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 33803
Date          Wed Jun  1 22:11:52 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781113.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 1.3E-31 3.7E-36  192.0  10.0  207   13-220     5-217 (217)
  2 >3d31_C Sulfate/molybdate ABC   99.9 3.2E-27 9.5E-32  167.8  13.4  205   15-223    78-295 (295)
  3 >2onk_C Molybdate/tungstate AB  99.9 1.2E-22 3.5E-27  142.8  10.5  156   17-173     2-165 (181)
  4 >2r6g_G Maltose transport syst  99.9 7.3E-21 2.2E-25  132.9  11.5  153   17-170     9-165 (172)
  5 >2r6g_F Maltose transport syst  99.8 3.4E-20   1E-24  129.2  12.4  141   16-171     8-148 (152)
  6 >3dhw_A D-methionine transport  93.4    0.15 4.5E-06   26.8   5.0   84  132-216   134-217 (217)
  7 >1eto_A FIS, factor for invers  75.2       4 0.00012   19.0   4.0   34  106-139    14-47  (53)
  8 >1ojl_A Transcriptional regula  71.9     4.7 0.00014   18.7   3.6   33  107-139    17-49  (51)
  9 >1umq_A Photosynthetic apparat  70.9     5.9 0.00017   18.1   4.0   36  104-139    40-75  (81)
 10 >3e7l_A Transcriptional regula  68.3     6.9  0.0002   17.7   4.0   37  104-140    18-54  (63)
 11 >1ntc_A Protein (nitrogen regu  67.7     6.1 0.00018   18.0   3.5   35  105-139    51-85  (91)
 12 >2ict_A Antitoxin HIGA; helix-  59.3      10  0.0003   16.9   3.3   31  106-136     9-39  (46)
 13 >2j8s_A ACRB, acriflavine resi  41.2      21 0.00061   15.1   7.5   26    3-28      9-34  (251)
 14 >2cw1_A SN4M; lambda CRO fold,  37.2      17  0.0005   15.6   1.6   16  118-133    13-28  (65)
 15 >2auw_A Hypothetical protein N  30.5      31 0.00093   14.1   3.8   32  108-139     4-35  (81)
 16 >3cec_A Putative antidote prot  29.0      33 0.00098   14.0   3.3   34  103-136    16-49  (56)
 17 >1g2h_A Transcriptional regula  24.1      41  0.0012   13.5   3.8   31  108-139    24-54  (61)

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=99.97  E-value=1.3e-31  Score=192.03  Aligned_cols=207  Identities=19%  Similarity=0.286  Sum_probs=173.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999999999999999999999706------7637999999999998555322222211122333210
Q gi|254781113|r   13 FPQLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFF------SDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGI   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~~~~~~~~i~~vig~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (217)
T 3dhw_A            5 MMWLLVRGVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIILLVWMIPFTRVIVG   84 (217)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHTTGGGGGGGGGGTTCSSSCCSSHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999999999999999999999999987344320189999999999999999999999999986455204


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~~~~~~~~~i~~~~~~~l~~i~~~~~eaA~~lG~s~~q~~~~v~lP~~~p~i~~~~~~~~~~~~~~~~~~  164 (217)
T 3dhw_A           85 TSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMG  164 (217)
T ss_dssp             CSSSHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTTTTHHHHHTCCTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             53018899898899724689899998888615027788860698742142673099769999999999999999999999


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~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~~l~~~l~~~~~rR  217 (217)
T 3dhw_A          165 GAVGAGGLGQIGYQYGYIGYNATVMN-TVLVLLVILVYLIQFAGDRIVRAVTRK  217 (217)
T ss_dssp             CSTTCCHHHHHHHHHHHSSCCTTHHH-HHHHHHHHHHHHHHHHCC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99987599999999999750189999-999999999999999999999985699


No 2  
>>3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} (C:)
Probab=99.95  E-value=3.2e-27  Score=167.85  Aligned_cols=205  Identities=10%  Similarity=0.107  Sum_probs=156.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------H
Q ss_conf             999999999999999999999999999999997067637999999999998555322222211122333----------2
Q gi|254781113|r   15 QLLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPH----------I   84 (226)
Q Consensus        15 ~~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~----------~   84 (226)
                      ..+++++++|+.++++++++++++|+++|+...+.+.+ .+............+|..+.....+.....          .
T Consensus        78 ~~~~~~l~~Tl~~~~~~~~~~~~ig~~~a~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (295)
T 3d31_C           78 RSVISSIFLSLYAGFLATLLALLLGAPTGYILARFDFP-GKRLVESIIDVPVVVPHTVAGIALLTVFGSRGLIGEPLESY  156 (295)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCT-THHHHHHHHHGGGTSCHHHHHHHHHHHHSTTSTTTGGGTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHC
T ss_conf             89999999999999999999999999999999963664-79999999999999999999999999997266324303321


Q ss_pred             HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10144333333100110000015789998875283368998651746356577875223576445677878898752679
Q gi|254781113|r   85 GIVFDSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTS  164 (226)
Q Consensus        85 g~~~~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~ts  164 (226)
                      .....+.+..+++..+...||+..+++++++++|++++|||+++|+|+||++|||++|++.|.++.+....++..+++..
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             HHHHHHHHHHHHHHH---HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999976999999999---99832357799999999999999999999999999986213747
Q gi|254781113|r  165 VASTITIPEIFQTAQ---RIVSTTYQPLIIYCELAFVYLILTSFCYIIQIKIESSVTQHTYS  223 (226)
Q Consensus       165 l~s~ig~~el~~~a~---~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~~lerr~~~~~~~  223 (226)
                      ....+|.++.+....   ...+.++   ....+.++++++++..+..+..++.||.++|||+
T Consensus       237 ~~~~l~~~~~~~~~~i~~~~~~~~~---~~~~a~~~i~~~~~~~~~~~~~~~~~r~~~~~r~  295 (295)
T 3d31_C          237 AVVILAYYPMVGPTLIYDRFISYGL---SASRPIAVLLILVTLSIFLVIRTLSAGWSIYDRD  295 (295)
T ss_dssp             HHHHHHCTTCCHHHHHHHHHHHSTT---TTTHHHHHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999958973199999999994489---9999999999999999999999999760364579


No 3  
>>2onk_C Molybdate/tungstate ABC transporter, permease protein; membrane protein; 3.10A {Archaeoglobus fulgidus} (C:69-249)
Probab=99.89  E-value=1.2e-22  Score=142.76  Aligned_cols=156  Identities=13%  Similarity=0.088  Sum_probs=130.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------CCC
Q ss_conf             999999999999999999999999999999706763799999999999855532222221112233321--------014
Q gi|254781113|r   17 LYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIG--------IVF   88 (226)
Q Consensus        17 l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g--------~~~   88 (226)
                      +++++++|+.+++++++++.++|+++|.... ..++..+...+........+|..+..+..++.....+        ...
T Consensus         2 ~~~~l~~Tl~~a~~~~~i~~~ig~~~a~~~~-~~~~~~~~~~~~~~~~~~~~p~~v~~~~~~~~~~~~~~~~~~~~~~~~   80 (181)
T 2onk_C            2 VWKVVLTTYYAALISTLIAVIFGTPLAYILA-RKSFPGKSVVEGIVDLPVVIPHTVAGIALLVVFGSSGLIGSFSPLKFV   80 (181)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SCCCSSHHHHHHHHHHHHHSCHHHHHHHHHHHHSTTSTTTTTCSSCCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             9999999999999999999999999999886-415631589999998741210122233310023553222221234544


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             43333331001100000157899988752833689986517463565778752235764456778788987526799999
Q gi|254781113|r   89 DSFVAIIISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVAST  168 (226)
Q Consensus        89 ~~~~~~ii~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~s~  168 (226)
                      ..+...+++..+...||...+++++++++|+++.|||+++|+|+||++|||++|++.|.+..+....++..+++.+....
T Consensus        81 ~~~~~~il~~~~~~~p~~~~~~~~~l~~i~~~~~eaA~~~Gas~~q~~~~I~lP~~~p~i~~~~~l~~~~~~~~~~~~~~  160 (181)
T 2onk_C           81 DALPGIVVAMLFVSVPIYINQAKEGFASVDVRLEHVARTLGSSPLRVFFTVSLPLSVRHIVAGAIMSWARGISEFGAVVV  160 (181)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHTTCCHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCHHHHT
T ss_pred             CCCCEEEEECCCCCCCCCCCCCHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCEEEEHHHHHHHHHHHHHHHH
T ss_conf             43320221011333333122200002235424564543269984340063448662763267518888769999888874


Q ss_pred             HHHHH
Q ss_conf             76999
Q gi|254781113|r  169 ITIPE  173 (226)
Q Consensus       169 ig~~e  173 (226)
                      +|.++
T Consensus       161 ~~~~~  165 (181)
T 2onk_C          161 IAYYP  165 (181)
T ss_dssp             TCCSS
T ss_pred             HCCCC
T ss_conf             32898


No 4  
>>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=99.85  E-value=7.3e-21  Score=132.92  Aligned_cols=153  Identities=18%  Similarity=0.109  Sum_probs=123.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCC
Q ss_conf             999999999999999999999999999999706763799999999999855532222221112233321----0144333
Q gi|254781113|r   17 LYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIG----IVFDSFV   92 (226)
Q Consensus        17 l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g----~~~~~~~   92 (226)
                      +++++++|+.++++++++++++|++.|..-.+.+.+. +............+|..+.....+..+...+    .......
T Consensus         9 ~~~~l~~Sl~~a~~~~~i~~~ig~~~a~~~~~~~~~~-~~~~~~~~~~~~~ip~~v~~~~~~~~~~~~~~~~~~~~~~~~   87 (172)
T 2r6g_G            9 VLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPG-KATLLKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTH   87 (172)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTT-SHHHHHHHHHTTSSCSSSHHHHHHHHHHHHHHHSTTSSTTSH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH-HHHHHHHHHCCCCCCCHHHEEEHHEECCCCCCCCCCCCCCCE
T ss_conf             9999864899999999999863103333332044147-889998762332133112011031002445651222246750


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        88 ~~ii~~~~~~~p~~~~~~~~~l~~i~~~~~eaA~~lGas~~~~f~~V~lP~~~p~i~~~~~l~f~~~~~~~~~~~~l~  165 (172)
T 2r6g_G           88 GGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLL  165 (172)
T ss_dssp             HHHHHHHTTTTHHHHHHHHHHHTTSCTHHHHHHHHTTCCHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTCCHHHHHHC
T ss_pred             EEEEECCCCCEEEEEEEEEHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECCEECC
T ss_conf             000000355115421100036413305655567754940777788888987654677788776443232300340114


No 5  
>>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=99.84  E-value=3.4e-20  Score=129.23  Aligned_cols=141  Identities=16%  Similarity=0.127  Sum_probs=116.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             99999999999999999999999999999997067637999999999998555322222211122333210144333333
Q gi|254781113|r   16 LLYAAIVVTLPIACISFVISLIIGFFIAVIRIFFSDTIISLIMHFYVWIFRGTPLLVQLFVIFYGLPHIGIVFDSFVAII   95 (226)
Q Consensus        16 ~l~~~l~~Tl~~~~~~~~i~~~lg~~la~~~~~~~~~~~~~~~~~~i~~~r~iP~lv~l~~~~f~~~~~g~~~~~~~~~i   95 (226)
                      .+++.+++|+.+++.+++++.++|+++|+...+.+.+. |...+...    ..|..+......++.          ...+
T Consensus         8 ~~~~~~~~tl~~a~~~~~~~~~~g~~~a~l~~r~~f~g-r~~l~~~~----~lp~~~p~~v~~~~~----------~~li   72 (152)
T 2r6g_F            8 PFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRG-KAVYRVLL----ILPYAAWFSDPTTAR----------TMLI   72 (152)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSSTT-HHHHHHHT----THHHHCTTTSHHHHH----------HHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-HHHHHHHH----HHHHHCHHCCCHHHH----------HHHH
T ss_conf             99999999999999999999999999999987422462-11413532----388880204821322----------2233


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1001100000157899988752833689986517463565778752235764456778788987526799999769
Q gi|254781113|r   96 ISLTLNFSAYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHIILPQTITTSAVPLSSEFISILKSTSVASTITI  171 (226)
Q Consensus        96 i~l~l~~~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~s~ig~  171 (226)
                      ++..+...|+..+.++++++++|++++||||++|+|+||++|||++|++.|.++++....++..+|+.+....+|.
T Consensus        73 ~a~~~~~~p~~~~~~~~~l~~i~~~l~eAA~~lGas~~~~~~~I~lP~~~p~il~~~~l~f~~~~~e~~~~~~l~g  148 (152)
T 2r6g_F           73 IVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLLTN  148 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGSCTHHHHHHHHTCCCSHHHHHHTTGGGTHHHHHHHHHHHHHHHHTCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             3455553224455444320244278999999749994011314631647899999999999999998789999947


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} (A:)
Probab=93.42  E-value=0.15  Score=26.82  Aligned_cols=84  Identities=8%  Similarity=-0.040  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             35657787522357644567787889875267999997699999999999832357799999999999999999999999
Q gi|254781113|r  132 RKQTIRHIILPQTITTSAVPLSSEFISILKSTSVASTITIPEIFQTAQRIVSTTYQPLIIYCELAFVYLILTSFCYIIQI  211 (226)
Q Consensus       132 ~~q~~~~iilPqal~~ilp~l~~~~i~lik~tsl~s~ig~~el~~~a~~i~~~~~~~~~~~~~~~~i~l~i~~~~~~l~~  211 (226)
                      .+.....-..|..++...-.+...+-... .....+.-+.+...........+............+++++++...+.+.+
T Consensus       134 ~~~v~lP~~~p~i~~~~~~~~~~~~~~~~-~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~l~~  212 (217)
T 3dhw_A          134 VRKVLLPEALPGLVNAATITLITLVGYSA-MGGAVGAGGLGQIGYQYGYIGYNATVMNTVLVLLVILVYLIQFAGDRIVR  212 (217)
T ss_dssp             HHHTTHHHHHHHHHHHHHHHHHHHHHHHH-HCCSTTCCHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHCC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             26730997699999999999999999999-99999875999999999997501899999999999999999999999999


Q ss_pred             HHHHH
Q ss_conf             99998
Q gi|254781113|r  212 KIESS  216 (226)
Q Consensus       212 ~lerr  216 (226)
                      ++|||
T Consensus       213 ~~~rR  217 (217)
T 3dhw_A          213 AVTRK  217 (217)
T ss_dssp             -----
T ss_pred             HHCCC
T ss_conf             85699


No 7  
>>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} (A:46-98)
Probab=75.24  E-value=4  Score=19.04  Aligned_cols=34  Identities=12%  Similarity=0.150  Sum_probs=28.8

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        14 E~~~I~~aL~~~~gn~s~aA~~Lgisr~tL~rkl   47 (53)
T 1eto_A           14 EQPLLDMVMQYTLGNQTRAALMMGINRGTLRKKL   47 (53)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999999929989999999798999999999


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=71.94  E-value=4.7  Score=18.69  Aligned_cols=33  Identities=21%  Similarity=0.377  Sum_probs=28.3

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        17 ~~~I~~aL~~~~Gn~~~aA~~LGisr~TL~rkl   49 (51)
T 1ojl_A           17 KEVILAALEKTGGNKTEAARQLGITRKTLLAKL   49 (51)
T ss_dssp             HHHHHHHHHTTTTCHHHHHHHHTSCHHHHHHHT
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999999929989999999888999999986


No 9  
>>1umq_A Photosynthetic apparatus regulatory protein; DNA-binding protein, response regulator, DNA binding domain, helix-turn-helix; NMR {Rhodobacter sphaeroides} (A:)
Probab=70.91  E-value=5.9  Score=18.12  Aligned_cols=36  Identities=11%  Similarity=0.062  Sum_probs=30.6

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        40 ~~E~~~I~~aL~~~~gn~~~aA~~Lgisr~TL~rkl   75 (81)
T 1umq_A           40 RVRWEHIQRIYEMCDRNVSETARRLNMHRRTLQRIL   75 (81)
T ss_dssp             HHHHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             999999999999998309999999698999999999


No 10 
>>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} (A:)
Probab=68.34  E-value=6.9  Score=17.75  Aligned_cols=37  Identities=14%  Similarity=0.124  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             0015789998875283368998651746356577875
Q gi|254781113|r  104 AYISEIIRSSIISIPKGQWDASYAIGLTRKQTIRHII  140 (226)
Q Consensus       104 ~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~ii  140 (226)
                      .+=.+.+..+++.-.-.+-+||+.+|.|+.+.++++-
T Consensus        18 ~~Er~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klk   54 (63)
T 3e7l_A           18 EFEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIK   54 (63)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999999999199899999998959999999999


No 11 
>>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} (A:)
Probab=67.66  E-value=6.1  Score=18.03  Aligned_cols=35  Identities=6%  Similarity=0.111  Sum_probs=29.3

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        51 ~e~~~i~~~L~~~~gn~~~aA~~LGisR~TL~rkl   85 (91)
T 1ntc_A           51 LERTLLTTALRHTQGHKQEAARLLGWGAATLTAKL   85 (91)
T ss_dssp             HHHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999999949949999999798999999999


No 12 
>>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=59.28  E-value=10  Score=16.86  Aligned_cols=31  Identities=13%  Similarity=0.128  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             1578999887528336899865174635657
Q gi|254781113|r  106 ISEIIRSSIISIPKGQWDASYAIGLTRKQTI  136 (226)
Q Consensus       106 ~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~  136 (226)
                      -.|+++.-++...-+|.|.|+.+|.|+...-
T Consensus         9 PGe~L~E~Le~~gis~~~lA~~lgvs~~~is   39 (46)
T 2ict_A            9 PGDIIQESLDELNVSLREFARAXEIAPSTAS   39 (46)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             7899999999979999999999977789999


No 13 
>>2j8s_A ACRB, acriflavine resistance protein B; membrane protein/complex, designed ankyrin repeat protein, multidrug resistance protein; HET: LMT LMU; 2.54A {Escherichia coli} PDB: 2dhh_A 1iwg_A 2dr6_A* 2drd_A* 2hqf_A 2hqg_A 2hqd_A 2hqc_A 2i6w_A 1oy6_A* 1oy9_A* 1oyd_A* 1oy8_A* 1oye_A 2rdd_A* 2w1b_A* 3d9b_A 1t9x_A* 1t9t_A* 1t9v_A* ... (A:505-567,A:868-1055)
Probab=41.19  E-value=21  Score=15.13  Aligned_cols=26  Identities=15%  Similarity=0.344  Sum_probs=13.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             30899999999999999999999999
Q gi|254781113|r    3 YEWFNLIIDSFPQLLYAAIVVTLPIA   28 (226)
Q Consensus         3 ~~w~~~~~~~~~~~l~~~l~~Tl~~~   28 (226)
                      |.||+-..|...+..-.++...+.-.
T Consensus         9 ~~~f~~~f~~~~~~y~~~~~~~~~~~   34 (251)
T 2j8s_A            9 FGWFNRMFEKSTHHYTDSVGGILRST   34 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSSS
T ss_pred             HHHHHHCCHHHHHHHHHHHHHCCHHH
T ss_conf             66631000344333466764210011


No 14 
>>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} (A:)
Probab=37.18  E-value=17  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 15 
>>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein structure initiative; 1.85A {Nitrosomonas europaea} (A:90-170)
Probab=30.46  E-value=31  Score=14.14  Aligned_cols=32  Identities=16%  Similarity=0.044  Sum_probs=23.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             78999887528336899865174635657787
Q gi|254781113|r  108 EIIRSSIISIPKGQWDASYAIGLTRKQTIRHI  139 (226)
Q Consensus       108 ~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i  139 (226)
                      +.+++=.+...-+|-+||.++|.|+.-+-.+-
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 16 
>>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=29.01  E-value=33  Score=14.00  Aligned_cols=34  Identities=9%  Similarity=0.098  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHH
Q ss_conf             0001578999887528336899865174635657
Q gi|254781113|r  103 SAYISEIIRSSIISIPKGQWDASYAIGLTRKQTI  136 (226)
Q Consensus       103 ~~~~~~i~r~~l~~v~~~~~EAA~alG~s~~q~~  136 (226)
                      .+.-.|+++.-++...-+|.|-|+.+|.|+.++-
T Consensus        16 p~HPGeiL~e~Le~~gis~~~lA~~lgvs~~~is   49 (56)
T 3cec_A           16 PIHPGEVIADILDDLDINTANFAEILGVSNQTIQ   49 (56)
T ss_dssp             CCCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHH
T ss_pred             CCCCCHHHHHHHHHCCCCHHHHHHHHCCCHHHHH
T ss_conf             9883399999999879999999999782789999


No 17 
>>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} (A:)
Probab=24.05  E-value=41  Score=13.48  Aligned_cols=31  Identities=3%  Similarity=0.140  Sum_probs=22.8

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             78999887528336899865174635657787
Q gi|254781113|r  108 EIIRSSIISIPKGQWDASYAIGLTRKQTIRHI  139 (226)
Q Consensus       108 ~i~r~~l~~v~~~~~EAA~alG~s~~q~~~~i  139 (226)
                      +.+..+++. ..+..+||+.+|.++...++++
T Consensus        24 ~~I~~aL~~-~gn~~~aA~~Lgisr~tL~rkl   54 (61)
T 1g2h_A           24 QVLKLFYAE-YPSTRKLAQRLGVSHTAIANKL   54 (61)
T ss_dssp             HHHHHHHHH-SCSHHHHHHHTTSCTHHHHHHH
T ss_pred             HHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999998403-8738999999586189999899


Done!