Query         gi|254780687|ref|YP_003065100.1| flagellar C-ring protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 318
No_of_seqs    160 out of 776
Neff          8.3 
Searched_HMMs 23785
Date          Tue May 31 17:32:10 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780687.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 2hp7_A Flagellar motor switch  100.0   1E-35 4.3E-40  251.9  22.9  179   28-212     5-183 (183)
  2 1o6a_A Putative flagelar motor  99.7 3.3E-17 1.4E-21  130.6  11.5   82  232-314    13-94  (96)
  3 1o9y_A HRCQ2; secretory protei  99.6 2.3E-15 9.5E-20  118.6  11.8   75  232-306     9-83  (84)
  4 1xkr_A Chemotaxis protein CHEC  98.8 4.5E-06 1.9E-10   57.6  21.2  179   30-213     7-202 (206)
  5 3hm4_A Chemotaxis protein CHEX  97.2   0.009 3.8E-07   36.0  11.5  145   39-201    10-155 (156)
  6 3hzh_B Chemotaxis operon prote  97.0   0.018 7.4E-07   34.1  14.5  149   40-201    18-168 (172)
  7 3h2d_A CHEC-like superfamily p  96.8   0.026 1.1E-06   33.0  13.4  145   38-201     6-153 (155)
  8 1squ_A CHEX protein; alpha-bet  95.5    0.13 5.3E-06   28.5  15.4  113   37-164     4-117 (155)
  9 2e63_A KIAA1787 protein; struc  50.7      10 0.00043   16.0   4.0   44  255-298   114-157 (170)
 10 3gt2_A Putative uncharacterize  30.0      21  0.0009   13.9   4.5   40  257-303    88-127 (142)
 11 1v6z_A Hypothetical protein TT  30.0      21  0.0009   13.9   3.3  103   43-152    20-135 (228)
 12 1saw_A Hypothetical protein FL  29.7      22 0.00091   13.9   4.3   36  253-288   177-219 (225)
 13 1nr9_A Protein YCGM; structura  24.1      27  0.0011   13.2   3.6   30  252-281   177-213 (223)
 14 2z0t_A Putative uncharacterize  23.1      29  0.0012   13.1   1.7   35  225-268     9-43  (109)
 15 3biq_A FACT complex subunit SP  23.0      29  0.0012   13.1   3.8   25  178-202   284-308 (467)
 16 3ne0_A Resuscitation promoting  22.1      30  0.0012   13.0   2.1   43  256-302   156-198 (214)
 17 1hmj_A RPB5, protein (subunit   22.1      30  0.0013   13.0   1.8   21  251-271    41-61  (78)
 18 1eik_A RNA polymerase subunit   21.3      28  0.0012   13.2   1.2   19  252-270    44-62  (77)

No 1  
>2hp7_A Flagellar motor switch protein FLIM; bacterial chemotaxis, flagellar switch complex, signaling protein; 2.00A {Thermotoga maritima}
Probab=100.00  E-value=1e-35  Score=251.93  Aligned_cols=179  Identities=15%  Similarity=0.137  Sum_probs=170.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCCEEEEEEECCCCCCEEEEEECHHHHHHH
Q ss_conf             66799999999999999999999986298079986472566799897116886399999736778339999887899999
Q gi|254780687|r   28 KKTIEKISSSLGYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLVITL  107 (318)
Q Consensus        28 ~~~~~~~~~~~~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p~~~~i~~~~pl~g~~ll~id~~l~~~l  107 (318)
                      ++...++++.++|+|+|.++..|++++|..++|++ ++++.+|+||++++|.|+++++++++||+|++++.+|++++|++
T Consensus         5 ske~l~~L~~I~e~far~~~~~l~~~lr~~~~v~~-~v~~~~~~ef~~~l~~p~~l~i~~~~pl~g~~ll~i~~~l~~~~   83 (183)
T 2hp7_A            5 SKEQLRTFQMIHENFGRALSTYLSGRLRTFVDVEI-SIDQLTYEEFIRSVMIPSFIVIFTGDVFEGSAIFEMRLDLFYTM   83 (183)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTSCCEEEE-EEEEEEHHHHHHHSCSSCEEEEEEETTCSSCEEEEECHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE-EEEEEEHHHHHHHCCCCEEEEEEEECCCCCCEEEEECHHHHHHH
T ss_conf             35466799999999999999999998688847999-46899899999658887289998604658807999886999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHHHHCHHHHCCCCCCCEEEEEEEE
Q ss_conf             98872788876666665657989999999999999999999851002732000002443110000124787189999988
Q gi|254780687|r  108 LENLLGASHETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDYLKKNTNRLSNEFVTTINMN  187 (318)
Q Consensus       108 id~~lGG~g~~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~e~vi~i~~~  187 (318)
                      ||++|||.|...   ++|+||+||.++++++++.++++|.++|+++.++++.+...++  |+++++++.|+|.+++++|+
T Consensus        84 vD~l~GG~g~~~---~~R~lT~iE~~i~~~i~~~~~~~l~~aw~~~~~~~~~~~~~e~--np~~~~i~~~~e~vv~~~f~  158 (183)
T 2hp7_A           84 LDIIMGGPGENP---PNRPPTEIETSIMRKEVTNMLTLLAQAWSDFQYFIPSIENVET--NPQFVQIVPPNEIVLLVTAS  158 (183)
T ss_dssp             HHHHHTCC-------CCSCCCHHHHHHHHHHHHHHHHHHHHHTHHHHCCCEEEEEEES--CGGGCCSSCTTSEEEEEEEE
T ss_pred             HHHHCCCCCCCC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEC--CHHHHCCCCCCCEEEEEEEE
T ss_conf             999748999988---9987868889999999999999999998533137740334233--86765638999859999999


Q ss_pred             EEECCEEEEEEEEEEHHHHHHHHHH
Q ss_conf             6667813799998504775256775
Q gi|254780687|r  188 MTIENVASSFVLIIPQETLLKTTLI  212 (318)
Q Consensus       188 v~~~~~~g~~~l~lP~~~l~~~~~~  212 (318)
                      +++|+.+|.+++|+||++++|++++
T Consensus       159 v~~g~~~g~~~i~iP~~~Lepi~~k  183 (183)
T 2hp7_A          159 VSWGEFTSFINVCWPFSLLEPLLEK  183 (183)
T ss_dssp             EEETTEEEEEEEEEEHHHHHHHHHC
T ss_pred             EEECCCCEEEEEEEHHHHHHHHCCC
T ss_conf             9989964299999638841433069


No 2  
>1o6a_A Putative flagelar motor switch protein FLIN; TM0680A, C- terminal proteolytic fragment of TM0680A, structural genomics, JCSG, PSI; 1.85A {Thermotoga maritima} SCOP: b.139.1.1 PDB: 1yab_A
Probab=99.73  E-value=3.3e-17  Score=130.63  Aligned_cols=82  Identities=20%  Similarity=0.286  Sum_probs=75.8

Q ss_pred             HHHHHHCEEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEEEEEECCCCHHHHH
Q ss_conf             99974080079999812343098994579997898257899738999999999999998788978999984258146788
Q gi|254780687|r  232 ARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRINFDQKSL  311 (318)
Q Consensus       232 ~~~l~~~~v~i~a~Lg~~~l~l~dil~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AVrI~~~i~~~~~~l  311 (318)
                      .+.++++||+++|+||+++++++|+++|++||||+|+++.+++++++|||+++|+|++|.+|+++||||++.+.++++ +
T Consensus        13 l~~l~di~v~l~~~lg~~~l~l~dl~~L~~Gdvi~l~~~~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~i~~~~~-~   91 (96)
T 1o6a_A           13 LELLLDIPLKVTVELGRTRMTLKRVLEMIHGSIIELDKLTGEPVDILVNGKLIARGEVVVIDENFGVRITEIVSPKER-L   91 (96)
T ss_dssp             HHHHTTCEEEEEEEEEEEEEEHHHHHHCCTTCEEEEEEETTCCEEEEETTEEEEEEEEEEETTEEEEEEEEECCHHHH-H
T ss_pred             HHHHCCCCEEEEEEEEEEEEEHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEECCCHHH-H
T ss_conf             466326608999999510856999846899999991798999789999999999999999999999999984194899-8


Q ss_pred             HHH
Q ss_conf             887
Q gi|254780687|r  312 KNF  314 (318)
Q Consensus       312 ~~~  314 (318)
                      +++
T Consensus        92 ~~l   94 (96)
T 1o6a_A           92 ELL   94 (96)
T ss_dssp             HHH
T ss_pred             HHH
T ss_conf             764


No 3  
>1o9y_A HRCQ2; secretory protein, HRP, type III secretion system, phytopathogenicity; 2.29A {Pseudomonas syringae} SCOP: b.139.1.1
Probab=99.64  E-value=2.3e-15  Score=118.58  Aligned_cols=75  Identities=17%  Similarity=0.170  Sum_probs=71.0

Q ss_pred             HHHHHHCEEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEEEEEECCCC
Q ss_conf             999740800799998123430989945799978982578997389999999999999987889789999842581
Q gi|254780687|r  232 ARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRINF  306 (318)
Q Consensus       232 ~~~l~~~~v~i~a~Lg~~~l~l~dil~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AVrI~~~i~~  306 (318)
                      ...+.++|++++++||+.+|+++|+++|++||||+|+...+++|++++||+++|+|++|.+|+++||||++.+..
T Consensus         9 ~~~l~~i~v~l~~~Lg~~~~~l~el~~L~~Gdvl~L~~~~~~~v~l~v~g~~i~~Gel~~~~~~~av~It~~i~~   83 (84)
T 1o9y_A            9 PPALDSLALDLTLRCGELRLTLAELRRLDAGTILEVTGISPGHATLCHGEQVVAEGELVDVEGRLGLQITRLVTR   83 (84)
T ss_dssp             --CCTTCEEEEEEEEEEEEEEHHHHHTCCTTCEEEECSSCTTEEEEEETTEEEEEEEEEEETTEEEEEEEEEC--
T ss_pred             HHHHHCCCEEEEEEEEEEEEEHHHHHCCCCCCEEECCCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEECC
T ss_conf             457717827999999310868999952899999994777999899999999999999999999999999991007


No 4  
>1xkr_A Chemotaxis protein CHEC; signal transduction, protein phosphatase, attractant; 1.75A {Thermotoga maritima} SCOP: d.252.1.1 PDB: 2f9z_A
Probab=98.82  E-value=4.5e-06  Score=57.63  Aligned_cols=179  Identities=11%  Similarity=0.042  Sum_probs=129.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCCE---EEEEEE-CCCCCCEEEEEECHHHHH
Q ss_conf             7999999999999999999999862980799864725667998971168863---999997-367783399998878999
Q gi|254780687|r   30 TIEKISSSLGYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENF---VFSQAS-LSSWSSNFFIGCSNNLVI  105 (318)
Q Consensus        30 ~~~~~~~~~~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p~---~~~i~~-~~pl~g~~ll~id~~l~~  105 (318)
                      ...++++++..--+...+++|+..++..|++++..++..+..++...++.+.   +..... ..++.|..++.++...+.
T Consensus         7 ~~~D~l~E~~NIg~G~AAtaLs~ll~~~v~l~vp~v~~~~~~~l~~~~~~~~~~~~~v~~~~~G~~~G~~ll~f~~~~a~   86 (206)
T 1xkr_A            7 RQKDLLKEIGNIGAGNAATAISYMINKKVEISVPNVEIVPISKVIFIAKDPEEIVVGVKMPVTGDIEGSVLLIMGTTVVK   86 (206)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSCEEEECCCEEEEEGGGGGGGSSCTTCEEEEEEEEEEESSCEEEEEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEHHHHHHHHCCCCCEEEEEEEEEECCCCEEEEEEECHHHHH
T ss_conf             99999999999988899999999859969998898999709999998468674299999985617646999995899999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHHHHC-------HH-HH-CCCC
Q ss_conf             999887278887666666565798999999999999999999985100273200000244311-------00-00-1247
Q gi|254780687|r  106 TLLENLLGASHETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDY-------LK-KN-TNRL  176 (318)
Q Consensus       106 ~lid~~lGG~g~~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~~~~~-------~~-~~-~~~~  176 (318)
                      .+++.|+|+.+.     ...++++.+...+..+.+.+..++-.+|+...+....+..|.....       .. .. ....
T Consensus        87 ~l~~~l~g~~~~-----~~~~~~e~~~sal~EigNIl~ga~~~~la~~l~~~i~~s~P~~~~d~~~~il~~~~~~~~~~~  161 (206)
T 1xkr_A           87 KILEILTGRAPD-----NLLNLDEFSASALREIGNIMCGTYVSALADFLGFKIDTLPPQLVIDMISAIFAEASIEELEDN  161 (206)
T ss_dssp             HHHHHHHSCCCS-----CSTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEECCCEEEEEEHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHCCCCCC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCEEEECCHHHHCCHHHHHHHCCC
T ss_conf             999985699988-----755537889999999999999999999999859966467998882460433476776542046


Q ss_pred             CCCEEEEEEEEEEE--C--CEEEEEEEEEEHHHHHHHHHHH
Q ss_conf             87189999988666--7--8137999985047752567754
Q gi|254780687|r  177 SNEFVTTINMNMTI--E--NVASSFVLIIPQETLLKTTLIS  213 (318)
Q Consensus       177 p~e~vi~i~~~v~~--~--~~~g~~~l~lP~~~l~~~~~~~  213 (318)
                      .++.++++...+.+  .  +..|.+.++.....+..+...+
T Consensus       162 ~~~~~l~i~t~~~~~~~~~~i~g~l~llp~~~s~~~L~~~L  202 (206)
T 1xkr_A          162 SEDQIVFVETLLKVEEEEEPLTSYMMMIPKPGYLVKIFERM  202 (206)
T ss_dssp             CCCEEEEEEEEEEETTSSSCEEEEEEEEECTTHHHHHHHTT
T ss_pred             CCCEEEEEEEEEEEEECCCCCEEEEEECCCHHHHHHHHHHC
T ss_conf             78659999999997620355469999914989999999983


No 5  
>3hm4_A Chemotaxis protein CHEX; YP_386777.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.30A {Desulfovibrio desulfuricans subsp} PDB: 3h4y_A*
Probab=97.15  E-value=0.009  Score=36.03  Aligned_cols=145  Identities=8%  Similarity=0.022  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCCEEEEEEE-CCCCCCEEEEEECHHHHHHHHHHHHCCCCC
Q ss_conf             9999999999999862980799864725667998971168863999997-367783399998878999999887278887
Q gi|254780687|r   39 GYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQAS-LSSWSSNFFIGCSNNLVITLLENLLGASHE  117 (318)
Q Consensus        39 ~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p~~~~i~~-~~pl~g~~ll~id~~l~~~lid~~lGG~g~  117 (318)
                      ..-|.......|++.++..+......++..       ..+.+.+.+++. ..+++|..++.++..++..++..|+|.+. 
T Consensus        10 ~npFi~at~~vl~~m~~~~v~~~~p~~~~~-------~~~~~~v~~~I~~~G~~~G~v~l~~~~~~a~~ia~~m~g~~~-   81 (156)
T 3hm4_A           10 AKPFVTATTNVLSTMAGIQPIPGQPYVKKN-------NVAKGDVSAVVGITGHKNGSISVTFTKQCAIAVVKAMLGDDI-   81 (156)
T ss_dssp             HHHHHHHHHHHHHHHHCCCCEECCCEECCS-------SCEEEEEEEEEEEESSSCEEEEEEECHHHHHHHHHHHHCSSC-
T ss_pred             EHHHHHHHHHHHHHHHCCCCEECCCEEECC-------CCCCCCEEEEEEEECCCCEEEEEEECHHHHHHHHHHHCCCCC-
T ss_conf             289899999999998499746388676256-------677888999999701552899999789999999999739996-


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHHHHCHHHHCCCCCCCEEEEEEEEEEECCEEEEE
Q ss_conf             66666656579899999999999999999998510027320000024431100001247871899999886667813799
Q gi|254780687|r  118 TIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDYLKKNTNRLSNEFVTTINMNMTIENVASSF  197 (318)
Q Consensus       118 ~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~e~vi~i~~~v~~~~~~g~~  197 (318)
                             .++++.-+..+..+.+.+.......++.. +....+..|.........-....+...+.+.|....|..  .+
T Consensus        82 -------~~~~e~~~da~~E~~N~i~G~~~~~l~~~-g~~~~ls~P~v~~g~~~~i~~~~~~~~~~i~f~~~~G~~--~i  151 (156)
T 3hm4_A           82 -------QDIIQDTKDAVGEVTNMISGQARAALSEM-GMTFQGATPSVIMGDGHTISHVTKSPVIAIPFKTNHGEF--TV  151 (156)
T ss_dssp             -------SCHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCCCEECCCEEEEEEEEEEEECCSSCCEEEEEECTTCCE--EE
T ss_pred             -------CCHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCEEEECCCEEEECCCCEEEECCCCCEEEEEEEECCCEE--EE
T ss_conf             -------40558999999999999899999999877-983750699289679824540689868999999569759--99


Q ss_pred             EEEE
Q ss_conf             9985
Q gi|254780687|r  198 VLII  201 (318)
Q Consensus       198 ~l~l  201 (318)
                      ++|+
T Consensus       152 ~i~l  155 (156)
T 3hm4_A          152 EFCL  155 (156)
T ss_dssp             EEEE
T ss_pred             EEEE
T ss_conf             9996


No 6  
>3hzh_B Chemotaxis operon protein (CHEX); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}
Probab=97.03  E-value=0.018  Score=34.11  Aligned_cols=149  Identities=6%  Similarity=-0.030  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHHHHHCCCE-EEEEECCCEEEEHHHHHHCCCCCEEEEEEE-CCCCCCEEEEEECHHHHHHHHHHHHCCCCC
Q ss_conf             999999999999862980-799864725667998971168863999997-367783399998878999999887278887
Q gi|254780687|r   40 YLYKKFLPKIFKEKMDLD-VDISYTSCQSGKFSHIIHSFKENFVFSQAS-LSSWSSNFFIGCSNNLVITLLENLLGASHE  117 (318)
Q Consensus        40 e~~~r~l~~~l~~~~~~~-v~v~~~~ve~~~~~e~i~~l~~p~~~~i~~-~~pl~g~~ll~id~~l~~~lid~~lGG~g~  117 (318)
                      .-|.......|+++++.. +...-...+...       .+.+-+.++.. ...+.|..++.++...+..+++.|+|++..
T Consensus        18 npFi~a~~~vl~~ml~~~~~~~~~~~~~~~~-------~~~~~v~~~Ig~~G~~~G~~~l~~~~~~a~~i~~~m~g~e~~   90 (172)
T 3hzh_B           18 EPFLDAASSVLRDMLLVENIEMGKPGLKSIN-------QKIKGVSVIVGLAGSVEGSIIIDMDIETALFVASKLNFEEYD   90 (172)
T ss_dssp             HHHHHHHHHHHHHHSCSSCCEECCCBSSCC-----------CCEEEEEEEEESSCEEEEEEECHHHHHHHHHHHHTSCCC
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEECCCC-------CCCCCEEEEEEEEECCCEEEEEEECHHHHHHHHHHHCCCCCC
T ss_conf             7889999999999859874345764104556-------778979999997424668999998999999999997599866


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHHHHCHHHHCCCCCCCEEEEEEEEEEECCEEEEE
Q ss_conf             66666656579899999999999999999998510027320000024431100001247871899999886667813799
Q gi|254780687|r  118 TIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDYLKKNTNRLSNEFVTTINMNMTIENVASSF  197 (318)
Q Consensus       118 ~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~e~vi~i~~~v~~~~~~g~~  197 (318)
                      ..+   ..++.+..+..+..+.+.+.......++.. +....+..|..... ....+..++...+.+.|....|+. -.+
T Consensus        91 ~~~---~e~~~e~~~dal~El~NiI~G~~~~~ls~~-g~~i~is~P~vi~g-~~~~i~~~~~~~i~ip~~~~~g~~-~~i  164 (172)
T 3hzh_B           91 DFD---DEETKEMVAATLTEVGNIIAGNFVTTLHAK-GFVFDITPPAFIYG-ENMKISNKGSEALIVPFSLPDGKI-IEV  164 (172)
T ss_dssp             CTT---STTHHHHHHHHHHHHHHHHHHHHHHTTTTS-SSCEEECCCEEECS-CSSCCCCCSSCEEEEEEECSSSCE-EEE
T ss_pred             CCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCEEEEECCEEEEC-CCEEEECCCCCEEEEEEEECCCCE-EEE
T ss_conf             677---531008899999999999999999999977-98387309979957-982775189978999999045988-999


Q ss_pred             EEEE
Q ss_conf             9985
Q gi|254780687|r  198 VLII  201 (318)
Q Consensus       198 ~l~l  201 (318)
                      ++++
T Consensus       165 ~ial  168 (172)
T 3hzh_B          165 NIAI  168 (172)
T ss_dssp             EEEE
T ss_pred             EEEE
T ss_conf             9999


No 7  
>3h2d_A CHEC-like superfamily protein; NP_719446.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Shewanella oneidensis mr-1} PDB: 3iic_A*
Probab=96.83  E-value=0.026  Score=33.01  Aligned_cols=145  Identities=8%  Similarity=0.075  Sum_probs=92.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCCEEEEEEE--CCCCCCEEEEEECHHHHHHHHHHHHCCC
Q ss_conf             99999999999999862980799864725667998971168863999997--3677833999988789999998872788
Q gi|254780687|r   38 LGYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQAS--LSSWSSNFFIGCSNNLVITLLENLLGAS  115 (318)
Q Consensus        38 ~~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p~~~~i~~--~~pl~g~~ll~id~~l~~~lid~~lGG~  115 (318)
                      +-.-|.......|+..++..+......++..       ..+...+.++..  ..++.|..++.++..++..++..|+|..
T Consensus         6 ~inpFi~a~~~vl~~m~~~~~~~~~~~~~~~-------~~~~~~i~~vi~~~~g~~~G~i~l~~~~~~a~~i~~~m~g~~   78 (155)
T 3h2d_A            6 FINPFLQSLLNVISTMASLELTPGKPQIKTD-------NLAKGDVSGLIGMVGPQTKGSLSITFEQKLVLQIMQNMLGEN   78 (155)
T ss_dssp             HHHHHHHHHHHHHHTTGGGCCEECCCEECCC-------SCCCEEEEEEEEEEETTEEEEEEEEECHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEECCCEEECC-------CCCCCCEEEEEEEECCCCCEEEEEEECHHHHHHHHHHHCCCC
T ss_conf             9889999999999998598855188553204-------556773999999863754479999978999999999862999


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHHHHCHHHHCCC-CCCCEEEEEEEEEEECCEE
Q ss_conf             876666665657989999999999999999999851002732000002443110000124-7871899999886667813
Q gi|254780687|r  116 HETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDYLKKNTNR-LSNEFVTTINMNMTIENVA  194 (318)
Q Consensus       116 g~~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~p~e~vi~i~~~v~~~~~~  194 (318)
                      .        .++++.....+..+.+.+++.....++.. +....+..|..... ....+. ..+...+.+.|..+.|.  
T Consensus        79 ~--------~~~de~~~da~~El~N~I~G~~~~~l~~~-g~~~~~s~P~vi~g-~~~~i~~~~~~~~~~i~f~t~~G~--  146 (155)
T 3h2d_A           79 P--------GKINEEVTDLVGEITNMVTGGAKNLLGQK-GYEFEMATPMVVSG-QGHTISHKANGTKIIMPFTSSYGT--  146 (155)
T ss_dssp             C--------SSCCHHHHHHHHHHHHHHHHHHHHHHHHT-TCCCEECCCEEEEE-EEEEEEECCSSCEEEEEEEETTEE--
T ss_pred             C--------CCCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCEEEECCCEEEEC-CCCEEECCCCCCEEEEEEECCCCC--
T ss_conf             8--------76468889899999999999999999857-98186049979937-983775178995899999827884--


Q ss_pred             EEEEEEE
Q ss_conf             7999985
Q gi|254780687|r  195 SSFVLII  201 (318)
Q Consensus       195 g~~~l~l  201 (318)
                      -.+++|+
T Consensus       147 ~~i~i~~  153 (155)
T 3h2d_A          147 AFIEVCF  153 (155)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEEE
T ss_conf             9999995


No 8  
>1squ_A CHEX protein; alpha-beta sandwich, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.40A {Thermotoga maritima} SCOP: d.252.1.1 PDB: 1xko_A
Probab=95.46  E-value=0.13  Score=28.50  Aligned_cols=113  Identities=5%  Similarity=0.010  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCCEEEEEEE-CCCCCCEEEEEECHHHHHHHHHHHHCCC
Q ss_conf             999999999999999862980799864725667998971168863999997-3677833999988789999998872788
Q gi|254780687|r   37 SLGYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQAS-LSSWSSNFFIGCSNNLVITLLENLLGAS  115 (318)
Q Consensus        37 ~~~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p~~~~i~~-~~pl~g~~ll~id~~l~~~lid~~lGG~  115 (318)
                      .+-.-|.......|++.++..+......++..       ..+.+.+.+++. ..++.|..++.++...+..+++.|+||.
T Consensus         4 e~in~f~~a~~~vl~~~~g~e~~~~~~~~~~~-------~~~~~~i~~~i~~~G~~~G~i~l~~~~~~a~~i~~~mlg~~   76 (155)
T 1squ_A            4 RIVNALIGSVYETIRDVLGIEPKTGKPSTVSH-------IEIPHSLVTVIGITGGIEGSLIYSFSSETALKVVSAMMGGM   76 (155)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCCCEECCCEECSS-------BCCCSSEEEEEEEEESCCEEEEEEECHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEC-------CCCCCCEEEEEEEECCCCEEEEEEECHHHHHHHHHHHHCCC
T ss_conf             99999999999999998599845078535403-------56788789999980366459999929999999999983899


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHH
Q ss_conf             8766666656579899999999999999999998510027320000024
Q gi|254780687|r  116 HETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFY  164 (318)
Q Consensus       116 g~~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~  164 (318)
                      ..       .++.+.....+..+.+.++.......+. .++...+..|.
T Consensus        77 ~~-------~~~~e~~~da~~El~N~I~G~~~~~l~~-~g~~i~~s~P~  117 (155)
T 1squ_A           77 EY-------NQLDELALSAIGELGNMTAGKLAMKLEH-LGKHVDITPPT  117 (155)
T ss_dssp             CC-------CSCCHHHHHHHHHHHHHHHHHHHHHHHT-TSCCEEECCCE
T ss_pred             CC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHH-CCCEEEECCCE
T ss_conf             87-------6423889999999999989999999986-79818725997


No 9  
>2e63_A KIAA1787 protein; structure genomics, neuralized domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=50.67  E-value=10  Score=16.00  Aligned_cols=44  Identities=16%  Similarity=0.135  Sum_probs=33.8

Q ss_pred             HHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEE
Q ss_conf             99457999789825789973899999999999999878897899
Q gi|254780687|r  255 DVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTI  298 (318)
Q Consensus       255 dil~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AV  298 (318)
                      ..-.+++||+|-+-...+..+..++||+.+..+-.+....=||+
T Consensus       114 ~~~~~~~GD~IG~~~~~~G~l~f~~NG~~~Gva~~~i~~~ly~~  157 (170)
T 2e63_A          114 DLDQLGEGDRVGVERTVAGELRLWVNGRDCGVAATGLPPRVWAV  157 (170)
T ss_dssp             CGGGCCSSCCEEEEECTTSCEEEEESSCEEEEEECCCCSCEEEE
T ss_pred             CCCCCCCCCEEEEEECCCCEEEEEECCEEEEEEECCCCCCEEEE
T ss_conf             64547768799999979976999989988368883899988999


No 10 
>3gt2_A Putative uncharacterized protein; P60 domain, antigen, unknown function; HET: EDO; 1.75A {Mycobacterium avium subsp}
Probab=29.99  E-value=21  Score=13.90  Aligned_cols=40  Identities=8%  Similarity=0.195  Sum_probs=27.6

Q ss_pred             HCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEEEEEEC
Q ss_conf             45799978982578997389999999999999987889789999842
Q gi|254780687|r  257 VTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDR  303 (318)
Q Consensus       257 l~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AVrI~~~  303 (318)
                      -++++||+|=++.....-|-+|+++-.+..+     ++.  |+|...
T Consensus        88 ~~~~pGDLvff~~~~~~HVgIyiG~g~~Iha-----g~~--v~i~~i  127 (142)
T 3gt2_A           88 QQARKGDLIFYGPEGTQSVAMYLGNNQMLEV-----GDV--VQVSPV  127 (142)
T ss_dssp             GGCCTTCEEEESGGGCSEEEEEEETTEEEEE-----SSB--EEEEEC
T ss_pred             CCCCCCEEEEECCCCCCEEEEEECCCEEEEC-----CCC--EEEEEE
T ss_conf             5799981899569999889999679969978-----995--899884


No 11 
>1v6z_A Hypothetical protein TTHA0657; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.00A {Thermus thermophilus HB8} SCOP: b.122.1.2 c.116.1.5 PDB: 2cx8_A* 2z0y_A*
Probab=29.97  E-value=21  Score=13.90  Aligned_cols=103  Identities=10%  Similarity=0.105  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCC-EEEEEEECC---CCCCEEEE---EECHHHHHHHHH--HHHC
Q ss_conf             99999999986298079986472566799897116886-399999736---77833999---988789999998--8727
Q gi|254780687|r   43 KKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKEN-FVFSQASLS---SWSSNFFI---GCSNNLVITLLE--NLLG  113 (318)
Q Consensus        43 ~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p-~~~~i~~~~---pl~g~~ll---~id~~l~~~lid--~~lG  113 (318)
                      ++.+.+.|+...+..+.+.-..-.  .+.+.+. +... .+..+....   +..-...+   .+.+.-.-.++.  .-+|
T Consensus        20 ~~Hl~~VLR~k~Gd~i~v~dg~g~--~~~~i~~-~~~~~~~~~~~~~~~~~~~~~~i~l~~~l~k~~~~e~il~k~tELG   96 (228)
T 1v6z_A           20 TRHLVEVLRARVGDRFTVFDGERE--ALAEVVD-LGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELG   96 (228)
T ss_dssp             HHHHHTTSCCCTTCEEEEECSSCE--EEEEEEE-CCSSCEEEEEEEECCCCSCSSCEEEEEECCSTTHHHHHHHHHHHTT
T ss_pred             HHHHHHCCCCCCCCEEEEEECCCC--EEEEEEE-CCCCEEEEEEEECCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHEE
T ss_conf             889996681999999999979988--8999997-1685389998640545588851589973028078999999988431


Q ss_pred             CCCCCCCCCCCC----CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             888766666656----579899999999999999999998510
Q gi|254780687|r  114 ASHETIPQLYNR----SLSTVEKKLAKRTIAQISAVLNQCIST  152 (318)
Q Consensus       114 G~g~~~~~~~~R----~lT~iE~~l~~~i~~~~~~~l~~a~~~  152 (318)
                      =. ...+-...|    .+.  +.+ ++++-..+.++...+-..
T Consensus        97 V~-~I~p~~sers~~~~~~--~~k-~~R~~~ii~~A~~Qsgr~  135 (228)
T 1v6z_A           97 AT-RIQPLVTRHSVPKEMG--EGK-LRRLRAVALEAAKQSGRV  135 (228)
T ss_dssp             CS-EEEEEECTTCSCSCCC--HHH-HHHHHHHHHHHHHHTTCS
T ss_pred             EE-EEEEECCCCCCHHHHH--HHC-CCHHHHHHHHHHHHCCCC
T ss_conf             17-9999700344212220--110-213789999999964994


No 12 
>1saw_A Hypothetical protein FLJ36880; structural genomics, fumarylacetoacetatehydrolase family, unknown function; 2.20A {Homo sapiens} SCOP: d.177.1.1
Probab=29.73  E-value=22  Score=13.87  Aligned_cols=36  Identities=14%  Similarity=0.147  Sum_probs=22.6

Q ss_pred             HHHHHCCCCCCEEECCCCC-------CCEEEEEECCEEEEEEE
Q ss_conf             9899457999789825789-------97389999999999999
Q gi|254780687|r  253 LKDVVTLKIGQVIPFLHRE-------KTCAILSANGKEIYSCE  288 (318)
Q Consensus       253 l~dil~L~vGDVI~L~~~~-------~~~v~v~v~g~~~f~g~  288 (318)
                      +.+.+.|.+||||-...+.       .|.|++.++|....+-+
T Consensus       177 lS~~~tL~pGDvI~TGTP~Gvg~l~~GD~v~~~i~glG~L~n~  219 (225)
T 1saw_A          177 VSKIITLEEGDIILTGTPKGVGPVKENDEIEAGIHGLVSMTFK  219 (225)
T ss_dssp             HHTTSCBCTTCEEECCCCSCCEEECTTCEEEEEETTTEEEEEE
T ss_pred             HHCCCEECCCCEEECCCCCCCCCCCCCCEEEEEECCEEEEEEE
T ss_conf             8679625999589828989875489998999998673559989


No 13 
>1nr9_A Protein YCGM; structural genomics, putative isomerase, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.70A {Escherichia coli} SCOP: d.177.1.1
Probab=24.09  E-value=27  Score=13.22  Aligned_cols=30  Identities=20%  Similarity=0.236  Sum_probs=20.7

Q ss_pred             CHHHHHCCCCCCEEECCCCCC-------CEEEEEECC
Q ss_conf             098994579997898257899-------738999999
Q gi|254780687|r  252 TLKDVVTLKIGQVIPFLHREK-------TCAILSANG  281 (318)
Q Consensus       252 ~l~dil~L~vGDVI~L~~~~~-------~~v~v~v~g  281 (318)
                      .+.+.+.|.+||+|-...+..       |.+++.++|
T Consensus       177 ~lS~~~tL~pGDvI~TGTP~Gvg~l~~GD~v~~~ieG  213 (223)
T 1nr9_A          177 YMSKFFTLKAGDVVLTGTPDGVGPLQSGDELTVTFDG  213 (223)
T ss_dssp             HHTTTSCBCTTCEEECCCCSCCEEECTTCEEEEEETT
T ss_pred             HHHCCCEECCCCEEECCCCCCCCCCCCCCEEEEEEEC
T ss_conf             9868872699988991998987178999999999989


No 14 
>2z0t_A Putative uncharacterized protein PH0355; alpha/beta protein, RNA binding protein, structural genomics, NPPSFA; 1.80A {Pyrococcus horikoshii} PDB: 1s04_A
Probab=23.08  E-value=29  Score=13.09  Aligned_cols=35  Identities=23%  Similarity=0.320  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHCEEEEEEEEEEEEECHHHHHCCCCCCEEECC
Q ss_conf             89999999997408007999981234309899457999789825
Q gi|254780687|r  225 EDLIDPFARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFL  268 (318)
Q Consensus       225 ~~~~~~l~~~l~~~~v~i~a~Lg~~~l~l~dil~L~vGDVI~L~  268 (318)
                      +.|-..++....    .++.+|..     +....+++||.|.+.
T Consensus         9 ~~~f~~I~~G~K----tiE~Rl~d-----~k~~~ik~GD~I~F~   43 (109)
T 2z0t_A            9 EEYIELIKAGKK----KIEGRLYD-----EKRRQIKPGDIIIFE   43 (109)
T ss_dssp             HHHHHHHHTTSC----CEEEEECC-----TTGGGCCTTCEEEEG
T ss_pred             CHHHHHHHCCCC----EEEEEECH-----HHHHHCCCCCEEEEE
T ss_conf             116899876998----89998042-----668728999999996


No 15 
>3biq_A FACT complex subunit SPT16; PITA-bread, aminopeptidase, chromatin, replication, activator, chromosomal protein, coiled coil, DNA damage; 1.73A {Saccharomyces cerevisiae} PDB: 3bip_A 3bit_A*
Probab=23.01  E-value=29  Score=13.08  Aligned_cols=25  Identities=8%  Similarity=-0.004  Sum_probs=17.0

Q ss_pred             CCEEEEEEEEEEECCEEEEEEEEEE
Q ss_conf             7189999988666781379999850
Q gi|254780687|r  178 NEFVTTINMNMTIENVASSFVLIIP  202 (318)
Q Consensus       178 ~e~vi~i~~~v~~~~~~g~~~l~lP  202 (318)
                      ..-++++.+.....+..+.+.-.+|
T Consensus       284 ~gd~vlvD~G~~y~gY~sDitRT~~  308 (467)
T 3biq_A          284 GNGCILASCGIRYNNYCSNITRTFL  308 (467)
T ss_dssp             CSEEEEEEECEEETTEECCEEEEEE
T ss_pred             CCCEEEEEECEEECCCCCCCEEEEE
T ss_conf             5998999835599956157437998


No 16 
>3ne0_A Resuscitation promoting factor interacting protei; cell WALL, peptidoglycan, hydrolase; 1.00A {Mycobacterium tuberculosis} PDB: 2xiv_A*
Probab=22.15  E-value=30  Score=12.97  Aligned_cols=43  Identities=9%  Similarity=0.171  Sum_probs=26.8

Q ss_pred             HHCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEEEEEE
Q ss_conf             94579997898257899738999999999999998788978999984
Q gi|254780687|r  256 VVTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITD  302 (318)
Q Consensus       256 il~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AVrI~~  302 (318)
                      .-++++||+|=+......-|-+|+++-.+..+    .+....|+|..
T Consensus       156 ~~~~~pGDLvff~~~~~~HVgIy~G~g~~Iha----~~~g~~V~i~~  198 (214)
T 3ne0_A          156 SSQMRRGDVIFYGPNGSQHVTIYLGNGQMLEA----PDVGLKVRVAP  198 (214)
T ss_dssp             GGGCCTTCEEEESGGGCSEEEEEEETTEEEEC----CSTTCBSEEEE
T ss_pred             CCCCCCCEEEEECCCCCCEEEEEECCCEEEEE----CCCCCCEEEEE
T ss_conf             27899971899569999879999669989997----98999789988


No 17 
>1hmj_A RPB5, protein (subunit H); RNA polymerase, archaea; NMR {Methanocaldococcus jannaschii} SCOP: d.78.1.1
Probab=22.06  E-value=30  Score=12.96  Aligned_cols=21  Identities=14%  Similarity=0.313  Sum_probs=16.2

Q ss_pred             ECHHHHHCCCCCCEEECCCCC
Q ss_conf             309899457999789825789
Q gi|254780687|r  251 TTLKDVVTLKIGQVIPFLHRE  271 (318)
Q Consensus       251 l~l~dil~L~vGDVI~L~~~~  271 (318)
                      =++...++|++||++.+-++-
T Consensus        41 DPva~~~g~~~GdiikI~R~S   61 (78)
T 1hmj_A           41 DPVIQEIGAKEGDVVRVIRKS   61 (78)
T ss_pred             CHHHHHHCCCCCCEEEEEECC
T ss_conf             997897389999489999748


No 18 
>1eik_A RNA polymerase subunit RPB5; RPBH, OCSP, NESG, protein structure initiative, structural genomics, PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.78.1.1
Probab=21.27  E-value=28  Score=13.18  Aligned_cols=19  Identities=11%  Similarity=0.420  Sum_probs=13.5

Q ss_pred             CHHHHHCCCCCCEEECCCC
Q ss_conf             0989945799978982578
Q gi|254780687|r  252 TLKDVVTLKIGQVIPFLHR  270 (318)
Q Consensus       252 ~l~dil~L~vGDVI~L~~~  270 (318)
                      ++...+++++|||+.+.++
T Consensus        44 Pva~~~g~k~GdvikI~R~   62 (77)
T 1eik_A           44 PVAKAIGAKRGDIVKIIRK   62 (77)
T ss_dssp             HHHHGGGCCTTCEEEEEEE
T ss_pred             HHHHHHCCCCCCEEEEEEC
T ss_conf             7254007878858999965


Done!