Query         gi|254780798|ref|YP_003065211.1| possible lolA type protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 204
No_of_seqs    112 out of 1275
Neff          8.8 
Searched_HMMs 23785
Date          Mon May 30 12:47:24 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780798.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2w7q_A Outer-membrane lipoprot 100.0 1.1E-32 4.5E-37  202.0  20.0  180   25-204    12-203 (204)
  2 1iwl_A P20, outer-membrane lip 100.0   3E-31 1.2E-35  193.9  19.0  167   34-203     1-178 (182)
  3 2yzy_A Putative uncharacterize  99.8 2.1E-18 8.7E-23  121.5  13.4  175   27-203     3-198 (200)
  4 3buu_A Uncharacterized LOLA su  99.0 1.1E-07 4.7E-12   61.0  17.6  170   25-195     2-222 (229)
  5 3bk5_A Putative outer membrane  97.8  0.0013 5.3E-08   38.2  16.9  167   30-196     4-233 (237)
  6 3m4w_A Sigma-E factor regulato  97.7  0.0022 9.2E-08   36.8  15.7  165   31-196     3-179 (295)
  7 2qgu_A Probable signal peptide  54.3     3.4 0.00014   18.8   1.0   14    5-18      1-14  (211)
  8 1dbg_A Chondroitinase B; beta   25.8      20 0.00086   14.5   1.2   15   33-47     28-42  (506)
  9 2v25_A Major cell-binding fact  20.9      22 0.00091   14.3   0.6   11    3-13      1-11  (259)
 10 1my6_A Iron (III) superoxide d  20.2     3.2 0.00014   19.0  -3.8   47   31-77     94-141 (199)

No 1  
>2w7q_A Outer-membrane lipoprotein carrier protein; periplasmic chaperone, lipoprotein transport, transport, periplasm, chaperone; 1.88A {Pseudomonas aeruginosa}
Probab=100.00  E-value=1.1e-32  Score=202.05  Aligned_cols=180  Identities=16%  Similarity=0.209  Sum_probs=141.8

Q ss_pred             HHCCCCCCCHHHHHHHHHHHCCCEEEEEEEEEECC------CEEEEEEEEECCCEEEEEECCCCEEEEEEECEEEEEEEC
Q ss_conf             40344431017999999861267069999996189------559999999669869999716641577751205999713
Q gi|254780798|r   25 NAAYPITKDQSVKKAIEHFLSIQTMQGTFLQEDAG------YVMKGEFFMARPSKFYFKYSSPSSVSLISDGSNIAVYNA   98 (204)
Q Consensus        25 ~a~~~~~~~~~~~~i~~~l~~~~t~~a~F~Q~~~~------~~~~G~~~~kkP~k~rw~y~~P~~~~iv~~g~~l~~~d~   98 (204)
                      .++.+...++.++++.++++++++++|+|+|+..+      ..++|+|+++||++|||+|.+|.++.+++||+++|+||+
T Consensus        12 ~~s~a~~~~~~~~kl~~~~~~~~s~~a~F~Q~~~~~~~~~~~~s~G~~~~~kP~k~r~~y~~P~~~~ii~~g~~l~~~d~   91 (204)
T 2w7q_A           12 RGSIAIDDSAAVQRLTGLLNKAQTLTARFSQLTLDGSGTRLQETAGQLSLKRPGLFRWHTDAPNEQLLISNGEKVWLYDP   91 (204)
T ss_dssp             -CCCSSCCHHHHHHHHHHHHTCSEEEEEEEEEEECTTSCCEEEEEEEEEEETTTEEEEEECSSSCEEEEEETTEEEEEET
T ss_pred             CCCCCCCCHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCEEEEEEEEEEEECCCEEEEEECCCCCEEEEECCCEEEEECC
T ss_conf             35344162789999999983676489999999965889747888999999809989999889850799984987999875


Q ss_pred             CCCCCCCHHHHHH----HHHHHCCHHHHHHHHCCCCCC-CCCCEEEEECCCCCCCCEEEEEEECCCCEEEEEEEEECCCC
Q ss_conf             3343210111111----233210001212221011322-35727997204666663479999369842999999967998
Q gi|254780798|r   99 KLDTWSVYPLRYM----AFSVIFSNNQHVIQESIQRVE-SNNSFITIFFKDDFMGNMISVTFDRLSYRLLNWKIMDSSRR  173 (204)
Q Consensus        99 ~~~q~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~i~l~f~~~~~~l~~~~i~D~~G~  173 (204)
                      +++++..++....    +..++.+.............. ..........+.........++|+.++..|++|++.|..|+
T Consensus        92 ~~~~v~~~~~~~~~~~~~~~~l~~~~~~l~~~~~v~~~~~~~~~~~~l~p~~~~~~~~~i~i~~~~~~l~~i~i~d~~g~  171 (204)
T 2w7q_A           92 DLEQVTIQKLDQRLTQTPALLLSGDISKISESFAITYKEGGNVVDFVLKPKTKDTLFDTLRLSFRSGKVNDMQMIDGVGQ  171 (204)
T ss_dssp             TTTEEEEECHHHHTTTCGGGGGGSCHHHHTTTEEEEEEEETTEEEEEEEESSSCSSCSEEEEEEETTEEEEEEEECTTCC
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHCCCHHHHHHHHHHHEECCCCEEEEEECCCCCCCCEEEEEEEECCCEEEEEEEEECCCC
T ss_conf             34523012321111113355642444566654201000258618999735677764689999955981899999968999


Q ss_pred             EEEEEEEEEECCCCCCHHHCCCCCC-CCCCCC
Q ss_conf             7999997432288689655126853-134489
Q gi|254780798|r  174 YSIIKILKYKENTVLDPKVFEIPYD-KIHNIN  204 (204)
Q Consensus       174 ~t~i~f~ni~~N~~i~~~~F~f~~~-~~~~~~  204 (204)
                      .|++.|+|++.|.++++++|+|.+| ++++|+
T Consensus       172 ~t~i~f~n~~~n~~i~~~~F~f~~P~g~eVi~  203 (204)
T 2w7q_A          172 RTNILFFDVKMNEALDAKQFTFDVPPGVDVIQ  203 (204)
T ss_dssp             EEEEEEEEEEESCCCCGGGGCCCCCTTCEEEC
T ss_pred             EEEEEEEEEEECCCCCHHHEEECCCCCCEEEC
T ss_conf             99999994560899896458897959976747


No 2  
>1iwl_A P20, outer-membrane lipoproteins carrier protein; unclosed beta barrel, protein transport; 1.65A {Escherichia coli} SCOP: b.125.1.1 PDB: 1ua8_A 2zpd_A 2zpc_A
Probab=100.00  E-value=3e-31  Score=193.90  Aligned_cols=167  Identities=15%  Similarity=0.238  Sum_probs=133.5

Q ss_pred             HHHHHHHHHHHCCCEEEEEEEEEEC------CCEEEEEEEEECCCEEEEEECCCCEEEEEEECEEEEEEECCCCCCCCHH
Q ss_conf             1799999986126706999999618------9559999999669869999716641577751205999713334321011
Q gi|254780798|r   34 QSVKKAIEHFLSIQTMQGTFLQEDA------GYVMKGEFFMARPSKFYFKYSSPSSVSLISDGSNIAVYNAKLDTWSVYP  107 (204)
Q Consensus        34 ~~~~~i~~~l~~~~t~~a~F~Q~~~------~~~~~G~~~~kkP~k~rw~y~~P~~~~iv~~g~~l~~~d~~~~q~~~~~  107 (204)
                      +++.+|+++|+++++++|+|+|+..      ..+++|+++++|||++||+|.+|.++.+++||+.+|+|||+++|+..++
T Consensus         1 d~~~~l~~~l~~~~s~~a~F~Q~~~~~~~~~~~~~~G~~~~~kp~~~r~~y~~P~~~~iv~~g~~l~~y~~~~~~v~~~~   80 (182)
T 1iwl_A            1 DAASDLKSRLDKVSSFHASFTQKVTDGSGAAVQEGQGDLWVKRPNLFNWHMTQPDESILVSDGKTLWFYNPFVEQATATW   80 (182)
T ss_dssp             CHHHHHHHHTTSCSEEEEEEEEEEEC-----CEEEEEEEEEETTTEEEEEECSSSCEEEEEESSEEEEEEGGGTEEEEEE
T ss_pred             CHHHHHHHHHHCCCEEEEEEEEEEECCCCCEEEEEEEEEEEEECCEEEEEECCCCEEEEEECCCEEEEECCCCCCCCCCC
T ss_conf             97899999984567389999999985889704789999999809989999858825999985968999755324012455


Q ss_pred             HHHHH----HHHHCCHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCEEEEEEEEECCCCEEEEEEEEEE
Q ss_conf             11112----33210001212221011322357279972046666634799993698429999999679987999997432
Q gi|254780798|r  108 LRYMA----FSVIFSNNQHVIQESIQRVESNNSFITIFFKDDFMGNMISVTFDRLSYRLLNWKIMDSSRRYSIIKILKYK  183 (204)
Q Consensus       108 ~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~f~~~~~~l~~~~i~D~~G~~t~i~f~ni~  183 (204)
                      .....    ...+............. ........+.++........+.|+|+.++ .|++|.+.|..|++|+|.|++ +
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~L~pk~~~~~~~~i~i~~~~~~-~l~~i~~~d~~g~~t~i~f~~-~  157 (182)
T 1iwl_A           81 LKDATGNTPFMLIARNQSSDWQQYNI-KQNGDDFVLTPKASNGNLKQFTINVGRDG-TIHQFSAVEQDDQRSSYQLKS-Q  157 (182)
T ss_dssp             GGGCCCCSHHHHHHHCCHHHHTTEEE-EEETTEEEEEESSSSCSEEEEEEEECTTC-CEEEEEEEETTCCEEEEEEEE-E
T ss_pred             HHHHHCCCHHHHHCCCCHHHHHHEEE-ECCCCEEEEEECCCCCCEEEEEEEECCCC-CEEEEEEEECCCCEEEEEEEC-C
T ss_conf             02321027467751541555543000-02351799988587767048999996899-698999997896999999980-0


Q ss_pred             CCCCCCHHHCCC-CCCCCCCC
Q ss_conf             288689655126-85313448
Q gi|254780798|r  184 ENTVLDPKVFEI-PYDKIHNI  203 (204)
Q Consensus       184 ~N~~i~~~~F~f-~~~~~~~~  203 (204)
                      .|.++++++|+| +++++++|
T Consensus       158 ~n~~i~~~~F~f~~P~g~eVi  178 (182)
T 1iwl_A          158 QNGAVDAAKFTFTPPQGVTVD  178 (182)
T ss_dssp             EESCCCGGGGSCCCCSSCEEE
T ss_pred             CCCCCCHHHEEECCCCCCEEE
T ss_conf             679999667889795998687


No 3  
>2yzy_A Putative uncharacterized protein TTHA1012; uncharacterized conserved protein, structural genomics, unknown function, NPPSFA; 1.60A {Thermus thermophilus HB8}
Probab=99.79  E-value=2.1e-18  Score=121.52  Aligned_cols=175  Identities=9%  Similarity=0.046  Sum_probs=122.8

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCEEEEEEEEE-ECC-CEEEEEE-EEECCCEEEEEECCCCE---EEEEEECEEEEEEECCC
Q ss_conf             344431017999999861267069999996-189-5599999-99669869999716641---57775120599971333
Q gi|254780798|r   27 AYPITKDQSVKKAIEHFLSIQTMQGTFLQE-DAG-YVMKGEF-FMARPSKFYFKYSSPSS---VSLISDGSNIAVYNAKL  100 (204)
Q Consensus        27 ~~~~~~~~~~~~i~~~l~~~~t~~a~F~Q~-~~~-~~~~G~~-~~kkP~k~rw~y~~P~~---~~iv~~g~~l~~~d~~~  100 (204)
                      +.|..++++++++.+.+++.++.++.+.-+ ..+ ...+-+. .+++|+++||+|.+|..   +.++.||+.+|.|+|++
T Consensus         3 ~~A~sa~eil~k~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~r~~~~~P~~~~g~~~l~dG~~~W~Y~p~~   82 (200)
T 2yzy_A            3 GLAQSAQEILDRVEKNLSTPWQATVQGRIQGPGGEEELLARVYALPQARLFRVEFLKPGSLEGNFTVITEKEVWNYLYLT   82 (200)
T ss_dssp             ---CHHHHHHHHHHHHTCSCEEEEEEEEC-----CCEEEEEEEEEGGGTEEEEEEEESTTTTTCEEEECSSCEEEEETTT
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCEEEEEEEEECCCCEEEEEEEEEEECCCEEEEEEECCCCCCCEEEEECCCEEEEEECCC
T ss_conf             20348999999999763545326999999937997478999999806987999991786557719999199999995778


Q ss_pred             CCCCCHHHHHHHHHH---HCCH---HHHHHHHCCCC--------CCCCCCEEEEECCCCCCCCEEEEEEECCCCEEEEEE
Q ss_conf             432101111112332---1000---12122210113--------223572799720466666347999936984299999
Q gi|254780798|r  101 DTWSVYPLRYMAFSV---IFSN---NQHVIQESIQR--------VESNNSFITIFFKDDFMGNMISVTFDRLSYRLLNWK  166 (204)
Q Consensus       101 ~q~~~~~~~~~~~~~---~~~~---~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~i~l~f~~~~~~l~~~~  166 (204)
                      +++.+.+........   ....   ...........        ........+.+ +.+.....+.++++.+++.+.+++
T Consensus        83 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~g~e~~~g~~~~~l~l~p-k~~~~~~~~~lwIdk~~~~p~k~~  161 (200)
T 2yzy_A           83 NQLVISPREKAKIQGLGFAPQGLGDLKALSEQVDLRLEGEVRLPEGMAWKLVGRS-KENQGFAAMELYILKADPRPLRFV  161 (200)
T ss_dssp             TEEEEEC------------------------CCEEEEEEEEEETTEEEEEEEEEC----CCCSEEEEEEETTTTEEEEEE
T ss_pred             CEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHCHHHCCCCEEECCCCEEEEEECC-CCCCCCEEEEEEEECCCCEEEEEE
T ss_conf             8389963632323345667204565666544110110342331896089997367-765542069999998999699999


Q ss_pred             EEECCCCE-EEEEEEEEECCCCCCHHHCCCCCCCCCCC
Q ss_conf             99679987-99999743228868965512685313448
Q gi|254780798|r  167 IMDSSRRY-SIIKILKYKENTVLDPKVFEIPYDKIHNI  203 (204)
Q Consensus       167 i~D~~G~~-t~i~f~ni~~N~~i~~~~F~f~~~~~~~~  203 (204)
                      +.|..|+. ++++|+|++ |..++++.|+|.+++..+|
T Consensus       162 ~~d~~g~~~~~~~~~~~k-~~~~~~~~f~~~P~~~~vi  198 (200)
T 2yzy_A          162 FLDEKGKVLADLKVVEFK-RTNLTEAQLKRYPKDAQVV  198 (200)
T ss_dssp             EECTTSCEEEEEEEEEEE-ECCCCHHHHTCCCTTCEEE
T ss_pred             EEECCCCEEEEEEEEEEE-ECCCCHHHCEECCCCCCEE
T ss_conf             994899989999999856-0799859957789998013


No 4  
>3buu_A Uncharacterized LOLA superfamily protein NE2245; PSI-2, protein structure initiative, midwest center for structural genomics; HET: MSE; 1.20A {Nitrosomonas europaea atcc 19718}
Probab=98.98  E-value=1.1e-07  Score=61.03  Aligned_cols=170  Identities=13%  Similarity=0.085  Sum_probs=109.2

Q ss_pred             HHCCCCCCCHHHHHHHHHHHCCCEEEEEEEEE-ECCC----EEEEEEEEECCCEEEEEECCCCE---EEEEEECEEEEEE
Q ss_conf             40344431017999999861267069999996-1895----59999999669869999716641---5777512059997
Q gi|254780798|r   25 NAAYPITKDQSVKKAIEHFLSIQTMQGTFLQE-DAGY----VMKGEFFMARPSKFYFKYSSPSS---VSLISDGSNIAVY   96 (204)
Q Consensus        25 ~a~~~~~~~~~~~~i~~~l~~~~t~~a~F~Q~-~~~~----~~~G~~~~kkP~k~rw~y~~P~~---~~iv~~g~~l~~~   96 (204)
                      .|+++..++++++++.+....-.++++..+=+ ..+.    ..+=..+-+-+.+....+.+|..   +.++.+|+.+|.|
T Consensus         2 ~a~~a~ta~eIl~k~d~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~kg~~k~li~f~~P~~~kG~~~L~~~d~~w~Y   81 (229)
T 3buu_A            2 NAKSAVTAQSILEKADEIRFPQDSFQVNVAIRTAAPDHAEDLYRYQVLSKGNENSIVMITEPASERGQAILMKGRDLWVF   81 (229)
T ss_dssp             ----CCCHHHHHHHHHHHHSCSSCEEEEEEEEEEETTEECCCEEEEEEEETTTEEEEEEEESTTTTTCEEEEETTEEEEE
T ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCEEEECCCCEEEE
T ss_conf             85234799999999987406799889999999975997469999999963993799999078202692999907761898


Q ss_pred             ECCCCCCCCHHHHHHHHHHHCCHHH---HHHHHC--------CCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCEE---
Q ss_conf             1333432101111112332100012---122210--------11322357279972046666634799993698429---
Q gi|254780798|r   97 NAKLDTWSVYPLRYMAFSVIFSNNQ---HVIQES--------IQRVESNNSFITIFFKDDFMGNMISVTFDRLSYRL---  162 (204)
Q Consensus        97 d~~~~q~~~~~~~~~~~~~~~~~~~---~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~i~l~f~~~~~~l---  162 (204)
                      .|.++++-+.+..+....-+...+.   +.....        ...+.......+.++......+.+.++++.+++.+   
T Consensus        82 lP~~~rv~ris~~~~~~~~f~~~D~~~~dl~~dy~~~~~~e~~~~g~~~yvlel~pk~~~~~Y~k~~~wIdk~~~~p~k~  161 (229)
T 3buu_A           82 MPSVSQPIRLSLSQRLTGQVANGDIARANFTGDYHPQLLRNESIDDEDYYVLELTGIDRSVTYQKVLLWVNQSNFRPYKA  161 (229)
T ss_dssp             CTTCSSCEEECTTSEEETTEEHHHHHCCCSBTTEEEEEEEEEEETTEEEEEEEEEESSTTSSCSEEEEEEETTTCCEEEE
T ss_pred             CCCCCCEEEECCCCCCCCCCCCCCHHHCCCCCCCEEEEEEEEEECCEEEEEEEEECCCCCCCCEEEEEEEECCCCEEEEE
T ss_conf             55568369955765556875433011120002334898400368884499999852788888669999999878889999


Q ss_pred             ---------------------------EEEEEEEC--CCCEEEEEEEEEECCCCCCHHHCCC
Q ss_conf             ---------------------------99999967--9987999997432288689655126
Q gi|254780798|r  163 ---------------------------LNWKIMDS--SRRYSIIKILKYKENTVLDPKVFEI  195 (204)
Q Consensus       163 ---------------------------~~~~i~D~--~G~~t~i~f~ni~~N~~i~~~~F~f  195 (204)
                                                 ..+.+.|.  .|..|.+.++++++| +++++.|.-
T Consensus       162 e~yd~~G~l~K~~~~~~~~~i~g~~~p~~~~~~~~~~~~~~T~l~~~~i~~~-~i~d~~Ft~  222 (229)
T 3buu_A          162 EFYSVSGRLLKTSRYENFDNILGEMRPTRIIMEDALKSGEVSVLDYSDMKLR-DLPDKIFTK  222 (229)
T ss_dssp             EEECTTSCEEEEEEEEEEEEETTEEEEEEEEEEESSSSCCEEEEEEEEEEEC-CCCGGGSST
T ss_pred             EEECCCCCEEEEEEEEEEEEECCEEEEEEEEEEECCCCCCEEEEEEEEEEEC-CCCHHHCCH
T ss_conf             9991799789999968539988999879999996877898899999851348-899487889


No 5  
>3bk5_A Putative outer membrane lipoprotein-sorting protein; putative outer membrane protein domain, PSI-2; HET: MSE; 2.00A {Vibrio parahaemolyticus rimd 2210633}
Probab=97.81  E-value=0.0013  Score=38.16  Aligned_cols=167  Identities=11%  Similarity=-0.021  Sum_probs=93.8

Q ss_pred             CCCCHHHHHHHHHHHCCCEEEEEEEE--E-ECCCEEEEEEEEE---CC---CEEEEEECCCCE---EEEEE-----ECEE
Q ss_conf             43101799999986126706999999--6-1895599999996---69---869999716641---57775-----1205
Q gi|254780798|r   30 ITKDQSVKKAIEHFLSIQTMQGTFLQ--E-DAGYVMKGEFFMA---RP---SKFYFKYSSPSS---VSLIS-----DGSN   92 (204)
Q Consensus        30 ~~~~~~~~~i~~~l~~~~t~~a~F~Q--~-~~~~~~~G~~~~k---kP---~k~rw~y~~P~~---~~iv~-----~g~~   92 (204)
                      ....++++++.+.-.+.++.+|.-.=  + ..|...+=.+-++   .+   .+....+..|..   +.+..     .++.
T Consensus         4 ~~g~eIa~~~~~~~~g~~~~~~~~~M~l~~~~g~~~~R~~~~~~~~~~~~~~ksli~f~~P~~~kGt~~L~~~~~~~~dd   83 (237)
T 3bk5_A            4 EKGLEIAQERKARDEGWGDSIATMEMILKNAQGESSTRLMRLKSLEVEGDGDKGLTIFDQPRDVTGTAFLNHSHTIGADD   83 (237)
T ss_dssp             HHHHHHHHHHHHTTCCCCEEEEEEEEEEECCC-CCEEEEEEEEEECCTTSCCEEEEEEEESTTTTTCEEEEECCSSSCCE
T ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCEEEEEEECCHHCCCCEEEEEECCCCCCC
T ss_conf             67999999977512487782699999999589989999999999980799837999993651105948998644689861


Q ss_pred             EEEEECCCCCCCCHHHHHHHHHHHCCHHHHH--------HHHC------CCCCCCCCCEEEEECCCCCCCCEEEEEEECC
Q ss_conf             9997133343210111111233210001212--------2210------1132235727997204666663479999369
Q gi|254780798|r   93 IAVYNAKLDTWSVYPLRYMAFSVIFSNNQHV--------IQES------IQRVESNNSFITIFFKDDFMGNMISVTFDRL  158 (204)
Q Consensus        93 l~~~d~~~~q~~~~~~~~~~~~~~~~~~~~~--------~~~~------~~~~~~~~~~~~~~~~~~~~~~~i~l~f~~~  158 (204)
                      .|.|.|.++.+-+.+...-...+........        ....      ...+.........++........+.++++.+
T Consensus        84 ~WlYlP~~~rv~RIs~s~k~~sfmGSDfsyeDl~~~~~~~~~~~l~~~~~~~g~~~~vle~~pk~~~~~Y~k~~~wIdk~  163 (237)
T 3bk5_A           84 QWLYLPALKRVKRISSRNKSGPFMGSEFAYEDLSSFEIEKYRFNHLKDEKFNGQDVFVLEQIPTDKNSGYTKQVVWLDKA  163 (237)
T ss_dssp             EEEEETTTTEEEECCGGGTTSBSTTSSCBGGGGSCCCGGGEEEEEEEEEEETTEEEEEEEEEESCTTSSEEEEEEEEETT
T ss_pred             EEEECCCCCCEEECCCCCCCCCCCCCEEEHHHHHCCCCCCCHHHHCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEECC
T ss_conf             58984778834985830146873344112134100320001122202211288069999952589877416999999977


Q ss_pred             CCEEEEEEEEECC--------------------------------CCEEEEEEEEEECCCCCCHHHCCCC
Q ss_conf             8429999999679--------------------------------9879999974322886896551268
Q gi|254780798|r  159 SYRLLNWKIMDSS--------------------------------RRYSIIKILKYKENTVLDPKVFEIP  196 (204)
Q Consensus       159 ~~~l~~~~i~D~~--------------------------------G~~t~i~f~ni~~N~~i~~~~F~f~  196 (204)
                      ++.+.+.+..|..                                |..|.+.+.++++|..|++++|.-.
T Consensus       164 ~~~p~k~e~yd~~G~l~K~~~~~~~~~~~~~~~~~~~~~m~~~~~g~~T~l~~~~i~~~~~l~d~~Ft~~  233 (237)
T 3bk5_A          164 HYRPLKVEFYDRKGALLKTLTFANYKQYLDKYWRAHTMAMTNHQTGKSTELNTSDLRFQTGLEENDFNKN  233 (237)
T ss_dssp             TCCEEEEEEEETTSCEEEEEEEEEEEEETTTEEEEEEEEEEETTTCCEEEEEEEEEEECCCCCGGGGCGG
T ss_pred             CCEEEEEEEECCCCCEEEEEEEEEEEECCCCEEEEEEEEEECCCCCCEEEEEEEEEECCCCCCHHHCCHH
T ss_conf             7679999999279969999994541320596443499999917889889999986781899894888987


No 6  
>3m4w_A Sigma-E factor regulatory protein RSEB; RSEA, RSEB, RSEP, stress response, sigma factor, periplasm, membrane, transmembrane; 2.30A {Escherichia coli} PDB: 2p4b_A 2v43_A 2v42_A
Probab=97.66  E-value=0.0022  Score=36.82  Aligned_cols=165  Identities=10%  Similarity=0.047  Sum_probs=102.2

Q ss_pred             CCCHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEEEEEE-CC--CEEEEEECCCCEEEEEEECEEEEEEECCCCCCCCHH
Q ss_conf             310179999998612670699999961895599999996-69--869999716641577751205999713334321011
Q gi|254780798|r   31 TKDQSVKKAIEHFLSIQTMQGTFLQEDAGYVMKGEFFMA-RP--SKFYFKYSSPSSVSLISDGSNIAVYNAKLDTWSVYP  107 (204)
Q Consensus        31 ~~~~~~~~i~~~l~~~~t~~a~F~Q~~~~~~~~G~~~~k-kP--~k~rw~y~~P~~~~iv~~g~~l~~~d~~~~q~~~~~  107 (204)
                      ++...++++.+..++ .++++.|+....+...+=.+.=. ..  ..-|.+.-.-.+..++-.|+.++.+.|+.+.+....
T Consensus         3 ~a~~lL~~m~~A~~~-lnY~g~fv~~~~~~~~s~ri~H~~~~~~e~erl~~LdG~~revir~~~~v~~~~p~~~~~~~~~   81 (295)
T 3m4w_A            3 ASGALLQQMNLASQS-LNYELSFISINKQGVESLRYRHARLDNRPLAQLLQMDGPRREVVQRGNEISYFEPGLEPFTLNG   81 (295)
T ss_dssp             HHHHHHHHHHHHHHH-SEEEEEEEEEETTEEEEEEEEEEECSSSEEEEEEECSSSCCEEEEETTEEEEECTTSCCEEEEC
T ss_pred             CHHHHHHHHHHHHHH-CCEEEEEEEECCCCEEEEEEEEEEECCEEEEEEEECCCCCEEEEEECCEEEEEECCCCCEEEEC
T ss_conf             489999999988875-7834999999099077899999980996999999559994289997999999907985278845


Q ss_pred             H--HHHHHHHHCCHHHHHHHHCCC------CCCCCCCEEEEECCCCCCCCEEEEEEECCCCEEEEEEEEECCCCEE-EEE
Q ss_conf             1--111233210001212221011------3223572799720466666347999936984299999996799879-999
Q gi|254780798|r  108 L--RYMAFSVIFSNNQHVIQESIQ------RVESNNSFITIFFKDDFMGNMISVTFDRLSYRLLNWKIMDSSRRYS-IIK  178 (204)
Q Consensus       108 ~--~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~i~l~f~~~~~~l~~~~i~D~~G~~t-~i~  178 (204)
                      -  ......++..........+..      ..-..........+.+..-....+|+|.++..+.+.++.|..|+.. .+.
T Consensus        82 ~~~~~~fp~~l~~~~~~l~~~Y~~~~~G~~RVAGR~a~vi~l~PkD~~Ry~y~lWiD~etgLpLk~~~~d~~g~vlEq~~  161 (295)
T 3m4w_A           82 DYIVDSLPSLIYTDFKRLSPYYDFISVGRTRIADRLCEVIRVVARDGTRYSYIVWMDTESKLPMRVDLLDRDGETLEQFR  161 (295)
T ss_dssp             SSCTTSSCGGGGCCHHHHTTTEEEEEEEEEEETTEEEEEEEEEETTSCSCEEEEEEETTTCCEEEEEEECTTSCEEEEEE
T ss_pred             CCCCCCCCCCCCCCHHHHHHCEEEEECCCCEECCCEEEEEEEEECCCCEEEEEEEEECCCCCEEEEEECCCCCCEEEEEE
T ss_conf             54556673114547556741544898688579993889999985799768899999878896887755047997999999


Q ss_pred             EEEEECCCCCCHHHCCCC
Q ss_conf             974322886896551268
Q gi|254780798|r  179 ILKYKENTVLDPKVFEIP  196 (204)
Q Consensus       179 f~ni~~N~~i~~~~F~f~  196 (204)
                      |+++..+..+++..|.++
T Consensus       162 ft~l~~~~~~~~~~~~~~  179 (295)
T 3m4w_A          162 VIAFNVNQDISSSMQTLA  179 (295)
T ss_dssp             EEEEEEESSCCHHHHHHH
T ss_pred             EEEEEECCCCCHHHHHCC
T ss_conf             999882788665564021


No 7  
>2qgu_A Probable signal peptide protein; NESG, RSR89, Q8XV73, X-RAY, structural genomics, PSI-2, protein structure initiative; HET: MSE PEF; 1.50A {Ralstonia solanacearum GMI1000}
Probab=54.33  E-value=3.4  Score=18.82  Aligned_cols=14  Identities=7%  Similarity=0.287  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             88999999999999
Q gi|254780798|r    5 LYKSVIGVVILFFY   18 (204)
Q Consensus         5 ~mk~i~~~~i~~~~   18 (204)
                      |||+++..+++.++
T Consensus         1 M~k~~~~~l~~~l~   14 (211)
T 2qgu_A            1 MFKKLLHSLVAGLT   14 (211)
T ss_dssp             --------------
T ss_pred             CHHHHHHHHHHHHH
T ss_conf             94899999999999


No 8  
>1dbg_A Chondroitinase B; beta helix, polysaccharide lyase, dematan sulfate; HET: MAN RAM GCU MXY G4D BGC; 1.70A {Pedobacter heparinus} SCOP: b.80.1.4 PDB: 1dbo_A* 1ofl_A* 1ofm_A*
Probab=25.79  E-value=20  Score=14.45  Aligned_cols=15  Identities=7%  Similarity=-0.024  Sum_probs=7.2

Q ss_pred             CHHHHHHHHHHHCCC
Q ss_conf             017999999861267
Q gi|254780798|r   33 DQSVKKAIEHFLSIQ   47 (204)
Q Consensus        33 ~~~~~~i~~~l~~~~   47 (204)
                      -...+.|++.+++.+
T Consensus        28 v~~~~tiq~Ai~~a~   42 (506)
T 1dbg_A           28 VASNETLYQVVKEVK   42 (506)
T ss_dssp             ECSHHHHHHHHHHCC
T ss_pred             CCCHHHHHHHHHCCC
T ss_conf             498589999997089


No 9  
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate, transport, ABC transport, virulence factor, receptor; 1.49A {Campylobacter jejuni}
Probab=20.85  E-value=22  Score=14.30  Aligned_cols=11  Identities=18%  Similarity=0.437  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHH
Q ss_conf             47889999999
Q gi|254780798|r    3 FLLYKSVIGVV   13 (204)
Q Consensus         3 ~~~mk~i~~~~   13 (204)
                      |+|+|.++.+.
T Consensus         1 m~~~k~l~~~~   11 (259)
T 2v25_A            1 MVFRKSLLKLA   11 (259)
T ss_dssp             -----------
T ss_pred             CCHHHHHHHHH
T ss_conf             96379999999


No 10 
>1my6_A Iron (III) superoxide dismutase; iron speroxide dismutase, thermophIle, reactive oxygen species, cyanobacteria, SOD, fesod; 1.60A {Thermosynechococcus elongatus} SCOP: a.2.11.1 d.44.1.1
Probab=20.23  E-value=3.2  Score=18.95  Aligned_cols=47  Identities=11%  Similarity=0.118  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHHHHHCCCEEEEEEEEEECCCEEEEEEEEE-CCCEEEEE
Q ss_conf             310179999998612670699999961895599999996-69869999
Q gi|254780798|r   31 TKDQSVKKAIEHFLSIQTMQGTFLQEDAGYVMKGEFFMA-RPSKFYFK   77 (204)
Q Consensus        31 ~~~~~~~~i~~~l~~~~t~~a~F~Q~~~~~~~~G~~~~k-kP~k~rw~   77 (204)
                      ........|++.+.+.+.|+.+|.+.-.+...+|-.++- .|++++..
T Consensus        94 p~~~l~~~I~~~FGS~d~fk~~F~~~a~~~~GsGW~wL~~~~~~l~i~  141 (199)
T 1my6_A           94 PTGDVAARINSAFGSYDEFKAQFKNAAATQFGSGWAWLVLEAGTLKVT  141 (199)
T ss_dssp             CCHHHHHHHHHHHSSHHHHHHHHHHHHHHCCSSEEEEEEEETTEEEEE
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEE
T ss_conf             898999999987489999999999988607776699999738953377


Done!