Query         gi|254780715|ref|YP_003065128.1| 50S ribosomal protein L19 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 141
No_of_seqs    113 out of 921
Neff          4.8 
Searched_HMMs 33803
Date          Wed Jun  1 15:53:42 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780715.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3i1n_P 50S ribosomal protein  100.0   2E-43       0  294.3   5.5  113    1-118     2-114 (115)
  2 >2zjr_M 50S ribosomal protein  100.0 8.5E-43       0  290.2   5.7  114   21-134     1-114 (143)
  3 >2ftc_K 39S ribosomal protein  100.0 1.2E-38 3.4E-43  264.2   8.0   98   21-119     1-98  (98)
  4 >3bbo_R Ribosomal protein L19; 100.0 1.1E-36 3.4E-41  251.6  -3.2   91   24-115     1-91  (91)
  5 >2j01_T 50S ribosomal protein  100.0 2.1E-31 6.1E-36  218.4   2.4   80   21-100     1-80  (80)
  6 >2e6z_A Transcription elongati  82.2     3.8 0.00011   21.2   5.8   51   21-82      5-55  (59)
  7 >1zq1_A Glutamyl-tRNA(Gln) ami  68.7     8.8 0.00026   18.9   5.8   62   24-96     12-75  (82)
  8 >1jb7_A Telomere-binding prote  66.6     8.5 0.00025   19.0   4.1   26   44-69     51-82  (180)
  9 >2d6f_A Glutamyl-tRNA(Gln) ami  56.0      15 0.00044   17.5   4.8   60   24-98     16-76  (81)
 10 >1nz9_A Transcription antiterm  50.4      18 0.00054   16.9   4.1   30   22-58      3-32  (58)
 11 >1ugp_B NitrIle hydratase beta  50.0     7.5 0.00022   19.4   1.4   35   21-56      3-41  (93)
 12 >2zzd_A Thiocyanate hydrolase   47.6     8.5 0.00025   19.0   1.4   35   21-56      4-42  (96)
 13 >3hht_B NitrIle hydratase beta  46.4     9.2 0.00027   18.8   1.4   35   21-56      2-40  (92)
 14 >1k0r_A NUSA; two component ar  45.2      22 0.00065   16.4   3.7   31   17-47     55-87  (92)
 15 >2qdy_B NitrIle hydratase subu  43.4      11 0.00032   18.4   1.4   32   21-53      7-42  (99)
 16 >2asb_A Transcription elongati  38.1      28 0.00084   15.7   3.7   31   17-47     44-76  (81)
 17 >2zou_A Spondin-1; beta-sandwi  33.2      34   0.001   15.3   5.1   32   21-57     31-63  (149)
 18 >1qzg_A Protection of telomere  33.2      34   0.001   15.3   3.4   28   43-70     43-78  (187)
 19 >1r3e_A TRNA pseudouridine syn  32.8      34   0.001   15.2   3.3   50   19-81     30-79  (85)
 20 >1vq8_T 50S ribosomal protein   32.6      35   0.001   15.2   5.4   68   23-99     23-92  (101)
 21 >1y43_B Aspergillopepsin II he  29.8      39  0.0011   14.9   4.9   42   23-83     56-97  (118)
 22 >3frn_A Flagellar protein FLGA  28.2      41  0.0012   14.7   4.4   47   22-74      1-47  (71)
 23 >2do3_A Transcription elongati  27.5      42  0.0013   14.6   3.3   29   23-58     17-45  (69)
 24 >3db3_A E3 ubiquitin-protein l  26.3      44  0.0013   14.5   6.9   65   23-88      3-67  (72)
 25 >3bbo_W Ribosomal protein L24;  26.1      23 0.00067   16.4   0.7   58   23-87     68-136 (140)
 26 >3kd4_A Putative protease; str  25.0      47  0.0014   14.4   5.4   21   18-38    100-120 (209)
 27 >3coo_A Spondin-1; reelin-N do  23.5      50  0.0015   14.2   4.2   32   21-57     46-78  (180)
 28 >1c05_A Ribosomal protein S4 d  22.7      52  0.0015   14.1   2.0   17   17-33      7-25  (83)
 29 >2nn6_I 3'-5' exoribonuclease   22.2      53  0.0016   14.0   3.0   20   24-43     61-80  (94)
 30 >2zjr_R 50S ribosomal protein   22.1      54  0.0016   14.0   2.8   58   23-87     15-83  (87)
 31 >3i4o_A Translation initiation  20.9      30  0.0009   15.6   0.5   13   23-35     53-65  (79)
 32 >1yz6_A Probable translation i  20.8      57  0.0017   13.8   3.1   16   20-35      4-19  (83)

No 1  
>>3i1n_P 50S ribosomal protein L19; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_P 3e1b_I 3e1d_I 1vs6_P 3i1p_P 3i1r_P 3i1t_P 3i20_P 3i22_P 2qam_P* 1p85_N 1p86_N 2awb_P 2gya_N 2gyc_N 2aw4_P 2i2v_P 2j28_P 2i2t_P* 2qao_P* ... (P:)
Probab=100.00  E-value=2e-43  Score=294.25  Aligned_cols=113  Identities=55%  Similarity=0.905  Sum_probs=109.6

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEC
Q ss_conf             93589997999999760279897378998999999835887740123453543136666433886300356130289991
Q gi|254780715|r    1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPL   80 (141)
Q Consensus         1 Mnli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl   80 (141)
                      +|+|+.+|++++     +.++|+|+|||||+|++++.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||+
T Consensus         2 ~~Li~~ie~~~~-----k~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvI~~~~~g~~~tftlR~i~~gvGVE~~fpl   76 (115)
T 3i1n_P            2 SNIIKQLEQEQM-----KQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQT   76 (115)
T ss_dssp             CCTTTHHHHTTC-----CSCCCCCCTTCCCEEEEEEECSSCEEEEEEECEEEEECCCGGGCCEEEECCBTTBCEEEEECT
T ss_pred             HHHHHHHHHHHH-----HCCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEEECCCCCEEEEEEEECCCCCEEEEEEC
T ss_conf             589999999984-----056998499989999999846885158899999999968984037988996377567999981


Q ss_pred             CCCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHHC
Q ss_conf             07861012220002046787687508884102201200
Q gi|254780715|r   81 YSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENT  118 (141)
Q Consensus        81 ~SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~~  118 (141)
                      |||+|++|+|+++|||||||||||||+.||+|||||+.
T Consensus        77 ~SP~I~~IeV~~~~kvRRaKLyYLR~~~gk~arike~~  114 (115)
T 3i1n_P           77 HSPVVDSISVKRRGAVRKAKLYYLRERTGKAARIKERL  114 (115)
T ss_dssp             TCTTTCEEECCSCBCCSCSCCGGGGGTCSGGGCCCBCC
T ss_pred             CCCCCCCEEEECCCCEEEEEEEEECCCCCHHHHHHHHC
T ss_conf             79982202443158152100555204722677644521


No 2  
>>2zjr_M 50S ribosomal protein L19; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (M:24-166)
Probab=100.00  E-value=8.5e-43  Score=290.23  Aligned_cols=114  Identities=53%  Similarity=0.907  Sum_probs=105.4

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCHHHHHH
Q ss_conf             89737899899999983588774012345354313666643388630035613028999107861012220002046787
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSK  100 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gkvRrak  100 (141)
                      +|+|++||||+|++++.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||||||+|++|+|+++|||||||
T Consensus         1 iP~f~~GD~V~V~~~i~eg~k~RvQ~f~GvvI~~~~~Gl~stftvRki~~gvGVEr~fpl~SP~I~~IeVirrgKvRRAK   80 (143)
T 2zjr_M            1 LPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAK   80 (143)
T ss_dssp             CCCCSSSEEEEEECCTTSSSCCCCEEEECCEEECCCCGGGCEEEEEEEETTEEEEEEEETTCTTEEEEEEEECCCCSSSC
T ss_pred             CCCCCCCCEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCEEEEEEEECCCCEEEEHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             99848998999999965888655116657899961788631477244525734477645419204233011021677888


Q ss_pred             HHHHCCCCCCEEEHHHHCCCCCCCCCCCCHHHHH
Q ss_conf             6875088841022012001212365432002333
Q gi|254780715|r  101 LYYLQDLRGKAARIKENTGKRAKALNEEVRRAAL  134 (141)
Q Consensus       101 LyYLR~~~gk~arik~~~~~~~~~~~~~~~~~~~  134 (141)
                      ||||||+.||+|||+++.................
T Consensus        81 LYYLR~~~gK~arike~~~~~~~~~~~~~~~~~~  114 (143)
T 2zjr_M           81 LYYLRELRGKAARIKSDRSRVMKDAARAQQDKAN  114 (143)
T ss_dssp             CGGGCC----------------------------
T ss_pred             HHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             8877725236778788876230011112200022


No 3  
>>2ftc_K 39S ribosomal protein L19, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (K:)
Probab=100.00  E-value=1.2e-38  Score=264.16  Aligned_cols=98  Identities=33%  Similarity=0.585  Sum_probs=95.0

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCHHHHHH
Q ss_conf             89737899899999983588774012345354313666643388630035613028999107861012220002046787
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSK  100 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gkvRrak  100 (141)
                      +|+|+|||+|+|++++.| +|+|+|.|+|+||+++++|+++||||||+++|+|||++||||||+|++|||+++|||||||
T Consensus         1 iP~f~~GD~v~V~~~i~e-~k~r~q~f~GvvI~~~~~g~~~tftlR~i~~g~GVE~~f~l~SP~I~~IeV~~~~kvrRaK   79 (98)
T 2ftc_K            1 IPEFYVGSILRVTTADPY-ASGKISQFLGICIQRSGRGLGATFILRNVIEGQGVEICFELYNPRVQEIQVVKLEKRLDDS   79 (98)
T ss_pred             CCCCCCCCEEEEEEEECC-CCEEEEEEEEEEEEEECCCCEEEEEEEEECCCCEEEEEEECCCCCCCEEEEEEECEEEEHH
T ss_conf             996379999999999778-8747887899999982389736999998328935999993889970237898406055200


Q ss_pred             HHHHCCCCCCEEEHHHHCC
Q ss_conf             6875088841022012001
Q gi|254780715|r  101 LYYLQDLRGKAARIKENTG  119 (141)
Q Consensus       101 LyYLR~~~gk~arik~~~~  119 (141)
                      ||||||+.||+|+|++++.
T Consensus        80 LyYLR~~~gk~a~ik~~~k   98 (98)
T 2ftc_K           80 LLYLRDALPEYSTFDVNMK   98 (98)
T ss_pred             EEEHHCCCCCCCCEECCCC
T ss_conf             0022228864443112359


No 4  
>>3bbo_R Ribosomal protein L19; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (R:143-233)
Probab=100.00  E-value=1.1e-36  Score=251.59  Aligned_cols=91  Identities=36%  Similarity=0.727  Sum_probs=88.9

Q ss_pred             CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCHHHHHHHHH
Q ss_conf             37899899999983588774012345354313666643388630035613028999107861012220002046787687
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSKLYY  103 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gkvRrakLyY  103 (141)
                      |+|||||+|++++.| +|+|+|.|+|+||+++++|+++||||||+++|+|||++||||||+|++|||+++||||||||||
T Consensus         1 f~~GD~v~V~~~i~e-~k~r~q~f~GvvI~~~~~g~~~tftlR~v~~g~gVE~~f~l~SP~i~~IeV~~~~kvrRaKLyY   79 (91)
T 3bbo_R            1 IRTGDIVQIRLEVPE-NKRRLSVYKGIVISRQNAGIHTTIRIRRIIAGVGVEIVFPLYSPNIKEIKVVSHRKVRKARLYY   79 (91)
T ss_dssp             SCCCSCCCCCCCBCC-CSSCCSCCBCCCCCSCBCCCSSSCBCBCCCCCSTTTCCCCCBSSSSSCCCCCCCSCCCCSCSSC
T ss_pred             CCCCCEEEEEEEECC-CCEEEEEEEEEEEEEECCCCCEEEEEEEECCCEEEEEEEECCCCCCCEEEEEECCCCCHHHHHH
T ss_conf             389989999999777-9875763589999985898634799999338724899985579975669998636300333344


Q ss_pred             HCCCCCCEEEHH
Q ss_conf             508884102201
Q gi|254780715|r  104 LQDLRGKAARIK  115 (141)
Q Consensus       104 LR~~~gk~arik  115 (141)
                      |||+.||+||||
T Consensus        80 LR~~~gk~arik   91 (91)
T 3bbo_R           80 LRDKLPRLSTFK   91 (91)
T ss_dssp             CCCSSTTCSSCC
T ss_pred             HCCCCCCCCCCC
T ss_conf             405866322539


No 5  
>>2j01_T 50S ribosomal protein L19; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (T:19-98)
Probab=99.96  E-value=2.1e-31  Score=218.44  Aligned_cols=80  Identities=51%  Similarity=0.968  Sum_probs=79.0

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCHHHHHH
Q ss_conf             89737899899999983588774012345354313666643388630035613028999107861012220002046787
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGKVRRSK  100 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gkvRrak  100 (141)
                      +|+|++||||+|++++.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++||||||+|++|||+++|||||||
T Consensus         1 iP~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftlR~i~~g~GVEr~f~l~SP~i~~IeVir~~kvRRAK   80 (80)
T 2j01_T            1 LPEFRPGDTVRVSYKVKEGNRTRIQDFEGIVIRIRRNGFNTTFTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGRARRAK   80 (80)
T ss_dssp             SCCCCSSCBBCCCCCCBTTBSCCCCCCBCEEEEEECCSSSCEEEEEEEETTEEEEEEECSSSSCSCCCBCCCCBCCSSSS
T ss_pred             CCCCCCCCEEEEEEEECCCCCCEEEEEEEEEEEEECCCCCEEEEEEEEECCCCEEEEEEECCCCCCEEEEEECCCEEHHH
T ss_conf             99828988999999975788413677556898983698630798888607864899999669987757887227301100


No 6  
>>2e6z_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:)
Probab=82.23  E-value=3.8  Score=21.23  Aligned_cols=51  Identities=22%  Similarity=0.272  Sum_probs=37.5

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCC
Q ss_conf             89737899899999983588774012345354313666643388630035613028999107
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYS   82 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~S   82 (141)
                      --.|.|||.|.|    .+|.-.   ...|.+++..    +.++|++-.-.+.+-..-||..+
T Consensus         5 ~~~f~pGD~VeV----~~GEl~---~l~G~V~sv~----gd~Vti~p~~~dL~~~l~~p~~~   55 (59)
T 2e6z_A            5 SSGFQPGDNVEV----CEGELI---NLQGKILSVD----GNKITIMPKHEDLKDMLEFPAQE   55 (59)
T ss_dssp             CSSCCTTSEEEE----CSSTTT---TCEEEECCCB----TTEEEEEECCSSCCSCEEEETTT
T ss_pred             CCCCCCCCEEEE----ECCEEC---CCEEEEEEEC----CCEEEEEECCCCCCCEEECCHHH
T ss_conf             255389998999----227753---7799999970----99899987642368615416798


No 7  
>>1zq1_A Glutamyl-tRNA(Gln) amidotransferase subunit D; X-RAY, 3D structure, asparaginase 1 family, GATD subfamily, lyase; 3.00A {Pyrococcus abyssi} (A:1-82)
Probab=68.67  E-value=8.8  Score=18.94  Aligned_cols=62  Identities=24%  Similarity=0.372  Sum_probs=37.5

Q ss_pred             CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEEC--CCCCCEEEEECCCCCEEEEEEEECCHH
Q ss_conf             3789989999998358877401234535431366664338863003--561302899910786101222000204
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKIS--YGEGMNRLFPLYSPMIQDITVIRRGKV   96 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~--~g~GVE~~fpl~SP~i~~Iev~r~gkv   96 (141)
                      ..+||.|+|...  +|.  .-..|+|+++-.---.-+.+++| |.-  +++|+..      -.|++||++.+++.
T Consensus        12 ~~vGD~VrV~~~--~~~--~~~~~eGilmP~~e~s~~d~iVi-KLdnGYNvGi~~------~~i~~ievlek~~~   75 (82)
T 1zq1_A           12 INVGDFVRITKE--EDG--EEVTYEGYIXPPYELSAGDTLVL-KLENGYNIGIAL------EKIRRIEVLERAKV   75 (82)
T ss_dssp             CCTTCEEEEEEE--SSS--SEEECCEEECCCCTTCCCSEEEE-EETTSCEEEEEG------GGEEEEEEEECCCC
T ss_pred             CCCCCEEEEEEE--CCC--CCEEEEEEECCCCCCCCCCEEEE-ECCCCCEEEEEH------HHEEEEEEECCCCC
T ss_conf             999987999992--388--85499999768865689998999-926881053037------89058998415778


No 8  
>>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA hydration, sodium ION, quadruplex DNA, DNA-binding protein/DNA complex; 1.86A {Sterkiella nova} (A:1-180)
Probab=66.61  E-value=8.5  Score=19.04  Aligned_cols=26  Identities=12%  Similarity=0.031  Sum_probs=12.6

Q ss_pred             CEEEEEEEEEE----CCCCC--CCEEEEEEEC
Q ss_conf             01234535431----36666--4338863003
Q gi|254780715|r   44 IQAYEGVCIAR----SGRGI--NKNFTVRKIS   69 (141)
Q Consensus        44 ~Q~F~GvvI~~----~~~G~--~stftvRki~   69 (141)
                      ...+-|||+..    +-+|-  -.||+|-.-+
T Consensus        51 ~vnvigVV~d~~~P~~s~g~d~~~tl~I~D~S   82 (180)
T 1jb7_A           51 PQHFYAVVIDATFPYKTNQERYICSLKIVDPT   82 (180)
T ss_dssp             CEEEEEEEEEECCCEECSSSCEEEEEEEEBTT
T ss_pred             EEEEEEEEEECCCCEECCCCEEEEEEEEECCC
T ss_conf             06899999862386336997189999998067


No 9  
>>2d6f_A Glutamyl-tRNA(Gln) amidotransferase subunit D; ligase, ligase/RNA complex; 3.15A {Methanothermobacterthermautotrophicus} (A:1-81)
Probab=56.03  E-value=15  Score=17.50  Aligned_cols=60  Identities=20%  Similarity=0.397  Sum_probs=35.2

Q ss_pred             CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEEC-CCCCCEEEEECCCCCEEEEEEEECCHHHH
Q ss_conf             3789989999998358877401234535431366664338863003-56130289991078610122200020467
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKIS-YGEGMNRLFPLYSPMIQDITVIRRGKVRR   98 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~-~g~GVE~~fpl~SP~i~~Iev~r~gkvRr   98 (141)
                      ..+||.|+|.   .++.     .|+|+++-..-..-+.+++|.=-. +++|+.       +.=.+||++.++....
T Consensus        16 ~~~GD~VrV~---k~~~-----~~eGilmPs~~~~~~d~iViKLdnGYNvGi~-------~~~i~ievlek~~~pk   76 (81)
T 2d6f_A           16 IDVGDMVLVE---KPDV-----TYEGMVLDRADDADDRHIVLKLENGYNIGVE-------ISDARIELLEKGSEPR   76 (81)
T ss_dssp             CCTTCEEEEE---CSSC-----EEEEEECCCCTTSCSSEEEEECTTSCEEEEE-------CTTCCCCEEECCC---
T ss_pred             CCCCCEEEEE---ECCE-----EEEEEEECCCCCCCCCEEEEECCCCCEEEEE-------HHHEEEEEEECCCCCC
T ss_conf             9999889999---7998-----9999996886678999899993787117656-------1251799985277654


No 10 
>>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} (A:)
Probab=50.42  E-value=18  Score=16.94  Aligned_cols=30  Identities=20%  Similarity=0.358  Sum_probs=21.7

Q ss_pred             CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCC
Q ss_conf             9737899899999983588774012345354313666
Q gi|254780715|r   22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRG   58 (141)
Q Consensus        22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G   58 (141)
                      -+|.+||.|+|    ..|   -.+-|+|.+..+....
T Consensus         3 ~~~~~Gd~V~I----~~G---pF~g~~G~V~~id~~k   32 (58)
T 1nz9_A            3 VAFREGDQVRV----VSG---PFADFTGTVTEINPER   32 (58)
T ss_dssp             CSCCTTCEEEE----CSG---GGTTCEEEEEEEETTT
T ss_pred             CCCCCCCEEEE----CCC---CCCCCEEEEEEEECCC
T ss_conf             23159999999----246---8999889999990889


No 11 
>>1ugp_B NitrIle hydratase beta subunit; complex, N-butyric acid, non-corrin cobalt, hydration, lyase; HET: BUA; 1.63A {Pseudonocardia thermophila} (B:134-226)
Probab=49.98  E-value=7.5  Score=19.40  Aligned_cols=35  Identities=29%  Similarity=0.526  Sum_probs=24.8

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEE----EEEEEEECC
Q ss_conf             897378998999999835887740123----453543136
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAY----EGVCIARSG   56 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F----~GvvI~~~~   56 (141)
                      -|.|.+||.|+|.- .....-+|++.|    .|++....+
T Consensus         3 ~prF~vGD~Vrvr~-~~~~~HtRlP~Y~RGk~G~I~~~~G   41 (93)
T 1ugp_B            3 PPKFKEGDVVRFST-ASPKGHARRARYVRGKTGTVVKHHG   41 (93)
T ss_dssp             CCSCCTTCEEEECC-CCCSSCCCCCGGGTTCEEEEEEEEE
T ss_pred             CCCCCCCCEEEECC-CCCCCCEECCHHHCCCEEEEEEEEC
T ss_conf             98357999889815-8999822176666687558999842


No 12 
>>2zzd_A Thiocyanate hydrolase subunit alpha; scnase, cobalt, metalloprotein, sulfenic acid, sulfinic acid, nitrIle hydratase, carbonyl sulfide; HET: FRU TLA BGC; 1.78A {Thiobacillus thioparus} PDB: 2dd4_A 2dxb_A 2dd5_A* 2dxc_A* (A:31-126)
Probab=47.62  E-value=8.5  Score=19.03  Aligned_cols=35  Identities=23%  Similarity=0.315  Sum_probs=24.6

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEE----EEEEEEECC
Q ss_conf             897378998999999835887740123----453543136
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAY----EGVCIARSG   56 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F----~GvvI~~~~   56 (141)
                      -|.|.+||.|+|.- .....-+|++.|    .|++....+
T Consensus         4 ~prF~vGD~Vrvr~-~~~~~HtRlP~Y~RGk~G~I~~~~g   42 (96)
T 2zzd_A            4 KSKFNVGDRVRIKD-LPDLFYTRTMTYTRGATGTIVRLVY   42 (96)
T ss_dssp             SCSSCTTCEEEECC-CCCSSCCSSCGGGTTCEEEEEEEEE
T ss_pred             CCCCCCCCEEEEEE-CCCCCCEECCHHHCCCEEEEEEEEC
T ss_conf             99458999999821-7999832485677888679999855


No 13 
>>3hht_B NitrIle hydratase beta subunit; alpha and beta proteins (A+B), lyase; 1.16A {Geobacillus pallidus} PDB: 2dpp_B 1v29_B (B:138-229)
Probab=46.44  E-value=9.2  Score=18.84  Aligned_cols=35  Identities=29%  Similarity=0.462  Sum_probs=24.2

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEE----EEEEEEECC
Q ss_conf             897378998999999835887740123----453543136
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAY----EGVCIARSG   56 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F----~GvvI~~~~   56 (141)
                      -|.|.+||.|+|.- .....-+|++.|    .|++....+
T Consensus         2 ~~rF~vGD~Vrvr~-~~~~~HtR~P~Y~RGk~G~I~~~~g   40 (92)
T 3hht_B            2 SPRFKVGERIKTKN-IHPTGHTRFPRYARDKYGVIDEVYG   40 (92)
T ss_dssp             CCSCCTTCEEEECC-CCCSSCCSCCGGGTTCEEEEEEEEE
T ss_pred             CCCCCCCCEEEEEC-CCCCCCCCCHHHHCCCEEEEEEEEC
T ss_conf             98578998778843-7999751254676787459998836


No 14 
>>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} (A:113-204)
Probab=45.24  E-value=22  Score=16.44  Aligned_cols=31  Identities=10%  Similarity=0.150  Sum_probs=19.5

Q ss_pred             HCCCCC--CCCCCCEEEEEEEEECCCCCCCEEE
Q ss_conf             027989--7378998999999835887740123
Q gi|254780715|r   17 SKRSLP--KFSPGDTLCVKTIITEGDKSRIQAY   47 (141)
Q Consensus        17 ~k~~~P--~f~~GD~v~V~~~i~eg~k~R~Q~F   47 (141)
                      .+..+|  .|++||.+++.+.-.+-.....|.|
T Consensus        55 ~~eqip~E~~~~Gdrik~~i~~V~~~~kg~~I~   87 (92)
T 1k0r_A           55 AAEQVPGESYEHGNRLRCYVVGVTRGAREPLIT   87 (92)
T ss_dssp             GGGSCTTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             HHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEE
T ss_conf             777599865899988999999999858997499


No 15 
>>2qdy_B NitrIle hydratase subunit beta; post translation, lyase; 1.30A {Rhodococcus erythropolis} (B:114-212)
Probab=43.43  E-value=11  Score=18.40  Aligned_cols=32  Identities=22%  Similarity=0.276  Sum_probs=22.8

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEE----EEEEEE
Q ss_conf             897378998999999835887740123----453543
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAY----EGVCIA   53 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F----~GvvI~   53 (141)
                      -|.|.+||.|+|.- .....-+|++.|    .|++..
T Consensus         7 ~~rF~vGD~Vrvr~-~~~~~HtRlP~YvRGk~G~I~~   42 (99)
T 2qdy_B            7 TTTFEVGQRVRVRD-EYVPGHIRMPAYCRGRVGTISH   42 (99)
T ss_dssp             CCCCCTTCEEEECC-CCCSSCCSCCGGGTTCEEEEEE
T ss_pred             CCCCCCCCEEEECC-CCCCCCEECCHHHCCCEEEEEE
T ss_conf             98679999899764-8999842276566687579986


No 16 
>>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} (A:1-81)
Probab=38.15  E-value=28  Score=15.75  Aligned_cols=31  Identities=10%  Similarity=0.150  Sum_probs=19.6

Q ss_pred             HCCCCC--CCCCCCEEEEEEEEECCCCCCCEEE
Q ss_conf             027989--7378998999999835887740123
Q gi|254780715|r   17 SKRSLP--KFSPGDTLCVKTIITEGDKSRIQAY   47 (141)
Q Consensus        17 ~k~~~P--~f~~GD~v~V~~~i~eg~k~R~Q~F   47 (141)
                      .+..+|  .|++||-+++.+.-.+-.....|.|
T Consensus        44 ~~eqip~E~~~~Gdrik~~i~~V~~~~kgp~I~   76 (81)
T 2asb_A           44 AAEQVPGESYEHGNRLRCYVVGVTRGAREPLIT   76 (81)
T ss_dssp             GGGSCTTCCCCTTCEEEEEEEEEECCSSSCEEE
T ss_pred             HHHCCCCCCCCCCCEEEEEEEEEEECCCCEEEE
T ss_conf             788699876799999999997999269826899


No 17 
>>2zou_A Spondin-1; beta-sandwich, extracellular protein, cell adhesion, extracellular matrix, glycoprotein, secreted; 1.45A {Homo sapiens} (A:)
Probab=33.25  E-value=34  Score=15.26  Aligned_cols=32  Identities=16%  Similarity=0.310  Sum_probs=23.6

Q ss_pred             CCC-CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC
Q ss_conf             897-3789989999998358877401234535431366
Q gi|254780715|r   21 LPK-FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR   57 (141)
Q Consensus        21 ~P~-f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~   57 (141)
                      .|+ +.||+.+.|++.-.++.     .|.|..|.-+..
T Consensus        31 ~~~~y~pG~~~~VtL~~~~~~-----~F~GFllqAr~~   63 (149)
T 2zou_A           31 DPDFYKPGTSYRVTLSAAPPS-----YFRGFTLIALRE   63 (149)
T ss_dssp             CCSSBCTTCEEEEEEEECTTC-----CBSEEEEEEEET
T ss_pred             CCCEECCCCEEEEEEECCCCC-----CCCEEEEEEEEC
T ss_conf             986055999799999815888-----503079898506


No 18 
>>1qzg_A Protection of telomeres protein 1; protrein-DNA complex, single-stranded telomeric DNA, DNA binding protein/DNA complex; HET: TMP; 1.90A {Schizosaccharomyces pombe} (A:)
Probab=33.23  E-value=34  Score=15.26  Aligned_cols=28  Identities=7%  Similarity=-0.067  Sum_probs=12.3

Q ss_pred             CCEEEEEEEEEEC------CCC--CCCEEEEEEECC
Q ss_conf             4012345354313------666--643388630035
Q gi|254780715|r   43 RIQAYEGVCIARS------GRG--INKNFTVRKISY   70 (141)
Q Consensus        43 R~Q~F~GvvI~~~------~~G--~~stftvRki~~   70 (141)
                      ....+-|||+...      ++|  --.||+|=.-+.
T Consensus        43 ~~VnvigVV~d~~~p~~s~~gg~d~~~tl~I~D~S~   78 (187)
T 1qzg_A           43 TIVNLFGIVKDFTPSRQSLHGTKDWVTTVYLWDPTC   78 (187)
T ss_dssp             EEEEEEEEEEEEEEEEECSSTTCCEEEEEEEECTTS
T ss_pred             CEEEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCC
T ss_conf             888899999103687126889987799999975887


No 19 
>>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase/RNA complex; HET: FHU; 2.10A {Thermotoga maritima} (A:225-309)
Probab=32.81  E-value=34  Score=15.21  Aligned_cols=50  Identities=16%  Similarity=0.219  Sum_probs=28.1

Q ss_pred             CCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECC
Q ss_conf             798973789989999998358877401234535431366664338863003561302899910
Q gi|254780715|r   19 RSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLY   81 (141)
Q Consensus        19 ~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~   81 (141)
                      .+.+.|..||.|.|.   .+++.     .-|+.++.     -++..+...-.|..+|..--+.
T Consensus        30 ~~~~~f~~gd~V~I~---~~~g~-----~iavG~~~-----~ss~el~~~~~g~~v~~~h~~~   79 (85)
T 1r3e_A           30 KEWDGFKKGEVVRVF---NEEGR-----LLALAEAE-----RNSSFLETLRKHERNERVLTLR   79 (85)
T ss_dssp             CEECCCCTTCEEEEE---CSSSC-----EEEEEEES-----SCTTCCCCSCC----CEEEEEE
T ss_pred             CCCCCCCCCCEEEEE---CCCCE-----EEEEEEEC-----CCCCEEEEEECCCCCCCEEEEC
T ss_conf             322457889999999---69991-----99999990-----7865156530358877488562


No 20 
>>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} (T:20-120)
Probab=32.57  E-value=35  Score=15.19  Aligned_cols=68  Identities=18%  Similarity=0.185  Sum_probs=37.1

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEE--CCCCCCEEEEECCCCCEEEEEEEECCHHHHH
Q ss_conf             7378998999999835887740123453543136666433886300--3561302899910786101222000204678
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKI--SYGEGMNRLFPLYSPMIQDITVIRRGKVRRS   99 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki--~~g~GVE~~fpl~SP~i~~Iev~r~gkvRra   99 (141)
                      .++.||+|.|   +.-..|+.    +|.|+.+....  ....|-.+  ...-|=+.-.|+|..++.=+...-....|-+
T Consensus        23 ~I~~GD~V~V---i~G~dkGk----~GkV~~V~~~~--~~V~Vegin~~k~~~k~~e~pIh~SnV~lv~~~~~~~~Rv~   92 (101)
T 1vq8_T           23 RVNAGDTVEV---LRGDFAGE----EGEVINVDLDK--AVIHVEDVTLEKTDGEEVPRPLDTSNVRVTDLDLEDEKREA   92 (101)
T ss_dssp             ECCTTCEEEE---CSSTTTTC----EEEEEEEETTT--TEEEETTCEEECSSSCEEECCBCGGGEEEEECCCCCHHHHH
T ss_pred             CEECCCEEEE---EECCCCCC----CCEEEEEECCC--CEEEECCEEEEECCCCEEECCCCHHHEEEEECCCCCCHHHH
T ss_conf             0316999999---15478997----51399998778--99999661899547982515446489799837679712533


No 21 
>>1y43_B Aspergillopepsin II heavy chain; proctase A, beta sandwich structure, hydrolase; 1.40A {Aspergillus niger var} (B:1-118)
Probab=29.84  E-value=39  Score=14.90  Aligned_cols=42  Identities=21%  Similarity=0.286  Sum_probs=26.6

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCC
Q ss_conf             7378998999999835887740123453543136666433886300356130289991078
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSP   83 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP   83 (141)
                      .+.+||.|.|++.-.-+.                   .-+++|-|.+.|.-+-+.+...+|
T Consensus        56 ~v~~GD~i~v~Vt~~s~~-------------------~g~~~i~n~s~g~t~t~t~s~~~~   97 (118)
T 1y43_B           56 TISEGDSIKVTVEATSKS-------------------SGSATVENLTTGQSVTHTFSGNVE   97 (118)
T ss_dssp             CCCTTCEEEEEEEEEETT-------------------EEEEEEEETTTTEEEEEEECSCCS
T ss_pred             CCCCCCEEEEEEEECCCC-------------------CEEEEEEECCCCEEEEEEEECCCC
T ss_conf             138999999999970799-------------------669999977799799999836899


No 22 
>>3frn_A Flagellar protein FLGA; structural genomics, periplasmic, PSI-2, protein structure initiative; 2.05A {Thermotoga maritima} (A:208-278)
Probab=28.24  E-value=41  Score=14.73  Aligned_cols=47  Identities=6%  Similarity=0.034  Sum_probs=31.4

Q ss_pred             CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCC
Q ss_conf             97378998999999835887740123453543136666433886300356130
Q gi|254780715|r   22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGM   74 (141)
Q Consensus        22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GV   74 (141)
                      |-++-||.|.|.+.  .++= .   ..-.-.+..+..++.++.|||...|--+
T Consensus         1 PlV~rG~~V~v~~~--~~g~-~---I~~~g~Al~~G~~Gd~IrVrN~~Sgkii   47 (71)
T 3frn_A            1 PDVVKGQVVPAYVD--MGSI-K---VTTFVEVLENGYLGETVRAMNVESRKYV   47 (71)
T ss_dssp             CSBCTTCEEEEEC-------------CEEEEESSCBCTTCEEEEEC--CCCEE
T ss_pred             CCCCCCCEEEEEEE--CCCE-E---EEEEEEECCCCCCCCEEEEEECCCCCEE
T ss_conf             51479988999960--5759-9---9997899878898988999988999989


No 23 
>>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:)
Probab=27.51  E-value=42  Score=14.65  Aligned_cols=29  Identities=24%  Similarity=0.338  Sum_probs=20.7

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCC
Q ss_conf             737899899999983588774012345354313666
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRG   58 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G   58 (141)
                      .|++||-|+|    ..|   +.+--.|+|+...+.-
T Consensus        17 ~F~~GDhVkV----i~G---~~~getGlVV~v~~d~   45 (69)
T 2do3_A           17 YFKMGDHVKV----IAG---RFEGDTGLIVRVEENF   45 (69)
T ss_dssp             SCCTTCEEEE----SSS---TTTTCEEEEEEECSSC
T ss_pred             CCCCCCEEEE----ECC---EECCCCEEEEEEECCE
T ss_conf             0579983899----064---6869628999993999


No 24 
>>3db3_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, tandem tudor domains, ligase, metal binding, DNA replication; HET: M3L; 2.40A {Homo sapiens} PDB: 3db4_A (A:90-161)
Probab=26.30  E-value=44  Score=14.51  Aligned_cols=65  Identities=9%  Similarity=0.100  Sum_probs=35.9

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEE
Q ss_conf             737899899999983588774012345354313666643388630035613028999107861012
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDI   88 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~I   88 (141)
                      ++.+||+|.|.|.+.+ .++|=--|.-.+-.++.+-...-+...=.+++--++-+--.|---|-+|
T Consensus         3 ~L~vG~~VMvNYN~d~-PkeRGfWYD~eI~~k~~tRt~kel~~~i~lG~d~l~dC~i~FvdEi~kI   67 (72)
T 3db3_A            3 DLEVGQVVXLNYNPDN-PKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKI   67 (72)
T ss_dssp             GCCTTCEEEEEECSSS-TTSCCEEEEEEEEEEEECSSCEEEEEEEECSSSEEEEEEESCTTCCBCC
T ss_pred             HCCCCCEEEEECCCCC-CHHCCCEEEEEEEEEECCCEEEEEEEEEEECCCCCCCCEEEEEEEEEEE
T ss_conf             8877769999758898-0024727889999843054120799999987872356379884325774


No 25 
>>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (W:1-140)
Probab=26.05  E-value=23  Score=16.38  Aligned_cols=58  Identities=21%  Similarity=0.258  Sum_probs=32.7

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC-----CCEEEEEEE------CCCCCCEEEEECCCCCEEE
Q ss_conf             7378998999999835887740123453543136666-----433886300------3561302899910786101
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI-----NKNFTVRKI------SYGEGMNRLFPLYSPMIQD   87 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~-----~stftvRki------~~g~GVE~~fpl~SP~i~~   87 (141)
                      .|+.||+|.|   +.-.+|+.    +|.|+++....-     +-+..-+.+      -.|-.++.-+|||.-++.=
T Consensus        68 ~i~kGD~V~V---i~G~dkGk----~G~V~~V~~~~~~V~Vegvn~~~~~~~~~~~~~~g~~~~~e~pi~~SnV~l  136 (140)
T 3bbo_W           68 HVKVGDTVKV---ISGGEKGK----IGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEAAIHSSNVML  136 (140)
T ss_dssp             CSCCSSCEEE---CSSSSTTC----CCSCCCCCSSSCCCCCSSCCCCCCBCCSCCSSSCCBSSCCCCCCCGGGEEE
T ss_pred             ECCCCCEEEE---EECCCCCC----EEEEEEEECCCCEEEEEEEEEEEEECCCCCCCCCCCEEEEECCEEHHHEEE
T ss_conf             1058999999---14789993----215999987799999974568996027766557884577861475688678


No 26 
>>3kd4_A Putative protease; structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: MSE; 2.00A {Parabacteroides distasonis atcc 8503} (A:1-209)
Probab=25.00  E-value=47  Score=14.36  Aligned_cols=21  Identities=14%  Similarity=0.086  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCCEEEEEEEEEC
Q ss_conf             279897378998999999835
Q gi|254780715|r   18 KRSLPKFSPGDTLCVKTIITE   38 (141)
Q Consensus        18 k~~~P~f~~GD~v~V~~~i~e   38 (141)
                      .-.+|.+++||+|...+.+..
T Consensus       100 ~~~~p~l~~Gdiie~~y~~~~  120 (209)
T 3kd4_A          100 VVVHTGLELGATIYLDYSIIT  120 (209)
T ss_dssp             EEECCSCCTTCEEEEEEEEEE
T ss_pred             EEECCCCCCCEEEEEEEEEEE
T ss_conf             998789898819999999977


No 27 
>>3coo_A Spondin-1; reelin-N domain, cell adhesion, extracellular matrix, glycoprotein, secreted; 2.00A {Homo sapiens} PDB: 2zot_A (A:)
Probab=23.50  E-value=50  Score=14.18  Aligned_cols=32  Identities=16%  Similarity=0.310  Sum_probs=23.8

Q ss_pred             CCC-CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC
Q ss_conf             897-3789989999998358877401234535431366
Q gi|254780715|r   21 LPK-FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR   57 (141)
Q Consensus        21 ~P~-f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~   57 (141)
                      .|. +.+|+++.|++.-.++.     .|.|..|.-++.
T Consensus        46 ~~~~y~pG~~~~Vtl~~~~~~-----~F~GFllqAr~~   78 (180)
T 3coo_A           46 DPDFYKPGTSYRVTLSAAPPS-----YFRGFTLIALRE   78 (180)
T ss_dssp             CCSEECTTCEEEEEEEECTTC-----CBSCCEEEEEET
T ss_pred             CCCCCCCCCEEEEEEEECCCC-----CCCEEEEEEECC
T ss_conf             887546998799999931788-----622389898216


No 28 
>>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} (A:77-159)
Probab=22.70  E-value=52  Score=14.09  Aligned_cols=17  Identities=35%  Similarity=0.814  Sum_probs=12.9

Q ss_pred             HCCCCCC--CCCCCEEEEE
Q ss_conf             0279897--3789989999
Q gi|254780715|r   17 SKRSLPK--FSPGDTLCVK   33 (141)
Q Consensus        17 ~k~~~P~--f~~GD~v~V~   33 (141)
                      .+-++|.  ++|||+|.|.
T Consensus         7 kkVdIPSy~~k~gD~I~ik   25 (83)
T 1c05_A            7 SRVNIPSYRVKPGQTIAVR   25 (83)
T ss_dssp             EECCCSSCBCCTTCEEEEC
T ss_pred             EEEEECCEEECCCCEEEEC
T ss_conf             6998434162178487502


No 29 
>>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} (I:76-169)
Probab=22.22  E-value=53  Score=14.02  Aligned_cols=20  Identities=35%  Similarity=0.544  Sum_probs=11.4

Q ss_pred             CCCCCEEEEEEEEECCCCCC
Q ss_conf             37899899999983588774
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSR   43 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R   43 (141)
                      |++||+|++.+.-.+-.+.+
T Consensus        61 ~~~Gd~V~~kV~~vd~~~~~   80 (94)
T 2nn6_I           61 FRPGDIVLAKVISLGDAQSN   80 (94)
T ss_dssp             CCSSSEEEEEEEEEETTTTE
T ss_pred             CCCCCEEEEEEEEECCCCCE
T ss_conf             67999999999986388973


No 30 
>>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (R:1-87)
Probab=22.08  E-value=54  Score=14.00  Aligned_cols=58  Identities=21%  Similarity=0.310  Sum_probs=31.5

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC-----CCEEEEEEE------CCCCCCEEEEECCCCCEEE
Q ss_conf             7378998999999835887740123453543136666-----433886300------3561302899910786101
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI-----NKNFTVRKI------SYGEGMNRLFPLYSPMIQD   87 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~-----~stftvRki------~~g~GVE~~fpl~SP~i~~   87 (141)
                      .|+.||+|.|   +.--+|++    +|.++++....-     +-+..-+.+      ..|--+++-.|+|..++.-
T Consensus        15 ~i~kGD~V~V---i~G~dkGk----~G~V~~V~~~~~~ViVegvN~~~~~~k~~~~~~~g~~~~~e~Pi~~SnV~l   83 (87)
T 2zjr_R           15 HFKKGDTVIV---LSGKHKGQ----TGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASKVAL   83 (87)
T ss_dssp             SSCTTSEEEC---CSSSSTTC----EEEEEEEETTTTEEEESSSCBCCCCCCTTSSSCCCCCCCBCCCBCSSSEEC
T ss_pred             EEECCCEEEE---EECCCCCC----EEEEEEEECCCCEEEEECCEEEEEEECCCCCCCCCCEEEEEEEEEHHHEEE
T ss_conf             1208999999---25589996----168999988899999957489998605644478887377764088677788


No 31 
>>3i4o_A Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis} (A:)
Probab=20.89  E-value=30  Score=15.55  Aligned_cols=13  Identities=23%  Similarity=0.417  Sum_probs=7.2

Q ss_pred             CCCCCCEEEEEEE
Q ss_conf             7378998999999
Q gi|254780715|r   23 KFSPGDTLCVKTI   35 (141)
Q Consensus        23 ~f~~GD~v~V~~~   35 (141)
                      -+.+||.|.|..+
T Consensus        53 ~I~~GD~V~Ve~~   65 (79)
T 3i4o_A           53 RILPEDRVVVELS   65 (79)
T ss_dssp             CCCTTCEEEEEEE
T ss_pred             EECCCCEEEEEEC
T ss_conf             9449999999967


No 32 
>>1yz6_A Probable translation initiation factor 2 alpha subunit; beta barrel, helical domain and alpha beta domain; 3.37A {Pyrococcus abyssi} (A:1-83)
Probab=20.75  E-value=57  Score=13.83  Aligned_cols=16  Identities=6%  Similarity=-0.014  Sum_probs=9.3

Q ss_pred             CCCCCCCCCEEEEEEE
Q ss_conf             9897378998999999
Q gi|254780715|r   20 SLPKFSPGDTLCVKTI   35 (141)
Q Consensus        20 ~~P~f~~GD~v~V~~~   35 (141)
                      .+.++++|+++...+.
T Consensus         4 ~~~~~~~G~~v~g~V~   19 (83)
T 1yz6_A            4 AREYPEEGEFVVATVK   19 (83)
T ss_dssp             CCSSCCTTCEEEEEEE
T ss_pred             CCCCCCCCCEEEEEEE
T ss_conf             0127999999999999


Done!