGklFGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~   79 (106)
T 2j01_I            1 ESNLKALEARIRAQAKRLAERKAEAERLKEILENLTLTIPVRAG-ETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKP   79 (106)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSTTTTTHHHHHHHTTCBCCCCCCBC-SSSBSSCCCHHHHHHHHHTTTCCCCCTTTTCCSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCCCHHHHHHHHHHHCCCEECHHHHHCCCC
T ss_conf             77899999988877543245667888888887655454442145-54330455799999999873296765646404564


Q ss_pred             CCCEEEEEEEEEECCCEEEEEEEEEE
Q ss_conf             43205499999963972999999997
Q gi|254780331|r  133 IKSVGIHNIMISLHADVSTTITLNVA  158 (179)
Q Consensus       133 Ik~~G~y~V~I~L~~~V~a~i~V~V~  158 (179)
                      ||++|.|+|+|+||++|+|+++|+|+
T Consensus        80 IK~~G~~~v~ikLh~~V~a~i~v~Vv  105 (106)
T 2j01_I           80 IKELGEYVLTYKPHPEVPIQLKVSVV  105 (106)
T ss_dssp             CCSCEEEECCCSSSSCCCCEEEECCC
T ss_pred             HHHEEEEEEEEEECCCEEEEEEEEEE
T ss_conf             12029999999964987999999999


No 5  
>>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} (J:122-197)
Probab=99.67  E-value=3.7e-18  Score=134.64  Aligned_cols=72  Identities=25%  Similarity=0.497  Sum_probs=68.1

Q ss_pred             HHHHHCCCCCCCCCCCCCCCHHHHHHHHHHC-CCCCCHHHHCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEC
Q ss_conf             3210002556543100341078999999860-887686663026564320549999996397299999999725
Q gi|254780331|r   88 KNFSLIRAAGDTGYLYGSVSSRDIADLLIEE-GFDVNRGQINLKSPIKSVGIHNIMISLHADVSTTITLNVARS  160 (179)
Q Consensus        88 ~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~-gi~I~k~~I~l~~pIk~~G~y~V~I~L~~~V~a~i~V~V~~~  160 (179)
                      .+++|.+++|++|+||||||++||+++|.++ |++|||++|.|| |||++|.|.|.++||++|+++++|+|.++
T Consensus         4 ~~i~i~~k~g~~gklFGSVt~~dIa~~l~~~~g~~idkk~I~l~-~IK~lG~y~v~i~Lh~~V~a~i~v~V~~e   76 (76)
T 3bbo_J            4 GAFKVKRKGGKGKLIFGSVTAQDLVDIIKSQLQKDIDKRLVSLP-EIRETGEYIAELKLHPDVTARVKINVFAN   76 (76)
T ss_dssp             CCCBCCCCBCTTSSBSSCCSSHHHHGGGTSSSSCCCCSTTCCSC-CCSSSSCEEECCCCBTTBCCCEEEBCCCC
T ss_pred             CEEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHCCCC-CCCCCEEEEEEEEECCCEEEEEEEEEEEC
T ss_conf             12667740454432213558899999986314870366405451-33235768999994499699999999969


No 6  
>>2j01_I 50S ribosomal protein L9; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (I:1-40)
Probab=99.63  E-value=4.6e-17  Score=127.80  Aligned_cols=40  Identities=60%  Similarity=0.942  Sum_probs=39.5

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECCC
Q ss_conf             3346520111758778388827763211014378730122
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRAN   53 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~aT   53 (179)
                      |+|||++||++||++||+|+|++|||||||||+|+|++||
T Consensus         1 m~VIL~~dv~~lG~~Gdiv~V~~GyaRN~Lip~~~A~~aT   40 (40)
T 2j01_I            1 MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLAT   40 (40)
T ss_dssp             CEEEECSCCSSSCSTTCEEECCHHHHHHTTTTTTSEEECC
T ss_pred             CEEEECCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHHCC
T ss_conf             9699905410279789899987157888731212320241


No 7  
>>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Bacillus stearothermophilus} (A:1-39)
Probab=99.62  E-value=8.5e-17  Score=126.11  Aligned_cols=39  Identities=41%  Similarity=0.721  Sum_probs=38.4

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECC
Q ss_conf             334652011175877838882776321101437873012
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRA   52 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~a   52 (179)
                      |||||++||++||++||+|+|++|||||||||+++|++|
T Consensus         1 mkVIL~~dv~~lGk~Gdvv~V~~GyaRN~LiP~~lA~~A   39 (39)
T 1div_A            1 MKVIFLKDVKGKGKKGEIKNVADGYANNFLFKQGLAIEA   39 (39)
T ss_dssp             CEEEECSBSSSBGGGTEEEECCTTHHHHTTTTTTSEEEC
T ss_pred             CEEEEECCCCCCCCCCCEEEECCHHHHHHHHHHHHHHHH
T ss_conf             979990441036988999998736688874066565351


No 8  
>>2hba_A BL17, 50S ribosomal protein L9; NTL9, K12M, RNA binding protein; 1.25A {Geobacillus stearothermophilus} (A:1-39)
Probab=99.61  E-value=9.3e-17  Score=125.86  Aligned_cols=39  Identities=41%  Similarity=0.762  Sum_probs=38.4

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEECCCCCEECC
Q ss_conf             334652011175877838882776321101437873012
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLLPKKKALRA   52 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~LiP~~~A~~a   52 (179)
                      |||||++||++||+.||+|+|++|||||||||+++|++|
T Consensus         1 mkVIL~~dv~~lGk~Gdvv~V~~GyaRN~LiP~~~A~~A   39 (39)
T 2hba_A            1 MKVIFLKDVKGMGKKGEIKNVADGYANNFLFKQGLAIEA   39 (39)
T ss_dssp             CEEEESSCBTTTBCTTCEEECCHHHHHHTTTTTTSEEEC
T ss_pred             CEEEECCCCCCCCCCCCEEEECCCCHHHHHCCCCCCHHC
T ss_conf             979982531057878999998661033451567953137


No 9  
>>3f6k_A Sortilin; protein sorting receptor, 10-bladed beta-propeller, Cys- rich domains, ssortilin, sortilin VPS10P-D, protein-peptide complex; HET: NAG BMA PGE; 2.00A {Homo sapiens} (A:89-139)
Probab=66.82  E-value=4  Score=21.02  Aligned_cols=30  Identities=23%  Similarity=0.448  Sum_probs=26.0

Q ss_pred             EEEEEEEECCCCCCCCCEEEECCCCEEEEEC
Q ss_conf             3346520111758778388827763211014
Q gi|254780331|r   14 MEVILLQNVTNLGPMGEVVKVKNGYARNYLL   44 (179)
Q Consensus        14 mkVIL~~dv~~lG~~Gdiv~Vk~GyaRN~Li   44 (179)
                      =||||+.||++ |..|-.+-.+.-|+.+|-.
T Consensus        15 gkViLt~dvs~-gs~g~riFrS~Dfg~tF~~   44 (51)
T 3f6k_A           15 GKVVLTAEVSG-GSRGGRIFRSSDFAKNFVQ   44 (51)
T ss_dssp             CCEEEEECCCT-TCSSCEEEEESSTTSSCEE
T ss_pred             CEEEEEECCCC-CCCCCCEEEEEECCCCCEE
T ss_conf             88999953346-7788618998009989648


No 10 
>>2zy9_A Mg2+ transporter MGTE; membrane protien, metal transport; 2.94A {Thermus thermophilus HB8} PDB: 2yvx_A (A:227-294)
Probab=51.00  E-value=4.6  Score=20.62  Aligned_cols=31  Identities=29%  Similarity=0.424  Sum_probs=22.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHC-CCCCCHH
Q ss_conf             556543100341078999999860-8876866
Q gi|254780331|r   95 AAGDTGYLYGSVSSRDIADLLIEE-GFDVNRG  125 (179)
Q Consensus        95 k~~e~gkLfGsVt~~dI~~~L~~~-gi~I~k~  125 (179)
                      =++++|+|.|-||..||...+.+. ...+...
T Consensus        29 Vvd~~gklvGiiT~~Di~~~~~~~~~~~~~~~   60 (68)
T 2zy9_A           29 VVDEEGRLVGIVTVDDVLDVLEAEATEDIHKL   60 (68)
T ss_dssp             EECTTSBEEEEEEHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCEEEEEEHHHHHHHHHHHHHHHHHHC
T ss_conf             01236947877559999998987515677640


No 11 
>>3fhm_A Uncharacterized protein ATU1752; CBS domain, prokaryotic, bound nucleotide, AMP, NADH, structural genomics, PSI-2; HET: AMP NAI; 2.70A {Agrobacterium tumefaciens str} (A:37-98)
Probab=50.77  E-value=7.3  Score=19.36  Aligned_cols=27  Identities=19%  Similarity=0.382  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             565431003410789999998608876
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEEGFDV  122 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~gi~I  122 (179)
                      ++++|+|.|-||..||...+..++...
T Consensus        28 vd~~~~lvGiiT~~Di~~~~~~~~~~~   54 (62)
T 3fhm_A           28 TDADGVVLGIFTERDLVKAVAGQGAAS   54 (62)
T ss_dssp             ECTTSCEEEEEEHHHHHHHHHHHGGGG
T ss_pred             EECCCEEEEEEEHHHHHHHHHHHCCCC
T ss_conf             958981999877789877565411575


No 12 
>>2yzi_A Hypothetical protein PH0107; sheet/helix/sheet/sheet/helix, structural genomics, unknown function, NPPSFA; 2.25A {Pyrococcus horikoshii} (A:14-73)
Probab=48.24  E-value=14  Score=17.59  Aligned_cols=44  Identities=18%  Similarity=0.244  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf             99887654321000255654310034107899999986088768
Q gi|254780331|r   80 GISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEEGFDVN  123 (179)
Q Consensus        80 ~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~gi~I~  123 (179)
                      +.+..+....+.---=++++|+|.|=||..||..++...+..++
T Consensus        15 ea~~~m~~~~i~~lpVvD~~~~lvGiiT~~Di~~~~~~~~~~~~   58 (60)
T 2yzi_A           15 EASRLXXEFDVGSLVVINDDGNVVGFFTKSDIIRRVIVPGLPYD   58 (60)
T ss_dssp             HHHHHHHHHTCSEEEEECTTSCEEEEEEHHHHHHHTTTTCCCTT
T ss_pred             HHHHHHHHCCCCEEEEECCCCCHHEEEHHHHHHHHHHHCCCCCC
T ss_conf             99999998699868530454202200008899988873166422


No 13 
>>1yav_A Hypothetical protein BSU14130; cystathionine beta synthase (CBS) domain, structural genomics, protein structure initiative, PSI; 2.10A {Bacillus subtilis} (A:89-159)
Probab=44.60  E-value=13  Score=17.81  Aligned_cols=28  Identities=18%  Similarity=0.133  Sum_probs=23.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf             5654310034107899999986088768
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEEGFDVN  123 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~gi~I~  123 (179)
                      ++++|+|.|-||..||...+...+-..+
T Consensus        33 Vd~~~~lvGiiT~~Di~~~~~~~~~~~~   60 (71)
T 1yav_A           33 ENDEQVFEGIFTRRVVLKELNKHIRSLN   60 (71)
T ss_dssp             ECTTCBEEEEEEHHHHHHHHHHHC----
T ss_pred             EEECCEEEEEEEHHHHHHHHHHHHHHHH
T ss_conf             8039999999889999999999999877


No 14 
>>3fbi_A Mediator of RNA polymerase II transcription subunit 7; proline-rich stretches, right-handed four-helix bundle, protein-protein complex; 2.80A {Saccharomyces cerevisiae} PDB: 3fbn_A (A:)
Probab=42.93  E-value=20  Score=16.53  Aligned_cols=59  Identities=7%  Similarity=-0.004  Sum_probs=29.8

Q ss_pred             CEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHCCCCCCC--CCCCCCC
Q ss_conf             730122014688877899999842234678999988765---4321000255654--3100341
Q gi|254780331|r   48 KALRANKENKILFESQRSVLEAANLEKKAKYEGISKDLA---KKNFSLIRAAGDT--GYLYGSV  106 (179)
Q Consensus        48 ~A~~aT~~n~~~~~~~~~~~~~~~~~~~~~a~~~~~~L~---~~~l~i~~k~~e~--gkLfGsV  106 (179)
                      +=..-|++|++.++..++...............-...++   .+-+-+.=..-.+  -++||+|
T Consensus        20 fwK~FT~ENl~kl~e~k~~~~~~~~~~~~~~~~~~r~~~~p~ELrfLvPP~~P~~g~Yr~FG~~   83 (84)
T 3fbi_A           20 YVKFFTQSNLEKLPKYKEKKAASAKQTAPNNSNGGSEEEITCALDYLIPPPXPKNQQYRAFGSI   83 (84)
T ss_dssp             GGGGCCHHHHHHHHHHHHHHHC---------------CCCCSGGGGGSCCCCCSSGGGSCSCCC
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCEEECCCC
T ss_conf             8885599999999999998775047767566565445689753313779767999963211335


No 15 
>>3kpb_A Uncharacterized protein MJ0100; CBS domain, S-adenosylmethionine, conformational change; HET: SAM; 1.60A {Methanocaldococcus jannaschii} PDB: 3kpd_A* 3kpc_A* (A:11-69)
Probab=42.29  E-value=15  Score=17.31  Aligned_cols=34  Identities=26%  Similarity=0.391  Sum_probs=25.2

Q ss_pred             HHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             2100025565431003410789999998608876
Q gi|254780331|r   89 NFSLIRAAGDTGYLYGSVSSRDIADLLIEEGFDV  122 (179)
Q Consensus        89 ~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~gi~I  122 (179)
                      .+.---=++++|+|-|=||..||...+.+....+
T Consensus        21 ~~~~~pVvd~~~~lvGiiT~~Di~~~~~~~~~~v   54 (59)
T 3kpb_A           21 NINHLPIVDEHGKLVGIITSWDIAKALAQNKKTI   54 (59)
T ss_dssp             TCSCEEEECTTSBEEEEECHHHHHHHHHTTCCBG
T ss_pred             CCCEEEEECCCCCEEEEEEHHHHHHHHCCCCCCH
T ss_conf             9819999908994999988999986441389799


No 16 
>>1y5h_A Hypothetical protein RV2626C; CBS domain, unknown function; 1.50A {Mycobacterium tuberculosis} (A:19-74)
Probab=36.11  E-value=16  Score=17.18  Aligned_cols=39  Identities=23%  Similarity=0.386  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCC
Q ss_conf             876543210002556543100341078999999860887
Q gi|254780331|r   83 KDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEEGFD  121 (179)
Q Consensus        83 ~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~gi~  121 (179)
                      +.+....+.=-.=++++|+|-|-||..||...+-.++..
T Consensus        14 ~lm~~~~i~~~pVVd~~g~lvGivT~rDi~~~~v~~~~~   52 (56)
T 1y5h_A           14 QYXREHDIGALPICGDDDRLHGXLTDRDIVIKGLAAGLD   52 (56)
T ss_dssp             HHHHHHTCSEEEEECGGGBEEEEEEHHHHHHTTGGGTCC
T ss_pred             HHHHHCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999984999752131323355441255665554203667


No 17 
>>2p9m_A Hypothetical protein MJ0922; structural genomics, southeast collaboratory for structural genomics, secsg; 2.59A {Methanocaldococcus jannaschii DSM2661} (A:76-138)
Probab=30.83  E-value=28  Score=15.65  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=19.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             5654310034107899999986
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      ++++|+|-|-||..|+..++.+
T Consensus        40 Vd~~g~lvGiiT~~Di~~~~~~   61 (63)
T 2p9m_A           40 VDKNNKLVGIISDGDIIRTISK   61 (63)
T ss_dssp             ECTTSBEEEEEEHHHHHHHHHH
T ss_pred             ECCCCEEEEEEEHHHHHHHHHH
T ss_conf             9579969999889999999998


No 18 
>>2p9m_A Hypothetical protein MJ0922; structural genomics, southeast collaboratory for structural genomics, secsg; 2.59A {Methanocaldococcus jannaschii DSM2661} (A:1-75)
Probab=30.69  E-value=31  Score=15.44  Aligned_cols=28  Identities=25%  Similarity=0.424  Sum_probs=23.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCCC
Q ss_conf             5654310034107899999986088768
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEEGFDVN  123 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~gi~I~  123 (179)
                      ++++|+|-|=||..||...+.+.+...+
T Consensus        45 vd~~~~lvGiit~~Di~~~~~~~~~~~~   72 (75)
T 2p9m_A           45 IDDENKVIGIVTTTDIGYNLIRDKYTLE   72 (75)
T ss_dssp             ECTTCBEEEEEEHHHHHHHHTTTCCCSS
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             3554146667777889998861443322


No 19 
>>3ddj_A CBS domain-containing protein; NP_344512.1, structural genomics, joint center for structural genomics, JCSG; HET: AMP; 1.80A {Sulfolobus solfataricus} (A:233-296)
Probab=30.40  E-value=37  Score=14.90  Aligned_cols=36  Identities=14%  Similarity=0.192  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             887654321000255654310034107899999986
Q gi|254780331|r   82 SKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        82 ~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      ++.+....+.---=+.++|+|-|-||..||...+..
T Consensus        18 ~~~m~~~~i~~lpVvDe~~~lvGIvT~~Di~~~~~~   53 (64)
T 3ddj_A           18 AAEXIVKRIGSLLILNKDNTIRGIITERDLLIALHH   53 (64)
T ss_dssp             HHHHHHHTCSEEEEECTTSCEEEEEEHHHHHHHHHH
T ss_pred             HHHHHHHCCCEEEEECCCCEEEEEEEHHHHHHHHHH
T ss_conf             999998299889999079989999889999999988


No 20 
>>2o16_A Acetoin utilization protein ACUB, putative; structural genomics, unknown function, PSI-2, protein structure initiative; 1.90A {Vibrio cholerae} (A:1-80)
Probab=30.38  E-value=32  Score=15.36  Aligned_cols=40  Identities=15%  Similarity=0.078  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             9887654321000255654310034107899999986088
Q gi|254780331|r   81 ISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEEGF  120 (179)
Q Consensus        81 ~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~gi  120 (179)
                      ..+.+....+.---=++++|++-|=||..||...+.....
T Consensus        27 a~~~m~~~~~~~lpVvd~~~~lvGiit~~Di~~~~~~~~~   66 (80)
T 2o16_A           27 AKHLMEALDIRHVPIVDANKKLLGIVSQRDLLAAQESSLQ   66 (80)
T ss_dssp             HHHHHHHHTCSEEEEECTTCBEEEEEEHHHHHHHHHHHCC
T ss_pred             HHHHHHHCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             9999998699755301454222333420015565222114


No 21 
>>3fv6_A YQZB protein; CBS domain dimer, metabolism regulator, central glycolytic gene regulator, transcription; 1.95A {Bacillus subtilis} PDB: 3fwr_A* 3fws_A* (A:22-96)
Probab=30.21  E-value=37  Score=14.88  Aligned_cols=39  Identities=13%  Similarity=0.114  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             887654321000255654310034107899999986088
Q gi|254780331|r   82 SKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEEGF  120 (179)
Q Consensus        82 ~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~gi  120 (179)
                      .+.+....+.---=++++|++.|-||..||...+...+.
T Consensus        18 ~~~m~~~~i~~~~Vvd~~~~~vGivT~~Di~~~~~~~~~   56 (75)
T 3fv6_A           18 ICTMFLEDVGTLFVVDRDAVLVGVLSRKDLLRASIGQQE   56 (75)
T ss_dssp             HHHHHHHTCSEEEEECTTSCEEEEEEHHHHHHHHTSCSC
T ss_pred             HHHHHHCCCCEEEEEECCCEEEEEEEHHHHHHHHHCCCC
T ss_conf             999997599489999699819999889999877761665


No 22 
>>3fio_A A cystathionine beta-synthase domain protein fused to A Zn-ribbon-like domain; PF1953,APC40009,cystathionine beta-synthase domain protein; 1.81A {Pyrococcus furiosus} PDB: 3ghd_A (A:)
Probab=29.34  E-value=18  Score=16.83  Aligned_cols=28  Identities=25%  Similarity=0.445  Sum_probs=22.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             5565431003410789999998608876
Q gi|254780331|r   95 AAGDTGYLYGSVSSRDIADLLIEEGFDV  122 (179)
Q Consensus        95 k~~e~gkLfGsVt~~dI~~~L~~~gi~I  122 (179)
                      -+.++|+|.|-||..||..++...+...
T Consensus        27 pV~~~~~lvGIiT~~Di~~~~~~~~~~~   54 (70)
T 3fio_A           27 VVXEGDEILGVVTERDILDKVVAKGKNP   54 (70)
T ss_dssp             EEEETTEEEEEEEHHHHHHHTTTTTCCG
T ss_pred             EEEECCEEEEEEEHHHHHHHHHHCCCCC
T ss_conf             9998999999985999999999669980


No 23 
>>2ef7_A Hypothetical protein ST2348; CBS-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.10A {Sulfolobus tokodaii str} (A:78-133)
Probab=29.32  E-value=31  Score=15.42  Aligned_cols=27  Identities=30%  Similarity=0.316  Sum_probs=22.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             565431003410789999998608876
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEEGFDV  122 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~gi~I  122 (179)
                      ++++|+|-|=||..||..++....-..
T Consensus        27 VD~~~~lvGiiT~~Di~k~~~~~~~~~   53 (56)
T 2ef7_A           27 VDDKGNLKGIISIRDITRAIDDXFETX   53 (56)
T ss_dssp             ECTTSCEEEEEEHHHHHHHHHHHC---
T ss_pred             EECCCEEEEEEEHHHHHHHHHHHHHHH
T ss_conf             938996999999999999998888876


No 24 
>>1zvd_A SMAD ubiquitination regulatory factor 2; ubiquitin ligasecatalytic mechanism,X-RAY tgfbeta; 2.10A {Homo sapiens} (A:153-224)
Probab=27.57  E-value=27  Score=15.83  Aligned_cols=41  Identities=24%  Similarity=0.127  Sum_probs=25.3

Q ss_pred             CCCCCCCCEEEECCCCEEE-EECCCCCEECCCCHHHHHHHHH
Q ss_conf             1758778388827763211-0143787301220146888778
Q gi|254780331|r   23 TNLGPMGEVVKVKNGYARN-YLLPKKKALRANKENKILFESQ   63 (179)
Q Consensus        23 ~~lG~~Gdiv~Vk~GyaRN-~LiP~~~A~~aT~~n~~~~~~~   63 (179)
                      .-+|---.+-....|..+. =|+|.|-.++.|.+|..++=..
T Consensus        23 e~l~L~F~~~~~~~g~~~~veLip~G~~i~VT~~N~~eYV~~   64 (72)
T 1zvd_A           23 GVLDHTFCVEHNAYGEIIQHELKPNGKSIPVNEENKKEYVRL   64 (72)
T ss_dssp             TTSCCCSEEEEEETTEEEEEESSTTCCCCCCTTTTHHHHHHH
T ss_pred             HHHCCEEEEEEECCCCCEEEECCCCCCCCCCHHHHHHHHHHH
T ss_conf             221362799860588613464489987663156449999999


No 25 
>>3gby_A Uncharacterized protein CT1051; CBS domain, structural genomics, PSI-2, protein structure initiative; HET: EPE; 1.66A {Chlorobium tepidum tls} (A:)
Probab=27.25  E-value=34  Score=15.18  Aligned_cols=36  Identities=28%  Similarity=0.345  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             887654321000255654310034107899999986
Q gi|254780331|r   82 SKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIE  117 (179)
Q Consensus        82 ~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~  117 (179)
                      ...+....+..--=++++|++.|-||..||.+.+.+
T Consensus        91 ~~~m~~~~~~~l~Vvd~~g~~~Givt~~di~~~l~~  126 (128)
T 3gby_A           91 LISVAAAKCSVVPLADEDGRYEGVVSRKRILGFLAE  126 (128)
T ss_dssp             HHHHHHCSSSEEEEECTTCBEEEEEEHHHHHHHHHT
T ss_pred             HHHHHHCEEEEEEEECCCCEEEEEEEHHHHHHHHHH
T ss_conf             787664122058999479979999999999999982


No 26 
>>2rc3_A CBS domain; in SITU proteolysis, BR, structural genomics, PSI-2, protein structure initiative; HET: NAD; 1.60A {Nitrosomonas europaea atcc 19718} (A:18-74)
Probab=25.84  E-value=31  Score=15.38  Aligned_cols=27  Identities=19%  Similarity=0.071  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             565431003410789999998608876
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEEGFDV  122 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~gi~I  122 (179)
                      +-++|+|.|=||..||...+...|...
T Consensus        28 Vvd~~~lvGIiT~~Dl~~~~~~~~~~~   54 (57)
T 2rc3_A           28 VMKDEKLVGILTERDFSRKSYLLDKPV   54 (57)
T ss_dssp             EEETTEEEEEEEHHHHHHHGGGSSSCG
T ss_pred             EEECCEEEEEEEEEEEEEECCCCCCCC
T ss_conf             950999998875310110011112344


No 27 
>>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker complexed with non-BRCT protein, three-helix bundle, parallel beta sheet; 2.50A {Homo sapiens} (C:131-151,C:232-259)
Probab=25.77  E-value=16  Score=17.29  Aligned_cols=11  Identities=64%  Similarity=1.011  Sum_probs=8.8

Q ss_pred             EEEECCCCCEE
Q ss_conf             11014378730
Q gi|254780331|r   40 RNYLLPKKKAL   50 (179)
Q Consensus        40 RN~LiP~~~A~   50 (179)
                      ||||+|-|...
T Consensus         1 rnyllpagysl   11 (49)
T 1kzy_C            1 RNYLLPAGYSL   11 (49)
T ss_dssp             GGSBCCCEEET
T ss_pred             HHCCCCCCCCC
T ss_conf             88007665341


No 28 
>>2ahq_A Sigma-54, RNA polymerase sigma factor RPON; sigma-54,sigma factors, solution structure, transcription; NMR {Aquifex aeolicus} PDB: 2o8k_A 2o9l_A (A:)
Probab=24.84  E-value=47  Score=14.28  Aligned_cols=23  Identities=39%  Similarity=0.700  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHH
Q ss_conf             41078999999860887686663
Q gi|254780331|r  105 SVSSRDIADLLIEEGFDVNRGQI  127 (179)
Q Consensus       105 sVt~~dI~~~L~~~gi~I~k~~I  127 (179)
                      +.+-..|++.|.++|+.|.++-|
T Consensus        37 PlSD~~I~~~L~~~Gi~IsRRTV   59 (76)
T 2ahq_A           37 PYSDQEIANILKEKGFKVARRTV   59 (76)
T ss_dssp             CCCHHHHHHHHTTTSSCCCHHHH
T ss_pred             CCCHHHHHHHHHHCCCCEEHHHH
T ss_conf             96499999999976997420319


No 29 
>>3ddj_A CBS domain-containing protein; NP_344512.1, structural genomics, joint center for structural genomics, JCSG; HET: AMP; 1.80A {Sulfolobus solfataricus} (A:104-154)
Probab=24.81  E-value=19  Score=16.75  Aligned_cols=23  Identities=17%  Similarity=0.095  Sum_probs=19.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             56543100341078999999860
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      ++++|+|-|-||..||...+.+.
T Consensus        27 vD~~~~lvGiiT~~Di~~~~~~~   49 (51)
T 3ddj_A           27 VDINDKPVGIVTEREFLLLYKDL   49 (51)
T ss_dssp             ECTTSCEEEEEEHHHHGGGGGGS
T ss_pred             EEECCCCCCEEECCCCCCCCCCC
T ss_conf             95234565112303444322256


No 30 
>>1pbj_A Hypothetical protein; structural genomics, CBS domain, PSI, protein structure initiative; 1.40A {Methanothermobacterthermautotrophicus str} (A:68-125)
Probab=24.32  E-value=29  Score=15.63  Aligned_cols=24  Identities=17%  Similarity=0.241  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             556543100341078999999860
Q gi|254780331|r   95 AAGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        95 k~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      .+-++|+|-|=||..||..++.+.
T Consensus        33 pVvd~~~lvGiiT~~Di~~~l~~~   56 (58)
T 1pbj_A           33 LVEEDDEIIGVISATDILRAKXAK   56 (58)
T ss_dssp             EEEETTEEEEEEEHHHHHHHHC--
T ss_pred             EEEECCEEEEEEEHHHHHHHHHHC
T ss_conf             999899999999999998734653


No 31 
>>3kxr_A Magnesium transporter, putative; cystathionine beta-synthase, Mg2+ transporter, structural genomics, PSI-2; 2.41A {Shewanella oneidensis mr-1} (A:53-61,A:121-205)
Probab=23.51  E-value=45  Score=14.40  Aligned_cols=23  Identities=35%  Similarity=0.469  Sum_probs=19.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             56543100341078999999860
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      ++++|+|-|-||..||.+.+.+.
T Consensus        42 vD~~g~lvGiiT~~Di~~~~~~~   64 (94)
T 3kxr_A           42 IDDAGELIGRVTLRAATALVREH   64 (94)
T ss_dssp             ECTTSBEEEEEEHHHHHHHHHHH
T ss_pred             ECCCCEEEEEEEHHHHHHHHHHH
T ss_conf             87699899998899999999999


No 32 
>>2nyc_A Nuclear protein SNF4; bateman2 domain, AMP kinase, protein binding; 1.90A {Saccharomyces cerevisiae} (A:16-89)
Probab=23.43  E-value=50  Score=14.11  Aligned_cols=38  Identities=18%  Similarity=0.238  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCC
Q ss_conf             88765432100025565431003410789999998608
Q gi|254780331|r   82 SKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEEG  119 (179)
Q Consensus        82 ~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~g  119 (179)
                      ...+....+.---=++++|+|-|-||..||...+...+
T Consensus        19 ~~~m~~~~~~~~pVvd~~g~lvGiit~~Di~~~~~~~~   56 (74)
T 2nyc_A           19 IQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGGI   56 (74)
T ss_dssp             HHHHHHHTCSEEEEECTTCBEEEEEEHHHHHHHHHTC-
T ss_pred             HHHHHHCCCCEEEEECCCCCCCCEEEHHHHHHHHHHCC
T ss_conf             99999879865854357995821552155788886045


No 33 
>>2uv4_A 5'-AMP-activated protein kinase subunit gamma-1; transferase, CBS domain, lipid synthesis, fatty acid biosynthesis; HET: AMP; 1.33A {Homo sapiens} PDB: 2uv5_A* 2uv6_A* 2uv7_A* (A:92-152)
Probab=22.87  E-value=43  Score=14.53  Aligned_cols=37  Identities=22%  Similarity=0.276  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             9988765432100025565431003410789999998
Q gi|254780331|r   80 GISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLI  116 (179)
Q Consensus        80 ~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~  116 (179)
                      +..+.+....+.---=++++|+|-|=||..||..++.
T Consensus        23 ~~~~~m~~~~~~~lpVvd~~g~lvGiit~~Di~~~~~   59 (61)
T 2uv4_A           23 TIINRLVEAEVHRLVVVDENDVVKGIVSLSDILQALV   59 (61)
T ss_dssp             HHHHHHHHHTCSEEEEECTTSBEEEEEEHHHHHHHHC
T ss_pred             HHHHHHHHCCCEEEEEECCCCEEEEEEEHHHHHHHHH
T ss_conf             9999898759349999948997999988999998886


No 34 
>>2d4z_A Chloride channel protein; CLC chloride channel cytoplasmic domain, CBS domains, ION channel regulatory subunit, transport protein; 3.10A {Torpedo marmorata} (A:196-250)
Probab=22.79  E-value=37  Score=14.94  Aligned_cols=24  Identities=21%  Similarity=0.224  Sum_probs=19.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             556543100341078999999860
Q gi|254780331|r   95 AAGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        95 k~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      -+-++|+|-|=||..|+..++.+.
T Consensus        29 pVv~~g~lvGiit~~Di~~~~~~~   52 (55)
T 2d4z_A           29 YVTSMGKLVGVVALAEIQAAIEGS   52 (55)
T ss_dssp             EEEETTEEEEEEEHHHHHHHHHC-
T ss_pred             EEEECCEEEEEEEHHHHHHHHHHH
T ss_conf             999899999998899999998765


No 35 
>>1zfj_A Inosine monophosphate dehydrogenase; IMPDH, CBS domains, oxidoreductase; HET: IMP; 1.90A {Streptococcus pyogenes} (A:160-217)
Probab=22.36  E-value=52  Score=13.98  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             56543100341078999999860
Q gi|254780331|r   96 AGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        96 ~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      ++++|+|-|=||..||...+...
T Consensus        31 vd~~~~lvGiiT~~Di~~~~~~~   53 (58)
T 1zfj_A           31 VDNSGRLSGLITIKDIEKVIEFP   53 (58)
T ss_dssp             ECTTSBEEEEEEHHHHHHHHHCT
T ss_pred             ECCCCCEEEEEEECCHHHHHHCC
T ss_conf             36789688899951314422075


No 36 
>>1nd7_A WW domain-containing protein 1; HECT, ubiquitin, ligase, WWP1; 2.10A {Homo sapiens} (A:152-225)
Probab=22.23  E-value=33  Score=15.21  Aligned_cols=23  Identities=17%  Similarity=0.049  Sum_probs=19.0

Q ss_pred             EEECCCCCEECCCCHHHHHHHHH
Q ss_conf             10143787301220146888778
Q gi|254780331|r   41 NYLLPKKKALRANKENKILFESQ   63 (179)
Q Consensus        41 N~LiP~~~A~~aT~~n~~~~~~~   63 (179)
                      ==|+|.|-.+..|.+|..++-..
T Consensus        43 ~eLip~G~~i~Vt~~N~~eYV~~   65 (74)
T 1nd7_A           43 HDLKLGGSNILVTEENKDEYIGL   65 (74)
T ss_dssp             EESSTTGGGCBCCTTTHHHHHHH
T ss_pred             EECCCCCCCCEEHHHHHHHHHHH
T ss_conf             64679998643068649999999


No 37 
>>2yzq_A Putative uncharacterized protein PH1780; sheet/helix/sheet/sheet/helix, structural genomics, unknown function, NPPSFA; HET: SAM; 1.63A {Pyrococcus horikoshii} (A:1-126)
Probab=20.97  E-value=56  Score=13.80  Aligned_cols=43  Identities=12%  Similarity=0.171  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             7899998876543210002556543100341078999999860
Q gi|254780331|r   76 AKYEGISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        76 ~~a~~~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      .........+....+..--=++++|++-|-||..||.+.+...
T Consensus        77 ~~l~~~~~~~~~~~~~~l~Vvd~~g~~~GiIt~~dil~~~~~~  119 (126)
T 2yzq_A           77 DTLKKAAKLMLEYDYRRVVVVDSKGKPVGILTVGDIIRRYFAK  119 (126)
T ss_dssp             SBHHHHHHHHHHHTCSEEEEECTTSCEEEEEEHHHHHHHTTTT
T ss_pred             CEEEHHCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCC
T ss_conf             1000010333222345431001134543158740323422222


No 38 
>>2d4z_A Chloride channel protein; CLC chloride channel cytoplasmic domain, CBS domains, ION channel regulatory subunit, transport protein; 3.10A {Torpedo marmorata} (A:1-81)
Probab=20.72  E-value=56  Score=13.77  Aligned_cols=22  Identities=32%  Similarity=0.499  Sum_probs=18.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             6543100341078999999860
Q gi|254780331|r   97 GDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        97 ~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      .++|+|-|-||..||..++...
T Consensus        53 ~e~~~lvGiit~~di~~~~~~~   74 (81)
T 2d4z_A           53 PDTNTLLGSIDRTEVEGLLQRR   74 (81)
T ss_dssp             TTTCBEEEEEEHHHHHHHHHHH
T ss_pred             CCCCEEEEEEEECCCCCHHHHH
T ss_conf             8873578998520121101221


No 39 
>>2oux_A Magnesium transporter; 10001B, structural genomics, PSI-2, protein structure initiative, nysgxrc; 2.16A {Enterococcus faecalis V583} (A:203-286)
Probab=20.60  E-value=57  Score=13.75  Aligned_cols=38  Identities=21%  Similarity=0.373  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             98876543210002556543100341078999999860
Q gi|254780331|r   81 ISKDLAKKNFSLIRAAGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        81 ~~~~L~~~~l~i~~k~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      ..+.+....+.---=++++|+|-|=||..||...+.+.
T Consensus        21 a~~~m~~~~~~~lpVvd~~~~lvGiit~~Di~~~~~~~   58 (84)
T 2oux_A           21 VAQTIRDYDFLAVPVTDYDDHLLGIVTVDDIIDVIDDE   58 (84)
T ss_dssp             HHHHHHHHTCSEEEEECTTCBEEEEEEHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCEEEEECCCCEEEEEEEHHHHHHHHHHH
T ss_conf             99999974986663886799699998899999999999


No 40 
>>3h1d_A E3 ubiquitin-protein ligase HUWE1; E3ligase, HECT, LOBE, alternative splicing, chromosomal rearrangement, cytoplasm, differentiation; 1.89A {Homo sapiens} PDB: 3g1n_A (A:176-248)
Probab=20.41  E-value=51  Score=14.06  Aligned_cols=22  Identities=23%  Similarity=0.232  Sum_probs=17.7

Q ss_pred             EECCCCCEECCCCHHHHHHHHH
Q ss_conf             0143787301220146888778
Q gi|254780331|r   42 YLLPKKKALRANKENKILFESQ   63 (179)
Q Consensus        42 ~LiP~~~A~~aT~~n~~~~~~~   63 (179)
                      =|+|.|--++.|.+|..++-..
T Consensus        44 eL~p~G~~i~VT~~N~~eYv~l   65 (73)
T 3h1d_A           44 DLKPNGANILVTEENKKEYVHL   65 (73)
T ss_dssp             GGSSCSSEEECCTTTHHHHHHH
T ss_pred             ECCCCCCCCCCCHHHHHHHHHH
T ss_conf             4588998773537889999999


No 41 
>>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, non-SMC subunit, ABC-type ATPase, WHD, ATP; HET: ATG; 3.10A {Haemophilus ducreyi} PDB: 3euk_A* (A:209-410)
Probab=20.34  E-value=57  Score=13.72  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=14.4

Q ss_pred             EEEEECCCCCEECCCCHHHHHHHHHH
Q ss_conf             21101437873012201468887789
Q gi|254780331|r   39 ARNYLLPKKKALRANKENKILFESQR   64 (179)
Q Consensus        39 aRN~LiP~~~A~~aT~~n~~~~~~~~   64 (179)
                      -|.||+|.+-.+.   +.+.++|.+.
T Consensus         9 ~~~~~~~~~~~vr---dAiedMEarL   31 (202)
T 3euj_A            9 LRDYLLPENSGVR---QAFQDMEAAL   31 (202)
T ss_dssp             GGGSSCCCCTTTT---HHHHC-----
T ss_pred             HHHHHHHHHHHHH---HHHHHHHHHH
T ss_conf             9999787566689---9999999999


No 42 
>>2j9l_A Chloride channel protein 5; domain, membrane, transport, CBS domain, CLC, disease mutation, ION channel, ION transport, transmembrane; HET: ATP; 2.30A {Homo sapiens} (A:115-185)
Probab=20.15  E-value=52  Score=13.98  Aligned_cols=24  Identities=17%  Similarity=0.371  Sum_probs=20.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             556543100341078999999860
Q gi|254780331|r   95 AAGDTGYLYGSVSSRDIADLLIEE  118 (179)
Q Consensus        95 k~~e~gkLfGsVt~~dI~~~L~~~  118 (179)
                      .+-++|+|-|=||..||..++.+.
T Consensus        29 pVvd~g~lvGiIT~~Di~~~~~~~   52 (71)
T 2j9l_A           29 LVTHNGRLLGIITKKDVLKHIAQM   52 (71)
T ss_dssp             EEEETTEEEEEEEHHHHHHHHHHH
T ss_pred             EEEECCEEEEEEEHHHHHHHHHHH
T ss_conf             799899899999899999999987


Done!