Query         gi|254780608|ref|YP_003065021.1| ribosomal large subunit pseudouridine synthase C [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 346
No_of_seqs    165 out of 5456
Neff          7.1 
Searched_HMMs 33803
Date          Wed Jun  1 15:31:39 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780608.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1v9f_A Ribosomal large subuni 100.0       0       0  453.2   9.8  300    7-328     4-317 (325)
  2 >1v9k_A Ribosomal large subuni 100.0       0       0  368.3   9.5  219   99-323     2-225 (228)
  3 >2i82_A Ribosomal large subuni 100.0       0       0  341.4   9.9  208   95-312     8-216 (217)
  4 >2gml_A Ribosomal large subuni 100.0       0       0  329.6   3.5  205   97-328     5-227 (237)
  5 >3dh3_A Ribosomal large subuni 100.0       0       0  317.7   4.7  197  104-327     2-216 (227)
  6 >2oml_A Ribosomal large subuni 100.0   2E-43       0  293.5   5.9  184   97-294     2-185 (189)
  7 >1ksk_A Ribosomal small subuni 100.0 1.2E-40 4.2E-45  275.8   5.1  170  103-300     2-171 (176)
  8 >1vio_A Ribosomal small subuni 100.0 1.6E-39 4.8E-44  268.9   6.3  178  103-303     2-185 (186)
  9 >1dm9_A Hypothetical 15.5 KD p  99.9 1.4E-23 4.1E-28  168.4   0.4  131   11-165     1-131 (133)
 10 >2olw_A Ribosomal large subuni  99.9 1.3E-22 3.8E-27  162.3   4.2  100   34-173     2-101 (119)
 11 >2olw_A Ribosomal large subuni  99.8 6.4E-21 1.9E-25  151.6   1.7   96  177-273     1-96  (98)
 12 >2k6p_A Uncharacterized protei  99.8 3.8E-20 1.1E-24  146.7   1.5   91   19-123     1-91  (92)
 13 >3dh3_A Ribosomal large subuni  99.0 2.9E-10 8.6E-15   84.4   5.2   54   15-69      3-56  (63)
 14 >1p9k_A ORF, hypothetical prot  98.9 4.7E-10 1.4E-14   83.1   2.1   69    1-69      3-72  (79)
 15 >1ksk_A Ribosomal small subuni  98.6 8.2E-08 2.4E-12   68.9   5.6   51   17-68      2-53  (58)
 16 >1vio_A Ribosomal small subuni  98.5 1.3E-07 3.9E-12   67.6   5.4   50   18-68      2-52  (57)
 17 >2vqe_D 30S ribosomal protein   98.1   1E-05   3E-10   55.7   6.8   50   20-70      1-52  (94)
 18 >3hp7_A Hemolysin, putative; s  98.1 2.2E-06 6.6E-11   59.9   3.2   55   14-68      2-59  (65)
 19 >3bbn_D Ribosomal protein S4;   97.9 1.1E-05 3.2E-10   55.6   3.9   53   19-71      8-61  (120)
 20 >3i1m_D 30S ribosomal protein   97.9 7.3E-06 2.2E-10   56.6   3.1   53   20-72      1-54  (94)
 21 >1h3f_A Tyrosyl-tRNA synthetas  97.6 0.00026 7.6E-09   46.9   6.9   62    7-68      5-70  (83)
 22 >1s1h_D 40S ribosomal protein   97.5 0.00011 3.3E-09   49.2   4.6   51   19-69      9-60  (99)
 23 >2cqj_A BRMS2, U3 small nucleo  97.3 0.00021 6.1E-09   47.5   3.5   52   18-69      7-61  (71)
 24 >2apo_A Probable tRNA pseudour  96.5   0.002   6E-08   41.2   2.9   71  105-188    15-85  (216)
 25 >2aus_C Pseudouridine synthase  96.4  0.0025 7.4E-08   40.7   3.0   83  105-200    15-97  (215)
 26 >2jan_A Tyrosyl-tRNA synthetas  95.8   0.011 3.2E-07   36.6   4.1   50   15-64      8-58  (88)
 27 >1sgv_A TRNA pseudouridine syn  92.5   0.057 1.7E-06   32.1   1.7   53  105-166     5-57  (87)
 28 >1k8w_A TRNA pseudouridine syn  92.1   0.068   2E-06   31.6   1.7   55  103-166    22-76  (108)
 29 >1r3e_A TRNA pseudouridine syn  92.0   0.071 2.1E-06   31.5   1.8   59  106-175     3-61  (92)
 30 >1c05_A Ribosomal protein S4 d  91.4    0.16 4.8E-06   29.2   3.0   25   45-69      1-26  (83)
 31 >1jil_A Tyrrs, tyrosyl-tRNA sy  91.1   0.046 1.4E-06   32.7   0.0   53   13-65    101-154 (174)
 32 >3kbg_A 30S ribosomal protein   90.4    0.42 1.2E-05   26.6   4.4   53   16-68      5-59  (81)
 33 >2ts1_A Tyrosyl-tRNA synthetas  89.1   0.086 2.5E-06   31.0   0.0   50   16-65    104-154 (174)
 34 >1fm0_D Molybdopterin converti  84.0     1.6 4.7E-05   23.0   4.2   53   17-71     24-78  (81)
 35 >2q5w_D Molybdopterin converti  83.7     1.4 4.3E-05   23.2   3.9   44   21-71     31-74  (77)
 36 >1vjk_A Molybdopterin converti  71.6     2.9 8.7E-05   21.3   2.6   51   21-71     42-95  (98)
 37 >2eh0_A KLP, kinesin-like prot  65.8     4.5 0.00013   20.1   2.5   22   46-67     82-103 (130)
 38 >2g1e_A Hypothetical protein T  65.3     8.2 0.00024   18.5   3.8   53   18-71     24-87  (90)
 39 >2g1l_A Kinesin-like protein K  64.9     6.2 0.00018   19.2   3.1   22   46-67     73-94  (104)
 40 >1rws_A Hypothetical protein P  64.7     2.7   8E-05   21.5   1.2   46   16-70     28-73  (77)
 41 >1wln_A Afadin; beta sandwich,  64.4     4.7 0.00014   20.0   2.4   10  101-110    64-73  (120)
 42 >1wgk_A Riken cDNA 2900073H19   63.1     5.3 0.00016   19.7   2.5   61   11-71     35-105 (114)
 43 >2ff4_A Probable regulatory pr  62.1       7 0.00021   18.9   2.9   25   44-68     59-83  (99)
 44 >1v8c_A MOAD related protein;   59.0      10  0.0003   17.9   3.3   46   21-70     28-83  (84)
 45 >3els_A PRE-mRNA leakage prote  56.6      11 0.00033   17.6   3.2   18  155-172    70-87  (158)
 46 >1tyg_B YJBS; alpha beta barre  54.7      12 0.00035   17.5   3.0   59    2-69     15-82  (87)
 47 >2hj1_A Hypothetical protein;   52.3     8.5 0.00025   18.4   2.0   38   26-70     48-85  (97)
 48 >1wxq_A GTP-binding protein; s  49.8     4.8 0.00014   19.9   0.4   24   45-68     54-77  (81)
 49 >2qjl_A URM1, ubiquitin-relate  49.6      16 0.00048   16.6   3.1   53   17-70     30-95  (99)
 50 >3dwg_C 9.5 kDa culture filtra  48.6      17 0.00051   16.4   3.1   27   45-71     60-90  (93)
 51 >3huh_A Virulence protein STM3  46.2      19 0.00057   16.1   3.6   50  252-315    20-71  (75)
 52 >2rk0_A Glyoxalase/bleomycin r  45.6      20 0.00059   16.1   3.5   45  252-313    19-63  (69)
 53 >1wwt_A Threonyl-tRNA syntheta  40.3      24 0.00071   15.5   5.3   61    1-68      5-71  (88)
 54 >3hvz_A Uncharacterized protei  39.5      23 0.00067   15.7   2.5   60    2-68      2-66  (78)
 55 >2k9x_A Tburm1, uncharacterize  36.3      16 0.00048   16.6   1.4   56   17-72     33-100 (110)
 56 >2eki_A DRG 1, developmentally  31.3      28 0.00083   15.1   1.9   16   52-67     69-84  (93)
 57 >3ct8_A Protein BH2160, putati  31.3      33 0.00098   14.6   4.8   47  252-310    21-67  (67)
 58 >2exd_A NFED short homolog; me  30.8      34   0.001   14.6   2.4   27   42-68     29-57  (80)
 59 >2csw_A Ubiquitin ligase prote  29.3      35   0.001   14.5   2.1   10  156-165    36-45  (145)
 60 >3ey7_A Biphenyl-2,3-DIOL 1,2-  27.4      39  0.0011   14.2   3.5   45  253-311    19-65  (67)
 61 >1vc3_B L-aspartate-alpha-deca  26.3      34   0.001   14.5   1.7   48    9-70     19-66  (96)
 62 >1yj5_C 5' polynucleotide kina  26.3      41  0.0012   14.1   2.3   22   46-67     72-95  (143)
 63 >1wv3_A Similar to DNA segrega  26.2      41  0.0012   14.1   2.6   27   43-69     54-81  (158)
 64 >2k5p_A THis protein, thiamine  26.1      41  0.0012   14.1   2.5   46   17-70     16-65  (78)
 65 >1tke_A Threonyl-tRNA syntheta  26.1      41  0.0012   14.1   2.5   45   16-67     15-59  (63)
 66 >1f0z_A THis protein; ubiquiti  24.8      42  0.0012   14.0   1.9   44   17-69     14-61  (66)
 67 >3kt9_A Aprataxin; FHA domain,  24.7      43  0.0013   13.9   2.8   24   45-68     65-90  (102)
 68 >3elx_A Ileal bIle acid-bindin  23.2      46  0.0014   13.7   5.7   48    1-53      1-51  (138)
 69 >2kmm_A Guanosine-3',5'-BIS(di  22.9      47  0.0014   13.7   3.3   45   17-68     17-61  (73)
 70 >2hd9_A UPF0310 protein PH1033  22.2      48  0.0014   13.7   1.8   42   32-73      8-49  (145)
 71 >3cuz_A MSA, malate synthase A  21.8      24 0.00072   15.5   0.2   27   31-57     53-79  (134)
 72 >1qf6_A THRRS, threonyl-tRNA s  21.7      41  0.0012   14.1   1.3   45   16-67     15-59  (63)
 73 >1nki_A Probable fosfomycin re  20.8      52  0.0015   13.4   4.7   61  245-323     9-70  (77)

No 1  
>>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=453.24  Aligned_cols=300  Identities=25%  Similarity=0.368  Sum_probs=235.6

Q ss_pred             EEE-EEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCC-CCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             049-9984113686689999987678898999999984990388788451121179-98899935655422233222234
Q gi|254780608|r    7 VQY-VVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQS-GQVVRIPPVINALNHIIKEQKIL   84 (346)
Q Consensus         7 ~~~-~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~-GD~I~i~~~~~~~~~~~~~~~~~   84 (346)
                      |++ ++|+++++|+|||+||++.++++||+.++++|++|+|+|||+++...+.+.. ++.+........           
T Consensus         4 ~~~~~~v~~~~~g~rl~~~L~~~~~~~sr~~~~~~i~~G~V~vng~~~~~~~~~~~~~~~~~~~~~~~~-----------   72 (325)
T 1v9f_A            4 VQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEE-----------   72 (325)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEECCCCCC-----------
T ss_conf             899999897648866999999866867999999999869989999991783206258989973254332-----------


Q ss_pred             CCCCCCCCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCC--CCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             55433432223454307861785688417653112235785332-332011011--111001333544534222404621
Q gi|254780608|r   85 DSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWV--DSKGQKPRLTHRLDQETSGILVVA  161 (346)
Q Consensus        85 ~~~~~~~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~--~~~~~~~~lVHRLDr~TSGlll~A  161 (346)
                          .........+..|||||++++|+|||+|++|||+.+.... +...+....  ......+++|||||++||||||+|
T Consensus        73 ----~~~~~~~~~~~~il~ed~~~ivvnKP~Gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~A  148 (325)
T 1v9f_A           73 ----EARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVA  148 (325)
T ss_dssp             -------CCCCCCCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCEEEEEEE
T ss_pred             ----CCCCCCCCCCCCEEEECCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCEEEE
T ss_conf             ----2233334454112510110578707888654898777888632321134443333342146532588986514664


Q ss_pred             CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCC
Q ss_conf             23101222102333322111200013456541000000012234655432111335555555303430101343202442
Q gi|254780608|r  162 RTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFC  241 (346)
Q Consensus       162 K~~~a~~~l~~~f~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~s  241 (346)
                      ||..+++.|+.+|+.+.+.|+|+|+|.|.+....+.+..+........      .......++.|.|+|.+..... .+|
T Consensus       149 k~~~~~~~l~~~~~~~~~~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~a~~~~~~~~~~~-~~s  221 (325)
T 1v9f_A          149 KTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRT------HMAVHPMGKPAVTHYRIMEHFR-VHT  221 (325)
T ss_dssp             SSHHHHHHHHHHHHTTCSEEEEEEEEESCCCCCEEEECCEEECSSCTT------CEEECTTSBCCEEEEEEEEECS-SEE
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCC------EEEECCCCCEEEEEEEEEEECC-CCE
T ss_conf             025889999987501210124234301354745662355335766653------0587688715789989865338-845


Q ss_pred             EEEEEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCH--------HCCCCCCCHHHHHHHHEEECCCCC-EEEEECCCC
Q ss_conf             04578612378999999996398000464446652210--------001344624131100043758896-499983997
Q gi|254780608|r  242 WLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGN--------FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP  312 (346)
Q Consensus       242 lv~~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~--------~~~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP  312 (346)
                      +++|+|.|||+||||+||+++||||+||.+||......        .......+++|||+.++|+||.++ .+.|+||+|
T Consensus       222 l~~~~~~TGR~HQIR~hla~~G~PIvGD~~Yg~~~~~~~~l~~g~~~~~~~~~~~~Lha~~l~~~~p~~~~~~~~~ap~P  301 (325)
T 1v9f_A          222 RLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIP  301 (325)
T ss_dssp             EEEEEESCCCTTHHHHHHHHTTCCBTTCTTTTCCCCCCTTCCHHHHHHHHHCCSCSEEEEEEEEECTTTCCEEEEECCCC
T ss_pred             EEEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHCCCCEEECCCCCCEEEEEECCH
T ss_conf             79999778831799999998399766877789855454433166777651586434653705857789998899991797


Q ss_pred             HHHHHHHHHHCCCCCC
Q ss_conf             8999999980898752
Q gi|254780608|r  313 AHMVKTWDSLGFKYDR  328 (346)
Q Consensus       313 ~~f~~~l~~l~~~~d~  328 (346)
                      ++|..+|+.|+++.+.
T Consensus       302 ~~f~~~l~~l~~~~~~  317 (325)
T 1v9f_A          302 QDMVELIEVMRADFEE  317 (325)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999997307765


No 2  
>>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=368.29  Aligned_cols=219  Identities=33%  Similarity=0.518  Sum_probs=179.4

Q ss_pred             CEEEEECCCEEEECCCCCCEEECCCCCCCC-CCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCC
Q ss_conf             307861785688417653112235785332-3320110111110013335445342224046212310122210233332
Q gi|254780608|r   99 SILLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMR  177 (346)
Q Consensus        99 ~~IiyED~~livinKPaGl~vhp~~g~~~~-~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~  177 (346)
                      +.|||||++|+|||||+|++|||+.+.... +..++...  ....++.+|||||++||||||+|||..+++.|+.+|+++
T Consensus         2 ~~Iiyed~~~~vvnKP~G~~~~~~~~~~~~tl~~~l~~~--~~~~~~~~vhRLD~~TSGlll~ak~~~~a~~l~~~~~~~   79 (228)
T 1v9k_A            2 DVIXYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALR--PEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK   79 (228)
T ss_dssp             CCEEEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHHHS--TTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTT
T ss_pred             CEEEEECCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHC--CCCCCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHH
T ss_conf             989996899999999999863899899536999999867--787653166404643221367523579999999998740


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHH
Q ss_conf             21112000134565410000000122346554321113355555553034301013432024420457861237899999
Q gi|254780608|r  178 RIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRV  257 (346)
Q Consensus       178 ~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRv  257 (346)
                      .+.|+|+|+|.|.+....+.+..++.........   .......+.+.|.++|.+....+ .+++++++|.|||+||||+
T Consensus        80 ~v~K~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~tGR~HQIR~  155 (228)
T 1v9k_A           80 GXQKDYLALVRGQWQSHVKSVQAPLLKNILQSGE---RIVRVSQEGKPSETRFKVEERYA-FATLVRCSPVTGRTHQIRV  155 (228)
T ss_dssp             CSEEEEEEEEESCCCTTCCEECCCEEEEECTTSC---EEEEECTTSBCCCEEEEEEEECS-SEEEEEEEESSCCTTHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCE---EEEECCCCCCCCCEEECHHHHCC-CCEEEEEEECCCCHHHHHH
T ss_conf             3454321034686422357522330000110101---55520788842215500555358-7379999947573578888


Q ss_pred             HHHHCCCCEECCCCCCCCCCCHH---CCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCHHHHHHHHHHC
Q ss_conf             99963980004644466522100---013446241311000437588964-9998399789999999808
Q gi|254780608|r  258 HALHMGCPIVGDHKYCANFKGNF---TSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLG  323 (346)
Q Consensus       258 hl~~~g~PivGD~~Yg~~~~~~~---~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~~f~~~l~~l~  323 (346)
                      ||+++||||+||.+||.......   ......+++|||++|+|+||.+++ +.|+||+|++|.++|+.|.
T Consensus       156 h~a~~g~PIvgD~~Y~~~~~~~~~~~~~~~~~~~~Lha~~l~f~~p~~~~~~~~~ap~P~~~~~~l~~~~  225 (228)
T 1v9k_A          156 HTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVXRIEAPXDEGLKRCLQKXR  225 (228)
T ss_dssp             HHHHTTCCBTTCTTTSCHHHHHHHHHTTCCCCSCCEEEEEEEEECTTTCCEEEEECCCCHHHHHHHHHHH
T ss_pred             HHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHCCCCEEECCCCCCEEEEEECCHHHHHHHHHHHH
T ss_conf             8885497213577413000002333202686237887150392879999889999178699999999987


No 3  
>>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=341.44  Aligned_cols=208  Identities=30%  Similarity=0.404  Sum_probs=170.7

Q ss_pred             CCCCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCC
Q ss_conf             34543078617856884176531122357853323320110111110013335445342224046212310122210233
Q gi|254780608|r   95 DFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESF  174 (346)
Q Consensus        95 ~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f  174 (346)
                      ......|||||++++|||||+|++|||+.+........+.  ......++.+|||||++||||||+||+.++++.|+.+|
T Consensus         8 ~~~~~~Ii~ed~~~ivinKP~gi~~~~~~~~~~~~~~~~~--~~~~~~~l~~vhRLD~~TSGllllak~~~~~~~l~~~~   85 (217)
T 2i82_A            8 QEPWLVILYQDDHIXVVNKPSGLLSVPGRLEEHKDSVXTR--IQRDYPQAESVHRLDXATSGVIVVALTKAAERELKRQF   85 (217)
T ss_dssp             CSSSCCEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHH--HHHHCTTCEESSCCCTTCEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCEEEEECCCCCCCCCCCCCCCCHHHHHH--HHHHCCCCCCCCCCCCCCCEEEEEEECHHHHHHHHHHH
T ss_conf             8999529997998999999999825799887760389997--64410332223455542101589860317777889876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHH
Q ss_conf             33221112000134565410000000122346554321113355555553034301013432024420457861237899
Q gi|254780608|r  175 RMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQ  254 (346)
Q Consensus       175 ~~~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQ  254 (346)
                      .++.+.|+|+|++.|.+....+.+..+............   .....+++.+.+.|.++... ..+|+++|+|.|||+||
T Consensus        86 ~~~~~~k~Y~a~~~g~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~-~~~s~~~~~~~TGr~HQ  161 (217)
T 2i82_A           86 REREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQK---VCYETGKPAQTEYEVVEYAA-DNTARVVLKPITGRSHQ  161 (217)
T ss_dssp             HTTCSEEEEEEEEESCCSSSEEEEECCEEECGGGTTCEE---ECTTTCBCCEEEEEEEEEET-TTEEEEEEEESSCCTTH
T ss_pred             HHCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCE---ECCCCCCCCCCEECCCCCCC-CCCEEEEEEECCCCHHH
T ss_conf             514010368988615446664067410123224332200---01224763001010111123-31047889850262378


Q ss_pred             HHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCC
Q ss_conf             99999963980004644466522100013446241311000437588964-99983997
Q gi|254780608|r  255 LRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLP  312 (346)
Q Consensus       255 IRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP  312 (346)
                      ||+||+++||||+||.+||......    ...|++|||++|+|+||.+++ +.|.||+|
T Consensus       162 IR~h~a~lg~PIlgD~~Yg~~~~~~----~~~~~~Lha~~l~f~~p~~ge~~~~~~p~P  216 (217)
T 2i82_A          162 LRVHXLALGHPILGDRFYASPEARA----XAPRLLLHAEXLTITHPAYGNSXTFKAPAD  216 (217)
T ss_dssp             HHHHHHHTTCCBTTCTTTSCHHHHH----TCSSCCEEEEEEEEECTTTCCEEEEECCCC
T ss_pred             HHHHHHHHCCEEECCCCCCCHHHCC----CCCCHHHHCCCCEEECCCCCCEEEEECCCC
T ss_conf             9999997197681676768855636----884666762767889989998899978999


No 4  
>>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} (A:)
Probab=100.00  E-value=0  Score=329.60  Aligned_cols=205  Identities=12%  Similarity=-0.003  Sum_probs=161.7

Q ss_pred             CCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCC
Q ss_conf             54307861785688417653112235785332332011011111001333544534222404621231012221023333
Q gi|254780608|r   97 LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM  176 (346)
Q Consensus        97 ~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~  176 (346)
                      .+..|||||+++||||||+|++|||+.....++...+..     ..++++|||||++||||||||++.+++..+..  ..
T Consensus         5 ~~~~ii~ed~~~ivvnKP~G~~~~~~~~~~~~~~~~l~~-----~~~~~~vhRLD~~TSGlll~a~~~~~~~~~~~--~~   77 (237)
T 2gml_A            5 HHHHHHGSDLVLIALNKPVGIVSTTEDGERDNIVDFVNH-----SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILR--AG   77 (237)
T ss_dssp             --------CCCEEEEEECTTCBCCSSSSCSSBHHHHSCC-----SSCCEEESCCCTTCEEEEEEESCHHHHHHHHH--HH
T ss_pred             CCCCCCCCCEEEEEEECCCCEEECCCCCCCCCCHHHCCC-----CCCEEECCCCCCCCCCCEEEECCHHHHHHHHH--HC
T ss_conf             555556852399999799938972289999974421576-----45611412468888885898416688888765--31


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHH
Q ss_conf             22111200013456541000000012234655432111335555555303430101343202442045786123789999
Q gi|254780608|r  177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR  256 (346)
Q Consensus       177 ~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIR  256 (346)
                      +.+.|+|+|+|.|.+....+.+..+....                   .+.+.+...... .++++++++|.|||+||||
T Consensus        78 ~~i~K~Y~a~v~G~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~-~~~~~v~~~~~tGR~HQIR  137 (237)
T 2gml_A           78 NDHEKEYLVTVDKPITEEFIRGXSAGVPI-------------------LGTVTKKCKVKK-EAPFVFRITLVQGLNRQIR  137 (237)
T ss_dssp             HHSCEEEEEEESSCCCHHHHHHHSSCCEE-------------------TTEECCCCEEEE-EETTEEEEEECCCSTTHHH
T ss_pred             CCCCEEEEEEECCCCCHHHHHHHHCCCEE-------------------CCEEEECHHHCC-CCCEEEEEEEECCCCHHHH
T ss_conf             35514887785267999999999759887-------------------775742000035-6654999998168861999


Q ss_pred             HHHHHCCCCEECCCCCCCCCCCH-----------------HCCCCCCCHHHHHHHHEEECCCCC-EEEEECCCCHHHHHH
Q ss_conf             99996398000464446652210-----------------001344624131100043758896-499983997899999
Q gi|254780608|r  257 VHALHMGCPIVGDHKYCANFKGN-----------------FTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLPAHMVKT  318 (346)
Q Consensus       257 vhl~~~g~PivGD~~Yg~~~~~~-----------------~~~~~~~r~~LHa~~l~f~hp~~~-~~~~~aplP~~f~~~  318 (346)
                      +||+++||||+||.+||......                 .......+++|||++++|+||.++ ++.|+||+|++|.++
T Consensus       138 ~h~~~~G~pI~gD~~y~~~~~~~~~l~~g~~~~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~t~e~~~~~~p~p~~~~~~  217 (237)
T 2gml_A          138 RXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKXEKTAEKG  217 (237)
T ss_dssp             HHHHHTTCCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHTTSTTCC------------------------------
T ss_pred             HHHHHCCCEEEEEEEEEECCEEECCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99998699766699999888880897997838999999999998763345666886667887666678877777777888


Q ss_pred             HHHHCCCCCC
Q ss_conf             9980898752
Q gi|254780608|r  319 WDSLGFKYDR  328 (346)
Q Consensus       319 l~~l~~~~d~  328 (346)
                      ++.|++.-+.
T Consensus       218 ~~~l~~~~~~  227 (237)
T 2gml_A          218 GRPASNGKRF  227 (237)
T ss_dssp             ----------
T ss_pred             CCCCCCCCCC
T ss_conf             8988899898


No 5  
>>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} (A:64-290)
Probab=100.00  E-value=0  Score=317.68  Aligned_cols=197  Identities=13%  Similarity=0.024  Sum_probs=160.3

Q ss_pred             ECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCC
Q ss_conf             17856884176531122357853323320110111110013335445342224046212310122210233332211120
Q gi|254780608|r  104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIY  183 (346)
Q Consensus       104 ED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y  183 (346)
                      ||+++||||||+||+|||+++...++.+++..+     .++.+|||||++|||||||||+.+++..++.+  .+.++|+|
T Consensus         2 Ed~~~ivinKP~Gl~~~~~~~~~~~l~~~l~~~-----~~l~~vhRLD~~TSGlll~ak~~~~~~~l~~~--~~~i~K~Y   74 (227)
T 3dh3_A            2 EDLVLIALNKPVGIVSTTEDGERDNIVDFVNHS-----KRVFPIGRLDKDSQGLIFLTNHGDLVNKILRA--GNDHEKEY   74 (227)
T ss_dssp             GGCCEEEEEECTTCBCCCCSSCTTBHHHHHTCS-----SCCEESSCCCTTCEEEEEEESCTTHHHHHHCG--GGCCCEEE
T ss_pred             CCEEEEECCCCCCEEECCCCCCCCCCHHHCCCC-----CCCCCCCCCCCCCCCEEEEECCCHHHHHHHHH--HCCCCCCC
T ss_conf             311356436665212033347777501101344-----43122465676763148994398799888763--12443221


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHCC
Q ss_conf             00134565410000000122346554321113355555553034301013432024420457861237899999999639
Q gi|254780608|r  184 WSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMG  263 (346)
Q Consensus       184 ~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~g  263 (346)
                      +|+|.|.+....+.+..+....                   ...+.+.+.... ..++++++.+.|||+||||+||+++|
T Consensus        75 ~a~v~G~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~-~~~~~~~~~~~tGr~hQIR~h~a~~g  134 (227)
T 3dh3_A           75 LVTVDKPITEEFIRGMSAGVPI-------------------LGTVTKKCKVKK-EAPFVFRITLVQGLNRQIRRMCEHFG  134 (227)
T ss_dssp             EEEESSCCCHHHHHHHHTCCBC-------------------SSSBCCCCEEEE-CSSSEEEEEESCCCTTHHHHHHHHTT
T ss_pred             CEEECCCCCHHHHHHHHCCCEE-------------------CCEEEEEEEEEE-CCCCEEEEEECCCCCHHHHHHHHHCC
T ss_conf             1276057999999999759984-------------------565744257752-26725899925885259999999879


Q ss_pred             CCEECCCCCCCCCCCH-----------------HCCCCCCCHHHHHHHHEEECCCCCE-EEEECCCCHHHHHHHHHHCCC
Q ss_conf             8000464446652210-----------------0013446241311000437588964-999839978999999980898
Q gi|254780608|r  264 CPIVGDHKYCANFKGN-----------------FTSPIQNKLYLHARYMDLPHPEGGR-LQITAPLPAHMVKTWDSLGFK  325 (346)
Q Consensus       264 ~PivGD~~Yg~~~~~~-----------------~~~~~~~r~~LHa~~l~f~hp~~~~-~~~~aplP~~f~~~l~~l~~~  325 (346)
                      |||+||.+||......                 .......+++|||+++.|+||.+++ ++|+||+|++|.++++.|+..
T Consensus       135 ~pI~gd~~y~~~~~~l~~l~~g~~r~l~~~e~~~~~~~~~~~~Lha~~l~f~~p~~~e~~~~~ap~p~~~~~~~~~l~~~  214 (227)
T 3dh3_A          135 YEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNG  214 (227)
T ss_dssp             CCEEEEEEEEETTEECTTCCTTCEEECCHHHHHHHHHTCCCCSSCC----------------------------------
T ss_pred             CEEEEEEEEEECCEECCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             96766999998787748979977388999999999987632456678876678877666788777777878889988899


Q ss_pred             CC
Q ss_conf             75
Q gi|254780608|r  326 YD  327 (346)
Q Consensus       326 ~d  327 (346)
                      .+
T Consensus       215 ~~  216 (227)
T 3dh3_A          215 KR  216 (227)
T ss_dssp             --
T ss_pred             CC
T ss_conf             99


No 6  
>>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} (A:)
Probab=100.00  E-value=2e-43  Score=293.51  Aligned_cols=184  Identities=20%  Similarity=0.177  Sum_probs=149.1

Q ss_pred             CCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCC
Q ss_conf             54307861785688417653112235785332332011011111001333544534222404621231012221023333
Q gi|254780608|r   97 LKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRM  176 (346)
Q Consensus        97 ~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~  176 (346)
                      .+..|||||++++|||||+|++|||+++.....   +..+.  ....+.+|||||++|||||||||+.+++..|..+|  
T Consensus         2 ~~~~vl~ed~~~ivinKP~g~~~~~~~~~~~~~---~~~~l--~~~~l~~vhRLD~~tsGlll~a~~~~~~~~l~~~~--   74 (189)
T 2oml_A            2 TRRKPENQPTRVILFNKPYDVLPQFTDEAGRKT---LKEFI--PVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPG--   74 (189)
T ss_dssp             ------CCCCCEEEEEECTTBCSCSSCCTTCBC---GGGTC--CCSSCEESSCCCTTCEEEEEEESCHHHHHHHHSTT--
T ss_pred             CCCCCCCCCCEEEEEECCCCEEEECCCCCCCCC---HHHHC--CCCCCEECCCCCCCCCCEEEEECCCHHHHHCCCCC--
T ss_conf             865778899889999899983860779988865---88963--71253473102612000799932530222103123--


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHH
Q ss_conf             22111200013456541000000012234655432111335555555303430101343202442045786123789999
Q gi|254780608|r  177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR  256 (346)
Q Consensus       177 ~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIR  256 (346)
                      +.+.|+|+|+|.|.+....+.+..+....................+++.+.+.|.++... ..++++++.|.|||+||||
T Consensus        75 ~~i~k~Y~a~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~tGr~hQIR  153 (189)
T 2oml_A           75 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKS-IPTSWLKITLYEGRNRQVR  153 (189)
T ss_dssp             SCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CTT-SCEEEEEEEESCCCTTHHH
T ss_pred             EEEEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCEEEEEEEEEEEE-CCCCEEEEEEECCCHHHHH
T ss_conf             037789999993279989999986494507851576579995356641024557888740-5650799999459779999


Q ss_pred             HHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHH
Q ss_conf             99996398000464446652210001344624131100
Q gi|254780608|r  257 VHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARY  294 (346)
Q Consensus       257 vhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~  294 (346)
                      +||+++||||+||.+||....      ...+++||||+
T Consensus       154 ~hl~~lg~pIvgD~~Y~~~~~------~~~~l~l~~~R  185 (189)
T 2oml_A          154 RMTAHVGFPTLRLIRYAMGDY------SLDNLANGEWR  185 (189)
T ss_dssp             HHHHHTTCCEEEEEEEEETTE------ECTTCCTTCEE
T ss_pred             HHHHHCCCEEEEEEEEEECCE------ECCCCCCCCCE
T ss_conf             999986996989899999998------50788998837


No 7  
>>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:59-234)
Probab=100.00  E-value=1.2e-40  Score=275.83  Aligned_cols=170  Identities=14%  Similarity=0.112  Sum_probs=133.4

Q ss_pred             EECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCC
Q ss_conf             61785688417653112235785332332011011111001333544534222404621231012221023333221112
Q gi|254780608|r  103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI  182 (346)
Q Consensus       103 yED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~  182 (346)
                      |||+++||||||+|++|||+.+....+.+.+.   .....++++|||||++|||||||||+.+++..+..  ..+.+.|+
T Consensus         2 Yed~~~ivvnKP~gl~~~~~~~~~~~~~~~l~---~~~~~~~~~vhRLD~~TSGlli~ak~~~~~~~~~~--~~~~~~k~   76 (176)
T 1ksk_A            2 QHGPRYFXLNKPQGYVCSTDDPDHPTVLYFLD---EPVAWKLHAAGRLDIDTTGLVLXTDDGQWSHRITS--PRHHCEKT   76 (176)
T ss_dssp             CCCCCEEEEEECTTCBSSSSCSSSCBGGGGCC---CTTGGGCEESSCCCTTCEEEEEEESCHHHHHHHHC--TTSCCCEE
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCCCCCCCCCC---CCCCCCEEEECCCCCCCCCEEEEECCHHHHHHHHH--HHCCCCEE
T ss_conf             57857999989998505665554431000012---44456365601388555755886058688887755--42388479


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHC
Q ss_conf             00013456541000000012234655432111335555555303430101343202442045786123789999999963
Q gi|254780608|r  183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM  262 (346)
Q Consensus       183 Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~  262 (346)
                      |+|+|.|.++.....+.....                ..+...+.|.+.....  ..+|+++|.|.|||+||||+||+++
T Consensus        77 y~~~v~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~--~~~s~~~~~~~tGr~HQIR~h~~~~  138 (176)
T 1ksk_A           77 YLVTLESPVADDTAEQFAKGV----------------QLHNEKDLTKPAVLEV--ITPTQVRLTISEGRYHQVKRXFAAV  138 (176)
T ss_dssp             EEEEESSCCCTTHHHHHHHCC----------------CCTTCSSCCCCCEEEE--EETTEEEEEESCCCTTHHHHHHHHT
T ss_pred             EEECCCCCCCHHHHHHHHEEE----------------EECCCEEEEEEEEEEC--CCCCEEEEEECCCCHHHHHHHHHHC
T ss_conf             984467888878977753025----------------6389575553468403--7996899996359839999999987


Q ss_pred             CCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECC
Q ss_conf             98000464446652210001344624131100043758
Q gi|254780608|r  263 GCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHP  300 (346)
Q Consensus       263 g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp  300 (346)
                      ||||+||.+||....     ....+++||||++-|+++
T Consensus       139 g~pI~gD~~Y~~~~~-----~~~~~l~l~~~r~l~~~e  171 (176)
T 1ksk_A          139 GNHVVELHRERIGGI-----TLDADLAPGEYRPLTEEE  171 (176)
T ss_dssp             TCCEEEEEEEEETTE-----ECCTTCCTTCEEECCHHH
T ss_pred             CCEEEEEEEEEECCC-----CCCCCCCCCCEEECCHHH
T ss_conf             997989999998865-----047989997515999999


No 8  
>>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:58-243)
Probab=100.00  E-value=1.6e-39  Score=268.86  Aligned_cols=178  Identities=15%  Similarity=0.112  Sum_probs=134.8

Q ss_pred             EECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCC
Q ss_conf             61785688417653112235785332332011011111001333544534222404621231012221023333221112
Q gi|254780608|r  103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKI  182 (346)
Q Consensus       103 yED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~  182 (346)
                      |||+++||||||+|++|||+.+...++...+.   .....++.+|||||++||||||||||.+++..+..++  +.++|+
T Consensus         2 yed~~~ivinKP~gl~~~~~~~~~~~~~~~l~---~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~--~~~~k~   76 (186)
T 1vio_A            2 IEEGQYFMLNKPQGCVCSNDDGDYPTIYQFFD---YPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPK--HHCEKT   76 (186)
T ss_dssp             SCCCCEEEEEECTTCBSSCCC--CCBGGGGSC---TTGGGGCEESSCCCTTCEEEEEEESCHHHHHHHHCTT--SCCCEE
T ss_pred             CCCCEEEEEECCCCCCCCCCCCCCEEEEEEEC---CCCCCEEEECCCCCCCCCCEEEEECCCCCCCCCCCCC--CCCCEE
T ss_conf             22210355402588643334432014542002---4533136540212401221378741775320001112--455201


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHC
Q ss_conf             00013456541000000012234655432111335555555303430101343202442045786123789999999963
Q gi|254780608|r  183 YWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHM  262 (346)
Q Consensus       183 Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIRvhl~~~  262 (346)
                      |+|+|.|.+......+........               +.  ......+... ...+++++++|.|||+||||+||+++
T Consensus        77 y~~~v~g~~~~~~~~~~~~~~~~~---------------~~--~~~~~~~~~~-~~~~~~~~~~~~tGr~hQIR~h~a~l  138 (186)
T 1vio_A           77 YLVTLADPVEENYSAACAEGILLR---------------GE--KEPTKPAKLE-ILDDYNVNLTISEGRYHQVKRMFAAL  138 (186)
T ss_dssp             EEEEESSCCCTTHHHHHHHCCCCT---------------TC--SSCCCCCEEE-ECSSSEEEEEESCCCTTHHHHHHHHT
T ss_pred             EEEEEEEECCHHHHHHHHCCEECC---------------CC--CCCEEEEEEC-CCCCCEEEEEECCCCCHHHHHHHHHC
T ss_conf             125998512044788985365616---------------83--0102332201-35684489885057607999999985


Q ss_pred             CCCEECCCCCCCCCCCH--H----CCCCCCCHHHHHHHHEEECCCCC
Q ss_conf             98000464446652210--0----01344624131100043758896
Q gi|254780608|r  263 GCPIVGDHKYCANFKGN--F----TSPIQNKLYLHARYMDLPHPEGG  303 (346)
Q Consensus       263 g~PivGD~~Yg~~~~~~--~----~~~~~~r~~LHa~~l~f~hp~~~  303 (346)
                      ||||+||.+||......  .    ......++.||++.+.|.||.+.
T Consensus       139 g~pIvgD~~yg~~~~~~~~~l~~g~~r~l~~~~l~~~~l~~~~~~~~  185 (186)
T 1vio_A          139 GNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLVEGGSHHHHH  185 (186)
T ss_dssp             TCCEEEEEEEEETTEECCTTCCTTCEEECCHHHHHHTC---------
T ss_pred             CCEEEEEEEEEECCCCCCCCCCCCCEEECCHHHHHHHHHCCCCCCCC
T ss_conf             99793889999887247999999762599999999999579865457


No 9  
>>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} (A:)
Probab=99.86  E-value=1.4e-23  Score=168.36  Aligned_cols=131  Identities=15%  Similarity=0.162  Sum_probs=101.9

Q ss_pred             EECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98411368668999998767889899999998499038878845112117998899935655422233222234554334
Q gi|254780608|r   11 VVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNL   90 (346)
Q Consensus        11 ~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~   90 (346)
                      +|+++++|||||+||++..+++||+.+++||++|+|+|||++++++++|+.||.|.+..............        .
T Consensus         1 iv~~~~~g~RLDk~L~~~~~~~sR~~a~~li~~G~V~VNG~~~~~s~~v~~gD~i~i~~~~~~~~~~~~~~--------~   72 (133)
T 1dm9_A            1 MKEKPAVEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRSKPSKIVELNATLTLRQGNDERTVIVKAI--------T   72 (133)
T ss_dssp             ----CTTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCTTCBCCTTCEEEEEETTEEEEEEECEE--------E
T ss_pred             CCCCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEECCCCCEECCCCEEEEEECCEEEEEEEEEE--------E
T ss_conf             99887764629999987867168999999998691888999734585615999899987998658999987--------6


Q ss_pred             CCCCCCCCCEEEEECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             322234543078617856884176531122357853323320110111110013335445342224046212310
Q gi|254780608|r   91 TKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRA  165 (346)
Q Consensus        91 ~~~~~~~~~~IiyED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~  165 (346)
                      ..........++|||++.+++|||+|+.+||..                ...++++|||||+.|||.|+++++.-
T Consensus        73 ~~~~~~~~~~~~~ed~~~~v~~kp~~~~~~~~~----------------~~~r~~~vgRLDk~~t~~ll~l~~dg  131 (133)
T 1dm9_A           73 EQRRPASEAALLYEETAESVEKREKMALARKLN----------------ALTMPHPDRRPDKKERRDLLRFKHGD  131 (133)
T ss_dssp             SCCCCHHHHGGGEEECHHHHHHHHHHHHHHHHH----------------HTC-----------------------
T ss_pred             ECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHC----------------CCCCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             225673035666323688711345777766522----------------45578899786859999999875589


No 10 
>>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:1-102,A:201-217)
Probab=99.86  E-value=1.3e-22  Score=162.27  Aligned_cols=100  Identities=20%  Similarity=0.187  Sum_probs=79.4

Q ss_pred             HHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCEEEECC
Q ss_conf             89999999849903887884511211799889993565542223322223455433432223454307861785688417
Q gi|254780608|r   34 FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNK  113 (346)
Q Consensus        34 r~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IiyED~~livinK  113 (346)
                      |++++++|++|.|+|||++++.++.      |.++                             ...|+|||++++|+||
T Consensus         2 Rr~~~~~i~~G~V~Vng~~v~~~d~------i~~~-----------------------------~~~I~yed~~~ivvnK   46 (119)
T 2olw_A            2 RQFIISENTMQKTSFRNHQVKRFSS------QRST-----------------------------RRKPENQPTRVILFNK   46 (119)
T ss_dssp             ----------------------------------------------------------------------CCCCEEEEEE
T ss_pred             CEEEECCCEEECCCCCCCCCCCCCC------CCCC-----------------------------CCCCCCCCCEEEEEEC
T ss_conf             5367068714212255422120554------0035-----------------------------5688789988999989


Q ss_pred             CCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCC
Q ss_conf             653112235785332332011011111001333544534222404621231012221023
Q gi|254780608|r  114 PAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTES  173 (346)
Q Consensus       114 PaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~  173 (346)
                      |+|++|||+.+...+   .+..+  ....++++|||||++|||||+|||+..+++.|+.+
T Consensus        47 P~g~~~~~~~~~~~~---tl~~~--~~~~~l~~vhRLDr~TSGLll~ak~~~~~~~L~~~  101 (119)
T 2olw_A           47 PYDVLPQFTDEAGRK---TLKEF--IPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQP  101 (119)
T ss_dssp             CTTBCSCSSCCTTSB---CGGGT--CCCCSCEESSCCCTTCEEEEEEESCHHHHHHHHCT
T ss_pred             CCCEEEECCCCCCCC---CHHHH--CCCCCCEECCCCCCCEEEEEEEECCCHHHHHHHHC
T ss_conf             999597077998887---68896--57126347531143120069984360565453110


No 11 
>>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} (A:103-200)
Probab=99.80  E-value=6.4e-21  Score=151.58  Aligned_cols=96  Identities=20%  Similarity=0.165  Sum_probs=74.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHH
Q ss_conf             22111200013456541000000012234655432111335555555303430101343202442045786123789999
Q gi|254780608|r  177 RRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLR  256 (346)
Q Consensus       177 ~~v~K~Y~Aiv~G~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slv~~~l~TGR~HQIR  256 (346)
                      |.|.|+|+|+|.|.++.....+.......................+++.|+|.|.++...+ .+|++++.|.|||+||||
T Consensus         1 r~v~K~Y~a~v~g~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~a~t~~~~~~~~~-~~s~~~i~l~tGr~HQIR   79 (98)
T 2olw_A            1 KRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSI-PTSWLKITLYEGRNRQVR   79 (98)
T ss_dssp             CCCCEEEEEEEESCCCHHHHHHHHHCCEETTEECCCCEEEEECCCTTCCCCSSCCC-CCSS-CEEEEEEEESCCCTTHHH
T ss_pred             CCCEEEEEEEEECCCCHHHHHHHHCCCEECCCEEEEEEEEEECCCCCCCCCCCEEEEEECC-CCEEEEEEEECCCHHHHH
T ss_conf             2221589999945688899999865936578535775699953554433101047774215-505899999159759999


Q ss_pred             HHHHHCCCCEECCCCCC
Q ss_conf             99996398000464446
Q gi|254780608|r  257 VHALHMGCPIVGDHKYC  273 (346)
Q Consensus       257 vhl~~~g~PivGD~~Yg  273 (346)
                      +||+++||||+||.+||
T Consensus        80 ~~la~~g~pI~gd~ry~   96 (98)
T 2olw_A           80 RMTAHVGFPTLRLIRYA   96 (98)
T ss_dssp             HHHHHTTCCEEEEEEEE
T ss_pred             HHHHHCCCEEEEEEEEE
T ss_conf             99998599798989999


No 12 
>>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} (A:)
Probab=99.77  E-value=3.8e-20  Score=146.69  Aligned_cols=91  Identities=13%  Similarity=0.136  Sum_probs=76.4

Q ss_pred             CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             66899999876788989999999849903887884511211799889993565542223322223455433432223454
Q gi|254780608|r   19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLK   98 (346)
Q Consensus        19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (346)
                      ||||+||++.+++.||+++++++++|.|+|||++++++++|+.||+|++.........              .......+
T Consensus         1 mRLD~~L~~~~~~~sr~~~~k~i~~g~I~VNg~~~~~~~~v~~gD~i~i~~~~~~~~~--------------~~~~~~~~   66 (92)
T 2k6p_A            1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCAKASKEVKAGDTISLHYLKGIEEY--------------TILQIPAL   66 (92)
T ss_dssp             CBHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEECCTTCBCCTTCEEEECCSSCCEEE--------------EECCCCCC
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEEEECCCCCCCCEEEEEECCCCEEE--------------EEEECCCC
T ss_conf             9678999872771599999999989979989899866247189999999848963689--------------99978865


Q ss_pred             CEEEEECCCEEEECCCCCCEEECCC
Q ss_conf             3078617856884176531122357
Q gi|254780608|r   99 SILLYEDSKIYVFNKPAGISVQGGS  123 (346)
Q Consensus        99 ~~IiyED~~livinKPaGl~vhp~~  123 (346)
                      ..|+|||++++|+|||||++|||+.
T Consensus        67 ~~i~yed~~~lvinKpagl~~hp~~   91 (92)
T 2k6p_A           67 KNVPRKDTHLYIAPKTKELEHHHHH   91 (92)
T ss_dssp             SCCCSSSTTSSEEECCCC-------
T ss_pred             CCCCHHHHCCCEEECHHCCCCCCCC
T ss_conf             8986455061598063216244457


No 13 
>>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} (A:1-63)
Probab=99.03  E-value=2.9e-10  Score=84.37  Aligned_cols=54  Identities=17%  Similarity=0.401  Sum_probs=50.1

Q ss_pred             HHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEEC
Q ss_conf             1368668999998767889899999998499038878845112117998899935
Q gi|254780608|r   15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPP   69 (346)
Q Consensus        15 ~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~   69 (346)
                      +++++|||+||+..+ +.||++++++|++|.|+|||++++++++|..||.|.+..
T Consensus         3 ~~~~~RLDk~La~~~-~~SR~~~~~li~~G~V~Vng~~vk~~~~v~~~d~I~v~~   56 (63)
T 3dh3_A            3 PDSSVRLNKYISESG-ICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNG   56 (63)
T ss_dssp             -CCCEEHHHHHHTTT-SSCHHHHHHHHHTTCEEETTEECCTTCEECTTCCEEETT
T ss_pred             CCCCCCHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCCCCCCCEEEECC
T ss_conf             988704999998778-851999999998793898999947888969999899999


No 14 
>>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} (A:)
Probab=98.90  E-value=4.7e-10  Score=83.07  Aligned_cols=69  Identities=17%  Similarity=0.063  Sum_probs=60.1

Q ss_pred             CCCCCCEEEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEEC
Q ss_conf             97668304999841136866899999876788989999999849903887884-5112117998899935
Q gi|254780608|r    1 MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP   69 (346)
Q Consensus         1 ~~~M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~   69 (346)
                      |+-|+.....++.....++|||+||++.....||++++++|..|.|+|||+++ +++++|..||.|.+..
T Consensus         3 m~~~~~~~~~~~~~~~~~~RLd~~L~~~~~~~SR~~a~~~I~~G~V~VNg~~v~~~~~~v~~gd~I~i~~   72 (79)
T 1p9k_A            3 MIHRMSNMATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAG   72 (79)
T ss_dssp             CCCSSCCCCEEECCSCSCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSEEEEETT
T ss_pred             HHHCCCCCCEEECCCCCCEEHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCCCCEEEECC
T ss_conf             1000147713864999719799999877883689999999984997989999277887989999999999


No 15 
>>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} (A:1-58)
Probab=98.58  E-value=8.2e-08  Score=68.91  Aligned_cols=51  Identities=18%  Similarity=0.254  Sum_probs=46.7

Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE
Q ss_conf             6866899999876788989999999849903887884-511211799889993
Q gi|254780608|r   17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP   68 (346)
Q Consensus        17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~   68 (346)
                      ..+|||+||++.. ..||++++++|+.|.|+|||+++ ++++.|..||.|.+.
T Consensus         2 ~~~RLDk~L~~~~-~~SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~d~I~i~   53 (58)
T 1ksk_A            2 SHXRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYD   53 (58)
T ss_dssp             CCEEHHHHHHHHH-TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTCCEEET
T ss_pred             CCCHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCCEECCCCEEEEE
T ss_conf             8400999998778-968999999998892999999946688580786769972


No 16 
>>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} (A:1-57)
Probab=98.53  E-value=1.3e-07  Score=67.60  Aligned_cols=50  Identities=16%  Similarity=0.298  Sum_probs=46.1

Q ss_pred             CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE
Q ss_conf             866899999876788989999999849903887884-511211799889993
Q gi|254780608|r   18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP   68 (346)
Q Consensus        18 g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~   68 (346)
                      .+|||+||++.. ..||++++++|++|+|+|||+++ ++++.|..||.|.+.
T Consensus         2 ~~RLDk~L~~~~-~~SR~~a~~lI~~g~V~Vng~~i~~~~~~v~~~d~i~v~   52 (57)
T 1vio_A            2 SLRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFE   52 (57)
T ss_dssp             CEEHHHHHHHHH-TCCHHHHHHHHHTTCEEETTEECCCTTCEECTTSCEEET
T ss_pred             CHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEECCCCCEEEEE
T ss_conf             558999999877-858999999998797899999915489586887878762


No 17 
>>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (D:100-193)
Probab=98.09  E-value=1e-05  Score=55.71  Aligned_cols=50  Identities=20%  Similarity=0.424  Sum_probs=43.9

Q ss_pred             CHHHHHHHH-CCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEECC
Q ss_conf             689999987-67889899999998499038878845-1121179988999356
Q gi|254780608|r   20 RLDRWFKNH-YPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIPPV   70 (346)
Q Consensus        20 RLd~~L~~~-~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~~~   70 (346)
                      |||.||.+. | ..|+.+++++|..|.|+|||++++ +++.|+.||.|++...
T Consensus         1 RLD~~l~r~~~-~~Tr~~ArqlI~hg~V~VNg~~v~~ps~~v~~gD~I~i~~~   52 (94)
T 2vqe_D            1 RLDNVVYRLGF-AVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK   52 (94)
T ss_dssp             BHHHHHHHTTS-SSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGG
T ss_pred             HHHHHHHHCCC-HHHHHHHHHHHHCCCEECCCEEEEECCEEECCCCCHHHHHH
T ss_conf             99999985352-00289888998706845088799753678528860012110


No 18 
>>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} (A:1-65)
Probab=98.08  E-value=2.2e-06  Score=59.87  Aligned_cols=55  Identities=16%  Similarity=0.195  Sum_probs=47.8

Q ss_pred             HHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCC--EECCEEE-CCCCCCCCCCEEEEE
Q ss_conf             113686689999987678898999999984990--3887884-511211799889993
Q gi|254780608|r   14 NDEENMRLDRWFKNHYPHINFVNLQKILRSGQV--RVDKKRV-KFNNRIQSGQVVRIP   68 (346)
Q Consensus        14 ~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V--~VNG~~v-k~~~~v~~GD~I~i~   68 (346)
                      +....+|||++|.+.--..||++++++|.+|.|  .|||+++ +|++.|..||.|.|.
T Consensus         2 ~~~~~~RLD~~L~~~g~~~Sr~~A~~lI~~G~V~~~VNg~~v~kp~~~v~~~d~i~v~   59 (65)
T 3hp7_A            2 NAXPKERVDVLAYKQGLFETREQAKRGVXAGLVVNVINGERYDKPGEKIDDGTELKLK   59 (65)
T ss_dssp             -CCCEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETTCCEEET
T ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEEECCEEECCCCCCCCCCCEEEEE
T ss_conf             9650889999999875812499999999859942320998956886787999989980


No 19 
>>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (D:82-201)
Probab=97.90  E-value=1.1e-05  Score=55.57  Aligned_cols=53  Identities=13%  Similarity=0.088  Sum_probs=44.4

Q ss_pred             CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCC
Q ss_conf             66899999876788989999999849903887884-511211799889993565
Q gi|254780608|r   19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVI   71 (346)
Q Consensus        19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~   71 (346)
                      +|||.++-+.-=.-|+.+++++|.+|.|.|||+++ ++++.|+.||.|.+.+..
T Consensus         8 ~RLD~~l~R~gfa~s~~~ARqlI~hghV~VNg~~v~~ps~~v~~gD~i~~~~~~   61 (120)
T 3bbn_D            8 MRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQ   61 (120)
T ss_dssp             SBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECSST
T ss_pred             HHHHHEEEECCCCCCHHHHHHHHHHHCEECCCEEECCCCEECCHHHHHHHCCHH
T ss_conf             753103550573357688889998751361548981657254616630010013


No 20 
>>3i1m_D 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ... (D:97-190)
Probab=97.90  E-value=7.3e-06  Score=56.60  Aligned_cols=53  Identities=15%  Similarity=0.129  Sum_probs=44.4

Q ss_pred             CHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEECCCC
Q ss_conf             6899999876788989999999849903887884-5112117998899935655
Q gi|254780608|r   20 RLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPPVIN   72 (346)
Q Consensus        20 RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~~~~   72 (346)
                      |||.+|-+.-=.-|+.+++++|..|.|+|||+++ +|++.|+.||+|.+.....
T Consensus         1 RLD~~l~r~gfa~S~~~ARqlI~hghv~VNg~~v~~ps~~vk~gD~i~i~~~~~   54 (94)
T 3i1m_D            1 RLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAK   54 (94)
T ss_dssp             STTHHHHTTTSCSSHHHHHHHHHTTCEESSSSBCCSTTCCCCTTCCEEECSSSC
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHCCEECCCEEEEEEEEEECCCCEEEECCCHH
T ss_conf             888886603125409999999985037608879976317705897788623232


No 21 
>>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} (A:350-432)
Probab=97.57  E-value=0.00026  Score=46.87  Aligned_cols=62  Identities=10%  Similarity=0.120  Sum_probs=50.0

Q ss_pred             EEEEEECHHHC---CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEE
Q ss_conf             04999841136---866899999876788989999999849903887884-511211799889993
Q gi|254780608|r    7 VQYVVVENDEE---NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIP   68 (346)
Q Consensus         7 ~~~~~V~~~~~---g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~   68 (346)
                      +..+.++.++.   ++|||.+|.+.==.-|+++.+++|+.|.|+|||+++ ++++.|..||.+.+.
T Consensus         5 ~p~~~i~~~~~~~~~~rl~~~l~~~gl~~S~~~ARrlI~~G~V~vN~~~v~~~~~~v~~~d~i~i~   70 (83)
T 1h3f_A            5 IPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQ   70 (83)
T ss_dssp             SCEEEECGGGCBTTEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEECSSCEEEE
T ss_pred             CCCEEECHHHHCCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEEE
T ss_conf             981574387832586349999998498677899999998599898999824877021589808998


No 22 
>>1s1h_D 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} (D:81-179)
Probab=97.53  E-value=0.00011  Score=49.15  Aligned_cols=51  Identities=12%  Similarity=-0.007  Sum_probs=43.9

Q ss_pred             CCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCCCEEEEEC
Q ss_conf             66899999876788989999999849903887884-5112117998899935
Q gi|254780608|r   19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSGQVVRIPP   69 (346)
Q Consensus        19 ~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~GD~I~i~~   69 (346)
                      +|||.++-+.-=.-|+.+++++|..|.|+|||+++ .|++.|+.||.|.+..
T Consensus         9 rRLD~il~R~gfa~s~~~ARqlI~HghI~VNg~~v~~Ps~~vk~gd~i~i~~   60 (99)
T 1s1h_D            9 RRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDF   60 (99)
T ss_dssp             GBHHHHHHHHTSSSSHHHHHHHHHHTCBEETTEECCCTTCBCCTTEECCBCS
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEEECCEEEECCCCCEEEE
T ss_conf             5078899981565889999999873772589999876246840587560556


No 23 
>>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=97.29  E-value=0.00021  Score=47.48  Aligned_cols=52  Identities=15%  Similarity=0.082  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEE-CCCCCCCCC--CEEEEEC
Q ss_conf             866899999876788989999999849903887884-511211799--8899935
Q gi|254780608|r   18 NMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRV-KFNNRIQSG--QVVRIPP   69 (346)
Q Consensus        18 g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~v-k~~~~v~~G--D~I~i~~   69 (346)
                      -+|||.+|.+.-=.-|+.+++++|..|.|+|||+++ +|++.|+.|  |.|.+.+
T Consensus         7 erRLd~~l~~~g~a~s~~~Ar~lI~~G~V~Vng~~v~~Ps~~v~~~~~d~I~~~~   61 (71)
T 2cqj_A            7 GRRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTRSMEDFVTWVD   61 (71)
T ss_dssp             EEEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEHHHHTTEEESC
T ss_pred             HCCHHHHHHHHCCCCCHHHHHHHHHHCEEEECCEEECCCCEEECCCCCCEEEEEC
T ss_conf             4126899998055278999999998498998999955698583589988699846


No 24 
>>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} (A:51-266)
Probab=96.45  E-value=0.002  Score=41.20  Aligned_cols=71  Identities=24%  Similarity=0.310  Sum_probs=46.5

Q ss_pred             CCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCC
Q ss_conf             78568841765311223578533233201101111100133354453422240462123101222102333322111200
Q gi|254780608|r  105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW  184 (346)
Q Consensus       105 D~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~  184 (346)
                      -+.|++||||+|+.+|.       +.+.+....  ...+.+-.+.||-..||+|+++-++.+ +.+..+   ....|+|.
T Consensus        15 ~~G~l~i~KP~g~tS~~-------vv~~~k~~~--~~~kvgh~GtLDp~a~GvLiv~ig~~T-kl~~~~---~~~~K~Y~   81 (216)
T 2apo_A           15 KYGVVVVDKPRGPTSHE-------VSTWVKKIL--NLDKAGHGGTLDPKVTGVLPVALERAT-KTIPMW---HIPPKEYV   81 (216)
T ss_dssp             HTEEEEEEECSSSCHHH-------HHHHHHHHT--TCSCEEESSCCCTTCEEEEEEEEGGGG-GGGGGT---TSSCEEEE
T ss_pred             CCCEEEEECCCCCCHHH-------HHHHHHHHH--CCCCCCCCCCCCCCCCCCHHHEECHHH-HHHHHH---CCCCCEEE
T ss_conf             49989997999899899-------999999984--877357787789634365532118653-221775---05882799


Q ss_pred             CCCC
Q ss_conf             0134
Q gi|254780608|r  185 SLVW  188 (346)
Q Consensus       185 Aiv~  188 (346)
                      |.+.
T Consensus        82 ~~~~   85 (216)
T 2apo_A           82 CLMH   85 (216)
T ss_dssp             EEEE
T ss_pred             EEEE
T ss_conf             9999


No 25 
>>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase/structural protein complex; 2.10A {Pyrococcus abyssi} PDB: 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3hjw_A* 3hjy_A (C:31-245)
Probab=96.38  E-value=0.0025  Score=40.65  Aligned_cols=83  Identities=22%  Similarity=0.272  Sum_probs=50.5

Q ss_pred             CCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCCC
Q ss_conf             78568841765311223578533233201101111100133354453422240462123101222102333322111200
Q gi|254780608|r  105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYW  184 (346)
Q Consensus       105 D~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~~~~v~K~Y~  184 (346)
                      -+.+|++|||.|+.+|-       +...+.....  ..+.+-.+-||-..||+++++-.+.+ +.+ ..|  ..-.|+|.
T Consensus        15 ~~G~l~~~KP~g~tS~~-------vv~~ik~~~~--~~kvGh~GTLDp~atGvl~i~vg~aT-kl~-~~~--~~~~K~Y~   81 (215)
T 2aus_C           15 QYGVINLDKPPGPTSHE-------VVAWIKRILN--LEKAGHGGTLDPKVSGVLPVALERAT-RVV-QAL--LPAGKEYV   81 (215)
T ss_dssp             HTEEEEEEECSSSCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG-GGG-GGG--TTCCEEEE
T ss_pred             CCCEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCCCCEEEEECHHH-HHH-HHH--CCCCCEEE
T ss_conf             78389995799899999-------9999998718--34257898789865034767873899-899-997--45885999


Q ss_pred             CCCCCCCCCCCCCCCC
Q ss_conf             0134565410000000
Q gi|254780608|r  185 SLVWGIPKNKKECIAN  200 (346)
Q Consensus       185 Aiv~G~~~~~~~~i~~  200 (346)
                      |.+..-...+..-++.
T Consensus        82 ~~~~~g~~t~t~d~~~   97 (215)
T 2aus_C           82 ALMHLHGDVPEDKIRA   97 (215)
T ss_dssp             EEEEESSCCCHHHHHH
T ss_pred             EEEEECCCCCCCHHHE
T ss_conf             9988723444440013


No 26 
>>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} (A:345-432)
Probab=95.82  E-value=0.011  Score=36.61  Aligned_cols=50  Identities=14%  Similarity=0.016  Sum_probs=39.4

Q ss_pred             HHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCE
Q ss_conf             1368668999998767889899999998499038878845-1121179988
Q gi|254780608|r   15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQV   64 (346)
Q Consensus        15 ~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~   64 (346)
                      -.+|++|..+|...=-..|++..+++|++|.|+|||+++. ++..+..+|.
T Consensus         8 ~~~~~~i~~lL~~~gl~~S~~earrlI~~GgV~IN~~~v~d~~~~i~~~~~   58 (88)
T 2jan_A            8 PGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEWVPQSSDF   58 (88)
T ss_dssp             SSSCCSHHHHHHHHTSCSSHHHHHHHHTTTCEEESSCEECCTTCCCCGGGS
T ss_pred             CCCCCCHHHHHHHCCCCCCHHHHHHHHHHCCEEECCEECCCCCCCCCHHHH
T ss_conf             578777999999828867899999999939999899981694330278782


No 27 
>>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, protein structure initiative; 1.90A {Mycobacterium tuberculosis H37RV} (A:1-60,A:206-232)
Probab=92.49  E-value=0.057  Score=32.08  Aligned_cols=53  Identities=26%  Similarity=0.426  Sum_probs=36.8

Q ss_pred             CCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCH
Q ss_conf             78568841765311223578533233201101111100133354453422240462123101
Q gi|254780608|r  105 DSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA  166 (346)
Q Consensus       105 D~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a  166 (346)
                      -+.|++||||.|+.+|.       +...+....+  ..+.+-..-||-..||+|+++-.+.+
T Consensus         5 ~~Gil~idKP~G~TS~~-------vv~~iKk~l~--~kKVGH~GTLDP~AtGvLiv~iG~aT   57 (87)
T 1sgv_A            5 GPGIVVIDKPAGMTSHD-------VVGRCRRIFA--TRRVGHAGTLDPMATGVLVIGIERAT   57 (87)
T ss_dssp             CSEEEEEEECTTCCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG
T ss_pred             CCEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECHHH
T ss_conf             98899997699899899-------9999999848--88556387889736423999989676


No 28 
>>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} (A:1-79,A:225-253)
Probab=92.08  E-value=0.068  Score=31.61  Aligned_cols=55  Identities=20%  Similarity=0.298  Sum_probs=37.5

Q ss_pred             EECCCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCH
Q ss_conf             6178568841765311223578533233201101111100133354453422240462123101
Q gi|254780608|r  103 YEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAA  166 (346)
Q Consensus       103 yED~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a  166 (346)
                      ++-+.|++||||.|+.+|.       +...+....+  ..+.+-..-||-..||||+++-.+.+
T Consensus        22 ~~~~Gil~idKP~G~TS~~-------vV~~vkk~l~--~kKVGH~GTLDP~AtGvLiv~iG~aT   76 (108)
T 1k8w_A           22 MDINGVLLLDKPQGMSSND-------ALQKVKRIYN--ANRAGHTGALDPLATGMLPICLGEAT   76 (108)
T ss_dssp             CCCCEEEEEEECTTCCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG
T ss_pred             CCCCEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECHHH
T ss_conf             8853699984799899899-------9999999858--99687686579746135999988888


No 29 
>>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima} (A:1-57,A:190-224)
Probab=92.05  E-value=0.071  Score=31.47  Aligned_cols=59  Identities=20%  Similarity=0.283  Sum_probs=38.0

Q ss_pred             CCEEEECCCCCCEEECCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHCCCCC
Q ss_conf             8568841765311223578533233201101111100133354453422240462123101222102333
Q gi|254780608|r  106 SKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFR  175 (346)
Q Consensus       106 ~~livinKPaGl~vhp~~g~~~~~~~~l~~~~~~~~~~~~lVHRLDr~TSGlll~AK~~~a~~~l~~~f~  175 (346)
                      +.|+.+|||.|+.+|-       +...+....+  ..+.+-..-||-..||+|+++-++.+  .|.++.+
T Consensus         3 nGil~idKP~G~TS~~-------vV~~iKk~l~--~kKVGH~GTLDP~AtGvLii~iG~aT--KL~~~~~   61 (92)
T 1r3e_A            3 HGILVAYKPKGPTSHD-------VVDEVRKKLK--TRKVGHGGTLDPFACGVLIIGVNQGT--RILELVR   61 (92)
T ss_dssp             CEEEEEEECSSSCHHH-------HHHHHHHHTT--CSCEEESSCCCTTCEEEEEEEEGGGG--GGGEEEE
T ss_pred             CEEEEEECCCCCCHHH-------HHHHHHHHHC--CCCCCCCCCCCCCCEEEEEEEECHHH--HHHEEEE
T ss_conf             5599996699899899-------9999999868--88787785679746446999988675--3323898


No 30 
>>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:77-159)
Probab=91.40  E-value=0.16  Score=29.22  Aligned_cols=25  Identities=28%  Similarity=0.494  Sum_probs=22.0

Q ss_pred             CCEECCEEEC-CCCCCCCCCEEEEEC
Q ss_conf             9038878845-112117998899935
Q gi|254780608|r   45 QVRVDKKRVK-FNNRIQSGQVVRIPP   69 (346)
Q Consensus        45 ~V~VNG~~vk-~~~~v~~GD~I~i~~   69 (346)
                      .|.|||+++. |++.+++||+|.+..
T Consensus         1 Hi~VNgkkVdIPSy~~k~gD~I~ik~   26 (83)
T 1c05_A            1 HILVDGSRVNIPSYRVKPGQTIAVRE   26 (83)
T ss_dssp             CEEETTEECCCSSCBCCTTCEEEECG
T ss_pred             CEECCCEEEEECCEEECCCCEEEECC
T ss_conf             63604369984341621784875020


No 31 
>>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} (A:247-420)
Probab=91.13  E-value=0.046  Score=32.66  Aligned_cols=53  Identities=6%  Similarity=0.073  Sum_probs=39.4

Q ss_pred             CHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEE
Q ss_conf             411368668999998767889899999998499038878845-11211799889
Q gi|254780608|r   13 ENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV   65 (346)
Q Consensus        13 ~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I   65 (346)
                      +....+.+|...|.+.--.-|++.++++|.+|.|+|||++++ +++.+..+|.+
T Consensus       101 ~~~~~~~~l~~lL~~~~l~~SkseaRrlI~~ggv~in~~ki~d~~~~i~~~~l~  154 (174)
T 1jil_A          101 TLSNDTTNIVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYALAPEDKI  154 (174)
T ss_dssp             ------------------------------------------------------
T ss_pred             EECCCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCEECHHHCC
T ss_conf             715888789999998388467999999998499899999813844400775704


No 32 
>>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} (A:1-81)
Probab=90.41  E-value=0.42  Score=26.60  Aligned_cols=53  Identities=21%  Similarity=0.258  Sum_probs=42.8

Q ss_pred             HCCCCHHHHHHHHCCCC-CHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEEEEE
Q ss_conf             36866899999876788-9899999998499038878845-11211799889993
Q gi|254780608|r   16 EENMRLDRWFKNHYPHI-NFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVVRIP   68 (346)
Q Consensus        16 ~~g~RLd~~L~~~~~~~-sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I~i~   68 (346)
                      ..++.|--||.+.++.. +...+++.+.+|.|.|||++.+ ..+.+-.-|+|+|+
T Consensus         5 ~~siPL~i~LRd~Lk~A~t~rEak~Il~~~~V~VDGkvr~D~~~pvG~mDVIsi~   59 (81)
T 3kbg_A            5 DQSVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFXDVIEIN   59 (81)
T ss_dssp             CSCEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTTCEEEET
T ss_pred             CCCCCCHHHHHHHHCCCCCHHHHHHHHHCCEEEECCEEECCCCCCCCEEEEEEEC
T ss_conf             1256543786446452265899999986793898999962389988706799979


No 33 
>>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} (A:246-419)
Probab=89.09  E-value=0.086  Score=30.96  Aligned_cols=50  Identities=8%  Similarity=0.106  Sum_probs=34.9

Q ss_pred             HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEEC-CCCCCCCCCEE
Q ss_conf             368668999998767889899999998499038878845-11211799889
Q gi|254780608|r   16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVK-FNNRIQSGQVV   65 (346)
Q Consensus        16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk-~~~~v~~GD~I   65 (346)
                      ..+.++..+|...--.-|++..+++|++|.|+|||++++ +++.+...|.+
T Consensus       104 ~~~~~l~~lL~~~gl~~S~seaRrlI~~ggv~in~~ki~d~~~~i~~~~~~  154 (174)
T 2ts1_A          104 GGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAEHRL  154 (174)
T ss_dssp             ---------------------------------------------------
T ss_pred             CCCCCHHHHHHHCCCCCCHHHHHHHHHCCCEEECCEEECCCCCCCCHHHCC
T ss_conf             799769999998598677899999998699898999823842201775714


No 34 
>>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} (D:)
Probab=84.03  E-value=1.6  Score=22.97  Aligned_cols=53  Identities=13%  Similarity=0.183  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHC--CCCEECCEEECCCCCCCCCCEEEEECCC
Q ss_conf             686689999987678898999999984--9903887884511211799889993565
Q gi|254780608|r   17 ENMRLDRWFKNHYPHINFVNLQKILRS--GQVRVDKKRVKFNNRIQSGQVVRIPPVI   71 (346)
Q Consensus        17 ~g~RLd~~L~~~~~~~sr~~~~~lir~--G~V~VNG~~vk~~~~v~~GD~I~i~~~~   71 (346)
                      .+..+...+...-..++  .++..+..  -.|.|||+.+..++.|+.||+|.+.|+.
T Consensus        24 ~~~tv~~l~~~L~~~~p--~~~~~l~~~~~~v~vn~~~v~~~~~l~~gdeVai~PPv   78 (81)
T 1fm0_D           24 DFPTVEALRQHMAAQSD--RWALALEDGKLLAAVNQTLVSFDHPLTDGDEVAFFPPV   78 (81)
T ss_dssp             CCSBHHHHHHHHHTTCH--HHHHHHCCTTCEEEETTEECCTTCBCCTTCEEEEECCC
T ss_pred             CCCCHHHHHHHHHHHCC--HHHHHHCCCCEEEECCCEECCCCCCCCCCCEEEEECCC
T ss_conf             99999999999987682--48886278958997284597999785999999996997


No 35 
>>2q5w_D Molybdopterin converting factor, subunit 1; MOCO, MPT synthase, MOAD, MOAE, transferase, molybdenum cofactor biosynthesis; 2.00A {Staphylococcus aureus} PDB: 2qie_B* (D:)
Probab=83.70  E-value=1.4  Score=23.22  Aligned_cols=44  Identities=27%  Similarity=0.417  Sum_probs=31.4

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCC
Q ss_conf             899999876788989999999849903887884511211799889993565
Q gi|254780608|r   21 LDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI   71 (346)
Q Consensus        21 Ld~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~   71 (346)
                      |-..|.+++|.+-.       +.-.|.|||+.++.++.|+.||.|.+.|+.
T Consensus        31 l~~~L~~~~~~~~~-------~~~~v~vN~~~v~~~~~l~dgDeVai~PPv   74 (77)
T 2q5w_D           31 FEDLLFERYPQINN-------KKFQVAVNEEFVQKSDFIQPNDTVALIPPV   74 (77)
T ss_dssp             HHHHHHHHCGGGTT-------CCCEEEETTEEECTTSEECTTCEEEEECSC
T ss_pred             HHHHHHHHCCCCCC-------HHHHHHCCCEECCCCCCCCCCCEEEEECCC
T ss_conf             99999987785511-------331341088076888670998999997998


No 36 
>>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PFU-562899-001, PSI, protein structure initiative; 1.51A {Pyrococcus furiosus} (A:)
Probab=71.60  E-value=2.9  Score=21.28  Aligned_cols=51  Identities=16%  Similarity=0.197  Sum_probs=31.1

Q ss_pred             HHHHHHHHCCCCCHHHH---HHHHHCCCCEECCEEECCCCCCCCCCEEEEECCC
Q ss_conf             89999987678898999---9999849903887884511211799889993565
Q gi|254780608|r   21 LDRWFKNHYPHINFVNL---QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVI   71 (346)
Q Consensus        21 Ld~~L~~~~~~~sr~~~---~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~   71 (346)
                      |-..|..++|.+....+   ..+...=.|.|||+.+..++.|+.||+|.+.|+.
T Consensus        42 l~~~L~~~~p~l~~~l~~~~~~~~~~~~v~vN~~~v~~~~~l~dgdeV~i~PPv   95 (98)
T 1vjk_A           42 LIEEIKKRHEKFKEEVFGEGYDEDADVNIAVNGRYVSWDEELKDGDVVGVFPPV   95 (98)
T ss_dssp             HHHHHHHHCGGGGGSCBCSSSCTTSSBEEEETTBCCCTTCBCCTTCEEEEESCC
T ss_pred             HHHHHHHHCCHHHHHHHHHCCCCCCCEEEEECCEECCCCCCCCCCCEEEEECCC
T ss_conf             999999867067888641101456547998678886989781999999997987


No 37 
>>2eh0_A KLP, kinesin-like protein KIF1B; FHA domain, KIAA0591, KIAA1448, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=65.83  E-value=4.5  Score=20.10  Aligned_cols=22  Identities=27%  Similarity=0.379  Sum_probs=8.2

Q ss_pred             CEECCEEECCCCCCCCCCEEEE
Q ss_conf             0388788451121179988999
Q gi|254780608|r   46 VRVDKKRVKFNNRIQSGQVVRI   67 (346)
Q Consensus        46 V~VNG~~vk~~~~v~~GD~I~i   67 (346)
                      +.|||.++.....|+.||+|++
T Consensus        82 t~vNg~~i~~~~~L~~GD~i~i  103 (130)
T 2eh0_A           82 TYVNGKRVSQPVQLRSGNRIIM  103 (130)
T ss_dssp             EEETTEECCSCEECCTTCBCEE
T ss_pred             EEECCEECCCCEECCCCCEEEE
T ss_conf             6999969465278799999998


No 38 
>>2g1e_A Hypothetical protein TA0895; MOAD, molybdopterin, transferase; NMR {Thermoplasma acidophilum} PDB: 2k22_A (A:)
Probab=65.34  E-value=8.2  Score=18.47  Aligned_cols=53  Identities=8%  Similarity=0.142  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHHCCCCCHHHHHHHHH-C-----C-CCEECCEEEC----CCCCCCCCCEEEEECCC
Q ss_conf             8668999998767889899999998-4-----9-9038878845----11211799889993565
Q gi|254780608|r   18 NMRLDRWFKNHYPHINFVNLQKILR-S-----G-QVRVDKKRVK----FNNRIQSGQVVRIPPVI   71 (346)
Q Consensus        18 g~RLd~~L~~~~~~~sr~~~~~lir-~-----G-~V~VNG~~vk----~~~~v~~GD~I~i~~~~   71 (346)
                      +..+..++......++.... +++. .     + .|.|||+.+.    .++.|+.||+|.+.|+.
T Consensus        24 ~~Tv~~ll~~L~~~~p~~~~-~l~~~~~~~~~~v~v~vNg~~v~~~~~~~t~l~~gD~V~ilPpv   87 (90)
T 2g1e_A           24 ISKISELLERLKVEYGSEFT-KQMYDGNNLFKNVIILVNGNNITSMKGLDTEIKDDDKIDLFPPV   87 (90)
T ss_dssp             CCBHHHHHHHHHHHSCHHHH-HHHCCSSCSTTTCEEEESSSBGGGTCSSSCBCCTTCEEEEECCT
T ss_pred             CCCHHHHHHHHHHHHHHHHH-HHHHHHHCHHHHEEEEEECCCCCCCCCCCCCCCCCCEEEEECCC
T ss_conf             99899999999967427899-99850102333504577030002344656537999999996888


No 39 
>>2g1l_A Kinesin-like protein KIF1C; transport, FHA domain, structural genomics consortium, SGC, transport protein; 2.60A {Homo sapiens} (A:)
Probab=64.89  E-value=6.2  Score=19.22  Aligned_cols=22  Identities=23%  Similarity=0.196  Sum_probs=9.1

Q ss_pred             CEECCEEECCCCCCCCCCEEEE
Q ss_conf             0388788451121179988999
Q gi|254780608|r   46 VRVDKKRVKFNNRIQSGQVVRI   67 (346)
Q Consensus        46 V~VNG~~vk~~~~v~~GD~I~i   67 (346)
                      +.|||++++....|+.||+|.+
T Consensus        73 t~vNg~~i~~~~~L~~gD~i~i   94 (104)
T 2g1l_A           73 TYVNGKLVTEPLVLKSGNRIVM   94 (104)
T ss_dssp             EEETTEECCSCEECCTTCEEEE
T ss_pred             CEECCEECCCCEECCCCCEEEE
T ss_conf             0899878024269999999998


No 40 
>>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural genomics, unknown function; NMR {Pyrococcus furiosus dsm 3638} (A:)
Probab=64.75  E-value=2.7  Score=21.52  Aligned_cols=46  Identities=24%  Similarity=0.378  Sum_probs=34.5

Q ss_pred             HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECC
Q ss_conf             3686689999987678898999999984990388788451121179988999356
Q gi|254780608|r   16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV   70 (346)
Q Consensus        16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~   70 (346)
                      .++..+..+|...  +++..       .=.|.+||..+..++.|+.||.|.|.++
T Consensus        28 ~~~~Tv~~ll~~L--~l~~~-------~v~v~vNg~~v~~~~~L~dgD~v~i~~~   73 (77)
T 1rws_A           28 REGMKVRDILRAV--GFNTE-------SAIAKVNGKVVLEDDEVKDGDFVEVIPV   73 (77)
T ss_dssp             CSSCCHHHHHHTT--TCSSC-------SSCEEETTEEECSSSCCCSSCCCBCSCC
T ss_pred             CCCCCHHHHHHHH--CCCCH-------HHHEEECCEECCCCCCCCCCCEEEEEEC
T ss_conf             9969999999980--99830-------1015599999699728699999999904


No 41 
>>1wln_A Afadin; beta sandwich, FHA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} (A:)
Probab=64.41  E-value=4.7  Score=20.01  Aligned_cols=10  Identities=30%  Similarity=0.245  Sum_probs=3.3

Q ss_pred             EEEECCCEEE
Q ss_conf             7861785688
Q gi|254780608|r  101 LLYEDSKIYV  110 (346)
Q Consensus       101 IiyED~~liv  110 (346)
                      |.|+++.+.+
T Consensus        64 I~~~~~~~~i   73 (120)
T 1wln_A           64 LTNMDGVVTV   73 (120)
T ss_dssp             EEESSSCEEE
T ss_pred             EEECCCCCEE
T ss_conf             9972464489


No 42 
>>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} (A:)
Probab=63.12  E-value=5.3  Score=19.67  Aligned_cols=61  Identities=13%  Similarity=0.243  Sum_probs=34.2

Q ss_pred             EECHHHCCCCHH---HHHHHHCCCCCHHHHHH--HHHCC-CCEECCEEEC----CCCCCCCCCEEEEECCC
Q ss_conf             984113686689---99998767889899999--99849-9038878845----11211799889993565
Q gi|254780608|r   11 VVENDEENMRLD---RWFKNHYPHINFVNLQK--ILRSG-QVRVDKKRVK----FNNRIQSGQVVRIPPVI   71 (346)
Q Consensus        11 ~V~~~~~g~RLd---~~L~~~~~~~sr~~~~~--lir~G-~V~VNG~~vk----~~~~v~~GD~I~i~~~~   71 (346)
                      .++....+..+.   .+|..++|.+.....-.  -++.+ .|.|||+.+.    .++.|+.||.|.+.|+.
T Consensus        35 ~~~~~~~~~Tv~~ll~~L~~~~p~l~~~l~d~~~~~~~~i~v~vN~~~v~~~~~~~t~l~~gDeV~i~Ppv  105 (114)
T 1wgk_A           35 ALPGQEEPWDIRNLLVWIKKNLLKERPELFIQGDSVRPGILVLINDADWELLGELDYQLQDQDSILFISTL  105 (114)
T ss_dssp             EECCCSSCCBHHHHHHHHTTTTCCSCHHHHCCSSSCCSSEEEEESSSBHHHHCTTTCBCCSSEEEEEEECS
T ss_pred             EECCCCCCCCHHHHHHHHHHHCCCCCHHHHCCCCCCCEEEEEEECCCEEEECCCCCCCCCCCCEEEEECCC
T ss_conf             70799987569999999998767522345314788505589997584246056866376997999997888


No 43 
>>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, transcription; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis H37RV} (A:290-388)
Probab=62.14  E-value=7  Score=18.89  Aligned_cols=25  Identities=24%  Similarity=0.437  Sum_probs=16.5

Q ss_pred             CCCEECCEEECCCCCCCCCCEEEEE
Q ss_conf             9903887884511211799889993
Q gi|254780608|r   44 GQVRVDKKRVKFNNRIQSGQVVRIP   68 (346)
Q Consensus        44 G~V~VNG~~vk~~~~v~~GD~I~i~   68 (346)
                      ..+.|||+++.....|+.||.|.|.
T Consensus        59 ~g~~vng~~v~~~~~L~~Gd~i~iG   83 (99)
T 2ff4_A           59 NGVHVQHERIRSAVTLNDGDHIRIC   83 (99)
T ss_dssp             SCCEETTEECSSEEEECTTCEEEET
T ss_pred             CCEEECCEECCCCEECCCCCEEEEC
T ss_conf             7857999998785678999999997


No 44 
>>1v8c_A MOAD related protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, protein binding; 1.60A {Thermus thermophilus} (A:1-84)
Probab=58.96  E-value=10  Score=17.89  Aligned_cols=46  Identities=13%  Similarity=0.372  Sum_probs=29.7

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHCC------CCEECCEEEC----CCCCCCCCCEEEEECC
Q ss_conf             899999876788989999999849------9038878845----1121179988999356
Q gi|254780608|r   21 LDRWFKNHYPHINFVNLQKILRSG------QVRVDKKRVK----FNNRIQSGQVVRIPPV   70 (346)
Q Consensus        21 Ld~~L~~~~~~~sr~~~~~lir~G------~V~VNG~~vk----~~~~v~~GD~I~i~~~   70 (346)
                      |-..|...+|++.    ..++..|      .|.|||+.++    .++.|+.||.|.+.|+
T Consensus        28 ll~~L~~~~p~~~----~~l~~~g~~~~~v~i~vNg~~i~~~~~~~t~l~dgDeVai~PP   83 (84)
T 1v8c_A           28 VLENLVRAYPALK----EELFEGEGLAERVSVFLEGRDVRYLQGLSTPLSPGATLDLFPP   83 (84)
T ss_dssp             HHHHHHHHCGGGH----HHHEETTEECTTCEEEETTEEGGGTTGGGCBCCTTCEEEEECS
T ss_pred             HHHHHHHHCCCCH----HHCCCCCCCCCEEEEEECCEEECCCCCCCCCCCCCCEEEEECC
T ss_conf             9999985786302----2003443510138999878774145788868699999999699


No 45 
>>3els_A PRE-mRNA leakage protein 1; intrinsically unstructured domain, forkhead-associated domain (FHA) domain, PRE-mRNA retention and splicing; 1.80A {Saccharomyces cerevisiae} (A:)
Probab=56.64  E-value=11  Score=17.63  Aligned_cols=18  Identities=11%  Similarity=-0.010  Sum_probs=7.9

Q ss_pred             CCEEEEECCCCHHHHHCC
Q ss_conf             240462123101222102
Q gi|254780608|r  155 SGILVVARTRAAAQHLTE  172 (346)
Q Consensus       155 SGlll~AK~~~a~~~l~~  172 (346)
                      .+-+++.++..+--.|..
T Consensus        70 ~~~~~iGR~~~~di~l~~   87 (158)
T 3els_A           70 TDLDDRTEIVVADIGIPE   87 (158)
T ss_dssp             ------CCCCCCSEEECC
T ss_pred             CCCCCCCCCCCCCEECCC
T ss_conf             532244775210377799


No 46 
>>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, biosynthetic protein; 3.15A {Bacillus subtilis} (B:)
Probab=54.65  E-value=12  Score=17.49  Aligned_cols=59  Identities=7%  Similarity=0.018  Sum_probs=36.0

Q ss_pred             CCCCCEEEEEECHH---H--CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEEEC
Q ss_conf             76683049998411---3--686689999987678898999999984990388788451----12117998899935
Q gi|254780608|r    2 SLMTYVQYVVVEND---E--ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRIPP   69 (346)
Q Consensus         2 ~~M~~~~~~~V~~~---~--~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i~~   69 (346)
                      .-|+.+-.++|...   .  ++..|..+|...  +++..       .=.|-|||..+..    ++.|+.||.|+|..
T Consensus        15 ~~~~~~m~I~vNG~~~~~~~e~~tl~~lL~~l--~~~~~-------~vaV~vN~~iVpr~~w~~~~L~~gD~IEIi~   82 (87)
T 1tyg_B           15 GHIGGRHMLQLNGKDVKWKKDTGTIQDLLASY--QLENK-------IVIVERNKEIIGKERYHEVELCDRDVIEIVH   82 (87)
T ss_dssp             -------CEEETTEEECCSSSCCBHHHHHHHT--TCTTS-------CCEEEETTEEECGGGTTTSBCCSSSEEEEEE
T ss_pred             CCCCCEEEEEECCEEEECCCCCCCHHHHHHHC--CCCCC-------EEEEEECCEECCHHHCCHHCCCCCCEEEEEE
T ss_conf             55388599999998988688886499999875--99988-------1999989998786787530599979999998


No 47 
>>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative; 2.10A {Haemophilus influenzae 86-028np} (A:)
Probab=52.29  E-value=8.5  Score=18.39  Aligned_cols=38  Identities=13%  Similarity=0.420  Sum_probs=27.4

Q ss_pred             HHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECC
Q ss_conf             987678898999999984990388788451121179988999356
Q gi|254780608|r   26 KNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV   70 (346)
Q Consensus        26 ~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~   70 (346)
                      .+.||++..       ....|=|=|+.++.++.|+.||+|+|+-+
T Consensus        48 l~~fPeidl-------~~~~vGIfgk~v~~d~~L~~GDRVEIYRP   85 (97)
T 2hj1_A           48 LSQFPEIDL-------STNKIGIFSRPIKLTDVLKEGDRIEIYRP   85 (97)
T ss_dssp             HHHCTTCCT-------TTSEEEEEECSCCTTCBCCTTCEEEECCC
T ss_pred             HHHCCCCCC-------CCCCEEEECCCCCCCCCCCCCCEEEEECC
T ss_conf             545966470-------10615568938588771789999999456


No 48 
>>1wxq_A GTP-binding protein; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 2.60A {Pyrococcus horikoshii OT3} (A:317-397)
Probab=49.76  E-value=4.8  Score=19.95  Aligned_cols=24  Identities=25%  Similarity=0.264  Sum_probs=20.6

Q ss_pred             CCEECCEEECCCCCCCCCCEEEEE
Q ss_conf             903887884511211799889993
Q gi|254780608|r   45 QVRVDKKRVKFNNRIQSGQVVRIP   68 (346)
Q Consensus        45 ~V~VNG~~vk~~~~v~~GD~I~i~   68 (346)
                      .+.+||+++..++.|+.||+|+|-
T Consensus        54 ~~~~~g~~v~~d~~L~dgDvV~Ii   77 (81)
T 1wxq_A           54 INARTKRRVGEDYELQFNDIVKIV   77 (81)
T ss_dssp             EETTTCSBCCTTCCCCTTEEEEEE
T ss_pred             EECCCCEEECCCCEECCCCEEEEE
T ss_conf             866776285698485689889999


No 49 
>>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A (A:)
Probab=49.61  E-value=16  Score=16.60  Aligned_cols=53  Identities=2%  Similarity=0.081  Sum_probs=32.2

Q ss_pred             CCCCHHH---HHHHHCCCCCHHHHHHHHHCC------CCEECCEEEC----CCCCCCCCCEEEEECC
Q ss_conf             6866899---999876788989999999849------9038878845----1121179988999356
Q gi|254780608|r   17 ENMRLDR---WFKNHYPHINFVNLQKILRSG------QVRVDKKRVK----FNNRIQSGQVVRIPPV   70 (346)
Q Consensus        17 ~g~RLd~---~L~~~~~~~sr~~~~~lir~G------~V~VNG~~vk----~~~~v~~GD~I~i~~~   70 (346)
                      .|..+..   .|.+++|...+. +.-....|      .|.|||+.++    .++.|+.||.|.+.|+
T Consensus        30 ~~~Tv~~li~~l~~~~p~~~~~-~~~~~~~~~~~~~~~v~vNg~~i~~~~~~~t~L~~gDeV~i~pp   95 (99)
T 2qjl_A           30 DPVTVGDLIDHIVSTMINNPND-VSIFIEDDSIRPGIITLINDTDWELEGEKDYILEDGDIISFTST   95 (99)
T ss_dssp             SCCBHHHHHHHHHHHTCSSGGG-HHHHEETTEECTTEEEEETTEEGGGGTGGGCBCCTTCEEEEEEC
T ss_pred             CCCCHHHHHHHHHHHCCCCHHH-HHHHCCCCCEEEEEEEEECCCEEECCCCCCCCCCCCCEEEEECC
T ss_conf             8888999999999874553034-33112345423228999879587817887758599799999678


No 50 
>>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis H37RV} PDB: 3dwm_A (C:)
Probab=48.63  E-value=17  Score=16.43  Aligned_cols=27  Identities=26%  Similarity=0.534  Sum_probs=21.2

Q ss_pred             CCEECCEEEC----CCCCCCCCCEEEEECCC
Q ss_conf             9038878845----11211799889993565
Q gi|254780608|r   45 QVRVDKKRVK----FNNRIQSGQVVRIPPVI   71 (346)
Q Consensus        45 ~V~VNG~~vk----~~~~v~~GD~I~i~~~~   71 (346)
                      .|.|||..+.    .++.|+.||+|.+.|+.
T Consensus        60 ~v~vNg~~v~~~~~~~t~l~~gDeV~ilPpv   90 (93)
T 3dwg_C           60 NIYVNDEDVRFSGGLATAIADGDSVTILPAV   90 (93)
T ss_dssp             EEEETTEEGGGTTGGGCBCCTTCEEEEEECC
T ss_pred             EEEECCEEECCCCCCCCCCCCCCEEEEECCC
T ss_conf             9998574510014766637998999996888


No 51 
>>3huh_A Virulence protein STM3117; structural genomics, nysgrc, target 13955A1BCT15P1, dioxygenase, PSI-2, protein structure initiative; 1.50A {Salmonella enterica subsp} PDB: 3hnq_A (A:78-152)
Probab=46.22  E-value=19  Score=16.12  Aligned_cols=50  Identities=18%  Similarity=0.265  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHCCCCEECCC--CCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCHHH
Q ss_conf             8999999996398000464--446652210001344624131100043758896499983997899
Q gi|254780608|r  252 THQLRVHALHMGCPIVGDH--KYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAHM  315 (346)
Q Consensus       252 ~HQIRvhl~~~g~PivGD~--~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~~f  315 (346)
                      -.+...||...|.+|.+.+  .+|....              .+++-|..|++..+++.++.|..-
T Consensus        20 ~d~~~~~L~~~Gv~i~~~p~~~~~~~~~--------------~~siYf~DPdG~~iEl~~~~~~~~   71 (75)
T 3huh_A           20 INDVVSEILQAGISIVEGPVERTGATGE--------------IMSIYIRDPDGNLIEISQYVEGHH   71 (75)
T ss_dssp             HHHHHHHHHHTTCCCSEEEEEEEETTEE--------------EEEEEEECTTCCEEEEEEC-----
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCC--------------EEEEEEECCCCCEEEEEEECCCCC
T ss_conf             7899999987186522387332268886--------------899999999999899988889876


No 52 
>>2rk0_A Glyoxalase/bleomycin resistance protein/dioxygenase domain; 11002Z, glyoxylase, PSI-II, newyork structural genomix research consortium (nysgrc); 2.04A {Frankia SP} (A:68-136)
Probab=45.62  E-value=20  Score=16.06  Aligned_cols=45  Identities=7%  Similarity=0.020  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCH
Q ss_conf             89999999963980004644466522100013446241311000437588964999839978
Q gi|254780608|r  252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPA  313 (346)
Q Consensus       252 ~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~  313 (346)
                      --+++.+|...|.++.+-.-.|.                 .+++.|..|.+..+++.++-|.
T Consensus        19 l~~~~~~L~~~gv~~~~~~~~g~-----------------~~siyf~DPdG~~iEl~~~~p~   63 (69)
T 2rk0_A           19 LDVLEERLAKAGAAFTPTQELPF-----------------GWILAFRDADNIALEAXLGREG   63 (69)
T ss_dssp             HHHHHHHHHHHTCCBCCCEEETT-----------------EEEEEEECTTCCEEEEEEECTT
T ss_pred             HHHHHHHHHHCCCEECCCCCCCC-----------------EEEEEEECCCCCEEEEEECCCC
T ss_conf             99999999978986478661798-----------------4999999999998999999985


No 53 
>>1wwt_A Threonyl-tRNA synthetase, cytoplasmic; TGS domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ligase; NMR {Homo sapiens} (A:)
Probab=40.33  E-value=24  Score=15.55  Aligned_cols=61  Identities=7%  Similarity=-0.097  Sum_probs=41.5

Q ss_pred             CCCCCCEEEEEECHH-----H-CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEE
Q ss_conf             976683049998411-----3-6866899999876788989999999849903887884511211799889993
Q gi|254780608|r    1 MSLMTYVQYVVVEND-----E-ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP   68 (346)
Q Consensus         1 ~~~M~~~~~~~V~~~-----~-~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~   68 (346)
                      +++|+.+=.++.+..     . .|..+..|.....+.+.+.       .=..+|||+.+..++.|..++.|++-
T Consensus         5 ~~~~~~~I~V~lpdg~~~~~~~~gtT~~dia~~i~~~~~~~-------~vaa~vng~l~dL~~~l~~d~~ve~i   71 (88)
T 1wwt_A            5 SSGDSKPIKVTLPDGKQVDAESWKTTPYQIACGISQGLADN-------TVIAKVNNVVWDLDRPLEEDCTLELL   71 (88)
T ss_dssp             CCCSCCEEEEECTTSCEEEEETTTCCHHHHHHHSSTTTGGG-------CCCEEESSSEECSSSCCCSSEEEEEC
T ss_pred             CCCCCCCEEEECCCCCEEECCCCCCCHHHHHHHHCHHHHHH-------HHEECCCCEEEEEEEECCCCCEEEEE
T ss_conf             55788757999799998971289977999999877778888-------87313298787501781899999999


No 54 
>>3hvz_A Uncharacterized protein; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.20A {Clostridium leptum dsm 753} (A:)
Probab=39.52  E-value=23  Score=15.70  Aligned_cols=60  Identities=10%  Similarity=0.140  Sum_probs=37.6

Q ss_pred             CCCCCEEEEEECHH-----HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEE
Q ss_conf             76683049998411-----36866899999876788989999999849903887884511211799889993
Q gi|254780608|r    2 SLMTYVQYVVVEND-----EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP   68 (346)
Q Consensus         2 ~~M~~~~~~~V~~~-----~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~   68 (346)
                      +||+.+=+++.+..     ..|.+.-.+.....+    ....+   .=..+|||+.+..++.|+.|+.|++-
T Consensus         2 ~l~~~~I~V~lpdG~~~~~~~g~T~~diA~~i~~----~l~~~---~v~a~vng~l~dL~~~l~~~~~veii   66 (78)
T 3hvz_A            2 DLAPEEVFVFTPKGDVISLPIGSTVIDFAYAIHS----AVGNR---XIGAKVDGRIVPIDYKVKTGEIIDVL   66 (78)
T ss_dssp             ----CEEEEECTTSCEEEEETTCBHHHHHHHHCH----HHHHT---EEEEEETTEEECTTCBCCTTCBEEEE
T ss_pred             CCCCCEEEEECCCCCEEECCCCCCHHHHHHHHHH----HHHHH---EEEEEECCEECCCCCCCCCCCEEEEE
T ss_conf             8778768998999976879999958898998700----36532---00379999999998885899999999


No 55 
>>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR {Trypanosoma brucei} (A:)
Probab=36.28  E-value=16  Score=16.62  Aligned_cols=56  Identities=20%  Similarity=0.270  Sum_probs=32.1

Q ss_pred             CCCCHHHHH---HHHCCCCCHHHHH----HHHHCC-CCEECCEEEC----CCCCCCCCCEEEEECCCC
Q ss_conf             686689999---9876788989999----999849-9038878845----112117998899935655
Q gi|254780608|r   17 ENMRLDRWF---KNHYPHINFVNLQ----KILRSG-QVRVDKKRVK----FNNRIQSGQVVRIPPVIN   72 (346)
Q Consensus        17 ~g~RLd~~L---~~~~~~~sr~~~~----~lir~G-~V~VNG~~vk----~~~~v~~GD~I~i~~~~~   72 (346)
                      .|..+..++   .+.+|.+.+....    .-++.+ .|.|||+.+.    .++.|+.||.|.+.|+.-
T Consensus        33 ~~~Tv~~ll~~L~~~~p~~~~~l~~~~~~~~~r~~i~v~VN~~~v~~~~~~~t~L~~gDeV~ilppvs  100 (110)
T 2k9x_A           33 TGTNLNGLVQLLKTNYVKERPDLLVDQTGQTLRPGILVLVNSCDAEVVGGMDYVLNDGDTVEFISTLH  100 (110)
T ss_dssp             GGCCHHHHHHHHTTTTCCSCHHHHBCSSSSSBCTTEEEEESSSBHHHHTSSCCCCCSSCEEEEEECCC
T ss_pred             CCCCHHHHHHHHHHHCCCCHHHCCCCCCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCEEEEECCCC
T ss_conf             99869999999998767303440244556650111899988956243888564859979999978887


No 56 
>>2eki_A DRG 1, developmentally-regulated GTP-binding protein 1; protein NEDD3, neural precursor cell expressed developmentally DOWN-regulated protein 3; NMR {Homo sapiens} (A:)
Probab=31.31  E-value=28  Score=15.11  Aligned_cols=16  Identities=19%  Similarity=0.459  Sum_probs=7.3

Q ss_pred             EECCCCCCCCCCEEEE
Q ss_conf             8451121179988999
Q gi|254780608|r   52 RVKFNNRIQSGQVVRI   67 (346)
Q Consensus        52 ~vk~~~~v~~GD~I~i   67 (346)
                      ++-.++.|+.||+|+|
T Consensus        69 ~vgl~~~L~dgDvV~I   84 (93)
T 2eki_A           69 KVGKDHTLEDEDVIQI   84 (93)
T ss_dssp             EECSSCCCCSSEEECE
T ss_pred             CCCCCCEECCCCEEEE
T ss_conf             6787628069999999


No 57 
>>3ct8_A Protein BH2160, putative glyoxalase; NP_243026.1, glyoxalase/bleomycin resistance protein/dioxygenase superfamily, structural genomics; HET: UNL; 2.10A {Bacillus halodurans c-125} (A:80-146)
Probab=31.30  E-value=33  Score=14.64  Aligned_cols=47  Identities=17%  Similarity=0.127  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECC
Q ss_conf             89999999963980004644466522100013446241311000437588964999839
Q gi|254780608|r  252 THQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAP  310 (346)
Q Consensus       252 ~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~ap  310 (346)
                      -.++..++...|.+|++.+.......            -..+.+.|..|++.++++.||
T Consensus        21 Vd~~~~~l~~~G~~i~~~p~~~~~~~------------~~~~~~~~~DPDG~~iEi~~P   67 (67)
T 3ct8_A           21 VDELTQKLKERGDPILYEDRHPFAGG------------PNHYAVFCEDPNRIKVEIVAP   67 (67)
T ss_dssp             HHHHHHHHHHHTCCBCCTTTTTCTTC------------TTCCEEEEECTTCCEEEEECC
T ss_pred             HHHHHHHHHHCCCEEECCCCCCCCCC------------CCEEEEEEECCCCCEEEEEEC
T ss_conf             89998889875977835998762689------------967999999899999999969


No 58 
>>2exd_A NFED short homolog; membrane protein; NMR {Pyrococcus horikoshii OT3} (A:)
Probab=30.75  E-value=34  Score=14.58  Aligned_cols=27  Identities=15%  Similarity=0.203  Sum_probs=21.0

Q ss_pred             HCCCCEECCEE--ECCCCCCCCCCEEEEE
Q ss_conf             84990388788--4511211799889993
Q gi|254780608|r   42 RSGQVRVDKKR--VKFNNRIQSGQVVRIP   68 (346)
Q Consensus        42 r~G~V~VNG~~--vk~~~~v~~GD~I~i~   68 (346)
                      ..|.|+++|..  +.....+..||.|+|-
T Consensus        29 ~~G~V~v~G~~W~A~s~~~i~~G~~V~V~   57 (80)
T 2exd_A           29 DHYLVEVEGDKWIAYSDEKLSLGDRVMVV   57 (80)
T ss_dssp             TCEEEEETTEEEEECCSSCCCTTCEEEEE
T ss_pred             CCEEEEECCEEEEEEECCCCCCCCEEEEE
T ss_conf             98999999989999979964899999999


No 59 
>>2csw_A Ubiquitin ligase protein RNF8; 11-stranded beta sandwich, ring finger protein 8, structural genomics, NPPSFA; NMR {Homo sapiens} (A:)
Probab=29.28  E-value=35  Score=14.53  Aligned_cols=10  Identities=20%  Similarity=0.066  Sum_probs=3.4

Q ss_pred             CEEEEECCCC
Q ss_conf             4046212310
Q gi|254780608|r  156 GILVVARTRA  165 (346)
Q Consensus       156 Glll~AK~~~  165 (346)
                      +.++|.+...
T Consensus        36 ~~~~iGR~~~   45 (145)
T 2csw_A           36 CEVTVGRGFG   45 (145)
T ss_dssp             CCEEEESSTT
T ss_pred             CEEEEECCCC
T ss_conf             7499837999


No 60 
>>3ey7_A Biphenyl-2,3-DIOL 1,2-dioxygenase III-related protein; integron cassette protein mobIle metagenome structural genomics, oxidoreductase, PSI-2; HET: MSE; 1.60A {Vibrio cholerae} PDB: 3ey8_A* (A:67-133)
Probab=27.35  E-value=39  Score=14.21  Aligned_cols=45  Identities=13%  Similarity=0.138  Sum_probs=33.6

Q ss_pred             HHHHHHHHHCCCCEECCCC--CCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCC
Q ss_conf             9999999963980004644--4665221000134462413110004375889649998399
Q gi|254780608|r  253 HQLRVHALHMGCPIVGDHK--YCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL  311 (346)
Q Consensus       253 HQIRvhl~~~g~PivGD~~--Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~apl  311 (346)
                      -.+..||.+.|.+|.+++.  +|....              ..++.|..|++..++|.++.
T Consensus        19 d~~~~~L~~~Gv~i~~~p~~~~~~~g~--------------~~siYf~DPdG~~iEl~~~p   65 (67)
T 3ey7_A           19 SDAXKHVEDQGVTIXEGPVKRTGAQGA--------------ITSFYFRDPDGNLIEVSTYS   65 (67)
T ss_dssp             HHHHHHHHHTTCCCCEEEEEEEETTEE--------------EEEEEEECTTCCEEEEEESC
T ss_pred             HHHHHHHHHCCCCEECCCCCCCCCCCC--------------EEEEEEECCCCCEEEEEECC
T ss_conf             899999997597400287232278886--------------89999999999999989776


No 61 
>>1vc3_B L-aspartate-alpha-decarboxylase heavy chain; tetramer, pyruvoyl group, riken structural genomics/proteomics initiative, RSGI; 1.50A {Thermus thermophilus} PDB: 2eeo_B (B:)
Probab=26.30  E-value=34  Score=14.54  Aligned_cols=48  Identities=15%  Similarity=0.171  Sum_probs=29.8

Q ss_pred             EEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECC
Q ss_conf             99984113686689999987678898999999984990388788451121179988999356
Q gi|254780608|r    9 YVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPV   70 (346)
Q Consensus         9 ~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~   70 (346)
                      .+-|-.-..|.|+..|...--    +       -+|.|.+||..+   ..++.||+|.|-.+
T Consensus        19 ~V~V~Nv~NG~Rf~TY~I~G~----~-------GSg~I~lNGAAA---rl~~~GD~vII~sy   66 (96)
T 1vc3_B           19 QVDIYDITNGARLTTYALPGE----R-------GSGVIGINGAAA---HLVKPGDLVILVAY   66 (96)
T ss_dssp             EEEEEETTTCCEEEEECEEEC----T-------TTTCEEEEGGGG---GTCCTTCEEEEEEE
T ss_pred             EEEEEECCCCCEEEEEEEECC----C-------CCCEEEECCHHH---EECCCCCEEEEEEC
T ss_conf             899999989948987999636----7-------668798558564---23599999999987


No 62 
>>1yj5_C 5' polynucleotide kinase-3' phosphatase FHA domain; beta sandwich, P-loop, transferase; 2.80A {Mus musculus} (C:)
Probab=26.28  E-value=41  Score=14.09  Aligned_cols=22  Identities=18%  Similarity=0.274  Sum_probs=11.5

Q ss_pred             CEECCEEECCC--CCCCCCCEEEE
Q ss_conf             03887884511--21179988999
Q gi|254780608|r   46 VRVDKKRVKFN--NRIQSGQVVRI   67 (346)
Q Consensus        46 V~VNG~~vk~~--~~v~~GD~I~i   67 (346)
                      +.|||+++...  +.|+.||+|.|
T Consensus        72 t~vNg~~i~~~~~~~L~~Gd~i~i   95 (143)
T 1yj5_C           72 STVGVHELKPGLSGSLSLGDVLYL   95 (143)
T ss_dssp             CEETTEECCTTCEEEECTTCEEES
T ss_pred             CEECCEECCCCEEEECCCCCEEEE
T ss_conf             378548804763898479999999


No 63 
>>1wv3_A Similar to DNA segregation ATPase and related proteins; structural genomics, unknown function; 1.75A {Staphylococcus aureus subsp} (A:81-238)
Probab=26.19  E-value=41  Score=14.08  Aligned_cols=27  Identities=11%  Similarity=0.208  Sum_probs=20.2

Q ss_pred             CCCCEECCEEEC-CCCCCCCCCEEEEEC
Q ss_conf             499038878845-112117998899935
Q gi|254780608|r   43 SGQVRVDKKRVK-FNNRIQSGQVVRIPP   69 (346)
Q Consensus        43 ~G~V~VNG~~vk-~~~~v~~GD~I~i~~   69 (346)
                      +|-+.+||+.+. ....|+.||+|.|..
T Consensus        54 ngt~~~n~~~~~~~~~~L~~Gd~i~iG~   81 (158)
T 1wv3_A           54 NTDVYINYELQEQLTNKAYIGDHIYVEG   81 (158)
T ss_dssp             TCCEEETTEECCSSEEEEETTCEEEETT
T ss_pred             CCCEEECCEEEECCEEECCCCCEEEECC
T ss_conf             9869987899725504304899999998


No 64 
>>2k5p_A THis protein, thiamine-biosynthesis protein; NESG, GMR137, structural genomics, PSI-2, protein structure initiative; NMR {Geobacter metallireducens gs-15} PDB: 3cwi_A (A:)
Probab=26.10  E-value=41  Score=14.07  Aligned_cols=46  Identities=9%  Similarity=0.169  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEEECC
Q ss_conf             686689999987678898999999984990388788451----121179988999356
Q gi|254780608|r   17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRIPPV   70 (346)
Q Consensus        17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i~~~   70 (346)
                      .+..|..+|...  +++..      +.=.|-+||+.+..    ++.|+.||.|.|...
T Consensus        16 ~~~tl~~lL~~l--~~~~~------~~iaV~vN~~iVpr~~w~~~~L~~gD~IeIi~~   65 (78)
T 2k5p_A           16 ESLNVTELLSAL--KVAQA------EYVTVELNGEVLEREAFDATTVKDGDAVEFLYF   65 (78)
T ss_dssp             SCEEHHHHHHHH--TCSCT------TTCCEEETTEECCTTHHHHCEECSSBCEEECCC
T ss_pred             CCCCHHHHHHHC--CCCCC------CEEEEEECCEEECHHHHCCCCCCCCCEEEEEEE
T ss_conf             998099999877--99889------879999899994778918044899799999958


No 65 
>>1tke_A Threonyl-tRNA synthetase; ligase; 1.46A {Escherichia coli} (A:1-63)
Probab=26.10  E-value=41  Score=14.07  Aligned_cols=45  Identities=13%  Similarity=-0.001  Sum_probs=31.4

Q ss_pred             HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEE
Q ss_conf             3686689999987678898999999984990388788451121179988999
Q gi|254780608|r   16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI   67 (346)
Q Consensus        16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i   67 (346)
                      ..|..+-.+.....+    +..++   .=..+|||+.+..++.|..++.|++
T Consensus        15 ~~g~T~~dia~~i~~----~~~~~---~v~a~vng~l~dL~~~l~~d~~ve~   59 (63)
T 1tke_A           15 DHAVSPMDVALDIGP----GLAKA---CIAGRVNGELVDACDLIENDAQLSI   59 (63)
T ss_dssp             SSCBCHHHHHHHHCH----HHHHH---CCEEEETTEEEETTCCBCSCEEEEE
T ss_pred             CCCCCHHHHHHHHCC----CHHHH---EEEEEECCEEECCCCCCCCCCEEEE
T ss_conf             899999999998670----01544---6999999999638844178758999


No 66 
>>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} (A:)
Probab=24.80  E-value=42  Score=14.00  Aligned_cols=44  Identities=7%  Similarity=0.141  Sum_probs=28.2

Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECC----CCCCCCCCEEEEEC
Q ss_conf             686689999987678898999999984990388788451----12117998899935
Q gi|254780608|r   17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKF----NNRIQSGQVVRIPP   69 (346)
Q Consensus        17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~----~~~v~~GD~I~i~~   69 (346)
                      +++.|..+|...  ++...       .=.|-+||..+..    ++.++.||.|.|..
T Consensus        14 ~~~tl~~lL~~~--~~~~~-------~vav~vN~~iv~k~~~~~~~l~~gD~ieiv~   61 (66)
T 1f0z_A           14 AGQTVHELLEQL--DQRQA-------GAALAINQQIVPREQWAQHIVQDGDQILLFQ   61 (66)
T ss_dssp             TTCCHHHHHHHH--TCCCS-------SEEEEETTEEECHHHHTTCCCCTTEEECEEE
T ss_pred             CCCCHHHHHHHC--CCCCC-------CEEEEECCEECCHHHCCCCCCCCCCEEEEEE
T ss_conf             999999999876--99998-------1999999999387882813489989999997


No 67 
>>3kt9_A Aprataxin; FHA domain, beta sandwich, beta sheet, AMP hydrolase, alternative splicing, disease mutation, DNA damage, DNA repair, DNA-binding; 1.65A {Homo sapiens} (A:)
Probab=24.69  E-value=43  Score=13.91  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=14.6

Q ss_pred             CCEECCEEECC--CCCCCCCCEEEEE
Q ss_conf             90388788451--1211799889993
Q gi|254780608|r   45 QVRVDKKRVKF--NNRIQSGQVVRIP   68 (346)
Q Consensus        45 ~V~VNG~~vk~--~~~v~~GD~I~i~   68 (346)
                      .+.|||+++.+  ...|+.||.|++.
T Consensus        65 gt~vng~~l~~~~~~~L~~gd~I~iG   90 (102)
T 3kt9_A           65 PTSIDSVVIGKDQEVKLQPGQVLHMV   90 (102)
T ss_dssp             CCEETTEECCBTCEEEECTTCCEEEE
T ss_pred             CEEECCEEECCCCCCCCCCCCEEEEE
T ss_conf             75899899468976164899999990


No 68 
>>3elx_A Ileal bIle acid-binding protein; ileal bIle acid-bindign protein, zebrafish, cholic acid, X- RAY structure, lipid-binding, transport; 1.60A {Danio rerio} PDB: 3elz_A* 3em0_A* (A:)
Probab=23.25  E-value=46  Score=13.73  Aligned_cols=48  Identities=13%  Similarity=-0.034  Sum_probs=33.0

Q ss_pred             CCCCCCEEEEEECHHHCCCCHHHHHHHHCCCCCHHHHHHHHHCC---CCEECCEEE
Q ss_conf             97668304999841136866899999876788989999999849---903887884
Q gi|254780608|r    1 MSLMTYVQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSG---QVRVDKKRV   53 (346)
Q Consensus         1 ~~~M~~~~~~~V~~~~~g~RLd~~L~~~~~~~sr~~~~~lir~G---~V~VNG~~v   53 (346)
                      |++|.........+.++   .|.||...  ++|....+.+-...   .|..||...
T Consensus         1 Ms~~~f~Gtwkl~~sEN---fd~~Lk~l--GV~~~~Rk~a~~~kp~~~I~~~Gd~~   51 (138)
T 3elx_A            1 MRGSAFNGKWETESQEG---YEPFCKLI--GIPDDVIAKGRDFKLVTEIVQNGDDF   51 (138)
T ss_dssp             --CCTTCEEEEEEEEES---HHHHHHHT--TCCHHHHHHTTTCCCEEEEEEETTEE
T ss_pred             CCCCCCEEEEEEEEEEC---HHHHHHHH--CCCHHHHHHHHCCCCEEEEEEECCEE
T ss_conf             97762207999984219---99999884--99999998876179769999909989


No 69 
>>2kmm_A Guanosine-3',5'-BIS(diphosphate) 3'- pyrophosphohydrolase; methods development, TGS domain, predominantly beta-sheet structure; NMR {Porphyromonas gingivalis} (A:)
Probab=22.88  E-value=47  Score=13.69  Aligned_cols=45  Identities=13%  Similarity=0.113  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEE
Q ss_conf             6866899999876788989999999849903887884511211799889993
Q gi|254780608|r   17 ENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIP   68 (346)
Q Consensus        17 ~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~   68 (346)
                      .|..+-.+.....+.+.+    +   .=..+|||+.+..++.|..|+.|++-
T Consensus        17 ~GtT~~dia~~i~~~l~~----~---~v~A~vng~l~dL~~~l~~~~~ve~i   61 (73)
T 2kmm_A           17 QGATALDFAYSLHSDLGD----H---CIGAKVNHKLVPLSYVLNSGDQVEVL   61 (73)
T ss_dssp             TTCBHHHHHHHHCSHHHH----T---EEEEEETTEECCTTCBCCSSSBEEEE
T ss_pred             CCCCHHHHHHHHCCCHHH----E---EEEEEECCEECCCCCCCCCCCEEEEE
T ss_conf             999631048774845023----6---89998898599888795899999999


No 70 
>>2hd9_A UPF0310 protein PH1033; structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: CIT; 1.35A {Pyrococcus horikoshii OT3} (A:)
Probab=22.21  E-value=48  Score=13.66  Aligned_cols=42  Identities=24%  Similarity=0.148  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEEECCCCC
Q ss_conf             898999999984990388788451121179988999356554
Q gi|254780608|r   32 INFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINA   73 (346)
Q Consensus        32 ~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i~~~~~~   73 (346)
                      .|+..++.....|-..++..+..+-.++++||.|.+..+...
T Consensus         8 ~s~e~~~~~~~~g~~~v~~gk~~~l~rikpGD~li~Y~~~~~   49 (145)
T 2hd9_A            8 TNRENWEVIKRHNVWGVPKKHKNTLSRVKPGDKLVIYVRQEK   49 (145)
T ss_dssp             ECHHHHHHHHHHCEEEECGGGHHHHTTCCTTCEEEEEECCEE
T ss_pred             CCHHHHHHHHHCCEEECCCCCHHHHHHCCCCCEEEEEECCCC
T ss_conf             799999999968888525765537861788887999955424


No 71 
>>3cuz_A MSA, malate synthase A; TIM barrel, cytoplasm, glyoxylate bypass, transferase, tricarboxylic acid cycle; 1.04A {Escherichia coli} PDB: 3cv1_A 3cv2_A* (A:399-532)
Probab=21.77  E-value=24  Score=15.48  Aligned_cols=27  Identities=11%  Similarity=0.047  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHHHCCCCEECCEEECCCC
Q ss_conf             889899999998499038878845112
Q gi|254780608|r   31 HINFVNLQKILRSGQVRVDKKRVKFNN   57 (346)
Q Consensus        31 ~~sr~~~~~lir~G~V~VNG~~vk~~~   57 (346)
                      .+||+++=+|++.|...-||+++....
T Consensus        53 EISR~QlWQWi~hg~~l~dG~~vt~~~   79 (134)
T 3cuz_A           53 EISRTSIWQWIHHQKTLSNGKPVTKAL   79 (134)
T ss_dssp             HHHHHHHHHHHHTTCBCTTSCBCCHHH
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHH
T ss_conf             999999999997677778884726999


No 72 
>>1qf6_A THRRS, threonyl-tRNA synthetase; tRNA(Thr), AMP, zinc, mRNA, aminoacylation, translational regulation, protein/RNA, ligase/RNA complex; HET: H2U AET G7M 5MU PSU AMP; 2.90A {Escherichia coli} (A:1-63)
Probab=21.74  E-value=41  Score=14.07  Aligned_cols=45  Identities=13%  Similarity=-0.001  Sum_probs=30.9

Q ss_pred             HCCCCHHHHHHHHCCCCCHHHHHHHHHCCCCEECCEEECCCCCCCCCCEEEE
Q ss_conf             3686689999987678898999999984990388788451121179988999
Q gi|254780608|r   16 EENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRI   67 (346)
Q Consensus        16 ~~g~RLd~~L~~~~~~~sr~~~~~lir~G~V~VNG~~vk~~~~v~~GD~I~i   67 (346)
                      ..|..+-.+.....+    +..++   .=..+|||+.+..++.|..++.|++
T Consensus        15 ~~g~T~~dia~~i~~----~~~~~---~v~a~vng~l~dL~~~l~~d~~ve~   59 (63)
T 1qf6_A           15 DHAVSPMDVALDIGP----GLAKA---CIAGRVNGELVDACDLIENDAQLSI   59 (63)
T ss_dssp             SSCBCHHHHHHHHCH----HHHHH---CSEEEETTEEEETTSCBCSCEECCE
T ss_pred             CCCCCHHHHHHHHCH----HHHHH---EEEEEECCEEEECCCCCCCCCEEEE
T ss_conf             899999999998653----12435---6999999999857851799988998


No 73 
>>1nki_A Probable fosfomycin resistance protein; potassium binding loop, manganese binding, transferase; 0.95A {Pseudomonas aeruginosa PAO1} (A:59-135)
Probab=20.82  E-value=52  Score=13.43  Aligned_cols=61  Identities=8%  Similarity=0.016  Sum_probs=42.2

Q ss_pred             EEECHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHHCCCCCCCHHHHHHHHEEECCCCCEEEEECCCCHH-HHHHHHHHC
Q ss_conf             7861237899999999639800046444665221000134462413110004375889649998399789-999999808
Q gi|254780608|r  245 MQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGRLQITAPLPAH-MVKTWDSLG  323 (346)
Q Consensus       245 ~~l~TGR~HQIRvhl~~~g~PivGD~~Yg~~~~~~~~~~~~~r~~LHa~~l~f~hp~~~~~~~~aplP~~-f~~~l~~l~  323 (346)
                      +..-+.--.+++.+|...|.|+.....=+                  ..++.|..|.+..+++.+.-|.. .......++
T Consensus         9 F~v~~~~~~~~~~~L~~~Gv~v~~~~~~~------------------~~siYf~DPdG~~iEl~~~~~~~~~~~~~~~~~   70 (77)
T 1nki_A            9 FGIAAADFARFAAQLRAHGVREWKQNRSE------------------GDSFYFLDPDGHRLEAHVGDLRSRLAACRQAPY   70 (77)
T ss_dssp             EEECHHHHHHHHHHHHHTTCCEEECCCSS------------------SCEEEEECTTCCEEEEESCCHHHHHHHHHHSCC
T ss_pred             ECCCHHHHHHHHHHHHHCCCCEECCCCCC------------------EEEEEEECCCCCEEEEEECCHHHCCCCCCCCCC
T ss_conf             12558899999999998899472489887------------------479999999999999998971341200446882


Done!