Query         gi|254781113|ref|YP_003065526.1| amino acid ABC transporter (permease) [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 226
No_of_seqs    117 out of 6342
Neff          7.4 
Searched_HMMs 23785
Date          Wed Jun  1 01:03:44 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781113.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3dhw_A D-methionine transport  100.0 5.1E-33 2.1E-37  198.9   9.9  207   13-220     5-217 (217)
  2 3d31_C Sulfate/molybdate ABC t 100.0 4.1E-28 1.7E-32  171.9  14.0  205   15-223    78-295 (295)
  3 2onk_C Molybdate/tungstate ABC  99.9 6.1E-26 2.6E-30  160.0  11.8  203   15-221    68-281 (284)
  4 2r6g_F Maltose transport syste  99.9 3.1E-21 1.3E-25  134.1  14.2  201   15-216   275-511 (514)
  5 2r6g_G Maltose transport syste  99.8 1.2E-18 5.2E-23  119.8  13.0  153   17-170    81-237 (296)
  6 3dhw_A D-methionine transport   88.9    0.17 7.3E-06   25.7   2.2   47  170-216   171-217 (217)
  7 1umq_A Photosynthetic apparatu  73.1     3.5 0.00015   18.6   4.0   35  106-140    42-76  (81)
  8 1eto_A FIS, factor for inversi  72.8     3.5 0.00015   18.5   4.0   33  107-139    60-92  (98)
  9 1ntc_A Protein (nitrogen regul  72.2       3 0.00013   18.9   3.5   34  106-139    52-85  (91)
 10 3e7l_A Transcriptional regulat  63.1     6.2 0.00026   17.2   4.0   35  105-139    19-53  (63)
 11 1g2h_A Transcriptional regulat  52.6     9.5  0.0004   16.1   3.8   35  104-139    20-54  (61)
 12 1ojl_A Transcriptional regulat  45.5      12 0.00052   15.5   3.6   31  109-139   272-302 (304)
 13 2cw1_A SN4M; lambda CRO fold,   37.2      12  0.0005   15.6   1.6   16  118-133    13-28  (65)
 14 1i3j_A I-TEVI, intron-associat  28.6      24   0.001   14.0   2.4   24  119-142    84-107 (116)

No 1  
>3dhw_A D-methionine transport system permease protein METI; ABC-transporter, methionine uptake transporter, membrane protein, amino-acid transport; 3.70A {Escherichia coli K12} SCOP: f.58.1.1
Probab=100.00  E-value=5.1e-33  Score=198.85  Aligned_cols=207  Identities=19%  Similarity=0.288  Sum_probs=166.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999999999999999999999970------67637999999999998555322222211122333210
Q gi|254781113|r   13 FPQLLYAAIVVTLPIACISFVISLIIGFFIAVIRIF------FSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGI   86 (226)
Q Consensus        13 ~~~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~------~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g~   86 (226)
                      .-.++++++++|+.+++.+++++.++|+++|+....      ..+++.......++.+++++|.+++++......+....
T Consensus         5 ~~~l~l~~~~~Tl~~a~~~~~~~~~ig~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~~~   84 (217)
T 3dhw_A            5 MMWLLVRGVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIILLVWMIPFTRVIVG   84 (217)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHTTGGGGGGGGGGTTCSSSCCSSHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999986444320089999999999999999999999999999999986


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             14433333310011000001578999887528336899865174635657787522357644567787889875267999
Q gi|254781113|r   87 VFDSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVA  166 (226)
Q Consensus        87 ~~~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~  166 (226)
                      ...++..+++++++...||+.+.++++++++|++++||||++|+|+||++|||++||++|.+++++.+.++..++++++.
T Consensus        85 ~~~~~~~~ii~~~~~~~~~~~~~~~~~l~~i~~~~~eAA~~lGas~~q~f~~vilP~~~p~ii~~~~~~~~~~i~~~~i~  164 (217)
T 3dhw_A           85 TSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMG  164 (217)
T ss_dssp             CSSSHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTTTTHHHHHTCCTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             12369999999999867999999999998589899999871898989996974199789999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             997699999999999832357799999999999999999999999999986213
Q gi|254781113|r  167 STITIPEIFQTAQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESSVTQH  220 (226)
Q Consensus       167 s~ig~~el~~~a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~~~~  220 (226)
                      +.+|.+++.....+.....++. +......+++.+++.....+.++++||++||
T Consensus       165 ~~ig~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~rR  217 (217)
T 3dhw_A          165 GAVGAGGLGQIGYQYGYIGYNA-TVMNTVLVLLVILVYLIQFAGDRIVRAVTRK  217 (217)
T ss_dssp             CSTTCCHHHHHHHHHHHSSCCT-THHHHHHHHHHHHHHHHHHHCC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9998879999999999986008-9999999999999999999999999975699


No 2  
>3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: f.58.1.1
Probab=99.96  E-value=4.1e-28  Score=171.89  Aligned_cols=205  Identities=11%  Similarity=0.121  Sum_probs=154.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------
Q ss_conf             99999999999999999999999999999999706763799999999999855532222221112233321---------
Q gi|254781113|r   15 QLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIG---------   85 (226)
Q Consensus        15 ~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g---------   85 (226)
                      ..+++++++|+.+++++++++.++|+++|....+.+.+. ++.......+...+|..+..+..+......|         
T Consensus        78 ~~~~~~i~~Tl~~a~~s~~i~~ilg~~~a~~l~~~~~~~-~~~~~~l~~~p~~~p~~v~~~~~~~~~~~~g~~~~~~~~~  156 (295)
T 3d31_C           78 RSVISSIFLSLYAGFLATLLALLLGAPTGYILARFDFPG-KRLVESIIDVPVVVPHTVAGIALLTVFGSRGLIGEPLESY  156 (295)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCTT-HHHHHHHHHGGGTSCHHHHHHHHHHHHSTTSTTTGGGTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHCC
T ss_conf             899999999999999999999999999999999645435-8999999999999998889999999861246533210102


Q ss_pred             -CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -0144333333100110000015789998875283368998651746356577875223576445677878898752679
Q gi|254781113|r   86 -IVFDSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTS  164 (226)
Q Consensus        86 -~~~~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~ts  164 (226)
                       ....++.+.+++.++...||..+.++++++++|++++|||+++|+|+||++|||++|++.|.++++....++..+++..
T Consensus       157 ~~~~~~~~~iii~~~~~~~p~~~~~~~~~l~~i~~~~~eAA~~~Gas~~~~~~~IiLP~~~p~i~~~~~l~f~~~~~~f~  236 (295)
T 3d31_C          157 IQFRDALPGIVVAMLFVSMPYLANSAREGFKSVDPRLENAARSLGAPLWKAFFFVTLPLSARYLLIGSVMTWARAISEFG  236 (295)
T ss_dssp             CCCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTCCH
T ss_pred             CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             67125789999999998074432015788873152699999984999366323533998999999999999999999999


Q ss_pred             HHHHHHHHHHHHH---HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999769999999---9999832357799999999999999999999999999986213747
Q gi|254781113|r  165 VASTITIPEIFQT---AQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESSVTQHTYS  223 (226)
Q Consensus       165 l~s~ig~~el~~~---a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~~~~~~~  223 (226)
                      ....+|..+....   -+...+.++   +...+.+++.++++..+..+.+++|||+++|||+
T Consensus       237 ~~~~l~~~~~~~~~~i~~~~~~~~~---~~a~a~a~il~ii~l~i~~~~~~L~~~~~~~~r~  295 (295)
T 3d31_C          237 AVVILAYYPMVGPTLIYDRFISYGL---SASRPIAVLLILVTLSIFLVIRTLSAGWSIYDRD  295 (295)
T ss_dssp             HHHHHHCTTCCHHHHHHHHHHHSTT---TTTHHHHHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCC
T ss_conf             9998848973499999999993489---9999999999999999999999999745033579


No 3  
>2onk_C Molybdate/tungstate ABC transporter, permease protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: f.58.1.1
Probab=99.93  E-value=6.1e-26  Score=159.99  Aligned_cols=203  Identities=13%  Similarity=0.098  Sum_probs=144.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--------
Q ss_conf             999999999999999999999999999999997067637999999999998555322222211122333210--------
Q gi|254781113|r   15 QLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGI--------   86 (226)
Q Consensus        15 ~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g~--------   86 (226)
                      ..+++++++|+.++++++++++++|+++|....+++.+ .+...+....+...+|.++..+...+.....+.        
T Consensus        68 ~~~~~~~~~Sl~~a~~s~~l~~~ig~~~a~~l~~~~~~-~~~~~~~l~~~p~~iP~~v~~~~~~~~~~~~~~~~~~~~~~  146 (284)
T 2onk_C           68 PAVWKVVLTTYYAALISTLIAVIFGTPLAYILARKSFP-GKSVVEGIVDLPVVIPHTVAGIALLVVFGSSGLIGSFSPLK  146 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCS-SHHHHHHHHHHHHHSCHHHHHHHHHHHHSTTSTTTTTCSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCH
T ss_conf             79999999999999999999999999999999982644-89999999997874451445666655331225567621000


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             14433333310011000001578999887528336899865174635657787522357644567787889875267999
Q gi|254781113|r   87 VFDSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVA  166 (226)
Q Consensus        87 ~~~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~  166 (226)
                      ....+.+.+++.++...||..++.+++++++|+++.|||+++|+|+||++|||++|++.|.++++....+...+++....
T Consensus       147 ~~~~~~~iil~~~~~~~p~~~~~~~~~l~~i~~~l~eaA~~lGas~~~~~~~IilP~~~p~i~~~~il~f~~~~~~~~~~  226 (284)
T 2onk_C          147 FVDALPGIVVAMLFVSVPIYINQAKEGFASVDVRLEHVARTLGSSPLRVFFTVSLPLSVRHIVAGAIMSWARGISEFGAV  226 (284)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCEEEHEEEHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             32106999999886146502223435531588568999997598935301102499999999999999999999999999


Q ss_pred             HHHHHHHHH---HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             997699999---9999998323577999999999999999999999999999862137
Q gi|254781113|r  167 STITIPEIF---QTAQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESSVTQHT  221 (226)
Q Consensus       167 s~ig~~el~---~~a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~~~~~  221 (226)
                      ..++.....   ...+...+.++..   ....+.+.++++..+..+.+++++|-+.+|
T Consensus       227 ~~l~~~~~~~~~~i~~~~~~~~~~~---~~a~a~il~~i~l~~~~~~~~l~~r~~~~~  281 (284)
T 2onk_C          227 VVIAYYPMIAPTLIYERYLSEGLSA---AMPVAAILILLSLAVFVALRIIVGREDVSE  281 (284)
T ss_dssp             HTTCCSSCCHHHHHHHHHHHHCGGG---THHHHHHHHHHHHHHHHHHHHTTC------
T ss_pred             HHHHCCCCHHHHHHHHHHHCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9882898529999999998058999---999999999999999999999997137743


No 4  
>2r6g_F Maltose transport system permease protein MALF; ABC transporter, catalytic intermediate, E. coli maltose transporter, MBP; HET: MAL ATP; 2.80A {Escherichia coli K12} SCOP: e.70.1.1 f.58.1.1 PDB: 3fh6_F
Probab=99.87  E-value=3.1e-21  Score=134.11  Aligned_cols=201  Identities=16%  Similarity=0.173  Sum_probs=136.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH---------
Q ss_conf             9999999999999999999999999999999970676379999999999985553222222111223-332---------
Q gi|254781113|r   15 QLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGL-PHI---------   84 (226)
Q Consensus        15 ~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~-~~~---------   84 (226)
                      +.+++.+.+|+..+++++++++++|++++....+. +...+...+....+...+|.++..+.+.+.+ +..         
T Consensus       275 ~~~~~sl~~t~~~a~~s~~l~~~~gl~la~~~~~~-~~r~~~~~~~l~~lP~~iP~iv~~l~~~~lf~~~~G~i~~~l~~  353 (514)
T 2r6g_F          275 KPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWE-ALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSA  353 (514)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS-SSTTHHHHHHHTTHHHHSCHHHHHHHHHHHTCSSSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHEEHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             89999999999998788999999999999998641-23511130251269999999999999999871244235556664


Q ss_pred             --HCCC----C---CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --1014----4---333333100110000015789998875283368998651746356577875223576445677878
Q gi|254781113|r   85 --GIVF----D---SFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSE  155 (226)
Q Consensus        85 --g~~~----~---~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~  155 (226)
                        |...    +   ...+.+++..+...||+..+++++++++|++++|||+.+|+|+||++|||++|++.|.+++.....
T Consensus       354 l~g~~~~~l~~~~~~~~~vil~~~~~~~P~~~~i~~~al~sIp~~l~EAA~idGAs~~q~f~~I~lPll~p~i~~~~il~  433 (514)
T 2r6g_F          354 LFGVKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIAS  433 (514)
T ss_dssp             TSSCCCCTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSCTHHHHHHHHTCCCSHHHHHHTTGGGTHHHHHHHHHHH
T ss_pred             CCCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHEEEHHHHHHHHHHHHHHH
T ss_conf             04888503137687799999999988887877765544316985899999975988622301130364699999999999


Q ss_pred             HHHHHHHHHHHHHHHH--------------HH-HHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8987526799999769--------------99-9999999983--235779999999999999999999999999998
Q gi|254781113|r  156 FISILKSTSVASTITI--------------PE-IFQTAQRIVS--TTYQPLIIYCELAFVYLILTSFCYIIQIKIESS  216 (226)
Q Consensus       156 ~i~lik~tsl~s~ig~--------------~e-l~~~a~~i~~--~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr  216 (226)
                      ++..+++..+...+.-              .| +.....+...  .....+....+.+++.++++..+..+..+..||
T Consensus       434 f~~~~~~F~~~~lLt~Ggp~~~~~~~~~~~t~~l~~~~y~~af~~~~~~~~g~AaAiavil~liv~~l~~i~~r~~r~  511 (514)
T 2r6g_F          434 FAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIATLIFLLVGALAIVNLKATRM  511 (514)
T ss_dssp             HHHHHTCHHHHHHHCSSCSBCSSCSSCCBSSCCHHHHHHHHHTSSSSCCCHHHHHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999888999994799875555565406889999999999851545678999999999999999999999999811


No 5  
>2r6g_G Maltose transport system permease protein MALG; ABC transporter, catalytic intermediate, E. coli maltose transporter, MBP; HET: MAL ATP; 2.80A {Escherichia coli K12} SCOP: f.58.1.1 PDB: 3fh6_G
Probab=99.79  E-value=1.2e-18  Score=119.85  Aligned_cols=153  Identities=18%  Similarity=0.107  Sum_probs=108.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCC
Q ss_conf             99999999999999999999999999999970676379999999999985553222222111223332101----44333
Q gi|254781113|r   17 LYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGIV----FDSFV   92 (226)
Q Consensus        17 l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g~~----~~~~~   92 (226)
                      ++.++.||+.+++.++++++++|.+.|..-.+.+.+..+..... ....-.+|..+.....+......|..    .....
T Consensus        81 ~~~~l~nSl~~a~~~~~~~~~i~~~~a~~l~r~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~~~g~~~~~~~~~~~  159 (296)
T 2r6g_G           81 VLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKG-MLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTH  159 (296)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTTSHHHHHH-HHHTTSSCSSSHHHHHHHHHHHHHHHSTTSSTTSH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHCCCH
T ss_conf             99999999999999999999999999999983478517999999-98622476779899999999861421344302336


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             333100110000015789998875283368998651746356577875223576445677878898752679999976
Q gi|254781113|r   93 AIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVASTIT  170 (226)
Q Consensus        93 ~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~s~ig  170 (226)
                      .+++...+...|+...+++++++++|++++|||+.+|+|+||++|||++|+..|.++.+..-.++..+++-......+
T Consensus       160 ~~vi~~~~~~~pf~~~~~~~~l~~ip~~l~EAA~~dGAs~~~~f~~I~lPll~p~i~~~~~l~fi~~~~~f~~~~~~~  237 (296)
T 2r6g_G          160 GGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLL  237 (296)
T ss_dssp             HHHHHHHTTTTHHHHHHHHHHHTTSCTHHHHHHHHTTCCHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTCCHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999999999899999999973407778889875993033243899847568999999999999999768888135


No 6  
>3dhw_A D-methionine transport system permease protein METI; ABC-transporter, methionine uptake transporter, membrane protein, amino-acid transport; 3.70A {Escherichia coli K12} SCOP: f.58.1.1
Probab=88.88  E-value=0.17  Score=25.70  Aligned_cols=47  Identities=9%  Similarity=-0.094  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             69999999999983235779999999999999999999999999998
Q gi|254781113|r  170 TIPEIFQTAQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESS  216 (226)
Q Consensus       170 g~~el~~~a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr  216 (226)
                      |.++.....+....+............+++++++...+.+.+++|||
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~rR  217 (217)
T 3dhw_A          171 GLGQIGYQYGYIGYNATVMNTVLVLLVILVYLIQFAGDRIVRAVTRK  217 (217)
T ss_dssp             HHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHCC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999860089999999999999999999999999975699


No 7  
>1umq_A Photosynthetic apparatus regulatory protein; DNA-binding protein, response regulator, DNA binding domain, helix-turn-helix; NMR {Rhodobacter sphaeroides} SCOP: a.4.1.12
Probab=73.07  E-value=3.5  Score=18.56  Aligned_cols=35  Identities=11%  Similarity=0.072  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             15789998875283368998651746356577875
Q gi|254781113|r  106 ISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHII  140 (226)
Q Consensus       106 ~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~ii  140 (226)
                      =-+.++.+++.-+-.+-+||+.||.|+...++|+-
T Consensus        42 Er~~I~~aL~~~~GN~s~AAr~LGIsR~TLyrklk   76 (81)
T 1umq_A           42 RWEHIQRIYEMCDRNVSETARRLNMHRRTLQRILA   76 (81)
T ss_dssp             HHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999999727799999997989999999999


No 8  
>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ...
Probab=72.82  E-value=3.5  Score=18.52  Aligned_cols=33  Identities=12%  Similarity=0.182  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             578999887528336899865174635657787
Q gi|254781113|r  107 SEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI  139 (226)
Q Consensus       107 ~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i  139 (226)
                      -+.++.+++.-.-.+.+||+.+|.|+...++|+
T Consensus        60 ~~~I~~aL~~~~gn~~~aA~~LGisR~tL~~kl   92 (98)
T 1eto_A           60 QPLLDMVMQYTLGNQTRAALMMGINRGTLRKKL   92 (98)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999999919988999999798999999999


No 9  
>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12
Probab=72.16  E-value=3  Score=18.88  Aligned_cols=34  Identities=6%  Similarity=0.114  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             1578999887528336899865174635657787
Q gi|254781113|r  106 ISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI  139 (226)
Q Consensus       106 ~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i  139 (226)
                      =.++++.+++...-.+.+||+.+|.|+-...+|+
T Consensus        52 Er~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Kl   85 (91)
T 1ntc_A           52 ERTLLTTALRHTQGHKQEAARLLGWGAATLTAKL   85 (91)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999968959999999798999999999


No 10 
>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus}
Probab=63.09  E-value=6.2  Score=17.17  Aligned_cols=35  Identities=14%  Similarity=0.151  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             01578999887528336899865174635657787
Q gi|254781113|r  105 YISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI  139 (226)
Q Consensus       105 ~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i  139 (226)
                      +=.+.++.+++.-+-.+-+||+.+|.++...++++
T Consensus        19 ~E~~~I~~aL~~~~gn~s~aA~~Lgi~r~tL~~kl   53 (63)
T 3e7l_A           19 FEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKI   53 (63)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999999919989999999897999999999


No 11 
>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12
Probab=52.55  E-value=9.5  Score=16.15  Aligned_cols=35  Identities=6%  Similarity=0.184  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             001578999887528336899865174635657787
Q gi|254781113|r  104 AYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHI  139 (226)
Q Consensus       104 ~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i  139 (226)
                      .|=-++++.+++.- .+..+||+.+|.|+...++++
T Consensus        20 ~~Ek~~I~~aL~~~-g~~~~aA~~Lgisr~tL~rKl   54 (61)
T 1g2h_A           20 FYEAQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKL   54 (61)
T ss_dssp             HHHHHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHH
T ss_pred             HHHHHHHHHHHHHC-CCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999999996-899999999797899999999


No 12 
>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}
Probab=45.47  E-value=12  Score=15.51  Aligned_cols=31  Identities=19%  Similarity=0.362  Sum_probs=16.4

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             8999887528336899865174635657787
Q gi|254781113|r  109 IIRSSIISIPKGQWDASYAIGLTRKQTIRHI  139 (226)
Q Consensus       109 i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i  139 (226)
                      .+..+++.-...+.+||+.+|+|+...+||+
T Consensus       272 ~I~~aL~~~~gn~~~aA~~LGisR~tLyrkl  302 (304)
T 1ojl_A          272 VILAALEKTGGNKTEAARQLGITRKTLLAKL  302 (304)
T ss_dssp             HHHHHHHTTTTCHHHHHHHHTSCHHHHHHHT
T ss_pred             HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999929989999999888999999986


No 13 
>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1
Probab=37.18  E-value=12  Score=15.59  Aligned_cols=16  Identities=44%  Similarity=0.464  Sum_probs=14.3

Q ss_pred             CCCHHHHHHHHCCCHH
Q ss_conf             8336899865174635
Q gi|254781113|r  118 PKGQWDASYAIGLTRK  133 (226)
Q Consensus       118 ~~~~~EAA~alG~s~~  133 (226)
                      |+.|.-|||++|.|..
T Consensus        13 dknqeyaaralglsqk   28 (65)
T 2cw1_A           13 DKNQEYAARALGLSQK   28 (65)
T ss_dssp             TSCHHHHHHHSSSCHH
T ss_pred             HHHHHHHHHHHCCHHH
T ss_conf             0028899998411699


No 14 
>1i3j_A I-TEVI, intron-associated endonuclease 1; protein-DNA complex, extended structure, Zn-finger, minor groove helix, helix-turn-helix; 2.20A {Enterobacteria phage T4} SCOP: d.285.1.1 PDB: 1t2t_A
Probab=28.59  E-value=24  Score=13.96  Aligned_cols=24  Identities=8%  Similarity=-0.025  Sum_probs=19.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             336899865174635657787522
Q gi|254781113|r  119 KGQWDASYAIGLTRKQTIRHIILP  142 (226)
Q Consensus       119 ~~~~EAA~alG~s~~q~~~~iilP  142 (226)
                      .+..|||+.+|.+.-.+.+|+-=|
T Consensus        84 ~S~~EAAr~Lgis~~TI~~RiKs~  107 (116)
T 1i3j_A           84 DCAADAARHFKISSGLVTYRVKSD  107 (116)
T ss_dssp             SSHHHHHHHHTCCHHHHHHHHHCT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             289999999689837789987088


Done!