Query         gi|254780172|ref|YP_003064585.1| general L-amino acid transport system permease protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 386
No_of_seqs    227 out of 3276
Neff          6.0 
Searched_HMMs 13730
Date          Mon May 23 10:26:24 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780172.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 d3dhwa1 f.58.1.1 (A:6-208) D-m  99.9 4.6E-24 3.3E-28  160.6  15.6  165  174-341     5-176 (203)
  2 d2onkc1 f.58.1.1 (C:1-252) Mol  99.7 1.3E-16 9.7E-21  115.8  16.9  162  170-332    44-211 (252)
  3 d3d31c1 f.58.1.1 (C:13-260) Su  99.7 1.5E-15 1.1E-19  109.4  19.4  165  170-335    42-214 (248)
  4 d2r6gf2 f.58.1.1 (F:261-504) M  99.4 9.4E-13 6.8E-17   92.7  12.7  156  173-328    17-188 (244)
  5 d2r6gg1 f.58.1.1 (G:7-296) Mal  99.4 2.8E-12   2E-16   89.9  11.4  154  172-328    74-231 (290)
  6 d1etxa_ a.4.1.12 (A:) FIS prot  69.5     2.6 0.00019   18.0   3.9   37  261-297    47-83  (89)
  7 d1ntca_ a.4.1.12 (A:) DNA-bind  62.9     3.1 0.00023   17.6   3.2   37  261-297    49-85  (91)
  8 d1umqa_ a.4.1.12 (A:) Photosyn  61.2     3.9 0.00028   17.0   3.8   35  263-297    20-54  (60)
  9 d1g2ha_ a.4.1.12 (A:) Transcri  41.7     8.1 0.00059   15.1   3.9   36  261-297    19-54  (61)
 10 d1i3ja_ d.285.1.1 (A:) DNA-bin  19.8      20  0.0014   12.8   2.5   22  277-298    65-86  (96)

No 1  
>d3dhwa1 f.58.1.1 (A:6-208) D-methionine transport system permease protein MetI {Escherichia coli [TaxId: 562]}
Probab=99.92  E-value=4.6e-24  Score=160.57  Aligned_cols=165  Identities=20%  Similarity=0.280  Sum_probs=131.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHH----HHHHHH---CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             02478779999999999987567----754441---27868899978988887614722899999999766415588773
Q gi|254780172|r  174 WGGLLVTLVISFFGIIISMPLGI----LLALGR---NSNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLFLPDTWDV  246 (386)
Q Consensus       174 ~gGl~~Tl~l~~~~~~~~~~lG~----llal~r---~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~lp~g~~~  246 (386)
                      +.|+..|+.+++.+..+++++|+    +++..+   ..+.+.+......+++++|++|.++++++.+.......  +.. 
T Consensus         5 l~~~~~tl~is~~~~~i~~ilg~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~v~~~~~~~~~~~~~--~~~-   81 (203)
T d3dhwa1           5 VRGVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIILLVWMIPFTRVIV--GTS-   81 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTGGGGGGGGGGTTCSSSCCSSHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTT--CCS-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCC-
T ss_conf             99999999999999999999999999999998744432008999999999999999999999999998635540--454-


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             87999999999998999899999999845866789999962168999999996998998620047999999961289999
Q gi|254780172|r  247 DKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISI  326 (386)
Q Consensus       247 ~~~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~KdTsL~~~  326 (386)
                      .....+++++++++.+|+.+++|+|++++|++|.|||+++|.|+||++++|++||+.+..+++..++++..+||++++..
T Consensus        82 ~~~~~~i~~~~~~~~p~~~~~~~~~l~~i~~~~~Eaa~~lGas~~q~~~~vilP~~~p~i~~~~~~~~~~~i~~~~~~~~  161 (203)
T d3dhwa1          82 IGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMGGA  161 (203)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTTTTHHHHHTCCTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHCCS
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             11999999999986489999999888843620689998869944424188409976999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999741
Q gi|254780172|r  327 INMFDLLGIVRVNFS  341 (386)
Q Consensus       327 Ig~~el~~~~~~~~~  341 (386)
                      +|..|+.....+...
T Consensus       162 ig~~~~~~~~~~~~~  176 (203)
T d3dhwa1         162 VGAGGLGQIGYQYGY  176 (203)
T ss_dssp             TTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             977599999999998


No 2  
>d2onkc1 f.58.1.1 (C:1-252) Molybdate/tungstate transport system permease protein WtpB (ModB) {Archaeoglobus fulgidus [TaxId: 2234]}
Probab=99.74  E-value=1.3e-16  Score=115.79  Aligned_cols=162  Identities=14%  Similarity=0.221  Sum_probs=130.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-----CCCC
Q ss_conf             111002478779999999999987567754441-2786889997898888761472289999999976641-----5588
Q gi|254780172|r  170 ETSLWGGLLVTLVISFFGIIISMPLGILLALGR-NSNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLF-----LPDT  243 (386)
Q Consensus       170 ~t~~~gGl~~Tl~l~~~~~~~~~~lG~llal~r-~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~-----lp~g  243 (386)
                      +...|..+..|+.+++.+.++++++|+.+|+.- +.+.+ .|........+..-+|.++.-+.....+...     ....
T Consensus        44 ~~~~~~~~~nSl~~~~~~~~i~~i~g~~la~~l~~~~~~-~~~~~~~~~~~p~~ip~~v~~~~~~~~~~~~~~~~~~~~~  122 (252)
T d2onkc1          44 DPAVWKVVLTTYYAALISTLIAVIFGTPLAYILARKSFP-GKSVVEGIVDLPVVIPHTVAGIALLVVFGSSGLIGSFSPL  122 (252)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCS-SHHHHHHHHHHHHHSCHHHHHHHHHHHHSTTSTTTTTCSS
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             978999999999999999999999999999999873132-1689999987521687177777776412332100012454


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Q ss_conf             77387999999999998999899999999845866789999962168999999996998998620047999999961289
Q gi|254780172|r  244 WDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSL  323 (386)
Q Consensus       244 ~~~~~~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~KdTsL  323 (386)
                      ...+.....+++.+....+|...++++|++++|+++.|||+++|.|++|++++|++|++.+..+.+..-.++..+||.+.
T Consensus       123 ~~~~~~~~iii~~~~~~~p~~~~~~~~~~~~i~~~~~eaA~~lGas~~~~~~~i~lP~~~p~i~~~~~l~~~~~~~~~~~  202 (252)
T d2onkc1         123 KFVDALPGIVVAMLFVSVPIYINQAKEGFASVDVRLEHVARTLGSSPLRVFFTVSLPLSVRHIVAGAIMSWARGISEFGA  202 (252)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_pred             CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             42001332110100112110368999999750388887887669983325469870876889999999999889999888


Q ss_pred             HHHHHHHHH
Q ss_conf             999999999
Q gi|254780172|r  324 ISIINMFDL  332 (386)
Q Consensus       324 ~~~Ig~~el  332 (386)
                      ...+|-.+-
T Consensus       203 ~~~~~~~~~  211 (252)
T d2onkc1         203 VVVIAYYPM  211 (252)
T ss_dssp             HHTTCCSSC
T ss_pred             HHHHCCCCC
T ss_conf             751148985


No 3  
>d3d31c1 f.58.1.1 (C:13-260) Sulfate/molybdate ABC transporter, permease protein {Methanosarcina acetivorans [TaxId: 2214]}
Probab=99.71  E-value=1.5e-15  Score=109.38  Aligned_cols=165  Identities=17%  Similarity=0.232  Sum_probs=131.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-C------C
Q ss_conf             1110024787799999999999875677544412-786889997898888761472289999999976641-5------5
Q gi|254780172|r  170 ETSLWGGLLVTLVISFFGIIISMPLGILLALGRN-SNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLF-L------P  241 (386)
Q Consensus       170 ~t~~~gGl~~Tl~l~~~~~~~~~~lG~llal~r~-s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~-l------p  241 (386)
                      +.+.+..+..|+.+++.+..++.++|..+|.... ++.+ .|........+-..+|.++.-+.....+... .      .
T Consensus        42 ~~~~~~~l~~Sl~~a~~s~~i~~~lg~~~a~~~~~~~~~-~~~~~~~l~~~p~~ip~vv~~~~~~~~~~~~~~~~~~~~~  120 (248)
T d3d31c1          42 NRSVISSIFLSLYAGFLATLLALLLGAPTGYILARFDFP-GKRLVESIIDVPVVVPHTVAGIALLTVFGSRGLIGEPLES  120 (248)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCT-THHHHHHHHHGGGTSCHHHHHHHHHHHHSTTSTTTGGGTT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCC
T ss_conf             989999999999999999999999999999999864651-2568999999999999720002445203432111112222


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             88773879999999999989998999999998458667899999621689999999969989986200479999999612
Q gi|254780172|r  242 DTWDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDS  321 (386)
Q Consensus       242 ~g~~~~~~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~KdT  321 (386)
                      .....+.+...+++.+....+|....++++++++|+++.|||+++|.|+||++|+|++||+.+..+.+..-.++..++|.
T Consensus       121 ~~~~~~~~~~iii~~~~~~~p~~~~~~~~~l~~i~~~~~eAA~~lGas~~~~~~~I~lP~~~p~i~~~~~l~f~~~~~~~  200 (248)
T d3d31c1         121 YIQFRDALPGIVVAMLFVSMPYLANSAREGFKSVDPRLENAARSLGAPLWKAFFFVTLPLSARYLLIGSVMTWARAISEF  200 (248)
T ss_dssp             TCCCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCEEEHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             11245642001001101100368888899997103368999876310423477898899999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             89999999999999
Q gi|254780172|r  322 SLISIINMFDLLGI  335 (386)
Q Consensus       322 sL~~~Ig~~el~~~  335 (386)
                      .....+|-...+..
T Consensus       201 ~~~~~l~~~~~~~~  214 (248)
T d3d31c1         201 GAVVILAYYPMVGP  214 (248)
T ss_dssp             HHHHHHHCTTCCHH
T ss_pred             HHHHHHCCCCCHHH
T ss_conf             98873318984099


No 4  
>d2r6gf2 f.58.1.1 (F:261-504) Maltose transport system permease protein MalF {Escherichia coli [TaxId: 562]}
Probab=99.45  E-value=9.4e-13  Score=92.69  Aligned_cols=156  Identities=17%  Similarity=0.206  Sum_probs=116.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-HH------HC--CCC
Q ss_conf             0024787799999999999875677544412786889997898888761472289999999976-64------15--588
Q gi|254780172|r  173 LWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLFMASIML-PL------FL--PDT  243 (386)
Q Consensus       173 ~~gGl~~Tl~l~~~~~~~~~~lG~llal~r~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~l-p~------~l--p~g  243 (386)
                      .|.-+..|+..++.+.+++.++|..+|..-..+....|......+-+-.-+|.++.-+.....+ |.      .+  ..+
T Consensus        17 ~~~~l~~t~~~~~~~~~~~~~~~~~lA~~l~~~~~~~~~~~~~~~~~p~~ip~~v~~~~~~~~~~~~~g~~~~~l~~~~~   96 (244)
T d2r6gf2          17 FLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFG   96 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSSTTHHHHHHHTTHHHHSCHHHHHHHHHHHTCSSSSHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCC
T ss_conf             99999999999999999999999999999984742047899999999998408899999999875235514666655302


Q ss_pred             CCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             773-------8799999999999899989999999984586678999996216899999999699899862004799999
Q gi|254780172|r  244 WDV-------DKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIG  316 (386)
Q Consensus       244 ~~~-------~~~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~  316 (386)
                      ...       ......+++......+|..-++++++++||+.++|||+..|-|+||++|+|++|+.....+...+-.++.
T Consensus        97 ~~~~~~~~~~~~~~~i~i~~v~~~~p~~~l~~~~~l~~I~~~l~EAA~idGAs~~~~f~~I~lPl~~p~i~~~~il~fi~  176 (244)
T d2r6gf2          97 VKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAF  176 (244)
T ss_dssp             CCCCTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSCTHHHHHHHHTCCCSHHHHHHTTGGGTHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHH
T ss_conf             67741012779999999999997102779999999975999998999974997657749998544689999999999999


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             996128999999
Q gi|254780172|r  317 LFKDSSLISIIN  328 (386)
Q Consensus       317 l~KdTsL~~~Ig  328 (386)
                      .+||-....+++
T Consensus       177 ~~~~f~~~~~l~  188 (244)
T d2r6gf2         177 NFNNFVLIQLLT  188 (244)
T ss_dssp             HHTCHHHHHHHC
T ss_pred             HCCHHHHHHHHC
T ss_conf             720056764425


No 5  
>d2r6gg1 f.58.1.1 (G:7-296) Maltose transport system permease protein MalG {Escherichia coli [TaxId: 562]}
Probab=99.38  E-value=2.8e-12  Score=89.88  Aligned_cols=154  Identities=16%  Similarity=0.121  Sum_probs=110.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH---HHHHCCCCCCCC
Q ss_conf             1002478779999999999987567754441-278688999789888876147228999999997---664155887738
Q gi|254780172|r  172 SLWGGLLVTLVISFFGIIISMPLGILLALGR-NSNIPVLRYACITFIELFRGVPLVTVLFMASIM---LPLFLPDTWDVD  247 (386)
Q Consensus       172 ~~~gGl~~Tl~l~~~~~~~~~~lG~llal~r-~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~---lp~~lp~g~~~~  247 (386)
                      +.|..+..|+.+++.+.+++.++|+..|.+- +++.+.-+.. ........-+|.++........   +....  .....
T Consensus        74 ~~~~~~~nSl~~a~~~~~~~~~ig~~~a~~l~r~~~~~~~~~-~~~~~~~~~~P~~v~~i~~~~~~~~~g~~~--~~~~~  150 (290)
T d2r6gg1          74 PVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATL-LKGMLIFQMFPAVLSLVALYALFDRLGEYI--PFIGL  150 (290)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTTSHHH-HHHHHHTTSSCSSSHHHHHHHHHHHHHHHS--TTSST
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCCCHHHEEEHHHCCCCCCCCC--CCCCC
T ss_conf             799998766776654555665677778888887441357899-987641311231230100220113347756--62135


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             79999999999989998999999998458667899999621689999999969989986200479999999612899999
Q gi|254780172|r  248 KLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISII  327 (386)
Q Consensus       248 ~~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~KdTsL~~~I  327 (386)
                      ....+++......-+|..-+++++++++|+.+.|||+.+|.|+||++++|++|+..+..+-...=.++..++|=....++
T Consensus       151 ~~~~~ii~~~~~~~pf~~~~~~~~l~~i~~~l~EAA~~~GAs~~~~f~~I~lPl~~p~i~~~~il~fi~~~~~f~~~~~~  230 (290)
T d2r6gg1         151 NTHGGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLL  230 (290)
T ss_dssp             TSHHHHHHHHTTTTHHHHHHHHHHHTTSCTHHHHHHHHTTCCHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCHHHHHHHCCCCEEEEEECCCHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEC
T ss_conf             74134422235503642001320541111666656865399778888998888631256667878766441101144111


Q ss_pred             H
Q ss_conf             9
Q gi|254780172|r  328 N  328 (386)
Q Consensus       328 g  328 (386)
                      +
T Consensus       231 ~  231 (290)
T d2r6gg1         231 L  231 (290)
T ss_dssp             C
T ss_pred             C
T ss_conf             3


No 6  
>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}
Probab=69.51  E-value=2.6  Score=18.00  Aligned_cols=37  Identities=14%  Similarity=0.023  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             9998999999998458667899999621689999999
Q gi|254780172|r  261 SAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       261 aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      .-+=.+.++.+++.-.--|.+||+.||+++..-.+++
T Consensus        47 ~e~E~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~kl   83 (89)
T d1etxa_          47 AEVEQPLLDMVMQYTRGNATRAALMMGINRGTLRKKL   83 (89)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999999929969999999897899999999


No 7  
>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}
Probab=62.87  E-value=3.1  Score=17.57  Aligned_cols=37  Identities=19%  Similarity=0.130  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             9998999999998458667899999621689999999
Q gi|254780172|r  261 SAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       261 aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      ..+=-+.++.+++.-.-.|.+||+.||+++....+++
T Consensus        49 ~~~E~~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Kl   85 (91)
T d1ntca_          49 PELERTLLTTALRHTQGHKQEAARLLGWGAATLTAKL   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999999959959999999798899999999


No 8  
>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}
Probab=61.18  E-value=3.9  Score=16.97  Aligned_cols=35  Identities=14%  Similarity=0.085  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             98999999998458667899999621689999999
Q gi|254780172|r  263 YIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       263 y~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      .--|.+..+++.-.-.+.+||+.||+|+..-++++
T Consensus        20 ~Er~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkm   54 (60)
T d1umqa_          20 VRWEHIQRIYEMCDRNVSETARRLNMHRRTLQRIL   54 (60)
T ss_dssp             HHHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999999966859999999898899999999


No 9  
>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}
Probab=41.68  E-value=8.1  Score=15.07  Aligned_cols=36  Identities=22%  Similarity=0.147  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             9998999999998458667899999621689999999
Q gi|254780172|r  261 SAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       261 aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      ..|=-+.++.+++.- .+..+||+.||+++...++++
T Consensus        19 ~~~Er~~I~~aL~~~-gn~~~aA~~Lgisr~tL~rKl   54 (61)
T d1g2ha_          19 GFYEAQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKL   54 (61)
T ss_dssp             SHHHHHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHC-CCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999999999987-899999999798899999999


No 10 
>d1i3ja_ d.285.1.1 (A:) DNA-binding domain of intron endonuclease I-TevI {Bacteriophage T4 [TaxId: 10665]}
Probab=19.77  E-value=20  Score=12.75  Aligned_cols=22  Identities=14%  Similarity=-0.053  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             6678999996216899999999
Q gi|254780172|r  277 KGQFEAANSLGLSYLQKMRLII  298 (386)
Q Consensus       277 ~GQ~EAA~alGls~~q~~~~Ii  298 (386)
                      ....|||++||.+...+.+++-
T Consensus        65 ~S~~EAar~lgi~~~tI~~R~k   86 (96)
T d1i3ja_          65 DCAADAARHFKISSGLVTYRVK   86 (96)
T ss_dssp             SSHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHC
T ss_conf             0699999994898378999975


Done!