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 33803
Date          Mon May 23 04:30:14 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780172.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >3dhw_A D-methionine transport 100.0 2.8E-27 8.3E-32  182.2  15.3  208  167-379     3-217 (217)
  2 >3d31_C Sulfate/molybdate ABC   99.9 1.1E-19 3.3E-24  136.6  19.7  211  170-385    77-294 (295)
  3 >2onk_C Molybdate/tungstate AB  99.8 5.5E-17 1.6E-21  120.4  15.3  162  173-334     2-168 (181)
  4 >2r6g_F Maltose transport syst  99.6 3.5E-15   1E-19  109.6  11.7  141  170-328     6-147 (152)
  5 >2r6g_G Maltose transport syst  99.6 4.5E-15 1.3E-19  109.0  11.5  159  170-328     6-165 (172)
  6 >1umq_A Photosynthetic apparat  71.4     5.2 0.00015   18.6   3.8   37  261-297    39-75  (81)
  7 >1ntc_A Protein (nitrogen regu  67.7     6.8  0.0002   17.9   3.7   40  258-297    46-85  (91)
  8 >1ojl_A Transcriptional regula  65.9     6.5 0.00019   18.0   3.3   37  261-297    13-49  (51)
  9 >1eto_A FIS, factor for invers  65.7     7.9 0.00023   17.5   5.8   39  259-297     9-47  (53)
 10 >2ict_A Antitoxin HIGA; helix-  59.1      10 0.00031   16.8   3.6   33  265-297    10-42  (46)
 11 >2auw_A Hypothetical protein N  51.9      14  0.0004   16.0   3.6   32  266-297     4-35  (81)
 12 >3e7l_A Transcriptional regula  42.5      19 0.00057   15.2   5.6   39  259-297    15-53  (63)
 13 >1g2h_A Transcriptional regula  29.0      31 0.00092   13.9   1.8   34  263-297    21-54  (61)
 14 >2w7n_A TRFB transcriptional r  27.0      35   0.001   13.6   2.1   24  272-295    30-53  (73)
 15 >2cw1_A SN4M; lambda CRO fold,  26.9      21 0.00064   14.9   0.7   31  275-311    12-42  (65)
 16 >2r6g_F Maltose transport syst  25.9      14 0.00041   16.0  -0.4   16  106-121     8-23  (97)
 17 >3cec_A Putative antidote prot  23.0      41  0.0012   13.2   3.6   34  264-297    19-52  (56)
 18 >1u7g_A Probable ammonium tran  21.0      45  0.0013   12.9   6.5   90  106-195    90-183 (385)

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} (A:)
Probab=99.95  E-value=2.8e-27  Score=182.21  Aligned_cols=208  Identities=16%  Similarity=0.208  Sum_probs=174.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             111111002478779999999999987567754441-------2786889997898888761472289999999976641
Q gi|254780172|r  167 SIVETSLWGGLLVTLVISFFGIIISMPLGILLALGR-------NSNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLF  239 (386)
Q Consensus       167 ~~V~t~~~gGl~~Tl~l~~~~~~~~~~lG~llal~r-------~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~  239 (386)
                      +++.+..|.++..|+.+++.+.++++++|+.+|..-       +...+.+........+.++++|.+..++......+..
T Consensus         3 ~~~~~~l~~~l~~tl~~~~~~~~i~~vig~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (217)
T 3dhw_A            3 EPMMWLLVRGVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIILLVWMIPFTRVI   82 (217)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHTTGGGGGGGGGGTTCSSSCCSSHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             78999999999999999999999999999999999999873443201899999999999999999999999999864552


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             55887738799999999999899989999999984586678999996216899999999699899862004799999996
Q gi|254780172|r  240 LPDTWDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFK  319 (386)
Q Consensus       240 lp~g~~~~~~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~K  319 (386)
                         +.....+...++++++++.+|+.+++|++++++|++|.|||+++|+|+||++++|++||+.+..+++..+.++..+|
T Consensus        83 ---~~~~~~~~~~ii~~~~~~~~~i~~~~~~~l~~i~~~~~eaA~~lG~s~~q~~~~v~lP~~~p~i~~~~~~~~~~~~~  159 (217)
T 3dhw_A           83 ---VGTSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVG  159 (217)
T ss_dssp             ---TCCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTTTTHHHHHTCCTHHHHHHTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             ---04530188998988997246898999988886150277888606987421426730997699999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             128999999999999999974101003551369999999999999999999999999998
Q gi|254780172|r  320 DSSLISIINMFDLLGIVRVNFSESTWISSVTPTTGLIFIGFVFWIFCFSISLYSVFIEKT  379 (386)
Q Consensus       320 dTsL~~~Ig~~el~~~~~~~~~~~~~~~~~~~~e~y~~~a~iY~ii~~~ls~~~~~lE~r  379 (386)
                      |++.+..+|..|+.+.......+..  .........+...+++++++....+..+++|||
T Consensus       160 ~~~~~~~ig~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~i~~~~~~~l~~~l~~~~~rR  217 (217)
T 3dhw_A          160 YSAMGGAVGAGGLGQIGYQYGYIGY--NATVMNTVLVLLVILVYLIQFAGDRIVRAVTRK  217 (217)
T ss_dssp             HHHHCCSTTCCHHHHHHHHHHHSSC--CTTHHHHHHHHHHHHHHHHHHHCC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999987599999999999750--189999999999999999999999999985699


No 2  
>>3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} (C:)
Probab=99.86  E-value=1.1e-19  Score=136.58  Aligned_cols=211  Identities=14%  Similarity=0.130  Sum_probs=166.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-------CCC
Q ss_conf             1110024787799999999999875677544412786889997898888761472289999999976641-------558
Q gi|254780172|r  170 ETSLWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLF-------LPD  242 (386)
Q Consensus       170 ~t~~~gGl~~Tl~l~~~~~~~~~~lG~llal~r~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~-------lp~  242 (386)
                      +.+.|.++..|+.+++.+.++++++|+.+|..........|......+.+...+|.++.....+......       ...
T Consensus        77 ~~~~~~~l~~Tl~~~~~~~~~~~~ig~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (295)
T 3d31_C           77 NRSVISSIFLSLYAGFLATLLALLLGAPTGYILARFDFPGKRLVESIIDVPVVVPHTVAGIALLTVFGSRGLIGEPLESY  156 (295)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCTTHHHHHHHHHGGGTSCHHHHHHHHHHHHSTTSTTTGGGTTT
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHC
T ss_conf             98999999999999999999999999999999996366479999999999999999999999999997266324303321


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf             87738799999999999899989999999984586678999996216899999999699899862004799999996128
Q gi|254780172|r  243 TWDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSS  322 (386)
Q Consensus       243 g~~~~~~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~KdTs  322 (386)
                      ....+..+..+++..++...|+..+++++++++|+++.|||+++|.|+||++++|++||+.+..+.+..-.++..++|..
T Consensus       157 ~~~~~~~~~~i~~~~~~~~p~~~~~~~~~l~~i~~~l~eAA~~~Gas~~~~f~~I~lP~~~p~i~~~~~l~~~~~~~~~~  236 (295)
T 3d31_C          157 IQFRDALPGIVVAMLFVSMPYLANSAREGFKSVDPRLENAARSLGAPLWKAFFFVTLPLSARYLLIGSVMTWARAISEFG  236 (295)
T ss_dssp             CCCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTCCH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             67123999999999999999999999999975050589999876998262127746996999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999999999974101003551369999999999999999999999999998433789
Q gi|254780172|r  323 LISIINMFDLLGIVRVNFSESTWISSVTPTTGLIFIGFVFWIFCFSISLYSVFIEKTLHKGSK  385 (386)
Q Consensus       323 L~~~Ig~~el~~~~~~~~~~~~~~~~~~~~e~y~~~a~iY~ii~~~ls~~~~~lE~rl~~~~r  385 (386)
                      ..+.+|-.+.+..........+.+  +..   -...++++.+++..+.....++.||..+.+|
T Consensus       237 ~~~~l~~~~~~~~~~i~~~~~~~~--~~~---~~a~~~i~~~~~~~~~~~~~~~~~r~~~~~r  294 (295)
T 3d31_C          237 AVVILAYYPMVGPTLIYDRFISYG--LSA---SRPIAVLLILVTLSIFLVIRTLSAGWSIYDR  294 (295)
T ss_dssp             HHHHHHCTTCCHHHHHHHHHHHST--TTT---THHHHHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHCC--HHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999995897319999999999448--999---9999999999999999999999976036457


No 3  
>>2onk_C Molybdate/tungstate ABC transporter, permease protein; membrane protein; 3.10A {Archaeoglobus fulgidus} (C:69-249)
Probab=99.76  E-value=5.5e-17  Score=120.42  Aligned_cols=162  Identities=14%  Similarity=0.172  Sum_probs=138.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC-----CCCCCCC
Q ss_conf             00247877999999999998756775444127868899978988887614722899999999766415-----5887738
Q gi|254780172|r  173 LWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLFL-----PDTWDVD  247 (386)
Q Consensus       173 ~~gGl~~Tl~l~~~~~~~~~~lG~llal~r~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~l-----p~g~~~~  247 (386)
                      .|.++..|+.+++++.++++++|+.+|.....+.+..|........+-+.+|.++..+..++++....     ..+...+
T Consensus         2 ~~~~l~~Tl~~a~~~~~i~~~ig~~~a~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~~   81 (181)
T 2onk_C            2 VWKVVLTTYYAALISTLIAVIFGTPLAYILARKSFPGKSVVEGIVDLPVVIPHTVAGIALLVVFGSSGLIGSFSPLKFVD   81 (181)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCCSSHHHHHHHHHHHHHSCHHHHHHHHHHHHSTTSTTTTTCSSCCTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             99999999999999999999999999998864156315899999987412101222333100235532222212345444


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        82 ~~~~~il~~~~~~~p~~~~~~~~~l~~i~~~~~eaA~~~Gas~~q~~~~I~lP~~~p~i~~~~~l~~~~~~~~~~~~~~~  161 (181)
T 2onk_C           82 ALPGIVVAMLFVSVPIYINQAKEGFASVDVRLEHVARTLGSSPLRVFFTVSLPLSVRHIVAGAIMSWARGISEFGAVVVI  161 (181)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCHHHHTT
T ss_pred             CCCEEEEECCCCCCCCCCCCCHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCEEEEHHHHHHHHHHHHHHHHH
T ss_conf             33202210113333331222000022354245645432699843400634486627632675188887699998888743


Q ss_pred             HHHHHHH
Q ss_conf             9999999
Q gi|254780172|r  328 NMFDLLG  334 (386)
Q Consensus       328 g~~el~~  334 (386)
                      |-.+.+.
T Consensus       162 ~~~~~~~  168 (181)
T 2onk_C          162 AYYPMIA  168 (181)
T ss_dssp             CCSSCCH
T ss_pred             CCCCCHH
T ss_conf             2898509


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} (F:269-326,F:360-453)
Probab=99.64  E-value=3.5e-15  Score=109.58  Aligned_cols=141  Identities=18%  Similarity=0.234  Sum_probs=115.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf             11100247877999999999998756775444-12786889997898888761472289999999976641558877387
Q gi|254780172|r  170 ETSLWGGLLVTLVISFFGIIISMPLGILLALG-RNSNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLFLPDTWDVDK  248 (386)
Q Consensus       170 ~t~~~gGl~~Tl~l~~~~~~~~~~lG~llal~-r~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~lp~g~~~~~  248 (386)
                      +++.|.-+..|+.++..+.+++.++|+.+|.. .+.+.|--|.     .|...             ++|+..|.-.---.
T Consensus         6 ~~~~~~~~~~tl~~a~~~~~~~~~~g~~~a~l~~r~~f~gr~~-----l~~~~-------------~lp~~~p~~v~~~~   67 (152)
T 2r6g_F            6 QKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAV-----YRVLL-------------ILPYAAWFSDPTTA   67 (152)
T ss_dssp             STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSSTTHHH-----HHHHT-------------THHHHCTTTSHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH-----HHHHH-------------HHHHHCHHCCCHHH
T ss_conf             7899999999999999999999999999999987422462114-----13532-------------38888020482132


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999899989999999984586678999996216899999999699899862004799999996128999999
Q gi|254780172|r  249 LLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISIIN  328 (386)
Q Consensus       249 ~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~KdTsL~~~Ig  328 (386)
                      +...+++..+...+|....++++++++|+++.|||+++|.|++|++++|++|++.+..++.....++..+||.+....+|
T Consensus        68 ~~~li~a~~~~~~p~~~~~~~~~l~~i~~~l~eAA~~lGas~~~~~~~I~lP~~~p~il~~~~l~f~~~~~e~~~~~~l~  147 (152)
T 2r6g_F           68 RTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLLT  147 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHGGGSCTHHHHHHHHTCCCSHHHHHHTTGGGTHHHHHHHHHHHHHHHHTCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             22233345555322445544432024427899999974999401131463164789999999999999999878999994


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} (G:73-244)
Probab=99.63  E-value=4.5e-15  Score=108.97  Aligned_cols=159  Identities=14%  Similarity=0.048  Sum_probs=126.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-CCCCCCCCH
Q ss_conf             1110024787799999999999875677544412786889997898888761472289999999976641-558877387
Q gi|254780172|r  170 ETSLWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLFMASIMLPLF-LPDTWDVDK  248 (386)
Q Consensus       170 ~t~~~gGl~~Tl~l~~~~~~~~~~lG~llal~r~s~~~~l~~~~~~~ie~~Rg~Pli~~lf~~~~~lp~~-lp~g~~~~~  248 (386)
                      +.+.|..+..|+.+++.+.++++++|+.+|..-.-.....|........+-..+|-++........+... .........
T Consensus         6 ~~~~~~~l~~Sl~~a~~~~~i~~~ig~~~a~~~~~~~~~~~~~~~~~~~~~~~ip~~v~~~~~~~~~~~~~~~~~~~~~~   85 (172)
T 2r6g_G            6 PFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLN   85 (172)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTTSHHHHHHHHHTTSSCSSSHHHHHHHHHHHHHHHSTTSSTT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHEEEHHEECCCCCCCCCCCCCC
T ss_conf             52799998648999999999998631033333320441478899987623321331120110310024456512222467


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999899989999999984586678999996216899999999699899862004799999996128999999
Q gi|254780172|r  249 LLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISIIN  328 (386)
Q Consensus       249 ~~~a~i~l~l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~n~~i~l~KdTsL~~~Ig  328 (386)
                      ...++++..+....|..-..+++++++|+.+.|||+++|.|+||++++|++|++.+....+..-.++..++|....+.++
T Consensus        86 ~~~~ii~~~~~~~p~~~~~~~~~l~~i~~~~~eaA~~lGas~~~~f~~V~lP~~~p~i~~~~~l~f~~~~~~~~~~~~l~  165 (172)
T 2r6g_G           86 THGGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLL  165 (172)
T ss_dssp             SHHHHHHHHTTTTHHHHHHHHHHHTTSCTHHHHHHHHTTCCHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTCCHHHHHHC
T ss_pred             CEEEEEECCCCCEEEEEEEEEHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECCEECC
T ss_conf             50000000355115421100036413305655567754940777788888987654677788776443232300340114


No 6  
>>1umq_A Photosynthetic apparatus regulatory protein; DNA-binding protein, response regulator, DNA binding domain, helix-turn-helix; NMR {Rhodobacter sphaeroides} (A:)
Probab=71.35  E-value=5.2  Score=18.56  Aligned_cols=37  Identities=14%  Similarity=0.080  Sum_probs=32.4

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        39 ~~~E~~~I~~aL~~~~gn~~~aA~~Lgisr~TL~rkl   75 (81)
T 1umq_A           39 DRVRWEHIQRIYEMCDRNVSETARRLNMHRRTLQRIL   75 (81)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999999998309999999698999999999


No 7  
>>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} (A:)
Probab=67.74  E-value=6.8  Score=17.88  Aligned_cols=40  Identities=18%  Similarity=0.100  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             9989998999999998458667899999621689999999
Q gi|254780172|r  258 AFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       258 l~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      -....+-.+.++..++.-...+.+||+.||+|+...++++
T Consensus        46 ~~~~~~e~~~i~~~L~~~~gn~~~aA~~LGisR~TL~rkl   85 (91)
T 1ntc_A           46 EAQPELERTLLTTALRHTQGHKQEAARLLGWGAATLTAKL   85 (91)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999999999949949999999798999999999


No 8  
>>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium} (A:254-304)
Probab=65.87  E-value=6.5  Score=17.98  Aligned_cols=37  Identities=22%  Similarity=0.254  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        13 ~~~E~~~I~~aL~~~~Gn~~~aA~~LGisr~TL~rkl   49 (51)
T 1ojl_A           13 VDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL   49 (51)
T ss_dssp             HHHHHHHHHHHHHTTTTCHHHHHHHHTSCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999999929989999999888999999986


No 9  
>>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} (A:46-98)
Probab=65.70  E-value=7.9  Score=17.48  Aligned_cols=39  Identities=15%  Similarity=0.021  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             989998999999998458667899999621689999999
Q gi|254780172|r  259 FASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       259 ~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      .-..+-.+.++..++.-.-.+.+||+.||+++....+++
T Consensus         9 ~~~~~E~~~I~~aL~~~~gn~s~aA~~Lgisr~tL~rkl   47 (53)
T 1eto_A            9 VLAEVEQPLLDMVMQYTLGNQTRAALMMGINRGTLRKKL   47 (53)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999999999999929989999999798999999999


No 10 
>>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 1.63A {Escherichia coli CFT073} (A:1-46)
Probab=59.11  E-value=10  Score=16.75  Aligned_cols=33  Identities=15%  Similarity=0.260  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             999999998458667899999621689999999
Q gi|254780172|r  265 AEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       265 aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      .|++|-=++...-.|.|.|+.+|.|+...-+.|
T Consensus        10 Ge~L~E~Le~~gis~~~lA~~lgvs~~~is~ii   42 (46)
T 2ict_A           10 GDIIQESLDELNVSLREFARAXEIAPSTASRLL   42 (46)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999979999999999977789999998


No 11 
>>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein structure initiative; 1.85A {Nitrosomonas europaea} (A:90-170)
Probab=51.94  E-value=14  Score=16.04  Aligned_cols=32  Identities=19%  Similarity=0.057  Sum_probs=23.6

Q ss_pred             HHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             99999998458667899999621689999999
Q gi|254780172|r  266 EVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       266 Ei~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      |-|++=.....--|-+||++||+++.-+..|=
T Consensus         4 e~F~~W~~r~gLsl~~AAeALGisrRmi~YY~   35 (81)
T 2auw_A            4 EXFGDWXHRNNLSLTTAAEALGISRRXVSYYR   35 (81)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999859999999999499999999997


No 12 
>>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} (A:)
Probab=42.54  E-value=19  Score=15.15  Aligned_cols=39  Identities=13%  Similarity=0.146  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             989998999999998458667899999621689999999
Q gi|254780172|r  259 FASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       259 ~~aAy~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      ....+-.+.+.-+++.-.-.+.+||+.||+++.+.++++
T Consensus        15 ~~~~~Er~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~kl   53 (63)
T 3e7l_A           15 AKKEFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKI   53 (63)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999999999999919989999999895999999999


No 13 
>>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} (A:)
Probab=28.98  E-value=31  Score=13.90  Aligned_cols=34  Identities=24%  Similarity=0.163  Sum_probs=24.2

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        21 ~Er~~I~~aL~~-~gn~~~aA~~Lgisr~tL~rkl   54 (61)
T 1g2h_A           21 YEAQVLKLFYAE-YPSTRKLAQRLGVSHTAIANKL   54 (61)
T ss_dssp             HHHHHHHHHHHH-SCSHHHHHHHTTSCTHHHHHHH
T ss_pred             HHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999998403-8738999999586189999899


No 14 
>>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli} (A:1-73)
Probab=27.03  E-value=35  Score=13.62  Aligned_cols=24  Identities=29%  Similarity=0.122  Sum_probs=18.4

Q ss_pred             HHHCCHHHHHHHHHHCCHHHHHHH
Q ss_conf             984586678999996216899999
Q gi|254780172|r  272 LQSISKGQFEAANSLGLSYLQKMR  295 (386)
Q Consensus       272 l~svp~GQ~EAA~alGls~~q~~~  295 (386)
                      +.-=.++|.|.|.++|+|+-....
T Consensus        30 VLV~G~~~~evA~~~Glsrq~V~~   53 (73)
T 2w7n_A           30 VLVDGKPQATFATSLGLTRGAVSQ   53 (73)
T ss_dssp             HHTTCCCHHHHHHHHTCCHHHHHH
T ss_pred             HHHCCCHHHHHHHHHCCHHHHHHH
T ss_conf             996882099999996730989999


No 15 
>>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} (A:)
Probab=26.92  E-value=21  Score=14.86  Aligned_cols=31  Identities=42%  Similarity=0.425  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             5866789999962168999999996998998620047
Q gi|254780172|r  275 ISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIV  311 (386)
Q Consensus       275 vp~GQ~EAA~alGls~~q~~~~IilPQAlr~~iP~l~  311 (386)
                      -+|.|--||+++|+|.--      +-..++.-+|-.+
T Consensus        12 edknqeyaaralglsqkl------ieevlkrglpvyv   42 (65)
T 2cw1_A           12 EDKNQEYAARALGLSQKL------IEEVLKRGLPVYV   42 (65)
T ss_dssp             TTSCHHHHHHHSSSCHHH------HHHHHHTTCCCBC
T ss_pred             HHHHHHHHHHHHCCHHHH------HHHHHHCCCCEEE
T ss_conf             600288999984116999------9999975995699


No 16 
>>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} (F:113-209)
Probab=25.93  E-value=14  Score=16.01  Aligned_cols=16  Identities=38%  Similarity=0.958  Sum_probs=12.7

Q ss_pred             HHEEEECHHHCCCHHH
Q ss_conf             6225525111430568
Q gi|254780172|r  106 FIFGNYPMAQRWRPIL  121 (386)
Q Consensus       106 ~lyG~YP~~e~WRv~l  121 (386)
                      +-|+.||.+..||..+
T Consensus         8 y~F~Ly~~~~~~rL~L   23 (97)
T 2r6g_F            8 YNFGLYPAGDEWQLAL   23 (97)
T ss_dssp             CCEEEEEETTEEEEEE
T ss_pred             EEEEEEECCCCEEEEE
T ss_conf             0158875288348999


No 17 
>>3cec_A Putative antidote protein of plasmid maintenance system; ZP_00107635.1, structural genomics, joint center for structural genomics; HET: MSE; 1.60A {Nostoc punctiforme pcc 73102} (A:1-56)
Probab=23.01  E-value=41  Score=13.16  Aligned_cols=34  Identities=24%  Similarity=0.219  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             8999999998458667899999621689999999
Q gi|254780172|r  264 IAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLI  297 (386)
Q Consensus       264 ~aEi~Rggl~svp~GQ~EAA~alGls~~q~~~~I  297 (386)
                      -+|+++-=++...-.|.|-|+++|.++.+.-..|
T Consensus        19 PGeiL~e~Le~~gis~~~lA~~lgvs~~~is~Ii   52 (56)
T 3cec_A           19 PGEVIADILDDLDINTANFAEILGVSNQTIQEVI   52 (56)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             3399999999879999999999782789999998


No 18 
>>1u7g_A Probable ammonium transporter; right handed helical bundle, transmembrane helices, ammonia channnel, membrane protein, RH protein; HET: MSE BOG; 1.40A {Escherichia coli} (A:)
Probab=21.04  E-value=45  Score=12.91  Aligned_cols=90  Identities=17%  Similarity=0.060  Sum_probs=46.6

Q ss_pred             HHEEEECHHHCCCHHHHHHHHHHHHHH-HHHCCHHHHHHHHH---HHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             622552511143056899999999999-74000111233346---89999988988513333574111111002478779
Q gi|254780172|r  106 FIFGNYPMAQRWRPILVFLTGSILLTP-MLIPSFPRKFLNSI---LLFGLFPIFSFFVLYGGLGLSIVETSLWGGLLVTL  181 (386)
Q Consensus       106 ~lyG~YP~~e~WRv~la~ill~vll~~-~l~~~~~~k~~~~l---~~~~~~pil~~~Ll~gg~gl~~V~t~~~gGl~~Tl  181 (386)
                      ..-|.+|....|--...|.+..+.+.. ...+|...+.+...   +....||..+.+...+|.....--.|.=||..+-+
T Consensus        90 ~~~~~~~~~~~~~f~~~faa~t~~I~~Gav~eR~~~~~~~i~~~l~~~~~y~~~a~wvw~~g~l~~lG~~DfaGg~vVH~  169 (385)
T 1u7g_A           90 AVXGSIYQYIHVAFQGSFACITVGLIVGALAERIRFPAVLIFVVVWLTLSYIPIAHXVWGGGLLASHGALDFAGGTVVHI  169 (385)
T ss_dssp             CEETTEEHHHHHHHHHHHHHHHHHHHHHHHGGGBCHHHHHHHHHHHHHHTHHHHHHHHHSSCHHHHHTCCCSSCTTTTHH
T ss_pred             CCCCCCHHHHHHHHHHHHHEEECCCCCCCCCCCCEEEEEEEHHHHHCCCCCCCEEEEECCCCCCCCCCCEEECCCEEEEE
T ss_conf             23333114677565320000211311132125641467663455650222471579961788534578610056326651


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999998756
Q gi|254780172|r  182 VISFFGIIISMPLG  195 (386)
Q Consensus       182 ~l~~~~~~~~~~lG  195 (386)
                      .-+..++..+..+|
T Consensus       170 ~aG~~gL~~a~~Lg  183 (385)
T 1u7g_A          170 NAAIAGLVGAYLIG  183 (385)
T ss_dssp             HHHHHHHHHHHHSC
T ss_pred             CCHHHHHHHHHHCC
T ss_conf             42398998887527


Done!