Query         gi|254780940|ref|YP_003065353.1| ribonuclease III [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 227
No_of_seqs    139 out of 3294
Neff          7.6 
Searched_HMMs 13730
Date          Wed Jun  1 10:59:40 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780940.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1o0wa1 a.149.1.1 (A:-1-167) R 100.0 2.9E-41 2.8E-45  271.1   6.7  147    4-150     9-162 (169)
  2 d2nuga1 a.149.1.1 (A:3-150) RN 100.0 6.5E-39 4.7E-43  256.6   9.6  137    6-150     2-140 (148)
  3 d1u61a_ a.149.1.1 (A:) Hypothe  99.9 2.1E-24 1.5E-28  167.4   3.5  107   37-144     5-123 (127)
  4 d1o0wa2 d.50.1.1 (A:168-236) R  99.7 6.5E-18 4.7E-22  127.4   8.7   68  156-223     1-68  (69)
  5 d2cpna1 d.50.1.1 (A:150-225) T  99.7   7E-17 5.1E-21  121.0   9.0   72  151-223     5-76  (76)
  6 d1uhza_ d.50.1.1 (A:) staufen   99.7 7.7E-17 5.6E-21  120.8   9.2   71  154-225     5-75  (89)
  7 d2nuga2 d.50.1.1 (A:151-218) R  99.7 8.1E-17 5.9E-21  120.7   8.0   68  156-224     1-68  (68)
  8 d1uila_ d.50.1.1 (A:) ATP-depe  99.6 1.7E-16 1.3E-20  118.6   6.5   74  151-226    22-103 (113)
  9 d1qu6a1 d.50.1.1 (A:1-90) dsRN  99.6 8.1E-17 5.9E-21  120.7   4.7   73  151-224     9-81  (90)
 10 d1di2a_ d.50.1.1 (A:) Double-s  99.6 3.7E-16 2.7E-20  116.6   8.0   67  157-224     2-68  (69)
 11 d1x49a1 d.50.1.1 (A:8-92) dsRN  99.6 2.2E-16 1.6E-20  118.0   5.7   71  153-224     5-75  (85)
 12 d1whna_ d.50.1.1 (A:) tRNA-dih  99.6 5.9E-16 4.3E-20  115.4   7.9   83  141-226    12-95  (128)
 13 d2dixa1 d.50.1.1 (A:7-79) Inte  99.6 4.4E-16 3.2E-20  116.2   7.1   68  155-224     2-69  (73)
 14 d1x47a1 d.50.1.1 (A:8-92) Dgcr  99.6 1.2E-15 8.7E-20  113.5   8.9   71  151-223     5-75  (85)
 15 d1whqa_ d.50.1.1 (A:) ATP-depe  99.6 8.3E-16 6.1E-20  114.4   6.1   68  154-223     5-73  (99)
 16 d1qu6a2 d.50.1.1 (A:91-179) ds  99.6 1.9E-15 1.4E-19  112.2   6.6   75  148-224     7-81  (89)
 17 d1t4oa_ d.50.1.1 (A:) RNase II  99.6 1.4E-15   1E-19  113.0   5.5   74  151-226     2-76  (81)
 18 d1x48a1 d.50.1.1 (A:8-83) dsRN  99.5 7.7E-15 5.6E-19  108.5   8.1   66  157-224     1-66  (76)
 19 d1ekza_ d.50.1.1 (A:) Staufen,  99.5 1.1E-15 8.1E-20  113.6   3.3   71  152-224     4-74  (76)
 20 d2dmya1 d.50.1.1 (A:8-91) Sper  99.5   2E-13 1.5E-17   99.8   9.7   68  154-227    11-78  (84)
 21 d2b7va1 d.50.1.1 (A:1-71) dsRN  99.5 7.3E-14 5.4E-18  102.5   7.2   65  153-223     2-66  (71)
 22 d2b7ta1 d.50.1.1 (A:1-73) dsRN  99.3 2.1E-12 1.6E-16   93.4   7.2   67  155-224     4-70  (73)
 23 d1ztda1 a.149.1.2 (A:2-125) Hy  70.4       3 0.00022   18.7   6.0   84   42-145     5-92  (124)
 24 d1aisa1 d.129.1.1 (A:1-92) TAT  41.6     9.3 0.00068   15.7   4.8   39  186-225    52-92  (92)
 25 d1kn0a_ d.50.1.3 (A:) The homo  33.8      12  0.0009   14.9   5.6   18  207-224   118-135 (184)
 26 d1mp9a1 d.129.1.1 (A:5-96) TAT  32.7      13 0.00094   14.8   4.0   39  186-225    52-92  (92)
 27 d2qale2 d.50.1.2 (E:9-77) Ribo  30.0      14   0.001   14.5   4.0   39  185-223    20-62  (69)
 28 d1qnaa1 d.129.1.1 (A:17-115) T  24.4      18  0.0013   13.9   5.7   39  186-225    50-90  (99)
 29 d2o3fa1 a.4.1.20 (A:1-83) Puta  22.0     7.3 0.00053   16.3  -0.4   41   55-97     23-66  (83)
 30 d2uube2 d.50.1.2 (E:5-73) Ribo  20.6      21  0.0016   13.4   5.9   38  186-223    21-62  (69)

No 1  
>d1o0wa1 a.149.1.1 (A:-1-167) RNase III endonuclease catalytic domain {Thermotoga maritima [TaxId: 2336]}
Probab=100.00  E-value=2.9e-41  Score=271.07  Aligned_cols=147  Identities=32%  Similarity=0.450  Sum_probs=135.2

Q ss_pred             CCHHHHHHHHCCCCCCHHHHHHHCCCHHHCC-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             5889999983696589899998424612126-------676654778874586886454787764104688789988888
Q gi|254780940|r    4 LRYSTLEKRIGYAFANRSLLEKALTHSSISH-------SYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFN   76 (227)
Q Consensus         4 ~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~-------~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~   76 (227)
                      ..++.||++|||+|+|++||.+||||+||..       ...++||||||||||||+++++++||.+||+.+||.+|.+|+
T Consensus         9 ~~~~~~e~~lgy~F~n~~Ll~~AlTH~S~~~~~~~~~~~~~~~nerLefLGDavL~~~v~~~l~~~~~~~~~g~ls~~~~   88 (169)
T d1o0wa1           9 KIVEEFQKETGINFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKS   88 (169)
T ss_dssp             HHHHHHHHHHCCCCSSHHHHHHHHBCHHHHHHHHHTTCTTCCCSHHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             99999999989863988999987668153654433233565321889999877999998999998641002001278999


Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC
Q ss_conf             88744334545431387720010366312375313333326699999999641554220012210256431110
Q gi|254780940|r   77 SLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS  150 (227)
Q Consensus        77 ~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~  150 (227)
                      .+|||++|+.+|..+||+++++++++........+++++||+|||+|||||+|+|++.|+.|+.++|.+.+...
T Consensus        89 ~lv~~~~La~ia~~~~l~~~i~~~~~~~~~~~~~~~kvlad~~EAliGAiylD~G~~~~~~~i~~~~~~~l~~i  162 (169)
T d1o0wa1          89 AAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRDRDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKI  162 (169)
T ss_dssp             HHTSHHHHHHHHHHTTHHHHCBCCHHHHHTTGGGCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCHHHHHHCCCHHHHCCCCCCCCHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             87418999999998181766424872654388665531220999999999993779999999999999999986


No 2  
>d2nuga1 a.149.1.1 (A:3-150) RNase III endonuclease catalytic domain {Aquifex aeolicus [TaxId: 63363]}
Probab=100.00  E-value=6.5e-39  Score=256.63  Aligned_cols=137  Identities=40%  Similarity=0.604  Sum_probs=125.0

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             89999983696589899998424612126676654778874586886454787764104688789988888887443345
Q gi|254780940|r    6 YSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCS   85 (227)
Q Consensus         6 ~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La   85 (227)
                      ++.||++|||+|+|++||.+||||+||...  .+|||||||||+||++++++|||.+||+.++|.||.+|+.+|||++|+
T Consensus         2 l~~le~~igy~F~n~~LL~~Alth~S~~~~--~~~erLeflGDavl~~~v~~~l~~~~p~~~~g~lt~~r~~lvsn~~La   79 (148)
T d2nuga1           2 LEQLEKKLGYTFKDKSLLEKALTHVSYSKK--EHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFN   79 (148)
T ss_dssp             HHHHHHHHTCCCSSHHHHHHHHBCTTTCSS--SCSHHHHHHHHHHHHHHHHHHHHHTCTTCCHHHHHHHHHHHTSHHHHH
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             889999989862888999998668576887--550999999988875455789985087751678877777764136766


Q ss_pred             HHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCC--CCHHHHHCCCCCCCCCC
Q ss_conf             454313877200103663123753133333266999999996415542--20012210256431110
Q gi|254780940|r   86 QVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIE--VAGTFVDKYWKQRALKS  150 (227)
Q Consensus        86 ~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~--~~~~~i~~~~~~~~~~~  150 (227)
                      .+|.++||++|++.+++.      .+++++||+|||+|||||+|+|++  .++.|+.++|.+.+...
T Consensus        80 ~~a~~lgl~~~i~~~~~~------~~~kilad~~EAiiGAiylD~g~~~~~~~~~i~~l~~~~i~~~  140 (148)
T d2nuga1          80 LLAQKLELHKFIRIKRGK------INETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSA  140 (148)
T ss_dssp             HHHHTTTGGGTCBSCTTC------CCHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCC------CHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             578885088998752642------0103657899998877642268779999999999999999988


No 3  
>d1u61a_ a.149.1.1 (A:) Hypothetical protein BC0111 {Bacillus cereus [TaxId: 1396]}
Probab=99.89  E-value=2.1e-24  Score=167.39  Aligned_cols=107  Identities=21%  Similarity=0.163  Sum_probs=88.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECC--------CCCCCCC
Q ss_conf             66547788745868864547877641046887899888888874433454543138772001036--------6312375
Q gi|254780940|r   37 QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSS--------DLRKDVC  108 (227)
Q Consensus        37 ~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~--------~~~~~~~  108 (227)
                      .-|...|||||||||+++|++|||.+|| .+||+||++|+.+||+++|+.++..+++++|+..+.        +......
T Consensus         5 ~~~~~~LefLGDAVl~l~v~~~L~~~~p-~~eg~Lt~~r~~lV~~~~la~~a~~l~l~~~l~~~e~~~~~~Grn~~~~~~   83 (127)
T d1u61a_           5 QLNSLALAYMGDAVYEQYIRYHLLQKGK-VRPNQLHRLGTSFVSAKAQAKVVYHLLETAFLTEEEEAVLRRGRNANSGTV   83 (127)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHHHHHHHCC-SCGGGHHHHHHHHHSHHHHHHHHHHHHHTTCSCHHHHHHHHHHTCCCSSCC
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             4484778987899999999999997189-990179999999924999999999907677764033431016775547777


Q ss_pred             C----CCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCC
Q ss_conf             3----13333326699999999641554220012210256
Q gi|254780940|r  109 S----FMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWK  144 (227)
Q Consensus       109 ~----~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~  144 (227)
                      +    ...+++||+|||+|||+|+|+|++.++.|+.+.+.
T Consensus        84 ~k~~~~~~y~lad~fEAliGalYLd~~~e~~~~~i~~~~~  123 (127)
T d1u61a_          84 PKNTDVQTYRHSTAFEALIGYHHLLNNRERLDEIVYKAIA  123 (127)
T ss_dssp             CTTCCHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             7666514777605999999999991888999999999998


No 4  
>d1o0wa2 d.50.1.1 (A:168-236) RNase III, C-terminal domain {Thermotoga maritima [TaxId: 2336]}
Probab=99.73  E-value=6.5e-18  Score=127.41  Aligned_cols=68  Identities=34%  Similarity=0.397  Sum_probs=66.3

Q ss_pred             CHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             52588987532022333343101020778884599999999989999996898999999999999974
Q gi|254780940|r  156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       156 dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      |||+.||||||+++..+|.|+++..+||+|++.|+|.|+++|..+++|.|+|||+||+.||+.||++|
T Consensus         1 d~Ks~LqE~~Qk~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~~~~g~g~sKK~Aeq~AA~~aL~~L   68 (69)
T d1o0wa2           1 DYKTALQEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAARIAYEKL   68 (69)
T ss_dssp             CHHHHHHHHHHHHHSSCCEEEEEEEECCTTSCEEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHH
T ss_conf             91789999999749999979999966888884299999989999999872899999999999999986


No 5  
>d2cpna1 d.50.1.1 (A:150-225) TAR RNA-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]}
Probab=99.68  E-value=7e-17  Score=121.04  Aligned_cols=72  Identities=33%  Similarity=0.374  Sum_probs=67.2

Q ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             0013452588987532022333343101020778884599999999989999996898999999999999974
Q gi|254780940|r  151 GKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       151 ~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      .....|||+.||||||+++...|+|.++.++|++|.+.|.|.|.+++.. ++|.|+|||+||+.||+.||++|
T Consensus         5 ~~~~~npks~LqE~~q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~-~~g~G~SKK~Aeq~AA~~aL~~L   76 (76)
T d2cpna1           5 QQSECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFI-EIGSGTSKKLAKRNAAAKMLLRV   76 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHTCCCCEEEEEEEECCSSSCEEEEEEEETTEE-EEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCEEEEEEECCEE-ECCCCCCHHHHHHHHHHHHHHHC
T ss_conf             6678897899999999749999979986643267775279999954224-11364529999999999999869


No 6  
>d1uhza_ d.50.1.1 (A:) staufen homolog 2 {Mouse (Mus musculus) [TaxId: 10090]}
Probab=99.68  E-value=7.7e-17  Score=120.79  Aligned_cols=71  Identities=21%  Similarity=0.288  Sum_probs=67.6

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCC
Q ss_conf             345258898753202233334310102077888459999999998999999689899999999999997488
Q gi|254780940|r  154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGI  225 (227)
Q Consensus       154 ~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi  225 (227)
                      ..||+++||||||++...+|+|+++.++||+|++.|+|.|.+++.. .+|.|+|||+||+.||+.||++||.
T Consensus         5 ~~~P~s~LqE~~Q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~~-~~g~g~SKK~Ae~~AA~~aL~~l~~   75 (89)
T d1uhza_           5 SSGPISRLAQIQQARKEKEPDYILLSERGMPRRREFVMQVKVGNEV-ATGTGPNKKIAKKNAAEAMLLQLGY   75 (89)
T ss_dssp             SSCHHHHHHHHHHHTTSCCCEEEEEEEESCSTTCEEEEEEEETTEE-EEEEESSHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCHHHHHHHHHHCCCCCCEEEECCCCCCCCCEEEEEEEEEEEEE-CCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             8881999999999649999979850244567750699999996564-0232037899999999999999676


No 7  
>d2nuga2 d.50.1.1 (A:151-218) RNase III, C-terminal domain {Aquifex aeolicus [TaxId: 63363]}
Probab=99.67  E-value=8.1e-17  Score=120.67  Aligned_cols=68  Identities=37%  Similarity=0.480  Sum_probs=64.8

Q ss_pred             CHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       156 dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      |||+.||||||+++..+|.|+++..+||+|++.|+|.|.+++. .++|.|+|||.||+.||+.||+.|.
T Consensus         1 d~Ks~LqE~~q~~~~~~P~Y~~~~~~g~~h~~~F~~~v~v~~~-~~~g~g~sKK~Aeq~AA~~aL~~Lk   68 (68)
T d2nuga2           1 DYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEY-RTLGEGKSKKEAEQRAAEELIKLLE   68 (68)
T ss_dssp             CHHHHHHHHHHHHHSCCCEEEEEEEESCGGGCEEEEEEEETTE-EEEEEESSHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHCCCCCCEEEEEEEECCCCCCEEEEEEEECCE-EEEEECCCHHHHHHHHHHHHHHHHC
T ss_conf             9078999999975999998999984188878479999998877-9999509999999999999999739


No 8  
>d1uila_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}
Probab=99.63  E-value=1.7e-16  Score=118.60  Aligned_cols=74  Identities=24%  Similarity=0.315  Sum_probs=64.0

Q ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEE-----CCEEEEEEEECCHHHHHHHHHHHHHHHC--
Q ss_conf             001345258898753202233334310102077888459999999-----9989999996898999999999999974--
Q gi|254780940|r  151 GKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEI-----SGLAPAQGMDCSKRAAEQVAAAEVLKRE--  223 (227)
Q Consensus       151 ~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v-----~g~~~g~g~g~SkK~Ae~~AA~~AL~kl--  223 (227)
                      ++...|||++||||||+++. +|.|++ ...||+|++.|+|.|.|     ++..+++|.|+|||+||+.||+.||++|  
T Consensus        22 ~wt~~n~Ks~LqE~~Qk~k~-~p~Y~i-~~~Gp~H~~~F~~~v~i~~~~~~~~~~~~G~G~sKK~AEq~AA~~~l~~L~~   99 (113)
T d1uila_          22 NWTLENAKARLNQYFQKEKI-QGEYKY-TQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYH   99 (113)
T ss_dssp             CCCHHHHHHHHHHHHHHSCC-CCCCEE-EEESCSTTCEEEEEEEEEETTTTEEEEEECCCSSHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHCCC-CCCEEE-EEECCCCCCEEEEEEEEEEECCCCEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             97014799999999986799-996598-5542688995999999942125976776406260999999999999999997


Q ss_pred             -CCC
Q ss_conf             -889
Q gi|254780940|r  224 -GIW  226 (227)
Q Consensus       224 -gi~  226 (227)
                       |++
T Consensus       100 ~g~i  103 (113)
T d1uila_         100 LGVI  103 (113)
T ss_dssp             HTSS
T ss_pred             CCCC
T ss_conf             4886


No 9  
>d1qu6a1 d.50.1.1 (A:1-90) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}
Probab=99.63  E-value=8.1e-17  Score=120.65  Aligned_cols=73  Identities=27%  Similarity=0.245  Sum_probs=66.5

Q ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             00134525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  151 GKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       151 ~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      +....|||+.||||||+++. .|.|.++..+||+|++.|+|.|.++|..+++|.|+|||+||+.||+.||+.|.
T Consensus         9 ~~~~~~y~s~LqE~~Qk~~~-~p~y~~~~~~Gp~h~~~F~v~v~v~~~~~~~g~G~sKK~Aeq~AA~~aL~~L~   81 (90)
T d1qu6a1           9 DLSAGFFMEELNTYRQKQGV-VLKYQELPNSGPPHDRRFTFQVIIDGREFPEGEGRSKKEAKNAAAKLAVEILN   81 (90)
T ss_dssp             CSSSCSHHHHHHHHHHHHTC-CCEEEEEESCBTTTBCCEEEEEESSSSCCCEEECCSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHCC-CCCEEEEEEECCCCCCEEEEEEEECCEEEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99977899999999998299-98579987107988744799999775664056787699999999999999998


No 10 
>d1di2a_ d.50.1.1 (A:) Double-stranded RNA-binding protein A, second dsRBD {Xenopus laevis [TaxId: 8355]}
Probab=99.63  E-value=3.7e-16  Score=116.61  Aligned_cols=67  Identities=34%  Similarity=0.439  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             25889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  157 AKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       157 pK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      |++.|||+||+++..+|.|+++.++||+|++.|.|.|.+++.. ++|.|+|||+||+.||+.||++|.
T Consensus         2 Pv~~LqE~~q~~~~~~P~Y~~~~~~G~~h~~~F~~~v~v~~~~-~~g~g~sKK~Aeq~AA~~aL~~L~   68 (69)
T d1di2a_           2 PVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFV-ETGSGTSKQVAKRVAAEKLLTKFK   68 (69)
T ss_dssp             HHHHHHHHHHHHTCCCCEEEEEEEESCGGGCEEEEEEEETTEE-EEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCEEEEEEEEEEE-EECCCCCHHHHHHHHHHHHHHHHC
T ss_conf             8389999999759999838999843787774168999986678-763767299999999999999845


No 11 
>d1x49a1 d.50.1.1 (A:8-92) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}
Probab=99.62  E-value=2.2e-16  Score=118.02  Aligned_cols=71  Identities=25%  Similarity=0.184  Sum_probs=66.0

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             134525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  153 FRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       153 ~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      ...|||++||||||+++. .|.|.++..+||+|++.|+|.|+|+|..+++|.|+|||+||+.||+.||+.|.
T Consensus         5 ~~~~yk~~L~E~~Qk~~~-~~~y~~~~~~Gp~h~~~F~~~v~v~g~~~~~g~g~sKK~Aeq~AA~~aL~~L~   75 (85)
T d1x49a1           5 TPGFYMDKLNKYRQMHGV-AITYKELSTSGPPHDRRFTFQVLIDEKEFPEAKGRSKQEARNAAAKLAVDILD   75 (85)
T ss_dssp             CTTHHHHHHHHHHHHHTC-CEEEEEEEEESCSSSCEEEEEEEESSCCCCCEEESSHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHCCC-CCEEEEEEECCCCCCCEEEEEEECCCEEEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             813399999999986699-97589987218988745899884184675055665599999999999999998


No 12 
>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]}
Probab=99.62  E-value=5.9e-16  Score=115.35  Aligned_cols=83  Identities=25%  Similarity=0.207  Sum_probs=68.4

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEE-CCHHHHHHHHHHHH
Q ss_conf             02564311100013452588987532022333343101020778884599999999989999996-89899999999999
Q gi|254780940|r  141 KYWKQRALKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMD-CSKRAAEQVAAAEV  219 (227)
Q Consensus       141 ~~~~~~~~~~~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g-~SkK~Ae~~AA~~A  219 (227)
                      .++............|||+.||||||+++..+|.|.++.+   .|++.|++.|.|+|..++.+.| +|||+||+.||+.|
T Consensus        12 ~~~~~~~r~~~p~~~~pKs~LqE~~Qk~~~~~P~Y~~~~~---~~~~~F~~~V~v~g~~~~s~~g~~SKK~AEq~AA~~A   88 (128)
T d1whna_          12 KMAIRFDRRAYPPQITPKMCLLEWCRREKLPQPVYETVQR---TIDRMFCSVVTVAEQKYQSTLWDKSKKLAEQTAAIVC   88 (128)
T ss_dssp             EECCCCCGGGSCTTCCHHHHHHHHHHHTTCCCCCCCEEEC---SSSCCEEEEEEETTEEEEESSCBSSHHHHHHHHHHHH
T ss_pred             EEEHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEC---CCCCCCEEEEEECCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             4237555301788998789999999863999976887622---5577777999988847651677453899999999999


Q ss_pred             HHHCCCC
Q ss_conf             9974889
Q gi|254780940|r  220 LKREGIW  226 (227)
Q Consensus       220 L~klgi~  226 (227)
                      |++||+-
T Consensus        89 L~~Lg~~   95 (128)
T d1whna_          89 LRSQGLP   95 (128)
T ss_dssp             HHHHTCS
T ss_pred             HHHHCCC
T ss_conf             9983898


No 13 
>d2dixa1 d.50.1.1 (A:7-79) Interferon-inducible double stranded RNA-dependent protein kinase activator A {Human (Homo sapiens) [TaxId: 9606]}
Probab=99.61  E-value=4.4e-16  Score=116.16  Aligned_cols=68  Identities=22%  Similarity=0.277  Sum_probs=63.7

Q ss_pred             CCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             4525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       155 ~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      +||++.||||||+++. .|.|+++.++||+|++.|+|.|.+++. .+.|.|+|||+||+.||+.||+.|.
T Consensus         2 K~Pis~L~E~~qk~~~-~p~y~~~~~~Gp~h~~~F~~~v~v~~~-~~~g~g~sKK~Aeq~AA~~al~~L~   69 (73)
T d2dixa1           2 KTPIQVLHEYGMKTKN-IPVYECERSDVQIHVPTFTFRVTVGDI-TCTGEGTSKKLAKHRAAEAAINILK   69 (73)
T ss_dssp             CCHHHHHHHHHHHTTC-CCEEEEEEEECSSSSCEEEEEEEETTE-EEEECSSCTTHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHCCC-CCEEEEEEEECCCCCCEEEEEEEEEEE-EEEECCCCHHHHHHHHHHHHHHHHH
T ss_conf             5877999999996798-988998653589887179999999889-9886146599999999999999987


No 14 
>d1x47a1 d.50.1.1 (A:8-92) Dgcr8 protein {Human (Homo sapiens) [TaxId: 9606]}
Probab=99.61  E-value=1.2e-15  Score=113.46  Aligned_cols=71  Identities=24%  Similarity=0.290  Sum_probs=64.1

Q ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             0013452588987532022333343101020778884599999999989999996898999999999999974
Q gi|254780940|r  151 GKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       151 ~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      .+..+|||+.||||||+.+..+|.|.++..+|++  +.|.|.|.++|..+++|.|+|||.||+.||+.||++|
T Consensus         5 n~~~K~p~s~LqE~~Qk~~~~~p~Y~~~~~~g~~--~~F~~~v~i~g~~~~~g~G~sKK~Aeq~AA~~AL~~L   75 (85)
T d1x47a1           5 NPNGKSEVCILHEYMQRVLKVRPVYNFFECENPS--EPFGASVTIDGVTYGSGTASSKKLAKNKAARATLEIL   75 (85)
T ss_dssp             CTTCCCHHHHHHHHHHHHTCSCCEEEEEECSSSS--CCEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCC--CCEEEEEEECCEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             8899598899999999829999973787547898--8889999999999744784129999999999999999


No 15 
>d1whqa_ d.50.1.1 (A:) ATP-dependent RNA helicase A, Dhx9 {Mouse (Mus musculus) [TaxId: 10090]}
Probab=99.58  E-value=8.3e-16  Score=114.43  Aligned_cols=68  Identities=22%  Similarity=0.381  Sum_probs=61.0

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEE-EEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             3452588987532022333343101020778884599999999989-999996898999999999999974
Q gi|254780940|r  154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLA-PAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       154 ~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~-~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ..|+|+.||||||++.. .|.|.+. ++||+|+++|+|.|.|+|.. +++|.|+|||+||+.||+.||+.|
T Consensus         5 ~~~~Ks~LqE~~qk~k~-~P~Y~~~-~~G~~h~~~F~~~v~v~g~~~~~~g~g~sKK~AEq~AA~~al~~L   73 (99)
T d1whqa_           5 SSGIKNFLYAWCGKRKM-TPAYEIR-AVGNKNRQKFMCEVRVEGFNYAGMGNSTNKKDAQSNAARDFVNYL   73 (99)
T ss_dssp             CCSSHHHHHHHHHHTTC-CCEEEEE-EEECSSSEEEEEEEECTTCSCCEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHCCC-CCEEEEE-CCCCCCCCEEEEEEEECCCCCEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             76688999999986899-9869984-024788860899998516543100577528899999999999999


No 16 
>d1qu6a2 d.50.1.1 (A:91-179) dsRNA-dependent protein kinase pkr {Human (Homo sapiens) [TaxId: 9606]}
Probab=99.57  E-value=1.9e-15  Score=112.20  Aligned_cols=75  Identities=19%  Similarity=0.088  Sum_probs=65.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             11000134525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  148 LKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       148 ~~~~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      ........|||++||||||+++. .|.|... ++||+|++.|.|.|.|+|..++.|.|+|||+||+.||+.||++|.
T Consensus         7 ~~~~~~~~n~~s~L~E~~Qk~~~-~~~y~~~-~~g~~h~~~F~~~v~i~g~~~~~g~G~sKK~Akq~AA~~Al~~L~   81 (89)
T d1qu6a2           7 SSEGLSMGNYIGLINRIAQKKRL-TVNYEQC-ASGVHGPEGFHYKCKMGQKEYSIGTGSTKQEAKQLAAKLAYLQIL   81 (89)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHSCC-EEEEEEE-EECSSSSSEEEEEEEEETTBCCEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCC-CCCEEEE-CCCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             77676532899999999996288-7642663-157878875699999897036665652699999999999999997


No 17 
>d1t4oa_ d.50.1.1 (A:) RNase III, C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=99.56  E-value=1.4e-15  Score=113.02  Aligned_cols=74  Identities=16%  Similarity=0.117  Sum_probs=62.5

Q ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEE-CCEEEEEEEECCHHHHHHHHHHHHHHHCCCC
Q ss_conf             001345258898753202233334310102077888459999999-9989999996898999999999999974889
Q gi|254780940|r  151 GKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEI-SGLAPAQGMDCSKRAAEQVAAAEVLKREGIW  226 (227)
Q Consensus       151 ~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v-~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~  226 (227)
                      +.++.|+|++||+|||+.+. .|.|+++...||+|.+ |.|.|.+ ++..++.|.|+|||.||++||+.||+++++|
T Consensus         2 ~~id~~~K~~L~e~~~~~g~-~P~Y~~~~~~~~~~~~-f~v~~~v~~~~~~~~g~g~SKK~AEq~AA~~aL~~~~~l   76 (81)
T d1t4oa_           2 DKLDMNAKRQLYSLIGYASL-RLHYVTVKKPTAVDPN-SIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKML   76 (81)
T ss_dssp             CCCCTTHHHHHHHHHCCGGG-CCEEEEEECCCSSCCC-EEEEEECTTCCEEEEEEESSHHHHHHHHHHHHHHCHHHH
T ss_pred             CCCCCCHHHHHHHHHHCCCC-CCEEEEECCCCCCCCC-EEEEEEEECCCEEEECCCCHHHHHHHHHHHHHHHHCCHH
T ss_conf             85556899999999830899-8579970147878898-899999966825876453301089999999999832288


No 18 
>d1x48a1 d.50.1.1 (A:8-83) dsRNA-dependent protein kinase pkr {Mouse (Mus musculus) [TaxId: 10090]}
Probab=99.54  E-value=7.7e-15  Score=108.48  Aligned_cols=66  Identities=20%  Similarity=0.204  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             25889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  157 AKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       157 pK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      |+++||||||++.. ++.|.+. ++||+|++.|+|.|.|+|..+++|.|+|||+||+.||+.||++|.
T Consensus         1 Y~s~L~E~~Qk~~~-~~~~~~~-~~G~~h~~~F~~~v~v~~~~~~~g~G~sKK~Aeq~AA~~Al~~L~   66 (76)
T d1x48a1           1 YIGLVNSFAQKKKL-SVNYEQC-EPNSELPQRFICKCKIGQTMYGTGSGVTKQEAKQLAAKEAYQKLL   66 (76)
T ss_dssp             HHHHHHHHHHHTTC-CEEEEEC-CCSSSSSCCEEEEEEESSCEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHCC-CCCCCCC-CCCCCCCCCEEEEEEECCEEECCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             94899999998689-9764447-769899975899999999995785762799999999999999997


No 19 
>d1ekza_ d.50.1.1 (A:) Staufen, domain III {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}
Probab=99.54  E-value=1.1e-15  Score=113.65  Aligned_cols=71  Identities=17%  Similarity=0.246  Sum_probs=65.2

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             0134525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  152 KFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       152 ~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      ...+||++.||||||+++.. |.|.++..+||+|++.|+|.|.+++. .++|.|+|||+||+.||+.||++|.
T Consensus         4 ~~~k~Pvs~L~E~~q~~~~~-~~y~~~~~~G~~h~~~F~~~v~v~~~-~~~g~G~SKK~Aeq~AA~~al~~L~   74 (76)
T d1ekza_           4 GDKKSPISQVHEIGIKRNMT-VHFKVLREEGPAHMKNFITACIVGSI-VTEGEGNGKKVSKKRAAEKMLVELQ   74 (76)
T ss_dssp             CCCSCHHHHHHHHHHHTTCC-CEEEESSSCCSSSCSCSSEEEEETTE-EEEECCCSTTSSSHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHCCCC-CEEEEEEEECCCCCEEEEEEEEEEEE-EEEECCCCHHHHHHHHHHHHHHHHH
T ss_conf             77889899999999967989-70899971379887089999998214-7660567699999999999999987


No 20 
>d2dmya1 d.50.1.1 (A:8-91) Spermatid perinuclear RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}
Probab=99.46  E-value=2e-13  Score=99.79  Aligned_cols=68  Identities=31%  Similarity=0.376  Sum_probs=60.3

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCC
Q ss_conf             34525889875320223333431010207788845999999999899999968989999999999999748899
Q gi|254780940|r  154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT  227 (227)
Q Consensus       154 ~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~t  227 (227)
                      ..||+++|+|+.     ..|+|+++.++||+|++.|+|.|.++|..+ .|.|+|||+||+.||+.||++|++-|
T Consensus        11 ~~n~~~~L~e~~-----~~~~Y~~~~~~Gp~h~~~F~~~v~v~g~~~-~g~G~SKK~Aeq~AA~~aL~~L~~~~   78 (84)
T d2dmya1          11 LMNALMRLNQIR-----PGLQYKLLSQSGPVHAPVFTMSVDVDGTTY-EASGPSKKTAKLHVAVKVLQAMGYPT   78 (84)
T ss_dssp             CTHHHHHHHHHS-----CSCCCEEEEEESCSSSCEEEEEEEETTEEE-EEEESSHHHHHHHHHHHHHHHHTCCC
T ss_pred             CCCHHHHHHHHC-----CCCEEEEEEEECCCCCCEEEEEEEECCEEE-ECCCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             449999998707-----898699977068988975999999999999-85899989999999999999948899


No 21 
>d2b7va1 d.50.1.1 (A:1-71) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}
Probab=99.45  E-value=7.3e-14  Score=102.46  Aligned_cols=65  Identities=23%  Similarity=0.258  Sum_probs=59.7

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             13452588987532022333343101020778884599999999989999996898999999999999974
Q gi|254780940|r  153 FRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       153 ~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ..+||++.|||+|+.     ++|++++++||+|++.|+|.|.|+|... +|.|+|||+||++||+.||++|
T Consensus         2 ~~Knpv~~L~E~~~~-----~~y~~~~~~G~~h~~~F~~~v~v~~~~~-~g~G~SKK~Ak~~AA~~aL~~L   66 (71)
T d2b7va1           2 SGKNPVMILNELRPG-----LKYDFLSESGESHAKSFVMSVVVDGQFF-EGSGRNKKLAKARAAQSALATV   66 (71)
T ss_dssp             CSSCHHHHHHHHCCS-----CEEEEEECCCCTTTCCEEEEEECSSCEE-EEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCC-----CEEEEEEEECCCCCCEEEEEEEECCEEE-EECCCCHHHHHHHHHHHHHHHH
T ss_conf             887989999997659-----8689925168998973999999999999-8168988999999999999998


No 22 
>d2b7ta1 d.50.1.1 (A:1-73) dsRNA-specific editase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}
Probab=99.31  E-value=2.1e-12  Score=93.44  Aligned_cols=67  Identities=25%  Similarity=0.312  Sum_probs=56.4

Q ss_pred             CCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             4525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       155 ~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      .+||+.|+++.+.  ...|.|.+++++||+|++.|+|.|.++|..+ +|.|+|||+||++||+.||+.|.
T Consensus         4 ~~pK~~l~~L~e~--~~~~~y~~~~~~G~~h~~~F~~~v~v~~~~~-~g~G~SKK~Aeq~AA~~aL~~l~   70 (73)
T d2b7ta1           4 VLPKNALMQLNEI--KPGLQYMLLSQTGPVHAPLFVMSVEVNGQVF-EGSGPTKKKAKLHAAEKALRSFV   70 (73)
T ss_dssp             SSSHHHHHHHHHH--CSCCEEEEEEEECSSSSCEEEEEEESSSSEE-EEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHC--CCCCEEEEEEEECCCCCCEEEEEEEECCEEE-ECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             8981999999851--8998799987128999964999999999999-91887499999999999999985


No 23 
>d1ztda1 a.149.1.2 (A:2-125) Hypothetical protein PF0609 {Pyrococcus furiosus [TaxId: 2261]}
Probab=70.42  E-value=3  Score=18.73  Aligned_cols=84  Identities=23%  Similarity=0.209  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHH
Q ss_conf             7887458688645478776--41046887899888888874433454543138772001036631237531333332669
Q gi|254780940|r   42 RLEFLGDRILGLLISTLLF--NHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVV  119 (227)
Q Consensus        42 rLEflGDavL~~~v~~~l~--~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~f  119 (227)
                      -|.-+||+.++|++|-.|-  .-.|...          -|-|.+|+---..-||...+.          +....-.+|..
T Consensus         5 gLak~GDSLiNfl~SlALte~lG~PTg~----------rVPnasLAiAle~a~Ls~~l~----------r~dkh~kGd~a   64 (124)
T d1ztda1           5 GLAKFGDSLINFLYSLALTEFLGKPTGD----------RVPNASLAIALELTGLSKNLR----------RVDKHAKGDYA   64 (124)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSCCCC----------CCCHHHHHHHHHHHTGGGGCC----------GGGTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCC----------CCCCHHHHHHHHHHHHHHCCC----------CCCCCCCCHHH
T ss_conf             5888718999999999999993898878----------788749999999970764088----------75667861799


Q ss_pred             HHHHHHHHHCCCCC--CCHHHHHCCCCC
Q ss_conf             99999996415542--200122102564
Q gi|254780940|r  120 ESLIAALYLDGGIE--VAGTFVDKYWKQ  145 (227)
Q Consensus       120 EA~iGAiy~d~G~~--~~~~~i~~~~~~  145 (227)
                      ||+++--|+.+-+.  .+-.++..-+.+
T Consensus        65 EA~iAyAWLeg~it~eEavEilk~nl~~   92 (124)
T d1ztda1          65 EALIAKAWLMGLISEREAVEIIKKNLYP   92 (124)
T ss_dssp             HHHHHHHHHTTSSCHHHHHHHHHTTCCG
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHCCH
T ss_conf             9999999993424099999999970758


No 24 
>d1aisa1 d.129.1.1 (A:1-92) TATA-box binding protein (TBP), C-terminal domain {Archaeon Pyrococcus woesei [TaxId: 2262]}
Probab=41.64  E-value=9.3  Score=15.69  Aligned_cols=39  Identities=28%  Similarity=0.393  Sum_probs=27.6

Q ss_pred             CCEEEEEEEECCEEEEEEEECCHHHHHHHHHH--HHHHHCCC
Q ss_conf             84599999999989999996898999999999--99997488
Q gi|254780940|r  186 DPRFTVVVEISGLAPAQGMDCSKRAAEQVAAA--EVLKREGI  225 (227)
Q Consensus       186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~--~AL~klgi  225 (227)
                      +|.-++.++..|+.+.+|. +|..+|++..++  ..|+++||
T Consensus        52 ~p~~~~lIF~sGkivitGa-kS~~~~~~a~~~i~~~l~~lGv   92 (92)
T d1aisa1          52 DPKVALLIFSSGKLVVTGA-KSVQDIERAVAKLAQKLKSIGV   92 (92)
T ss_dssp             SSCCEEEECTTSEEEEEEE-SSHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCEEEEEECCCEEEEECC-CCHHHHHHHHHHHHHHHHHCCC
T ss_conf             9958999978988999826-9999999999999999998389


No 25 
>d1kn0a_ d.50.1.3 (A:) The homologous-pairing domain of Rad52 recombinase {Human (Homo sapiens) [TaxId: 9606]}
Probab=33.85  E-value=12  Score=14.93  Aligned_cols=18  Identities=17%  Similarity=0.237  Sum_probs=13.2

Q ss_pred             CHHHHHHHHHHHHHHHCC
Q ss_conf             989999999999999748
Q gi|254780940|r  207 SKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       207 SkK~Ae~~AA~~AL~klg  224 (227)
                      .+|+|...|=++|+.++|
T Consensus       118 a~KeA~TDAlKRA~~~FG  135 (184)
T d1kn0a_         118 ARKEAVTDGLKRALRSFG  135 (184)
T ss_dssp             HHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             988888799999999977


No 26 
>d1mp9a1 d.129.1.1 (A:5-96) TATA-box binding protein (TBP), C-terminal domain {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}
Probab=32.67  E-value=13  Score=14.81  Aligned_cols=39  Identities=23%  Similarity=0.308  Sum_probs=26.4

Q ss_pred             CCEEEEEEEECCEEEEEEEECCHHHHHHHHHH--HHHHHCCC
Q ss_conf             84599999999989999996898999999999--99997488
Q gi|254780940|r  186 DPRFTVVVEISGLAPAQGMDCSKRAAEQVAAA--EVLKREGI  225 (227)
Q Consensus       186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~--~AL~klgi  225 (227)
                      +|.-++-++..|+.+.+|. +|..+++....+  ..|+++||
T Consensus        52 ~p~~t~lIF~SGkivitGa-ks~~~~~~a~~~~~~~L~~~G~   92 (92)
T d1mp9a1          52 SPKITSLIFKSGKMVVTGA-KSTDELIKAVKRIIKTLKKYGM   92 (92)
T ss_dssp             TTTEEEEECTTSEEEEECC-SSHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCEEEEEECCCEEEEECC-CCHHHHHHHHHHHHHHHHHCCC
T ss_conf             9957999985887999825-9999999999999999998189


No 27 
>d2qale2 d.50.1.2 (E:9-77) Ribosomal S5 protein, N-terminal domain {Escherichia coli [TaxId: 562]}
Probab=29.98  E-value=14  Score=14.53  Aligned_cols=39  Identities=18%  Similarity=0.021  Sum_probs=28.5

Q ss_pred             CCCEEEEEEEECCE----EEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             88459999999998----9999996898999999999999974
Q gi|254780940|r  185 HDPRFTVVVEISGL----APAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       185 ~~~~f~v~v~v~g~----~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ....|.+-|.+++.    -+|.|.+..-..|-++|..+|-++|
T Consensus        20 r~~~f~alVvvGn~~G~vG~G~gKa~ev~~Ai~KA~~~Ak~nl   62 (69)
T d2qale2          20 RIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNM   62 (69)
T ss_dssp             CCCCCEEEEEEECSSSBCCEEEEECSSHHHHHHHHHHHHHSSC
T ss_pred             CEEEEEEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHHHCC
T ss_conf             6258999999467998194766514508999999999998692


No 28 
>d1qnaa1 d.129.1.1 (A:17-115) TATA-box binding protein (TBP), C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}
Probab=24.41  E-value=18  Score=13.91  Aligned_cols=39  Identities=21%  Similarity=0.337  Sum_probs=26.9

Q ss_pred             CCEEEEEEEECCEEEEEEEECCHHHHHHHHHH--HHHHHCCC
Q ss_conf             84599999999989999996898999999999--99997488
Q gi|254780940|r  186 DPRFTVVVEISGLAPAQGMDCSKRAAEQVAAA--EVLKREGI  225 (227)
Q Consensus       186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~--~AL~klgi  225 (227)
                      +|.-++-++..|+.+.+|. +|..+|++.+.+  ..|+++|+
T Consensus        50 ~P~~t~lIF~SGKivitGa-ks~~~~~~a~~~i~~~l~k~g~   90 (99)
T d1qnaa1          50 EPKTTALIFASGKMVCTGA-KSEDFSKMAARKYARIVQKLGF   90 (99)
T ss_dssp             TTTEEEEEETTSEEEEEEE-SSHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCEEEEEECCCEEEEECC-CCHHHHHHHHHHHHHHHHHCCC
T ss_conf             9839999976977999646-9999999999999999998499


No 29 
>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}
Probab=22.05  E-value=7.3  Score=16.31  Aligned_cols=41  Identities=17%  Similarity=0.227  Sum_probs=28.5

Q ss_pred             HHHHHHHHC---CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             478776410---4688789988888887443345454313877200
Q gi|254780940|r   55 ISTLLFNHF---DSAKEGELSVRFNSLVSAETCSQVARELDLASFI   97 (227)
Q Consensus        55 v~~~l~~~~---p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l   97 (227)
                      |++|+..+.   +..+-.+++  ...-||..++.+.|+++|+..|-
T Consensus        23 ia~yil~~~~~~~~~si~~lA--~~~~vS~sTi~Rf~kklG~~gf~   66 (83)
T d2o3fa1          23 LADYILAHPHKAIESTVNEIS--ALANSSDAAVIRLCKSLGLKGFQ   66 (83)
T ss_dssp             HHHHHHHCHHHHHTCCHHHHH--HHTTCCHHHHHHHHHHTTCSSHH
T ss_pred             HHHHHHCCHHHHHHCCHHHHH--HHHCCCHHHHHHHHHHHCCCCHH
T ss_conf             999998299999883199999--99798998999999995899899


No 30 
>d2uube2 d.50.1.2 (E:5-73) Ribosomal S5 protein, N-terminal domain {Thermus thermophilus [TaxId: 274]}
Probab=20.56  E-value=21  Score=13.44  Aligned_cols=38  Identities=18%  Similarity=0.038  Sum_probs=27.7

Q ss_pred             CCEEEEEEEECCE----EEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             8459999999998----9999996898999999999999974
Q gi|254780940|r  186 DPRFTVVVEISGL----APAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       186 ~~~f~v~v~v~g~----~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ...|.+-|.+++.    -+|.|.+..-..|-++|..+|-++|
T Consensus        21 ~~~f~alvvvGn~~G~vG~G~gKa~ev~~Ai~KA~~~Ak~nm   62 (69)
T d2uube2          21 RFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNM   62 (69)
T ss_dssp             EEEEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHHHHSE
T ss_pred             EEEEEEEEEEECCCCCEEECCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             257999999978998492023322088999999999998692


Done!