Query         gi|254780470|ref|YP_003064883.1| translation initiation factor IF-1 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 110
No_of_seqs    112 out of 663
Neff          2.4 
Searched_HMMs 33803
Date          Wed Jun  1 13:07:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780470.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1hr0_W Translation initiation 100.0 8.9E-33 2.6E-37  211.3  -0.5   70    2-109     2-71  (71)
  2 >1ah9_A IF1, initiation factor  99.9 5.5E-27 1.6E-31  177.6   5.4   71    2-110     1-71  (71)
  3 >3i4o_A Translation initiation  99.9 5.3E-27 1.6E-31  177.7   5.3   72    1-110     7-79  (79)
  4 >1d7q_A Translation initiation  99.7 1.8E-17 5.3E-22  122.4   7.9   71    1-110    25-95  (143)
  5 >2oqk_A Putative translation i  99.6 2.6E-16 7.6E-21  115.6   5.8   71    1-110    26-96  (117)
  6 >1jt8_A EIF-1A, probable trans  99.6   1E-16   3E-21  118.0   3.6   71    1-110    14-85  (102)
  7 >2dgy_A MGC11102 protein; EIF-  97.0  0.0034   1E-07   39.4   7.5   64    8-110    16-80  (111)
  8 >1t9h_A YLOQ, probable GTPase   96.7  0.0041 1.2E-07   38.9   6.1   63    8-108    10-72  (75)
  9 >1u0l_A Probable GTPase ENGC;   96.4   0.012 3.5E-07   36.2   6.7   60    8-107    10-69  (73)
 10 >2id0_A Exoribonuclease 2; RNA  94.0    0.22 6.6E-06   28.8   6.7   77    8-110     5-85  (86)
 11 >2wp8_J Exosome complex exonuc  93.7    0.17   5E-06   29.5   5.5   75    8-110     2-90  (90)
 12 >2c35_B Human RPB7, DNA-direct  87.5     2.2 6.6E-05   23.0   6.4   74    8-109     4-81  (92)
 13 >1go3_E DNA-directed RNA polym  85.2       3   9E-05   22.2   6.1   74    8-109     4-80  (107)
 14 >2bx2_L Ribonuclease E, RNAse   83.6     1.6 4.7E-05   23.8   4.1   76    8-110     6-84  (94)
 15 >2b8k_G B16, DNA-directed RNA   81.5       2   6E-05   23.2   4.0   76    7-110     3-80  (133)
 16 >1y14_B B16, RPB7, DNA-directe  81.3     4.4 0.00013   21.3   6.9   74    8-109     4-79  (89)
 17 >2ckz_B C25, DNA-directed RNA   80.1     4.1 0.00012   21.5   5.2   77    8-110     4-85  (138)
 18 >2vnu_D Exosome complex exonuc  78.7     3.6 0.00011   21.8   4.5   75    8-110     2-90  (90)
 19 >3h0g_G DNA-directed RNA polym  75.4     1.3 3.9E-05   24.3   1.5   74    8-109     4-79  (89)
 20 >2rcn_A Probable GTPase ENGC;   75.3     3.5  0.0001   21.8   3.7   48   56-107    56-107 (111)
 21 >3go5_A Multidomain protein wi  66.0     5.9 0.00017   20.5   3.1   62    7-110    19-80  (84)
 22 >1wi5_A RRP5 protein homolog;   47.6      23 0.00067   17.2   4.1   67    6-110    22-93  (119)
 23 >3cw2_C Translation initiation  46.3      24  0.0007   17.0   4.9   71    7-110    13-83  (85)
 24 >1hh2_P NUSA, N utilization su  45.8      24 0.00071   17.0   5.1   60    8-109     9-68  (87)
 25 >2waq_E DNA-directed RNA polym  44.6     8.2 0.00024   19.7   0.9   74    8-109     4-80  (100)
 26 >2d0b_A RNAse HIII, ribonuclea  42.7      14  0.0004   18.4   1.8   15   65-79     38-52  (82)
 27 >1y43_B Aspergillopepsin II he  42.1      14 0.00042   18.4   1.8   35   74-108    46-80  (118)
 28 >2ifr_A Scytalidopepsin B; enz  37.9      22 0.00064   17.3   2.2   36   73-108    71-106 (206)
 29 >2khj_A 30S ribosomal protein   37.1      33 0.00098   16.2   6.1   69    7-110    33-101 (109)
 30 >1luz_A Protein K3, protein K2  35.3      28 0.00084   16.6   2.5   27   84-110    56-82  (88)
 31 >2k52_A Uncharacterized protei  31.5      41  0.0012   15.7   6.0   66    6-110     6-71  (80)
 32 >2khi_A 30S ribosomal protein   29.4      45  0.0013   15.4   5.1   65    7-110    32-101 (115)
 33 >3k3s_A Altronate hydrolase; s  27.0      26 0.00076   16.8   1.1   32   70-103     7-43  (105)
 34 >2b3w_A Hypothetical protein Y  26.8      34 0.00099   16.2   1.7   18   86-103    26-43  (77)
 35 >2g3r_A Tumor suppressor P53-b  24.4      46  0.0014   15.4   2.0   43    8-67     21-63  (73)
 36 >1s5u_A Protein YBGC; structur  21.0      62  0.0018   14.6   2.1   27   84-110    71-97  (125)

No 1  
>>1hr0_W Translation initiation factor; ribosomal subunit, ribosome, IF1; 3.20A {Escherichia coli} (W:)
Probab=99.97  E-value=8.9e-33  Score=211.31  Aligned_cols=70  Identities=50%  Similarity=0.821  Sum_probs=66.8

Q ss_pred             CCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEE
Q ss_conf             75645999789998158981799981667765333233544333445555444555554455568828999912511201
Q gi|254780470|r    2 PKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKH   81 (110)
Q Consensus         2 ~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~   81 (110)
                      .|||.|+++|+|+|+|||++|||+|                                      +||+.|+||+|||||+|
T Consensus         2 kke~~i~~eG~V~e~lpn~~F~V~L--------------------------------------eng~~vla~isGKmR~~   43 (71)
T 1hr0_W            2 KEKDTIRTEGVVTEALPNATFRVKL--------------------------------------DSGPEILAYISGKMRMH   43 (71)
T ss_dssp             CCSCCCCCEEECCCCCTTTBCCCEE--------------------------------------SSSCBCCCEECHHHHHT
T ss_pred             CCCCEEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCHHHHE
T ss_conf             8530589999999985997999998--------------------------------------99999999957755301


Q ss_pred             EEEEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             6477029969999746757843598842
Q gi|254780470|r   82 RIRISLGDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        82 ~IRIl~GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      +|||++||+|+|||||||||||||+||-
T Consensus        44 ~IrIl~GDrV~VE~spYDltkGRIv~R~   71 (71)
T 1hr0_W           44 YIRILPGDRVVVEITPYDPTRGRIVYRK   71 (71)
T ss_dssp             CCCCCTTCEEEEECCTTCTTCCEECSCC
T ss_pred             EEEECCCCEEEEEECCCCCCCEEEEECC
T ss_conf             5987599999999774569937799739


No 2  
>>1ah9_A IF1, initiation factor 1; ribosome binding, protein-RNA interaction, OB fold; NMR {Escherichia coli} (A:)
Probab=99.93  E-value=5.5e-27  Score=177.64  Aligned_cols=71  Identities=48%  Similarity=0.793  Sum_probs=68.9

Q ss_pred             CCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEE
Q ss_conf             75645999789998158981799981667765333233544333445555444555554455568828999912511201
Q gi|254780470|r    2 PKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKH   81 (110)
Q Consensus         2 ~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~   81 (110)
                      |||+.+|++|+|+++|||++|+|+|                                      +||+.++||++||||++
T Consensus         1 aK~~~~e~~G~V~~~L~~~~f~V~l--------------------------------------~dg~~~~a~i~GKmRk~   42 (71)
T 1ah9_A            1 AKEDNIEMQGTVLETLPNTMFRVEL--------------------------------------ENGHVVTAHISGKMRKN   42 (71)
T ss_dssp             CCSCCEECCEEEEEECSSSEEEEEE--------------------------------------TTSCEEEEEECSSGGGT
T ss_pred             CCCCCEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEECCCHHHEE
T ss_conf             9863389999999986997899995--------------------------------------79979999846423302


Q ss_pred             EEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             64770299699997467578435988429
Q gi|254780470|r   82 RIRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        82 ~IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +|+|++||+|.||+||||++||||+||||
T Consensus        43 ri~I~~GD~V~Ve~~~yd~~kgrIi~Ryr   71 (71)
T 1ah9_A           43 YIRILTGDKVTVELTPYDLSKGRIVFRSR   71 (71)
T ss_dssp             TCCCCTTCEECCEECSSCTTEEEECSCCC
T ss_pred             EEEECCCCEEEEEECCCCCCCEEEEEECC
T ss_conf             79964999999997766799398999749


No 3  
>>3i4o_A Translation initiation factor IF-1; cytoplasm, protein biosynthesis; 1.47A {Mycobacterium tuberculosis} (A:)
Probab=99.93  E-value=5.3e-27  Score=177.71  Aligned_cols=72  Identities=47%  Similarity=0.794  Sum_probs=68.2

Q ss_pred             CCC-CCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEE
Q ss_conf             975-6459997899981589817999816677653332335443334455554445555544555688289999125112
Q gi|254780470|r    1 MPK-EETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMR   79 (110)
Q Consensus         1 M~K-ed~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmR   79 (110)
                      |+| |+.+|++|+|+|+|||++|+|+|                                      +||+.++||++||||
T Consensus         7 m~kke~~~e~~G~V~~~L~~~~f~V~l--------------------------------------~dg~~~~~~i~GKmr   48 (79)
T 3i4o_A            7 MAKKDGAIEVEGRVVEPLPNAMFRIEL--------------------------------------ENGHKVLAHISGKMR   48 (79)
T ss_dssp             -----CCSEEEEEEEEEETTTEEEEEE--------------------------------------TTSCEEEEEECHHHH
T ss_pred             CCCCCCEEEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEECCCCEE
T ss_conf             666325499999999988998899997--------------------------------------899999997145035


Q ss_pred             EEEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             0164770299699997467578435988429
Q gi|254780470|r   80 KHRIRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        80 k~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +++|+|++||+|.||+||||+|||||+||||
T Consensus        49 k~rI~I~~GD~V~Ve~~~yd~~kg~Ii~Ryr   79 (79)
T 3i4o_A           49 QHYIRILPEDRVVVELSPYDLSRGRIVYRYK   79 (79)
T ss_dssp             HTTCCCCTTCEEEEEEETTEEEEEEEEEECC
T ss_pred             EEEEEECCCCEEEEEECCCCCCCEEEEEECC
T ss_conf             7579944999999996777788588999839


No 4  
>>1d7q_A Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding protein; NMR {Homo sapiens} (A:)
Probab=99.72  E-value=1.8e-17  Score=122.37  Aligned_cols=71  Identities=18%  Similarity=0.323  Sum_probs=66.9

Q ss_pred             CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf             97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r    1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK   80 (110)
Q Consensus         1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk   80 (110)
                      |++++..++.|+|+++|+|+.|+|++                                      .||..++|+++||||+
T Consensus        25 ~~~~~~~e~~g~V~~~lG~~~~~V~~--------------------------------------~dg~~~l~~ipgK~Rk   66 (143)
T 1d7q_A           25 LVFKEDGQEYAQVIKMLGNGRLEAMC--------------------------------------FDGVKRLCHIRGKLRK   66 (143)
T ss_dssp             CCCCCTTEEEEEEEEECSSSEEEEEE--------------------------------------TTTEEEEEECCSGGGG
T ss_pred             CCCCCCCEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCCCEE
T ss_conf             14699981899999973997899997--------------------------------------8998999996266402


Q ss_pred             EEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             164770299699997467578435988429
Q gi|254780470|r   81 HRIRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                       +|+|..||.|.|+++|||++||+|+|||.
T Consensus        67 -~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~   95 (143)
T 1d7q_A           67 -KVWINTSDIILVGLRDYQDNKADVILKYN   95 (143)
T ss_dssp             -SCCCCTTCEEEEECSSSSSSCCEEEEEEC
T ss_pred             -EEEEECCCEEEEECCCCCCCEEEEEEECC
T ss_conf             -57980799999941567685789999779


No 5  
>>2oqk_A Putative translation initiation factor EIF-1A; malaria, eukaryotic initiation factor (EIF), SGC, structural genomics; 1.80A {Cryptosporidium parvum iowa II} (A:)
Probab=99.64  E-value=2.6e-16  Score=115.64  Aligned_cols=71  Identities=20%  Similarity=0.330  Sum_probs=66.6

Q ss_pred             CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf             97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r    1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK   80 (110)
Q Consensus         1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk   80 (110)
                      |++++..++.|.|+++|+|+.|+|++                                      +||..++|+++||||+
T Consensus        26 ~~~~~~~e~~g~V~~~~G~~~~~V~~--------------------------------------~dg~~~l~~ipgK~Rk   67 (117)
T 2oqk_A           26 LVFKEEGQEYGQVQRXLGNGRLDAYC--------------------------------------FDGQKRLCHIRGKXRK   67 (117)
T ss_dssp             CCCCCTTEEEEEEEEEEETTEEEEEE--------------------------------------TTSCEEEEECCHHHHH
T ss_pred             ECCCCCCEEEEEEEEECCCCEEEEEE--------------------------------------CCCCEEEEEECCCCCC
T ss_conf             21699982899999973997899998--------------------------------------8999999997421201


Q ss_pred             EEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             164770299699997467578435988429
Q gi|254780470|r   81 HRIRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                       +|+|..||.|.|+++|||.+||+|+|||.
T Consensus        68 -~iwI~~GD~VlVe~~~~d~~kg~Iv~r~~   96 (117)
T 2oqk_A           68 -KVWVNPGDIVLVSLRDFQDSKGDIILKYT   96 (117)
T ss_dssp             -HSCCCTTCEEEEEECTTCTTEEEEEEECC
T ss_pred             -EEEEECCCEEEEECCCCCCCEEEEEEECC
T ss_conf             -17980899999943257896899999889


No 6  
>>1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel, translation factor; NMR {Methanocaldococcus jannaschii} (A:)
Probab=99.63  E-value=1e-16  Score=117.96  Aligned_cols=71  Identities=27%  Similarity=0.488  Sum_probs=66.1

Q ss_pred             CCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEE
Q ss_conf             97564599978999815898179998166776533323354433344555544455555445556882899991251120
Q gi|254780470|r    1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRK   80 (110)
Q Consensus         1 M~Ked~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk   80 (110)
                      |++.+..++.|.|+++|+|+.|+|++.                                      ||+.++|+++||||+
T Consensus        14 ~~~~~~~e~~~~V~~~lG~~~~~V~~~--------------------------------------~G~~~la~i~gK~rk   55 (102)
T 1jt8_A           14 IPRKEENEILGIIEQMLGASRVRVRCL--------------------------------------DGKTRLGRIPGRLKN   55 (102)
T ss_dssp             CSCCSSCCEEEEEECSSCSSEEEEEEE--------------------------------------TTEEEEEECCHHHHH
T ss_pred             CCCCCCCEEEEEEEEECCCCEEEEEEC--------------------------------------CCCEEEEEECCCEEE
T ss_conf             799988989999999829988999979--------------------------------------999999998476020


Q ss_pred             EEEEEECCCEEEEEECCCCC-CCCEEEEEEC
Q ss_conf             16477029969999746757-8435988429
Q gi|254780470|r   81 HRIRISLGDKVKVAMNPYDM-TRARITYRFK  110 (110)
Q Consensus        81 ~~IRIl~GDkV~Ve~SPYDL-tkGRItyR~K  110 (110)
                       +|+|..||.|.|+++|||+ +||+|+|||+
T Consensus        56 -~iwI~~GD~VlV~~~~~~~k~kg~Iv~r~~   85 (102)
T 1jt8_A           56 -RIWVREGDVVIVKPWEVQGDQKCDIIWRYT   85 (102)
T ss_dssp             -HHCCCSCEEEEECCBCCTTSEEEEEEEESS
T ss_pred             -EEEECCCCEEEEEEECCCCCCEEEEEEECC
T ss_conf             -158559999999951178996799999889


No 7  
>>2dgy_A MGC11102 protein; EIF-1A, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:)
Probab=97.02  E-value=0.0034  Score=39.39  Aligned_cols=64  Identities=19%  Similarity=0.117  Sum_probs=54.5

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf             99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL   87 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~   87 (110)
                      +.=+.|+.++-|..|.|..                                      .+|...+|++.||||+ ++-|-.
T Consensus        16 q~i~~V~~~~G~n~~eV~c--------------------------------------~dG~~rl~~ipgKfrk-~vWIk~   56 (111)
T 2dgy_A           16 QQIVRVLRTPGNNLHEVET--------------------------------------AQGQRFLVSMPSKYRK-NIWIKR   56 (111)
T ss_dssp             CEEEEEEECCSSSEEEEEC--------------------------------------TTSCEEEEECCTTCCS-CCCCCS
T ss_pred             CEEEEEEECCCCCEEEEEC--------------------------------------CCCCEEEEEECCCCCC-CEEEEC
T ss_conf             6999996426984499996--------------------------------------9999999996321123-257945


Q ss_pred             CCEEEEEECC-CCCCCCEEEEEEC
Q ss_conf             9969999746-7578435988429
Q gi|254780470|r   88 GDKVKVAMNP-YDMTRARITYRFK  110 (110)
Q Consensus        88 GDkV~Ve~SP-YDLtkGRItyR~K  110 (110)
                      ||-|.|+.-+ ++-.||-|+|+|-
T Consensus        57 GD~VlV~~~~~~~k~k~dIv~~y~   80 (111)
T 2dgy_A           57 GDFLIVDPIEEGEKVKAEISFVLC   80 (111)
T ss_dssp             SCEEEEEECSSCSSCCEEEEEECC
T ss_pred             CCEEEEEEHHHCCCCEEEEEEECC
T ss_conf             999999873546873499999769


No 8  
>>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} (A:1-75)
Probab=96.74  E-value=0.0041  Score=38.91  Aligned_cols=63  Identities=17%  Similarity=0.131  Sum_probs=48.4

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf             99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL   87 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~   87 (110)
                      .+.|.|+.... ..|.|+.+..                                   .++..+.|.+.|++|+..+++++
T Consensus        10 ~~~G~Vi~~~~-~~y~V~~~~~-----------------------------------~~g~~~~c~~RG~lr~~~~~~~V   53 (75)
T 1t9h_A           10 MPEGKIIKALS-GFYYVLDESE-----------------------------------DSDKVIQCRGRGIFRKNKITPLV   53 (75)
T ss_dssp             CCEEEEEEEET-TEEEEEECSS-----------------------------------SSCEEEEEESCSSCCSCCCCCCB
T ss_pred             CCCEEEEEEEC-CEEEEEECCC-----------------------------------CCCEEEEEEECCHHCCCCCCCCC
T ss_conf             78708999999-9999996368-----------------------------------88759999975321057998843


Q ss_pred             CCEEEEEECCCCCCCCEEEEE
Q ss_conf             996999974675784359884
Q gi|254780470|r   88 GDKVKVAMNPYDMTRARITYR  108 (110)
Q Consensus        88 GDkV~Ve~SPYDLtkGRItyR  108 (110)
                      ||.|.+  +|.|-.+|.|+--
T Consensus        54 GD~V~~--~~~~~~~G~I~~I   72 (75)
T 1t9h_A           54 GDYVVY--QAENDKEGYLMEI   72 (75)
T ss_dssp             TCEEEE--ECCTTSCEEEEEE
T ss_pred             CEEEEE--EECCCCCEEEEEE
T ss_conf             369999--9779980799998


No 9  
>>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} (A:1-73)
Probab=96.42  E-value=0.012  Score=36.21  Aligned_cols=60  Identities=20%  Similarity=0.297  Sum_probs=45.3

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf             99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL   87 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~   87 (110)
                      .+.|.|+.... ..|.|+.+                                     .++.++.|.+.|++|+.++..+.
T Consensus        10 ~~~G~Vi~~~~-~~y~V~~~-------------------------------------d~~~~~~c~~RG~lr~~~~~~~V   51 (73)
T 1u0l_A           10 RRRGIVVSFHS-NMVTVEDE-------------------------------------ETGERILCKLRGKFRLQNLKIYV   51 (73)
T ss_dssp             CEEEEEEEEET-TEEEEEET-------------------------------------TTCCEEEEEECGGGTTTTCCCCT
T ss_pred             CCEEEEEEEEC-CEEEEEEC-------------------------------------CCCEEEEEEECCEECCCCCCCEE
T ss_conf             41179999979-89999978-------------------------------------99919999944322058998000


Q ss_pred             CCEEEEEECCCCCCCCEEEE
Q ss_conf             99699997467578435988
Q gi|254780470|r   88 GDKVKVAMNPYDMTRARITY  107 (110)
Q Consensus        88 GDkV~Ve~SPYDLtkGRIty  107 (110)
                      ||+|.++  |-+-..|.|+-
T Consensus        52 GD~V~~~--~~~~~~g~I~~   69 (73)
T 1u0l_A           52 GDRVEYT--PDETGSGVIEN   69 (73)
T ss_dssp             TCEEEEE--CCCSSSEEEEE
T ss_pred             CEEEEEE--ECCCCCEEEEE
T ss_conf             2089998--87898289999


No 10 
>>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} (A:559-644)
Probab=94.04  E-value=0.22  Score=28.80  Aligned_cols=77  Identities=17%  Similarity=0.258  Sum_probs=47.9

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---EEEEEECCCEEEEE-E
Q ss_conf             9978999815898179998166776533323354433344555544455555445556882---89999125112016-4
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNA---VVIAYTAGRMRKHR-I   83 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~---~VlA~isGKmRk~~-I   83 (110)
                      +++|+|+...|.+.| |+|..+                         +-+|.-|+|.+...   ..-...+..-+++- -
T Consensus         5 ~~~g~V~~I~~~G~f-V~l~~~-------------------------~~eGli~~s~l~~~~~~~~~~~~~l~~~~~~~~   58 (86)
T 2id0_A            5 RFAAEIVDISRGGXR-VRLVDN-------------------------GAIAFIPAPFLHAVRDELVCSQENGTVQIKGET   58 (86)
T ss_dssp             CEEEEEEEEETTEEE-EEETTT-------------------------CCEEEEEGGGTCSCGGGEEEETTTTEEEETTEE
T ss_pred             EEEEEEEEEEECCEE-EEEECC-------------------------CEEEEEEHHHCCCCCCEEEEECCCCEEEECCCE
T ss_conf             489999889706399-998269-------------------------649999856647776448980222156405987


Q ss_pred             EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             770299699997467578435988429
Q gi|254780470|r   84 RISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        84 RIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      ..-+||+|+|.+.--|..+|||.+..|
T Consensus        59 ~~~~Gd~V~vkv~~vd~~~~kI~l~l~   85 (86)
T 2id0_A           59 VYKVTDVIDVTIAEVRXETRSIIARPV   85 (86)
T ss_dssp             EEETTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             EEECCCEEEEEEEEEECCCCEEEEEEC
T ss_conf             995799999999998345584899978


No 11 
>>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, cytoplasm, RNA-binding, RNA binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} (J:888-977)
Probab=93.65  E-value=0.17  Score=29.53  Aligned_cols=75  Identities=16%  Similarity=0.170  Sum_probs=46.9

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----------CEEEEEECC
Q ss_conf             997899981589817999816677653332335443334455554445555544555688-----------289999125
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDN-----------AVVIAYTAG   76 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~-----------~~VlA~isG   76 (110)
                      +++|.|+.+-+|+.| |+|+.                         .|-+|.-+++.+++           +.+..-.++
T Consensus         2 ~f~g~I~~V~~~G~f-V~l~~-------------------------~g~EGlV~~~~l~~d~~~~~~D~~~~~L~g~~t~   55 (90)
T 2wp8_J            2 TETGYVIKVFNNGIV-VLVPK-------------------------FGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTN   55 (90)
T ss_dssp             EEEEEEEEECSSEEE-EECTT-------------------------TCCEEEEEGGGTCSCGGGCEEETTTTEEEECCTT
T ss_pred             EEEEEEEEEEECCEE-EEECC-------------------------CCCEEEEEHHHCCCCCCCEEECHHHCEEEEEECC
T ss_conf             488999999957199-99708-------------------------9718999820079975424775688778632207


Q ss_pred             CEEEEEEEEECCCEEEEEECCCC---CCCCEEEEEEC
Q ss_conf             11201647702996999974675---78435988429
Q gi|254780470|r   77 RMRKHRIRISLGDKVKVAMNPYD---MTRARITYRFK  110 (110)
Q Consensus        77 KmRk~~IRIl~GDkV~Ve~SPYD---LtkGRItyR~K  110 (110)
                      +  .....+-+||+|+|.++--|   +.+++|-+.+|
T Consensus        56 ~--~~~~~~~igd~V~V~v~~vd~~~~~~~~i~f~L~   90 (90)
T 2wp8_J           56 S--DKPRDVYVFDKVEVQVRSVMDPITSKRKAELLLK   90 (90)
T ss_dssp             C--CSCEEEETTCEEEEEECCCCCSSSCCCCCCEEEC
T ss_pred             C--CCCEEEECCCEEEEEEEECCCCCCCCEEEEEEEC
T ss_conf             7--4650997499999999985676678615999849


No 12 
>>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} (B:81-172)
Probab=87.54  E-value=2.2  Score=23.02  Aligned_cols=74  Identities=8%  Similarity=0.027  Sum_probs=46.2

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCC----EEEEEE
Q ss_conf             9978999815898179998166776533323354433344555544455555445556882899991251----120164
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGR----MRKHRI   83 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGK----mRk~~I   83 (110)
                      .++|.|+...+.+.| |++.                           +-+|.-++|......+.-.-.-.    -+....
T Consensus         4 i~~G~V~~v~~~G~F-V~l~---------------------------~~eGli~~s~l~~~~~~~~~~~~~~~~~~~~~~   55 (92)
T 2c35_B            4 VVDAVVTQVNKVGLF-TEIG---------------------------PMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDI   55 (92)
T ss_dssp             EEEEEEEEEETTEEE-EEET---------------------------TEEEEEEGGGSCTTEEEESSSSSCEEEETTSCS
T ss_pred             EEEEEEEEECCCEEE-EEEE---------------------------CCCEEECCHHCCCEEEECCCCCCEEEEECCCCC
T ss_conf             999999987278699-9960---------------------------631120101102303203456532798315770


Q ss_pred             EEECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             77029969999746757843598842
Q gi|254780470|r   84 RISLGDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        84 RIl~GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      .+-+||+|+|.+.-.|..++||.+.+
T Consensus        56 ~~~vGd~V~v~V~~vd~~~~~i~~~l   81 (92)
T 2c35_B           56 VIQQDDEIRLKIVGTRVDKNDIFAIG   81 (92)
T ss_dssp             EEETTCEEEEEEEEEEEETTEEEEEE
T ss_pred             EECCCCEEEEEEEEEEECCCCCEEEE
T ss_conf             88899999999999983437847999


No 13 
>>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} (E:81-187)
Probab=85.22  E-value=3  Score=22.23  Aligned_cols=74  Identities=19%  Similarity=0.169  Sum_probs=45.6

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE---EEECCCEEEEEEE
Q ss_conf             9978999815898179998166776533323354433344555544455555445556882899---9912511201647
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVI---AYTAGRMRKHRIR   84 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~Vl---A~isGKmRk~~IR   84 (110)
                      .++|+|+.+.|.+.| |.|.                           |-+|.-|+|-+...-+.   ...+--.+...-+
T Consensus         4 ~~~g~V~~i~~~G~f-V~l~---------------------------g~~Glv~is~l~~~~~~~~~~~~~~~~~~~~~~   55 (107)
T 1go3_E            4 LIEGEVVDVVEFGSF-VRLG---------------------------PLDGLIHVSQIMDDYVSYDPKREAIIGKETGKV   55 (107)
T ss_dssp             EEEEEEEEEETTEEE-EECS---------------------------SSEEEEEGGGSCSSCEEECCC--CEEETTTCCE
T ss_pred             EEEEEEEEEEEEEEE-EEEC---------------------------CCEEEEEEHHCCCCCEECCHHHCEECCCCCCEE
T ss_conf             999999999732999-9955---------------------------805999811328985865756651314333579


Q ss_pred             EECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             7029969999746757843598842
Q gi|254780470|r   85 ISLGDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        85 Il~GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      +-+||+|+|.+.-.|..++||.+..
T Consensus        56 ~~~Gd~v~vkV~~vd~~~~~i~l~~   80 (107)
T 1go3_E           56 LEIGDYVRARIVAISLKAERKRGSK   80 (107)
T ss_dssp             ECTTCEEEEEEEEEECCC-----CE
T ss_pred             EECCCEEEEEEEEEECHHCCCCCCE
T ss_conf             9089999999999803005555670


No 14 
>>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A (L:43-126,L:209-218)
Probab=83.61  E-value=1.6  Score=23.84  Aligned_cols=76  Identities=16%  Similarity=0.216  Sum_probs=44.8

Q ss_pred             EEEEEEEECCCC--CCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-EEECCCEEEEEEE
Q ss_conf             997899981589--8179998166776533323354433344555544455555445556882899-9912511201647
Q gi|254780470|r    8 EFSGIVSELLPN--ANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVI-AYTAGRMRKHRIR   84 (110)
Q Consensus         8 e~~G~V~E~LPn--a~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~Vl-A~isGKmRk~~IR   84 (110)
                      .+.|.|+...|.  +.| |+|.                          ++.+|.-++|......+. -.-..+.+...=.
T Consensus         6 i~~G~V~~I~~f~~GaF-Vel~--------------------------~~~~Glihis~l~~~~~~~~~~~~~~~~~~~~   58 (94)
T 2bx2_L            6 IYKGKITRIEPSLEAAF-VDYG--------------------------AERHGFLPLKEIAREYFPANYSAHGRPNIKDV   58 (94)
T ss_dssp             EEEEEEEEEETTTTEEE-EESS--------------------------SSSCEEEEGGGSCGGGCC-------CCCGGGT
T ss_pred             EEEEEEEECCCCCCEEE-EEEC--------------------------CCCCEEEEHHHCCHHHCCCCCCCCCCCCHHHH
T ss_conf             89999953278876689-9508--------------------------99745888588385550455333456566773


Q ss_pred             EECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             70299699997467578435988429
Q gi|254780470|r   85 ISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        85 Il~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      .-+||+|+|.+.--|+.++||.+.++
T Consensus        59 ~~~Gd~V~V~V~~vd~~~~~i~lsl~   84 (94)
T 2bx2_L           59 LREGQEVIVQIDKEERGNKGAALTTF   84 (94)
T ss_dssp             CCTTCEEEEEEEECCCTTCCCEEESS
T ss_pred             CCCCCEEEEEECCCCCCCCCCCCCCC
T ss_conf             57998888985145444557553345


No 15 
>>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} (G:83-215)
Probab=81.53  E-value=2  Score=23.23  Aligned_cols=76  Identities=8%  Similarity=-0.033  Sum_probs=42.5

Q ss_pred             EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCE--EEEEEE
Q ss_conf             999789998158981799981667765333233544333445555444555554455568828999912511--201647
Q gi|254780470|r    7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRM--RKHRIR   84 (110)
Q Consensus         7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKm--Rk~~IR   84 (110)
                      -.++|+|+.+.+.+.| |+|..                           .+|.-|+|.....-+.--.+..+  +.-.=+
T Consensus         3 ~~~~G~V~~i~~~G~f-V~l~~---------------------------~~Gli~~s~l~~~~~~d~~~~~~~~~~~~~~   54 (133)
T 2b8k_G            3 EVVDGTVVSCSQHGFE-VQVGP---------------------------MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDV   54 (133)
T ss_dssp             EEEEEEEEEEETTEEE-EECTT---------------------------SEEEEEGGGSCSSCCCBSSCSSCEEECSSCE
T ss_pred             EEEEEEEEEECCCEEE-EEECC---------------------------CEEEEEEEECCCCCCCCCCCCEEEEECCCCE
T ss_conf             0999999976266489-98207---------------------------1689661006775421600052789438829


Q ss_pred             EECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             70299699997467578435988429
Q gi|254780470|r   85 ISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        85 Il~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +-+||.|+|.+--.|..++||....|
T Consensus        55 ~~~G~~v~vkVl~vd~~~~~i~ls~k   80 (133)
T 2b8k_G           55 ITIKSRIRVKIEGCISQVSSIHAIGS   80 (133)
T ss_dssp             EETTCEEEEEEEEEEEETTEEEEEEE
T ss_pred             EECCCEEEEEEEEEECCCCEEEEEEE
T ss_conf             93799999999998626570489999


No 16 
>>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} (B:83-171)
Probab=81.34  E-value=4.4  Score=21.30  Aligned_cols=74  Identities=8%  Similarity=-0.010  Sum_probs=46.0

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE--EEECCCEEEEEEEE
Q ss_conf             9978999815898179998166776533323354433344555544455555445556882899--99125112016477
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVI--AYTAGRMRKHRIRI   85 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~Vl--A~isGKmRk~~IRI   85 (110)
                      .++|.|+.+.|.+.| |++..                           -+|.-++|......+.  .-.+-.++...-++
T Consensus         4 i~~g~V~~v~~~G~F-V~l~~---------------------------~eg~v~~s~l~~d~~~~~~~~~~~~~~~~~~~   55 (89)
T 1y14_B            4 VVDGTVVSCSQHGFE-VQVGP---------------------------MKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVI   55 (89)
T ss_dssp             EEEEEEEEEETTEEE-EEETT---------------------------EEEEEEGGGSCTTCEECC-----CEECSSCEE
T ss_pred             EEEEEEEEEECCCEE-EEECC---------------------------CCEEEEEEECCCCCCCCHHHCEEEEECCCEEE
T ss_conf             899999998157389-99056---------------------------21787732003321147567278984188199


Q ss_pred             ECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             029969999746757843598842
Q gi|254780470|r   86 SLGDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        86 l~GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      -+||+|+|.+.-.|..++||.+.+
T Consensus        56 ~~Gd~V~vkV~~vd~~~~~i~l~l   79 (89)
T 1y14_B           56 TIKSRIRVKIEGCISQVSSIHAIG   79 (89)
T ss_dssp             CTTCEEEEEEEEEEEETTEEEEEE
T ss_pred             CCCCEEEEEEEEEECCCCCCEEEE
T ss_conf             189999999999980648738999


No 17 
>>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} (B:81-218)
Probab=80.15  E-value=4.1  Score=21.45  Aligned_cols=77  Identities=12%  Similarity=0.084  Sum_probs=48.9

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-----EEECCCEEEEE
Q ss_conf             9978999815898179998166776533323354433344555544455555445556882899-----99125112016
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVI-----AYTAGRMRKHR   82 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~Vl-----A~isGKmRk~~   82 (110)
                      .++|+|+.+.+-+.| |.|..                         ++.+|.-|+|.+...-+-     +.+..+-+...
T Consensus         4 i~~G~V~~v~~~Gif-V~L~~-------------------------~~~egli~~s~L~d~~~~~~~~~~~~~~~~~~~~   57 (138)
T 2ckz_B            4 IVTGWISKCTAEGIK-VSLLG-------------------------IFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETK   57 (138)
T ss_dssp             EEEEEEEEEETTEEE-EECTT-------------------------SCCCEEEETTTSCTTCEEETTTTEEEEECC--CE
T ss_pred             EEEEEEEEECCCEEE-EEECC-------------------------CCCCEEEEHHHCCCCCEECHHCCEEEEECCCCCC
T ss_conf             999999715165499-99338-------------------------7365385077678985793112559972487456


Q ss_pred             EEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             4770299699997467578435988429
Q gi|254780470|r   83 IRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        83 IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      -..-+||+|++.+---|+.+++|.+..|
T Consensus        58 ~~~~~Gd~V~vkV~~vd~~~~~i~lsl~   85 (138)
T 2ckz_B           58 LYFDVNEKIRFRIEREVFVDVKPKSPKE   85 (138)
T ss_dssp             EEECTTCEEEEEEEEEEECCCCC-----
T ss_pred             EEECCCCEEEEEEEEEEEECCCCCCCCC
T ss_conf             0975899899999999964279987310


No 18 
>>2vnu_D Exosome complex exonuclease RRP44; rRNA processing, RNA degradation, cytoplasm, RNA-binding, RNA processing, DIS3P, nucleus, hydrolase; HET: 1PE; 2.30A {Saccharomyces cerevisiae} (D:671-760)
Probab=78.72  E-value=3.6  Score=21.81  Aligned_cols=75  Identities=16%  Similarity=0.153  Sum_probs=43.8

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----------CCCEEEEEECC
Q ss_conf             9978999815898179998166776533323354433344555544455555445556-----------88289999125
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYL-----------DNAVVIAYTAG   76 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~-----------~~~~VlA~isG   76 (110)
                      +++|.|+.+-+|+.| |.|+..                         |-+|.-+++..           ..+.+..--++
T Consensus         2 ~~~g~Is~V~~~Gi~-V~l~~~-------------------------giEG~V~l~~l~~d~~~~~~D~~~~~l~g~~t~   55 (90)
T 2vnu_D            2 TETGYVIKVFNNGIV-VLVPKF-------------------------GVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTN   55 (90)
T ss_dssp             EEEEEEEEEETTEEE-EEETTT-------------------------TEEEEEEHHHHCSCGGGCEEETTTTEEEECCTT
T ss_pred             EEEEEEEEEEECEEE-EEEECC-------------------------CCEEEEECCCCCCCCCCEEECHHHCEEEEEEEC
T ss_conf             489999999957299-998089-------------------------748999801179985405875578389866606


Q ss_pred             CEEEEEEEEECCCEEEEEECCC---CCCCCEEEEEEC
Q ss_conf             1120164770299699997467---578435988429
Q gi|254780470|r   77 RMRKHRIRISLGDKVKVAMNPY---DMTRARITYRFK  110 (110)
Q Consensus        77 KmRk~~IRIl~GDkV~Ve~SPY---DLtkGRItyR~K  110 (110)
                      +  ...+.+-+||+|+|.++--   ++.+.+|-+.++
T Consensus        56 ~--~~~~~~~lgd~V~V~v~~v~~~~~~~~~i~f~L~   90 (90)
T 2vnu_D           56 S--DKPRDVYVFDKVEVQVRSVXDPITSKRKAELLLK   90 (90)
T ss_dssp             C--SSCEEEETTCEEEEEEC--------CCEEEC---
T ss_pred             C--CCCEEEECCCEEEEEEEEECCCCCCCEEEEEEEC
T ss_conf             7--4643997389999999991576668545999959


No 19 
>>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (G:84-172)
Probab=75.41  E-value=1.3  Score=24.31  Aligned_cols=74  Identities=12%  Similarity=0.017  Sum_probs=43.1

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECC--CEEEEEEEE
Q ss_conf             997899981589817999816677653332335443334455554445555544555688289999125--112016477
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAG--RMRKHRIRI   85 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isG--KmRk~~IRI   85 (110)
                      .++|+|+...+.+.|- +|.                           |-+|.-|+|.....-+.--...  .++...-.+
T Consensus         4 i~~G~V~~i~~~G~FV-~l~---------------------------~~eG~v~~s~l~~d~~~~~~~~~~~~~~~~~~~   55 (89)
T 3h0g_G            4 VVDAIVTTVNKMGFFA-NIG---------------------------PLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVI   55 (89)
T ss_dssp             EEECCCCEEETTEEEC-CBT---------------------------TBCCEEEGGGSCTTCCCBSSSSSCBEESSSCEE
T ss_pred             EEEEEEEEEECCEEEE-EEE---------------------------CCCEEEEHHHCCCCCCCCHHHCEEEEEECCEEE
T ss_conf             9999996880555999-940---------------------------641574412115543116004448986188199


Q ss_pred             ECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             029969999746757843598842
Q gi|254780470|r   86 SLGDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        86 l~GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      -+||+|+|.+.-.|..++||.+..
T Consensus        56 ~~Gd~V~vkV~~vd~~~~~i~l~l   79 (89)
T 3h0g_G           56 EKGSNVRLKIVGTRTDATEIFAIA   79 (89)
T ss_dssp             CSSCCEEEEEEEEEESSSCEEEEE
T ss_pred             CCCCEEEEEEEEEECCCCCCEEEE
T ss_conf             489999999999963527837999


No 20 
>>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium LT2} (A:1-111)
Probab=75.30  E-value=3.5  Score=21.83  Aligned_cols=48  Identities=13%  Similarity=0.055  Sum_probs=34.0

Q ss_pred             CCCCCCCCCCCCCEEEEEECCCEEEEEEEEECCCEEEEEECCCCC----CCCEEEE
Q ss_conf             555544555688289999125112016477029969999746757----8435988
Q gi|254780470|r   56 NDGVDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDM----TRARITY  107 (110)
Q Consensus        56 ~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~GDkV~Ve~SPYDL----tkGRIty  107 (110)
                      .++.+.|-.++|.++.|++-|+++.    ++.||+|.+....=.+    ..|-|+-
T Consensus        56 ~G~~y~V~~~dG~~~~C~~Rg~~~~----~vvGD~V~~~~~~e~~~~~~~~GvIe~  107 (111)
T 2rcn_A           56 FGMHADVESADGEVHRCNIRRTIRS----LVTGDRVVWRPGKAAAEGVNVKGIVEA  107 (111)
T ss_dssp             ETTEEEEEETTSCEEEEEECTTCCC----CCBTCEEEEECBC-------CCEEEEE
T ss_pred             ECCEEEEECCCCCEEEEEECCCCCC----CCCCCEEEEEECCCCCCCCCCCEEEEE
T ss_conf             8988999979997899886676789----988967998226765556676469999


No 21 
>>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} (A:136-219)
Probab=66.04  E-value=5.9  Score=20.55  Aligned_cols=62  Identities=19%  Similarity=0.246  Sum_probs=42.1

Q ss_pred             EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEE
Q ss_conf             99978999815898179998166776533323354433344555544455555445556882899991251120164770
Q gi|254780470|r    7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRIS   86 (110)
Q Consensus         7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl   86 (110)
                      -.+.|+|....|.+.| |+|..+                                     ...-+.|+|---    =+.-
T Consensus        19 ~~~~g~V~~i~~~G~f-V~l~~~-------------------------------------~~eGlv~~sel~----~~~~   56 (84)
T 3go5_A           19 QNWPAIVYRLKLSGTF-VYLPEN-------------------------------------NXLGFIHPSERY----AEPR   56 (84)
T ss_dssp             CEEEEEEEEEETTEEE-EEETTT-------------------------------------TEEEEECGGGCS----SCCC
T ss_pred             CEEEEEEEEEECCCCE-EEECCC-------------------------------------CEEEEECCCCCC----CCCC
T ss_conf             9999999999748718-984378-------------------------------------789996354124----4467


Q ss_pred             CCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             299699997467578435988429
Q gi|254780470|r   87 LGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        87 ~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +||+|+|-+.-.|..+|||..-.|
T Consensus        57 vGd~v~v~v~~vd~~~~~i~lslk   80 (84)
T 3go5_A           57 LGQVLDARVIGFREVDRTLNLSLK   80 (84)
T ss_dssp             TTCEEEEEEEEEETTTTEEEEECS
T ss_pred             CCCEEEEEEEEEECCCCEEEEEEC
T ss_conf             574899999999843767999965


No 22 
>>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} (A:)
Probab=47.56  E-value=23  Score=17.16  Aligned_cols=67  Identities=9%  Similarity=0.136  Sum_probs=43.6

Q ss_pred             EEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCE-----EE
Q ss_conf             5999789998158981799981667765333233544333445555444555554455568828999912511-----20
Q gi|254780470|r    6 TLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRM-----RK   80 (110)
Q Consensus         6 ~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKm-----Rk   80 (110)
                      --.+.|.|+.+.|.+.|- .|.                                     .++..-+.|++-=-     ..
T Consensus        22 G~~v~g~V~~v~~~G~fV-~l~-------------------------------------~~~~~g~i~~sels~~~~~~~   63 (119)
T 1wi5_A           22 GMLLTGTVSSLEDHGYLV-DIG-------------------------------------VDGTRAFLPLLKAQEYIRQKN   63 (119)
T ss_dssp             TCEEEEEEEEECSSEEEE-ECC-------------------------------------CSSCEEEEEHHHHHHHHHHHS
T ss_pred             CCEEEEEEEEEEEEEEEE-ECC-------------------------------------CCCCEEEEEHHHHCCCCCCCC
T ss_conf             978999999884018999-514-------------------------------------554027876999352112347


Q ss_pred             EEEEEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             164770299699997467578435988429
Q gi|254780470|r   81 HRIRISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        81 ~~IRIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      -.=.+-+||.|+|-+---|..++||..-+|
T Consensus        64 ~~~~~~vGd~i~v~V~~vd~~~~~i~ls~k   93 (119)
T 1wi5_A           64 KGAKLKVGQYLNCIVEKVKGNGGVVSLSVG   93 (119)
T ss_dssp             SSCCCCTTCEEEEEEEECCTTSCEEEEECC
T ss_pred             CCCEEEEEEEEEEEEEEEECCCCEEEEECH
T ss_conf             300021001899999998379858998401


No 23 
>>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B (C:1-85)
Probab=46.34  E-value=24  Score=17.04  Aligned_cols=71  Identities=15%  Similarity=0.143  Sum_probs=42.7

Q ss_pred             EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEE
Q ss_conf             99978999815898179998166776533323354433344555544455555445556882899991251120164770
Q gi|254780470|r    7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRIS   86 (110)
Q Consensus         7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl   86 (110)
                      -.+.|.|+...+++.|- +|..                        .+|-+|.-|+|-...        ++++.-.=..-
T Consensus        13 ~~v~g~V~~i~~~G~~V-~l~~------------------------~~~i~G~i~~s~ls~--------~~~~~~~~~~~   59 (85)
T 3cw2_C           13 EILIATVKQVFDYGSYV-SLDE------------------------YGGLQAFLPWSEVSS--------KWVKNIRDVLK   59 (85)
T ss_dssp             CEEEEEEEECCSSSBEE-EETT------------------------TTSEECBBCGGGSSC--------SSCCCHHHHSC
T ss_pred             CEEEEEEEEEECCEEEE-EECC------------------------CCCCEEEEEHHHCCC--------CCCCCHHHHCC
T ss_conf             99999999997554899-9756------------------------799089989899588--------65589888188


Q ss_pred             CCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             299699997467578435988429
Q gi|254780470|r   87 LGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        87 ~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +||+|++-+.--|..+|||..-.|
T Consensus        60 vG~~V~v~V~~vd~~~~ri~LS~k   83 (85)
T 3cw2_C           60 ENRKVIVKVIRVDRRKGTVDVSLK   83 (85)
T ss_dssp             TTCEEEEEECCCCSSSCCCBEEST
T ss_pred             CCCEEEEEEEEEECCCCCEEEEEE
T ss_conf             999999999665255744378984


No 24 
>>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} (P:129-215)
Probab=45.82  E-value=24  Score=16.99  Aligned_cols=60  Identities=13%  Similarity=-0.025  Sum_probs=41.4

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEEC
Q ss_conf             99789998158981799981667765333233544333445555444555554455568828999912511201647702
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRISL   87 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl~   87 (110)
                      .++|+|....+.+.| |.|.                                       |  +-|++.-+--..+=..-+
T Consensus         9 iv~g~V~~i~~~G~~-V~l~---------------------------------------~--~~g~ip~~e~~~~~~~~~   46 (87)
T 1hh2_P            9 VTTAEVIRVMGEWAD-IRIG---------------------------------------K--LETRLPKKEWIPGEEIKA   46 (87)
T ss_dssp             EEEEEEEEECSSEEE-EEET---------------------------------------T--EEEEEEGGGSCTTCCCCT
T ss_pred             EEEEEEEEEECCCEE-EECC---------------------------------------C--EEEEECHHHCCCCCCCCC
T ss_conf             899999999614359-9618---------------------------------------6--168717788698656799


Q ss_pred             CCEEEEEECCCCCCCCEEEEEE
Q ss_conf             9969999746757843598842
Q gi|254780470|r   88 GDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        88 GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      ||++++-+.--|..++||..-.
T Consensus        47 G~~i~~~v~~vd~~~~~i~ls~   68 (87)
T 1hh2_P           47 GDLVKVYIIDVVKTTKGPKILV   68 (87)
T ss_dssp             TCEEEEEEEEEEEETTEEEEEE
T ss_pred             CCEEEEEEEEEEECCCCCEEEE
T ss_conf             9989999999987488977999


No 25 
>>2waq_E DNA-directed RNA polymerase RPO7 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_E 2pmz_E 3hkz_E (E:81-180)
Probab=44.58  E-value=8.2  Score=19.72  Aligned_cols=74  Identities=23%  Similarity=0.116  Sum_probs=43.3

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE---EEEEECCCEEEEEEE
Q ss_conf             99789998158981799981667765333233544333445555444555554455568828---999912511201647
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAV---VIAYTAGRMRKHRIR   84 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~---VlA~isGKmRk~~IR   84 (110)
                      .++|.|+.+.|.+.| |+|..             .              +|.-|+|-....-   .-...+.+.+...-.
T Consensus         4 ~~~g~V~~v~~~G~f-V~l~~-------------~--------------~Glv~~s~ls~~~~~~~~~~~~~~~~~~~~~   55 (100)
T 2waq_E            4 VVEGEVLQVDNYGIF-VNLGP-------------M--------------DGLVHISQITDDTLKYDNVRGIIFGEKSKKV   55 (100)
T ss_dssp             CCCEEEEEECSSEEE-EBCSS-------------S--------------BBCEESTTBCSSSSCCCCCSSSCSCBCSSSB
T ss_pred             EEEEEEEEEECCEEE-EEECC-------------C--------------CCEEEEHHHCCCCCCCCHHHCEEEECCCCEE
T ss_conf             999999998547199-97148-------------7--------------7539752327874203455163774478829


Q ss_pred             EECCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             7029969999746757843598842
Q gi|254780470|r   85 ISLGDKVKVAMNPYDMTRARITYRF  109 (110)
Q Consensus        85 Il~GDkV~Ve~SPYDLtkGRItyR~  109 (110)
                      +-+||+|+|-+.--|..+++|.+|.
T Consensus        56 ~~vGd~v~vkV~~vd~~~~~i~~~i   80 (100)
T 2waq_E           56 IQKGDKVRARVISVASTVTGRLPRI   80 (100)
T ss_dssp             CCTTCEEBCEEEEEECCC---CCEE
T ss_pred             EECCCEEEEEEEEEECCCCCCCCCE
T ss_conf             9589999999999967877656707


No 26 
>>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A (A:1-82)
Probab=42.67  E-value=14  Score=18.44  Aligned_cols=15  Identities=27%  Similarity=0.558  Sum_probs=12.3

Q ss_pred             CCCCEEEEEECCCEE
Q ss_conf             688289999125112
Q gi|254780470|r   65 LDNAVVIAYTAGRMR   79 (110)
Q Consensus        65 ~~~~~VlA~isGKmR   79 (110)
                      .++..|.+|-|||+-
T Consensus        38 ~~~~tIt~Y~SGKVl   52 (82)
T 2d0b_A           38 RPDVVITAYRSGKVL   52 (82)
T ss_dssp             CTTCEEEEETTSEEE
T ss_pred             CCCCEEEEEECCEEE
T ss_conf             799589999577899


No 27 
>>1y43_B Aspergillopepsin II heavy chain; proctase A, beta sandwich structure, hydrolase; 1.40A {Aspergillus niger var} (B:1-118)
Probab=42.12  E-value=14  Score=18.35  Aligned_cols=35  Identities=23%  Similarity=0.215  Sum_probs=27.4

Q ss_pred             ECCCEEEEEEEEECCCEEEEEECCCCCCCCEEEEE
Q ss_conf             12511201647702996999974675784359884
Q gi|254780470|r   74 TAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR  108 (110)
Q Consensus        74 isGKmRk~~IRIl~GDkV~Ve~SPYDLtkGRItyR  108 (110)
                      -+.-+.--.|.|.+||.+.+.+.....++|+++..
T Consensus        46 P~~a~~~~~~~v~~GD~i~v~Vt~~s~~~g~~~i~   80 (118)
T 1y43_B           46 PDYAYDFSDITISEGDSIKVTVEATSKSSGSATVE   80 (118)
T ss_dssp             TSCCEEETTCCCCTTCEEEEEEEEEETTEEEEEEE
T ss_pred             CCCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEEE
T ss_conf             68841526641389999999999707996699999


No 28 
>>2ifr_A Scytalidopepsin B; enzyme-transition state analog complex, hydrolase; HET: TA2 AAR; 1.95A {Scytalidium lignicola} (A:)
Probab=37.91  E-value=22  Score=17.27  Aligned_cols=36  Identities=22%  Similarity=0.235  Sum_probs=26.4

Q ss_pred             EECCCEEEEEEEEECCCEEEEEECCCCCCCCEEEEE
Q ss_conf             912511201647702996999974675784359884
Q gi|254780470|r   73 YTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR  108 (110)
Q Consensus        73 ~isGKmRk~~IRIl~GDkV~Ve~SPYDLtkGRItyR  108 (110)
                      |-..-..--.|.|.+||.+.+.+.....++|+|+..
T Consensus        71 ~P~~a~~~~~~~v~~GD~i~v~V~~~s~~~g~~~i~  106 (206)
T 2ifr_A           71 YPEVSDDFSGITISEGDSIQMSVTATSDTSGSATLE  106 (206)
T ss_dssp             ESSCEEEC--CCCCTTCEEEEEEEEEETTEEEEEEE
T ss_pred             CCCCCCCCCCCEECCCCEEEEEEEECCCCCEEEEEE
T ss_conf             488755625421289998999999747996799999


No 29 
>>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} (A:)
Probab=37.14  E-value=33  Score=16.19  Aligned_cols=69  Identities=19%  Similarity=0.259  Sum_probs=41.3

Q ss_pred             EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEEE
Q ss_conf             99978999815898179998166776533323354433344555544455555445556882899991251120164770
Q gi|254780470|r    7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRIS   86 (110)
Q Consensus         7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRIl   86 (110)
                      -.+.|+|+...|++.|- .+.                          .|-.|.-|+|-...        .+...-.=.+-
T Consensus        33 ~iv~g~V~~v~~~G~~V-~~~--------------------------~~~~G~v~~s~l~~--------~~~~~~~~~~~   77 (109)
T 2khj_A           33 AIVTGKVTAVDAKGATV-ELA--------------------------DGVEGYLRASEASR--------DRVEDATLVLS   77 (109)
T ss_dssp             SEEEEEEEEECSSCEEE-ECS--------------------------TTCBCCBCTTCCCS--------SSSSSGGGSCC
T ss_pred             CEEEEEEEEEECCEEEE-EEC--------------------------CEEEEHEEHHHHCC--------CCCCCHHHHEE
T ss_conf             99999999998968999-989--------------------------81860110224244--------53149778203


Q ss_pred             CCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             299699997467578435988429
Q gi|254780470|r   87 LGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        87 ~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      +||.|++-+.--|..+|||..-.|
T Consensus        78 vG~~v~v~V~~vd~~~~~i~lSlk  101 (109)
T 2khj_A           78 VGDEVEAKFTGVDRKNRAISLSVR  101 (109)
T ss_dssp             TTCEEEEEEEEEETTTTEEEEETT
T ss_pred             CCCEEEEEEEEEECCCCEEEEEEE
T ss_conf             242799999999899999999834


No 30 
>>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus WR} (A:)
Probab=35.25  E-value=28  Score=16.58  Aligned_cols=27  Identities=30%  Similarity=0.381  Sum_probs=23.3

Q ss_pred             EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             770299699997467578435988429
Q gi|254780470|r   84 RISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        84 RIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      ..-+||+|++.+---|..++||...+|
T Consensus        56 ~~~vGd~v~~kVl~vd~~~~~i~LS~K   82 (88)
T 1luz_A           56 DKLVGKTVKVKVIRVDYTKGYIDVNYK   82 (88)
T ss_dssp             HHHTTCEEEEEEEEEETTTTEEEEEEE
T ss_pred             HHHCCCEEEEEEEEECCEEEEEEEHHH
T ss_conf             975395699999998360147984155


No 31 
>>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} (A:)
Probab=31.54  E-value=41  Score=15.65  Aligned_cols=66  Identities=12%  Similarity=0.239  Sum_probs=41.8

Q ss_pred             EEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEEEE
Q ss_conf             59997899981589817999816677653332335443334455554445555544555688289999125112016477
Q gi|254780470|r    6 TLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRIRI   85 (110)
Q Consensus         6 ~ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~IRI   85 (110)
                      --.+.|.|+...+.+.| |.|.                                      ++..=+.+++-=-....=.+
T Consensus         6 G~~~~g~V~~v~~~G~f-V~l~--------------------------------------~~i~Gli~~~~ls~~~~~~~   46 (80)
T 2k52_A            6 GKFYKGVVTRIEKYGAF-INLN--------------------------------------EQVRGLLRPRDMISLRLENL   46 (80)
T ss_dssp             TCEEEEEEEEEETTEEE-EEEE--------------------------------------TTEEEEECGGGCSSCCGGGC
T ss_pred             CCEEEEEEEEEECCEEE-EEEC--------------------------------------CCEEEEEEHHHCCCCCCCCC
T ss_conf             99999999999787799-9965--------------------------------------55789999126256423364


Q ss_pred             ECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             0299699997467578435988429
Q gi|254780470|r   86 SLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        86 l~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      -+||+|++.+.--|..++||..-.|
T Consensus        47 ~vG~~v~v~V~~vd~~~~~i~lS~k   71 (80)
T 2k52_A           47 NVGDEIIVQAIDVRPEKREIDFKYI   71 (80)
T ss_dssp             CTTCEEEEEEEEEETTTTEEEEEEC
T ss_pred             EECEEEEEEEEEEECCCCEEEEEEE
T ss_conf             0110299999999998899989987


No 32 
>>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} (A:)
Probab=29.42  E-value=45  Score=15.44  Aligned_cols=65  Identities=20%  Similarity=0.268  Sum_probs=39.8

Q ss_pred             EEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCEEEEEE---
Q ss_conf             99978999815898179998166776533323354433344555544455555445556882899991251120164---
Q gi|254780470|r    7 LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVVIAYTAGRMRKHRI---   83 (110)
Q Consensus         7 ie~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~~~VlA~isGKmRk~~I---   83 (110)
                      -.+.|.|+...|.+.|- .|.                                      ++..-+.+++-=-...++   
T Consensus        32 ~iv~G~V~~v~~~G~fV-~l~--------------------------------------~~~~g~i~~~els~~~~~~~~   72 (115)
T 2khi_A           32 TKLTGRVTNLTDYGCFV-EIE--------------------------------------EGVEGLVHVSEMDWTNKNIHP   72 (115)
T ss_dssp             CEEEEEEEEEETTEEEE-ECS--------------------------------------TTCEEEEETTSSSCSSTTCSS
T ss_pred             CEEEEEEEEEECCEEEE-EEC--------------------------------------CCCCEEEEEEEECCCCCCCCC
T ss_conf             99999999996875999-989--------------------------------------857223787631344422232


Q ss_pred             --EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             --770299699997467578435988429
Q gi|254780470|r   84 --RISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        84 --RIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                        .+-+||.|.|-+---|..+|||..-.|
T Consensus        73 ~~~~~~G~~v~v~V~~vd~~~~ri~lS~k  101 (115)
T 2khi_A           73 SKVVNVGDVVEVMVLDIDEERRRISLGLK  101 (115)
T ss_dssp             TTTCCTTCEEEEEEEEEETTTTEEEECCC
T ss_pred             EEEEECCCEEEEEEEEEECCCCEEEEEEE
T ss_conf             04884386699999999899999999987


No 33 
>>3k3s_A Altronate hydrolase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE; 2.15A {Shigella flexneri 2a str} (A:)
Probab=26.97  E-value=26  Score=16.84  Aligned_cols=32  Identities=25%  Similarity=0.254  Sum_probs=24.1

Q ss_pred             EEEEECCCEEEE-----EEEEECCCEEEEEECCCCCCCC
Q ss_conf             999912511201-----6477029969999746757843
Q gi|254780470|r   70 VIAYTAGRMRKH-----RIRISLGDKVKVAMNPYDMTRA  103 (110)
Q Consensus        70 VlA~isGKmRk~-----~IRIl~GDkV~Ve~SPYDLtkG  103 (110)
                      -.-|.+|+|++.     .|++-+.|.|-|.+.+  |.+|
T Consensus         7 ~~~~~~~~~~~~~~~~~~l~l~~~DNVaVAl~d--l~~G   43 (105)
T 3k3s_A            7 HHHHSSGRENLYFQGXQYIKIHALDNVAVALAD--LAEG   43 (105)
T ss_dssp             --------------CCSEECCSTTCSEEEESSC--BCTT
T ss_pred             CCCCCCCHHHHHHCCCCEEECCCCCCEEEECCC--CCCC
T ss_conf             221456422032327988871899989996774--6999


No 34 
>>2b3w_A Hypothetical protein YBIA; structure, NESG, structural genomics, COG 3236, PSI, protein structure initiative; NMR {Escherichia coli} (A:1-27,A:119-168)
Probab=26.85  E-value=34  Score=16.16  Aligned_cols=18  Identities=11%  Similarity=-0.163  Sum_probs=14.4

Q ss_pred             ECCCEEEEEECCCCCCCC
Q ss_conf             029969999746757843
Q gi|254780470|r   86 SLGDKVKVAMNPYDMTRA  103 (110)
Q Consensus        86 l~GDkV~Ve~SPYDLtkG  103 (110)
                      .-||+..||-||+|---|
T Consensus        26 ~~Gd~~LVE~Sp~D~~WG   43 (77)
T 2b3w_A           26 YGAPAKLVEHTENDAYWG   43 (77)
T ss_dssp             GGTTEEEEECCSSCCSSS
T ss_pred             CCCCCEEEECCCCCCCCC
T ss_conf             739988996799998446


No 35 
>>2g3r_A Tumor suppressor P53-binding protein 1; tandem tudor domains, cell cycle/transcription complex; 1.25A {Homo sapiens} (A:1-58,A:109-123)
Probab=24.35  E-value=46  Score=15.38  Aligned_cols=43  Identities=19%  Similarity=0.273  Sum_probs=28.0

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             997899981589817999816677653332335443334455554445555544555688
Q gi|254780470|r    8 EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDN   67 (110)
Q Consensus         8 e~~G~V~E~LPna~FrV~L~~~d~~~~~~~~l~~~~~~~f~~~g~~~g~~g~~~~s~~~~   67 (110)
                      -++|.++.-+-...||...+++-     .|+.-+|---            -.||||.++|
T Consensus        21 fysg~i~rd~g~~rfrl~fdd~~-----ecev~gkdil------------lcdpisleqg   63 (73)
T 2g3r_A           21 FYSGKITRDVGAGKYKLLFDDGY-----ECDVLGKDIL------------LCDPISLEQG   63 (73)
T ss_dssp             EEEEEEEEEEETTEEEEEETTSC-----EEEEEGGGEE------------CCSSCCHHHH
T ss_pred             EEEEEEEEECCCCEEEEEECCCC-----EEEECHHHCE------------EECCCCHHHH
T ss_conf             88689999737988999984899-----3785268817------------8278474455


No 36 
>>1s5u_A Protein YBGC; structural genomics, hypothetical protein, thioesterase fold, PSI, protein structure initiative; 1.70A {Escherichia coli} (A:1-125)
Probab=21.02  E-value=62  Score=14.62  Aligned_cols=27  Identities=11%  Similarity=0.236  Sum_probs=22.8

Q ss_pred             EEECCCEEEEEECCCCCCCCEEEEEEC
Q ss_conf             770299699997467578435988429
Q gi|254780470|r   84 RISLGDKVKVAMNPYDMTRARITYRFK  110 (110)
Q Consensus        84 RIl~GDkV~Ve~SPYDLtkGRItyR~K  110 (110)
                      .+..||++.|+.......+.+++++++
T Consensus        71 ~~~~gd~i~v~~~~~~~~~~~~~~~~~   97 (125)
T 1s5u_A           71 PARLDDMLEIQTEITSMRGTSLVFTQR   97 (125)
T ss_dssp             CCCTTCEEEEEEEEEEECSSEEEEEEE
T ss_pred             HHCCCCEEEEEEEEEECCCEEEEEEEE
T ss_conf             312684278899998759759999999


Done!