Query         gi|254780523|ref|YP_003064936.1| flagellar hook-associated protein FlgL [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 357
No_of_seqs    142 out of 3151
Neff          10.7
Searched_HMMs 33803
Date          Wed Jun  1 18:19:40 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780523.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >2d4x_A Flagellar HOOK-associa 100.0 7.7E-34 2.3E-38  205.2  17.3  247   42-327     1-248 (248)
  2 >1ucu_A Phase 1 flagellin; fla 100.0 3.5E-32   1E-36  196.0  20.5  183   43-320     1-184 (184)
  3 >1io1_A Phase 1 flagellin; bet 100.0 9.5E-28 2.8E-32  171.3  15.5  166   55-315     1-167 (168)
  4 >2zbi_A Flagellin homolog; fla 100.0 1.6E-27 4.8E-32  170.0  15.9  168   57-319     2-170 (174)
  5 >1ory_B Flagellin; flagellar c  97.3 0.00012 3.4E-09   42.9   2.4   45  307-351     2-46  (55)
  6 >1ucu_A Phase 1 flagellin; fla  96.8  0.0033 9.7E-08   34.9   6.1   42    4-45      2-43  (80)
  7 >1ucu_A Phase 1 flagellin; fla  96.1   0.018 5.4E-07   30.7   6.3   55  297-351    16-71  (80)
  8 >2d4y_A HAP1, flagellar HOOK-a  92.0    0.55 1.6E-05   22.5  13.7   93   39-131    57-152 (376)
  9 >3bj4_A Potassium voltage-gate  19.5      42  0.0012   12.0   4.4   27  290-316    14-40  (49)
 10 >3hfe_A Potassium voltage-gate  15.7      52  0.0015   11.5   3.1   20  290-309     7-26  (31)

No 1  
>>2d4x_A Flagellar HOOK-associated protein 3; multi-domain protein, alpha-helical bundle, complex all- beta folds, structural protein; 1.90A {Salmonella typhimurium} (A:)
Probab=100.00  E-value=7.7e-34  Score=205.20  Aligned_cols=247  Identities=14%  Similarity=0.105  Sum_probs=174.5

Q ss_pred             HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             21289999999999999999999999999999999999998888999999999999851378889889999999998656
Q gi|254780523|r   42 GLQLGARVTSILEWEQEKNHIAERLHSNSLVTKRLSTSQAHLSSMQKIVQDMVGPLVILLEGKTDNNKFPINAGMLRDSY  121 (357)
Q Consensus        42 ~sddp~~~~~~~~l~~~~~~l~~~~~n~~~a~~~l~~~e~~L~~i~~~l~~~~~~~v~a~n~t~~~~d~~~~a~e~~~~~  121 (357)
                      -||||+++.++++|+.+++++++|.+|+..+.+||+++|++|.++.++|+|+|+++++++||++++++|.+++.|+.+++
T Consensus         1 ~SDDp~~~~~a~~l~~~~~~~~q~~~Ni~~a~~~l~~ae~aL~~i~~~l~~~k~l~vqa~ngt~s~~dr~~i~~ei~~l~   80 (248)
T 2d4x_A            1 MSDDPIAASQAVVLSQAQAQNSQYALARTFATQKVSLEESVLSQVTTAIQTAQEKIVYAGNGTLSDDDRASLATDLQGIR   80 (248)
T ss_dssp             -----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99688999999999999999999999999999999999999999999999999999975147765222899988999988


Q ss_pred             HHHHHHHHH-HCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             777777652-0024304105665443212233333222222210001013454322245665321123332210012334
Q gi|254780523|r  122 ESFVTFANM-TDEGQYLFSGINSSEKPLNGYFTKDSLAKKSFDQMLQGFLEENSKSLLAGQHLEVSSMNAQQMTDFIKQL  200 (357)
Q Consensus       122 ~~l~~~aN~-~~~g~~~f~G~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  200 (357)
                      +++.+++|+ +++|.|+|+|.....+||.................................            .......
T Consensus        81 ~~i~~~an~t~~~g~~lf~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~  148 (248)
T 2d4x_A           81 DQLMNLANSTDGNGRYIFAGYKTEAAPFDQATGGYHGGEKSVTQQVDSARTMVIGHTGAQI------------FNSITSN  148 (248)
T ss_dssp             HHHHHHHTCBCTTSCBTTSTTCTTSCSBCTTTCCBCSCSSCEEEECSSSCEEEESCCHHHH------------HSCCCTT
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHH------------HCCCCCC
T ss_conf             9999998621024531125755466530046754435332111123544322224332011------------0133312


Q ss_pred             CCCCCCCCCCCCEEECCCCCCCEEECCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             44445665432001115665200000256410223203531011233333210023344555113566777778999999
Q gi|254780523|r  201 EDKFSDDEYWANNWSNASDHNIKYRIKDTEGIDVSANVNMRGIRDIMFVAVIGTEFLSKNLTDGARNVLTKKMLSTVQQG  280 (357)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a  280 (357)
                                                 ..............................................+..++.+
T Consensus       149 ---------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a  201 (248)
T 2d4x_A          149 ---------------------------AVPEPDGSDSEKNLFVMLDTAIAALKTPVEGNNVEKEKAAAAIDKTNRGLKNS  201 (248)
T ss_dssp             ---------------------------CCCCTTSCCCCCCHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------------------CCCCCCCCCCCHHHHHHHHCCCCCHHCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             ---------------------------22222322100023444200000100000000001110001112234678999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf             99999999986689999999999899999999986433327888999
Q gi|254780523|r  281 LSGIIEQRAVLGISEKNINEERVFLQNKNNIIDTYISKSIGVEQHTA  327 (357)
Q Consensus       281 ~~~i~~~~a~lGa~~~~l~~~~~~l~~~~~~l~~~~s~l~daD~ae~  327 (357)
                      ++.+...++.+|++++|++...+.+.....++++.+++++|+|++++
T Consensus       202 ~~~~~~~~~~~g~~~~~l~~~~~~~~~~~~~~~~~~s~i~d~D~a~v  248 (248)
T 2d4x_A          202 LNNVLTVRAELGTQLSELSTLDSLGSDRALGQKLQMSNLVDVDWNSV  248 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCC-----------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99999999998299999999999899999999999888763283259


No 2  
>>1ucu_A Phase 1 flagellin; flagellar filament, cryo-electron microscopy, helical reconstruction, structural protein; 4.00A {Salmonella typhimurium} (A:41-169,A:400-454)
Probab=100.00  E-value=3.5e-32  Score=195.99  Aligned_cols=183  Identities=10%  Similarity=0.021  Sum_probs=156.6

Q ss_pred             HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             12899999999999999999999999999999999999988889999999999998513788898899999999986567
Q gi|254780523|r   43 LQLGARVTSILEWEQEKNHIAERLHSNSLVTKRLSTSQAHLSSMQKIVQDMVGPLVILLEGKTDNNKFPINAGMLRDSYE  122 (357)
Q Consensus        43 sddp~~~~~~~~l~~~~~~l~~~~~n~~~a~~~l~~~e~~L~~i~~~l~~~~~~~v~a~n~t~~~~d~~~~a~e~~~~~~  122 (357)
                      ||||++++++.+|+.++.++++|.+|++.+.+||+++|++|.++.++|+|+|+++++++||+++++||.+++.|+.++++
T Consensus         1 SDDpa~~a~s~~l~s~i~~l~q~~~N~~~a~s~lqtae~aL~~i~~iLqrirelavqaangt~s~~dR~ai~~Ei~~L~~   80 (184)
T 1ucu_A            1 KDDAAGQAIANRFTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLN   80 (184)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             10699999999999999999999999999999999999999999999999999999761688765668888877555555


Q ss_pred             HHHHHHHH-HCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77777652-00243041056654432122333332222222100010134543222456653211233322100123344
Q gi|254780523|r  123 SFVTFANM-TDEGQYLFSGINSSEKPLNGYFTKDSLAKKSFDQMLQGFLEENSKSLLAGQHLEVSSMNAQQMTDFIKQLE  201 (357)
Q Consensus       123 ~l~~~aN~-~~~g~~~f~G~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (357)
                      +|.+++|. .++|.|+|.|.....+||...................                                  
T Consensus        81 ei~~ian~T~fnG~~Lf~Gs~~~t~~~~~~~~~~~~~~~~~~~~~~----------------------------------  126 (184)
T 1ucu_A           81 EIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQINSQT----------------------------------  126 (184)
T ss_dssp             HHHHHHHHCCBTTBCTTTSCEEEEEECSSSTTCEEEEEECCCSTTT----------------------------------
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCEEEECCCCCCCCC----------------------------------
T ss_conf             5555542456655432144554315521444411231033333222----------------------------------


Q ss_pred             CCCCCCCCCCCEEECCCCCCCEEECCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             44456654320011156652000002564102232035310112333332100233445551135667777789999999
Q gi|254780523|r  202 DKFSDDEYWANNWSNASDHNIKYRIKDTEGIDVSANVNMRGIRDIMFVAVIGTEFLSKNLTDGARNVLTKKMLSTVQQGL  281 (357)
Q Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~  281 (357)
                                                                                   ..........++..||.++
T Consensus       127 -------------------------------------------------------------~~~~~~~a~~~~~~~d~ai  145 (184)
T 1ucu_A          127 -------------------------------------------------------------LGLAATTTENPLQKIDAAL  145 (184)
T ss_dssp             -------------------------------------------------------------TTCCCSCCSSHHHHHHHHH
T ss_pred             -------------------------------------------------------------CCCHHHHHHHHHHHHHHHH
T ss_conf             -------------------------------------------------------------3324788999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999998668999999999989999999998643332
Q gi|254780523|r  282 SGIIEQRAVLGISEKNINEERVFLQNKNNIIDTYISKSI  320 (357)
Q Consensus       282 ~~i~~~~a~lGa~~~~l~~~~~~l~~~~~~l~~~~s~l~  320 (357)
                      ..|...|+++|+.||||++....|....++++...|+||
T Consensus       146 ~~~~~~r~~lga~qnrl~~~~~nl~~~~~n~~~a~s~i~  184 (184)
T 1ucu_A          146 AQVDTLRSDLGAVQNRFNSAITNLGNTVNNLTSVRSRIE  184 (184)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999879999999999999999999999854687


No 3  
>>1io1_A Phase 1 flagellin; beta-folium, structural protein; 2.00A {Salmonella typhimurium} (A:1-117,A:348-398)
Probab=99.96  E-value=9.5e-28  Score=171.33  Aligned_cols=166  Identities=10%  Similarity=0.035  Sum_probs=138.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-CC
Q ss_conf             99999999999999999999999999988889999999999998513788898899999999986567777776520-02
Q gi|254780523|r   55 WEQEKNHIAERLHSNSLVTKRLSTSQAHLSSMQKIVQDMVGPLVILLEGKTDNNKFPINAGMLRDSYESFVTFANMT-DE  133 (357)
Q Consensus        55 l~~~~~~l~~~~~n~~~a~~~l~~~e~~L~~i~~~l~~~~~~~v~a~n~t~~~~d~~~~a~e~~~~~~~l~~~aN~~-~~  133 (357)
                      |+.++.++++|.+|+..+.+||+++|++|.++.++|+|+||++++++||+++++||.+++.|+.++++++.+++|++ ++
T Consensus         1 lrsqi~~l~q~~~N~~da~s~lqtAe~aL~~i~~iL~rirelavqaaNgt~s~~DR~ai~~Ei~qL~~eI~~ianst~fn   80 (168)
T 1io1_A            1 FTANIKGLTQASRNANDGISIAQTTEGALNEINNNLQRVRELAVQSANSTNSQSDLDSIQAEITQRLNEIDRVSGQTQFN   80 (168)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHCCBT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             94166659999998999999999999999999999999999999850578999999999999999999999999736208


Q ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             43041056654432122333332222222100010134543222456653211233322100123344444566543200
Q gi|254780523|r  134 GQYLFSGINSSEKPLNGYFTKDSLAKKSFDQMLQGFLEENSKSLLAGQHLEVSSMNAQQMTDFIKQLEDKFSDDEYWANN  213 (357)
Q Consensus       134 g~~~f~G~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  213 (357)
                      |.|+|.|.....+||....................                                             
T Consensus        81 G~~Lf~Gs~t~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------  115 (168)
T 1io1_A           81 GVKVLAQDNTLTIQVGANDGETIDIDLKQINSQTL---------------------------------------------  115 (168)
T ss_dssp             TBCTTTSCEEEEEECSSSTTCEEEEEECCCSTTTT---------------------------------------------
T ss_pred             CCCCCCCCCCEEEEECCCCCCCEEEECCCCCCCCC---------------------------------------------
T ss_conf             80112567725897237765313653143320103---------------------------------------------


Q ss_pred             EECCCCCCCEEECCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11156652000002564102232035310112333332100233445551135667777789999999999999998668
Q gi|254780523|r  214 WSNASDHNIKYRIKDTEGIDVSANVNMRGIRDIMFVAVIGTEFLSKNLTDGARNVLTKKMLSTVQQGLSGIIEQRAVLGI  293 (357)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~i~~~~a~lGa  293 (357)
                                                                        .........++..||.++..|...|+.+|+
T Consensus       116 --------------------------------------------------~~t~~~a~~~~~~~d~a~~~v~~~r~~lga  145 (168)
T 1io1_A          116 --------------------------------------------------GLAATTTENPLQKIDAALAQVDTLRSDLAA  145 (168)
T ss_dssp             --------------------------------------------------TCCCSCCSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --------------------------------------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             --------------------------------------------------544788999999999999999999987658


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999899999999986
Q gi|254780523|r  294 SEKNINEERVFLQNKNNIIDTY  315 (357)
Q Consensus       294 ~~~~l~~~~~~l~~~~~~l~~~  315 (357)
                      .|||||+....+....++++..
T Consensus       146 ~qnr~~~t~~nl~~~~~n~~~a  167 (168)
T 1io1_A          146 VQNRFNSAITNLGNTVNNLTSA  167 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9885899999899999999851


No 4  
>>2zbi_A Flagellin homolog; flagellum, structural protein; 2.00A {Sphingomonas SP} (A:1-113,A:232-292)
Probab=99.96  E-value=1.6e-27  Score=170.04  Aligned_cols=168  Identities=12%  Similarity=0.105  Sum_probs=141.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HCCCC
Q ss_conf             99999999999999999999999998888999999999999851378889889999999998656777777652-00243
Q gi|254780523|r   57 QEKNHIAERLHSNSLVTKRLSTSQAHLSSMQKIVQDMVGPLVILLEGKTDNNKFPINAGMLRDSYESFVTFANM-TDEGQ  135 (357)
Q Consensus        57 ~~~~~l~~~~~n~~~a~~~l~~~e~~L~~i~~~l~~~~~~~v~a~n~t~~~~d~~~~a~e~~~~~~~l~~~aN~-~~~g~  135 (357)
                      .++.++++|.+|+..+.+||+++|++|.++.++|+|+|+++++++||+++++||.+++.|+.+++++|.+++|+ .++|.
T Consensus         2 sqi~~l~q~~rN~~da~s~lqtAe~aL~~i~~iLqrireLavQAaNgt~s~~Dr~ai~~Ei~qL~~eI~~ian~T~fnG~   81 (174)
T 2zbi_A            2 AQIKGLTQAQRNANDGISLAQTAEGALGEISNNLQRIRELAVQASNGTNTQTDRDALQAEVTQLQSEIQRVAEQTSFNGQ   81 (174)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHCEETTE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             05666999998799999999999999999999999999999987257999999999999999999999999985223276


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             04105665443212233333222222210001013454322245665321123332210012334444456654320011
Q gi|254780523|r  136 YLFSGINSSEKPLNGYFTKDSLAKKSFDQMLQGFLEENSKSLLAGQHLEVSSMNAQQMTDFIKQLEDKFSDDEYWANNWS  215 (357)
Q Consensus       136 ~~f~G~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  215 (357)
                      |+|.|.....+||.....+........                                                     
T Consensus        82 ~Lf~Gs~~~~~~~~~~~~~~~~~~~~~-----------------------------------------------------  108 (174)
T 2zbi_A           82 KLLDGSFNGVQFQIGANAGETIGVSKI-----------------------------------------------------  108 (174)
T ss_dssp             ESSBSCCCEEEEECSSSTTCEEEEECC-----------------------------------------------------
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHC-----------------------------------------------------
T ss_conf             644332100011100000023322101-----------------------------------------------------


Q ss_pred             CCCCCCCEEECCCCCCEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             15665200000256410223203531011233333210023344555113566777778999999999999999866899
Q gi|254780523|r  216 NASDHNIKYRIKDTEGIDVSANVNMRGIRDIMFVAVIGTEFLSKNLTDGARNVLTKKMLSTVQQGLSGIIEQRAVLGISE  295 (357)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~i~~~~a~lGa~~  295 (357)
                                                                .....+.........++..||.++..|...|+.+|+.|
T Consensus       109 ------------------------------------------~~~~~~v~t~~~a~~ai~~id~ai~~v~~~r~~lGa~q  146 (174)
T 2zbi_A          109 ------------------------------------------XNAQTTVSSFTNAQQTITQIDNALKDINTARADLGAVQ  146 (174)
T ss_dssp             ------------------------------------------CBCSTCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ------------------------------------------CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ------------------------------------------34222301177799999999999999999999875799


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999998999999999864333
Q gi|254780523|r  296 KNINEERVFLQNKNNIIDTYISKS  319 (357)
Q Consensus       296 ~~l~~~~~~l~~~~~~l~~~~s~l  319 (357)
                      ||||.....+....++++...|.-
T Consensus       147 nrl~~t~~nl~~~~~n~~aa~S~~  170 (174)
T 2zbi_A          147 NRFTSTVANLQSXTENLSSALEHH  170 (174)
T ss_dssp             HHHHHHHC----------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999998630


No 5  
>>1ory_B Flagellin; flagellar chaperone, cytosolic export chaperone, FLIS, FLIC; 2.45A {Aquifex aeolicus} (B:)
Probab=97.31  E-value=0.00012  Score=42.94  Aligned_cols=45  Identities=9%  Similarity=0.053  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999986433327888999999999999999999999997368
Q gi|254780523|r  307 NKNNIIDTYISKSIGVEQHTAHAQLSTLINKIEMSYMITTKLQKL  351 (357)
Q Consensus       307 ~~~~~l~~~~s~l~daD~ae~~t~l~~~q~~~qas~~~~a~i~~~  351 (357)
                      +..++++...|.|+|+|+++++++|.+.++..|++..+.++..+.
T Consensus         2 ~~~~N~~aA~SrI~DaD~A~E~~~~tk~qIL~Qa~~amLaQAN~~   46 (55)
T 1ory_B            2 VAKDNTDNAESIIRNVDFAKEMTEFTKYQIRMQSGVAMLAQANAL   46 (55)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHCHHHHHHHHCCCC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             268789999846540559999999999999999999999998526


No 6  
>>1ucu_A Phase 1 flagellin; flagellar filament, cryo-electron microscopy, helical reconstruction, structural protein; 4.00A {Salmonella typhimurium} (A:1-40,A:455-494)
Probab=96.83  E-value=0.0033  Score=34.86  Aligned_cols=42  Identities=12%  Similarity=-0.075  Sum_probs=34.1

Q ss_pred             CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHC
Q ss_conf             132189999999999999999999999997202204642128
Q gi|254780523|r    4 TGISTSSIFERMNILTKELNKDSVKLHEEMVTGQSSDYGLQL   45 (357)
Q Consensus         4 ~~Ist~~~~~~~~~~l~~~~~~l~~~~~qlsTGk~i~~~sdd   45 (357)
                      ++|.|+...-...+++...+..+.+..++||||.||+++--|
T Consensus         2 m~In~Ni~alna~r~l~~~~~~l~~sm~rLSSG~RINsADaD   43 (80)
T 1ucu_A            2 QVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSADSD   43 (80)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCTTTSCCC
T ss_pred             EEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHCH
T ss_conf             199740999999999999999999999986114864782131


No 7  
>>1ucu_A Phase 1 flagellin; flagellar filament, cryo-electron microscopy, helical reconstruction, structural protein; 4.00A {Salmonella typhimurium} (A:1-40,A:455-494)
Probab=96.10  E-value=0.018  Score=30.71  Aligned_cols=55  Identities=11%  Similarity=0.097  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999989999999998643-3327888999999999999999999999997368
Q gi|254780523|r  297 NINEERVFLQNKNNIIDTYIS-KSIGVEQHTAHAQLSTLINKIEMSYMITTKLQKL  351 (357)
Q Consensus       297 ~l~~~~~~l~~~~~~l~~~~s-~l~daD~ae~~t~l~~~q~~~qas~~~~a~i~~~  351 (357)
                      .+......+....+.+.+++- +--|+|+|+++++|.+.++..|++..+.++..++
T Consensus        16 ~l~~~~~~l~~sm~rLSSG~RINsADaD~A~E~~~~tk~qIL~Qa~~amLaQAN~~   71 (80)
T 1ucu_A           16 NLNKSQSALGTAIERLSSGLRINSADSDYATEVSNMSRAQILQQAGTSVLAQANQV   71 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCCTTTSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCHCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999999861148647821319999999999999999999999997416


No 8  
>>2d4y_A HAP1, flagellar HOOK-associated protein 1; multi-domain protein, alpha-helical bundle, complex all- beta folds, structural protein; 2.10A {Salmonella typhimurium} (A:1-268,A:356-463)
Probab=91.99  E-value=0.55  Score=22.49  Aligned_cols=93  Identities=8%  Similarity=-0.084  Sum_probs=59.6

Q ss_pred             CCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCHHHHHHHHH
Q ss_conf             4642128999999999999999999999999999999-99999988889999999999998513--78889889999999
Q gi|254780523|r   39 SDYGLQLGARVTSILEWEQEKNHIAERLHSNSLVTKR-LSTSQAHLSSMQKIVQDMVGPLVILL--EGKTDNNKFPINAG  115 (357)
Q Consensus        39 i~~~sddp~~~~~~~~l~~~~~~l~~~~~n~~~a~~~-l~~~e~~L~~i~~~l~~~~~~~v~a~--n~t~~~~d~~~~a~  115 (357)
                      ...|.+.+.....+.+.+.-..++.+....+...... -......+.+|+.++.++-++=.+-.  .+.....+...+..
T Consensus        57 s~~P~~~~~R~~vl~~a~~L~~~~n~~~~~L~~l~~~~~~~i~~~V~~iN~l~~~Ia~LN~~I~~~~~~~~g~~~ndLlD  136 (376)
T 2d4y_A           57 VSNAEDPAARQALIGKAEGLVNQFKTTDQYLRDQDKQVNIAIGSSVAQINNYAKQIANLNDQISRMTGVGAGASPNDLLD  136 (376)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------CHHHH
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf             86879889999999999999999999999999999999999999999999999999999999999861468999067789


Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9986567777776520
Q gi|254780523|r  116 MLRDSYESFVTFANMT  131 (357)
Q Consensus       116 e~~~~~~~l~~~aN~~  131 (357)
                      +-.+++++|-.+..-+
T Consensus       137 qRD~ll~eLS~~i~i~  152 (376)
T 2d4y_A          137 QRDQLVSELNKIVGVE  152 (376)
T ss_dssp             HHHHHHHHHHHHSCEE
T ss_pred             HHHHHHHHHHHHCCCE
T ss_conf             9999999987660704


No 9  
>>3bj4_A Potassium voltage-gated channel subfamily KQT member 1; coiled coil, alternative splicing, deafness, disease mutation, glycoprotein, ION transport; 2.00A {Homo sapiens} (A:)
Probab=19.49  E-value=42  Score=12.02  Aligned_cols=27  Identities=11%  Similarity=0.303  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             866899999999998999999999864
Q gi|254780523|r  290 VLGISEKNINEERVFLQNKNNIIDTYI  316 (357)
Q Consensus       290 ~lGa~~~~l~~~~~~l~~~~~~l~~~~  316 (357)
                      .+|+|.||+|.-...++.....+++.+
T Consensus        14 tIGaRLNRvedKvtqmDq~Ln~itdmL   40 (49)
T 3bj4_A           14 TIGARLNRVEDKVTQLDQRLALITDML   40 (49)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             398899889999999999999999999


No 10 
>>3hfe_A Potassium voltage-gated channel subfamily KQT member 1; coiled coil, trimer, alternative splicing, atrial fibrillation, cell membrane; 1.70A {Homo sapiens} PDB: 3hfc_A (A:)
Probab=15.74  E-value=52  Score=11.51  Aligned_cols=20  Identities=10%  Similarity=0.257  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             86689999999999899999
Q gi|254780523|r  290 VLGISEKNINEERVFLQNKN  309 (357)
Q Consensus       290 ~lGa~~~~l~~~~~~l~~~~  309 (357)
                      .+|+|.||+|.--..++...
T Consensus         7 tigarlnrvedkvtq~dq~l   26 (31)
T 3hfe_A            7 TIGARLNRVEDKVTQLDQRL   26 (31)
T ss_dssp             SHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHH
T ss_conf             08888878999998887766


Done!