Query         gi|254780614|ref|YP_003065027.1| F0F1 ATP synthase subunit epsilon [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 135
No_of_seqs    108 out of 1581
Neff          7.1 
Searched_HMMs 33803
Date          Wed Jun  1 15:51:01 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780614.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 >1aqt_A ATP synthase; hydrolas 100.0 9.2E-31 2.7E-35  212.4  18.2  121    4-124     1-121 (138)
  2 >2e5y_A ATP synthase epsilon c 100.0 3.2E-30 9.5E-35  209.0  14.8  117    4-121     1-117 (133)
  3 >2hld_H ATP synthase delta cha 100.0   4E-30 1.2E-34  208.4   9.7  115    2-116     5-120 (138)
  4 >2qe7_H ATP synthase subunit e 100.0 2.9E-30 8.5E-35  209.3   1.5  110    4-114     1-110 (135)
  5 >2rq6_A ATP synthase epsilon c  99.9 1.4E-23   4E-28  167.6  10.0   85    6-91      2-86  (86)
  6 >2w6j_H F1-ATPase delta subuni  99.9 6.1E-25 1.8E-29  176.0  -0.7   89    2-90     33-123 (123)
  7 >2ck3_H ATP synthase delta cha  99.9   3E-24 8.8E-29  171.7  -0.5   88    2-89     11-100 (100)
  8 >3hqx_A UPF0345 protein aciad0  88.7     1.8 5.3E-05   23.2   7.3   82    1-83      4-99  (111)
  9 >3eo6_A Protein of unknown fun  50.6      18 0.00053   16.9   7.7   69    8-77     10-89  (106)
 10 >1vq8_E 50S ribosomal protein   41.2      25 0.00075   16.0   4.3   57    8-64      3-59  (79)
 11 >1u8s_A Glycine cleavage syste  26.7      29 0.00087   15.6   1.4   17    1-17      1-17  (86)

No 1  
>>1aqt_A ATP synthase; hydrolase, ATPase, epsilon subunit; 2.30A {Escherichia coli} (A:)
Probab=99.98  E-value=9.2e-31  Score=212.38  Aligned_cols=121  Identities=24%  Similarity=0.341  Sum_probs=113.3

Q ss_pred             CCEEEEEEECCCCEEECCEEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEEEECCCCEEEEECCEEEEEE
Q ss_conf             44026999848863752213199996057335776898002667068807996268840354226756999499699998
Q gi|254780614|r    4 VNDLHFELVSPEKCVFSGEVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHRYVVIGGICDIVPSHCTVLS   83 (135)
Q Consensus         4 ~~~~~l~ivtP~~~i~~~~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~~~V~gG~~~v~~~~v~Il~   83 (135)
                      +++|+|+|+||++.+|+++|++|++||.+|+|||||||+|+|+.|.||+++++..++.+..|+|+|||++|.+|+|+|++
T Consensus         1 a~~l~l~IvtP~~~~~~~~v~~v~~~t~~G~~gILp~H~p~it~L~~G~i~i~~~~~~~~~~~v~gG~~~v~~~~v~I~~   80 (138)
T 1aqt_A            1 GSTYHLDVVSAEQQMFSGLVEKIQVTGSEGELGIYPGHAPLLTAIKPGMIRIVKQHGHEEFIYLSGGILEVQPGNVTVLA   80 (138)
T ss_dssp             -CCEEEEEEESSCEEEEEEEEEEEEEBSSSEEEECTTCCCEEEEECSEEEEEEETTTEEEEEEESSEEEEEETTEEEEEE
T ss_pred             CCEEEEEEECCCCEEEECEEEEEEEECCCCCEEECCCCCCEEEECCCCEEEEEECCCCEEEEEEECCEEEECCCEEEEEH
T ss_conf             96599999989855882457899997694375776898240231436579999859979999984889996699599992


Q ss_pred             ECCEEHHHCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             11220768599999999999999965078889999999999
Q gi|254780614|r   84 ETILPMDNACLQALEKRIDEVCSDLNNICDVDQRFQMEQLL  124 (135)
Q Consensus        84 ~~a~~~~~iD~~~a~~~~e~a~~~l~~~~~~~~~~~~~~~~  124 (135)
                      ++|++.++||.+++++.++++++.+++..+..++..++..+
T Consensus        81 ~~a~~~~~id~~~~~~~~~~a~~~l~~~~~~~~~~~~e~~l  121 (138)
T 1aqt_A           81 DTAIRGQDLDEARAMEAKRKAEEHISSSHGDVDYAQASAEL  121 (138)
T ss_dssp             SSEEEGGGCCHHHHHHHHHHHHHHHTTCSSSHHHHHHHHHH
T ss_pred             HHEEECCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             14075502999999999999999987087708999999999


No 2  
>>2e5y_A ATP synthase epsilon chain; F1FO ATP synthase, F1-ATPase, epsilon subunit, hydrolase; HET: ATP; 1.92A {Bacillus SP} PDB: 2e5t_A 2e5u_A (A:)
Probab=99.97  E-value=3.2e-30  Score=209.01  Aligned_cols=117  Identities=17%  Similarity=0.328  Sum_probs=108.1

Q ss_pred             CCEEEEEEECCCCEEECCEEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEEEECCCCEEEEECCEEEEEE
Q ss_conf             44026999848863752213199996057335776898002667068807996268840354226756999499699998
Q gi|254780614|r    4 VNDLHFELVSPEKCVFSGEVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHRYVVIGGICDIVPSHCTVLS   83 (135)
Q Consensus         4 ~~~~~l~ivtP~~~i~~~~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~~~V~gG~~~v~~~~v~Il~   83 (135)
                      |++|+|+|+||++.+|+++|++|++||.+|+|||||||+|+|+.|+||+++|+.+ +.++.|+|+|||++|.+|.|+|++
T Consensus         1 M~~l~l~IvtP~~~~~~~~v~~v~~~~~~G~~gILp~H~p~i~~L~~G~i~i~~~-~~~~~~~v~gG~~~v~~~~v~Il~   79 (133)
T 2e5y_A            1 MKTIHVSVVTPDGPVYEDDVEMVSVKAKSGELGILPGHIPLVAPLEISAARLKKG-GKTQYIAVSGGFLEVRPDKVTILA   79 (133)
T ss_dssp             CCCEEEEEEETTEEEEEEEESEEEEEETTEEEEECTTCCCEEEEEEEEEEEEEET-TEEEEEEEEEEEEEEETTEEEEEE
T ss_pred             CCEEEEEEECCCCEEEEEEEEEEEEECCCCCEEECCCCCCCEEECCCEEEEEEEC-CCEEEEEEECCEEEEECCEEEEEE
T ss_conf             9758999996985388445889999669538154479824111214507999844-766999975640388558589998


Q ss_pred             ECCEEHHHCCHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             11220768599999999999999965078889999999
Q gi|254780614|r   84 ETILPMDNACLQALEKRIDEVCSDLNNICDVDQRFQME  121 (135)
Q Consensus        84 ~~a~~~~~iD~~~a~~~~e~a~~~l~~~~~~~~~~~~~  121 (135)
                      +.|++.++||.+++++.++++++.+++..+..+.+.+.
T Consensus        80 ~~a~~~~~id~~~~~~~~~~a~~~l~~~~~~~~~~~~~  117 (133)
T 2e5y_A           80 QAAERAEDIDVLRAKAAKERAERRLQSQQDDIDFKRAE  117 (133)
T ss_dssp             SSEEEGGGCCHHHHHHHHHHHHHHHTCCSSCCCHHHHH
T ss_pred             EEEEEHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             01888401899999999999999987086629999999


No 3  
>>2hld_H ATP synthase delta chain, mitochondrial; ATP phosphorylase (H+ transporting), F1FO, F1- ATPase, hydrolase; HET: ANP; 2.80A {Saccharomyces cerevisiae} PDB: 3fks_H (H:)
Probab=99.96  E-value=4e-30  Score=208.39  Aligned_cols=115  Identities=19%  Similarity=0.327  Sum_probs=108.7

Q ss_pred             CCCCEEEEEEECCCCEEECC-EEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEEEECCCCEEEEECCEEE
Q ss_conf             84440269998488637522-13199996057335776898002667068807996268840354226756999499699
Q gi|254780614|r    2 SLVNDLHFELVSPEKCVFSG-EVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHRYVVIGGICDIVPSHCT   80 (135)
Q Consensus         2 ~M~~~~~l~ivtP~~~i~~~-~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~~~V~gG~~~v~~~~v~   80 (135)
                      +|+++|+|+|+||++.+|+| +|++|++||.+|+|||||||+|+|+.|+||+++|+.+++.+..|+++||++.+.++.|+
T Consensus         5 ~m~~~l~l~ivTP~~~~~~~~~V~~v~~~t~~G~~gILp~H~p~it~L~~G~i~i~~~~~~~~~~~~~gg~~~~~~~~v~   84 (138)
T 2hld_H            5 AASSGLKLQFALPHETLYSGSEVTQVNLPAKSGRIGVLANHVPTVEQLLPGVVEVMEGSNSKKFFISGGFATVQPDSQLC   84 (138)
T ss_dssp             ------CEEEECSSCBCCC--CCSEEEEECSSSEEEECSSCCCCEEEECSSEEEEEETTEEEEEECCCEEEEECTTSCEE
T ss_pred             CCCCCEEEEEECCCCCEECCCCEEEEEEECCCCCEEECCCCCCEEEEEECCEEEEEECCCEEEEEECCCEEEEECCCEEE
T ss_conf             66884699998696406778846999996685274575898350234107747984035515787406629993583799


Q ss_pred             EEEECCEEHHHCCHHHHHHHHHHHHHHHHHCCCHHH
Q ss_conf             998112207685999999999999999650788899
Q gi|254780614|r   81 VLSETILPMDNACLQALEKRIDEVCSDLNNICDVDQ  116 (135)
Q Consensus        81 Il~~~a~~~~~iD~~~a~~~~e~a~~~l~~~~~~~~  116 (135)
                      |+++.|++.++||.+++++.++++++++++..+.+.
T Consensus        85 Il~~~a~~~~~id~~~a~~~~~~a~~~l~~~~~~~~  120 (138)
T 2hld_H           85 VTAIEAFPLESFSQENIKNLLAEAKKNVSSSDAREA  120 (138)
T ss_dssp             EEESCC-CHHHHC-CHHHHHHHGGGTTTTTC--CHH
T ss_pred             EEEEEEECHHHCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             995130025455999999999999988706988899


No 4  
>>2qe7_H ATP synthase subunit epsilon; blockage of ATP hydrolysis, F1-ATPase, single particle analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} (H:)
Probab=99.96  E-value=2.9e-30  Score=209.31  Aligned_cols=110  Identities=23%  Similarity=0.383  Sum_probs=103.3

Q ss_pred             CCEEEEEEECCCCEEECCEEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEEEECCCCEEEEECCEEEEEE
Q ss_conf             44026999848863752213199996057335776898002667068807996268840354226756999499699998
Q gi|254780614|r    4 VNDLHFELVSPEKCVFSGEVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHRYVVIGGICDIVPSHCTVLS   83 (135)
Q Consensus         4 ~~~~~l~ivtP~~~i~~~~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~~~V~gG~~~v~~~~v~Il~   83 (135)
                      |++|+|+|+||++.+|+++|++|++||.+|+|||||||+|+|+.|.||+++|+.+++ ++.|||+|||++|.+|.|+|++
T Consensus         1 M~~l~l~ivtP~~~~~~~~v~~v~~~~~~G~~gIlp~H~p~it~L~~G~i~i~~~~~-~~~~~v~gG~~~v~~~~v~Il~   79 (135)
T 2qe7_H            1 MATVQVDIVTPERKVFQGEADIVIARGVEGELGVMAGHIPLVTPLKTAPVRIKQGDK-ETLIAVSGGFLEVRPDKVNILA   79 (135)
T ss_dssp             CCCCEEEEBCSSCBCCCSCCSCEEECBSSSCEEECSCCCCCCCCBCSSCCCBCTTSC-CBCCBCCSCCEEECSSEEEECC
T ss_pred             CCEEEEEEECCCCEEEECEEEEEEEECCCCCEEECCCCCCEEEECCCCCEEEECCCC-EEEEEECCCEEEECCCEEEEEE
T ss_conf             973799999798448824578999966943756658980427881378333221565-1567614786998599799997


Q ss_pred             ECCEEHHHCCHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             1122076859999999999999996507888
Q gi|254780614|r   84 ETILPMDNACLQALEKRIDEVCSDLNNICDV  114 (135)
Q Consensus        84 ~~a~~~~~iD~~~a~~~~e~a~~~l~~~~~~  114 (135)
                      +.|++.++||.+++++.++++++++++..+.
T Consensus        80 ~~a~~~~~id~~~a~~~~~~a~~~l~~~~~~  110 (135)
T 2qe7_H           80 DTAELPEEIDVERAKKAKARHETILKRLDKT  110 (135)
T ss_dssp             SSCBCTTTSCHHHHHHHHHTTTTTTTTCCSS
T ss_pred             HHEEEHHHCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             3068840189999999999999998645624


No 5  
>>2rq6_A ATP synthase epsilon chain; F1FO ATP synthase, F1-ATPase, epsilon subunit, ATP synthesis, CF1, hydrogen ION transport, hydrolase; NMR {Thermosynechococcus elongatus} PDB: 2rq7_A (A:1-86)
Probab=99.90  E-value=1.4e-23  Score=167.62  Aligned_cols=85  Identities=25%  Similarity=0.513  Sum_probs=80.8

Q ss_pred             EEEEEEECCCCEEECCEEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEEEECCCCEEEEECCEEEEEEEC
Q ss_conf             02699984886375221319999605733577689800266706880799626884035422675699949969999811
Q gi|254780614|r    6 DLHFELVSPEKCVFSGEVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHRYVVIGGICDIVPSHCTVLSET   85 (135)
Q Consensus         6 ~~~l~ivtP~~~i~~~~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~~~V~gG~~~v~~~~v~Il~~~   85 (135)
                      +|+|+|+||++.+|+++|++|++|+.+|++||||||+|+++.|.||+++++. +++++.|+|+|||+++.+|+|+|+++.
T Consensus         2 t~~l~IvtP~~~~~~~~v~~v~~~t~~G~~gIl~~H~p~i~~L~~g~~~i~~-~~~~~~~~v~gG~l~v~~n~v~Ila~~   80 (86)
T 2rq6_A            2 VMTVRVIAPDKTVWDAPAEEVILPSTTGQLGILSNHAPLLTALETGVMRVRQ-DREWVAIALMGGFAEVENNEVTILVNG   80 (86)
T ss_dssp             CEEEEEECSSSEEEEEEESEEEECCTTSCEEEESSCCSEEEEECSEEEEEES-SSCEEEEEECSEEEEECSSCEEEEESC
T ss_pred             EEEEEEECCCCEEEECEEEEEEEECCCCCEEECCCCCCEEEEEECCEEEEEE-CCCEEEEEEECCEEEEECCEEEEEEEE
T ss_conf             7899999699558834468999987944726658981646773177899997-895899999578899979999999705


Q ss_pred             CEEHHH
Q ss_conf             220768
Q gi|254780614|r   86 ILPMDN   91 (135)
Q Consensus        86 a~~~~~   91 (135)
                      |+++|+
T Consensus        81 a~~~en   86 (86)
T 2rq6_A           81 AERGDT   86 (86)
T ss_dssp             EECSTT
T ss_pred             EEECCC
T ss_conf             787111


No 6  
>>2w6j_H F1-ATPase delta subunit; ATP phosphorylase (H+ transporting), transit peptide, F1FO ATP synthase, ATP phosphorylase; 3.84A {Bos taurus} PDB: 2w6h_H 2w6i_H (H:1-123)
Probab=99.89  E-value=6.1e-25  Score=176.01  Aligned_cols=89  Identities=24%  Similarity=0.492  Sum_probs=84.7

Q ss_pred             CCCCEEEEEEECCCCEEECC-EEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEEEECCCCEEEEE-CCEE
Q ss_conf             84440269998488637522-131999960573357768980026670688079962688403542267569994-9969
Q gi|254780614|r    2 SLVNDLHFELVSPEKCVFSG-EVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHRYVVIGGICDIV-PSHC   79 (135)
Q Consensus         2 ~M~~~~~l~ivtP~~~i~~~-~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~~~V~gG~~~v~-~~~v   79 (135)
                      .||++|+|+|+||++.+|++ +|++|++||.+|+|||||||+|+++.|+||+++++.++++++.|+|+|||++|. +|+|
T Consensus        33 ~m~~~l~L~IvTP~~~~~~g~~V~~V~~~t~~G~~gILpnH~p~it~L~~G~i~i~~~~~~~~~~~V~gG~l~V~~~n~v  112 (123)
T 2w6j_H           33 AGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSKYFVSSGSVTVNADSSV  112 (123)
T ss_dssp             ------CCCEECSSCEEEC-----CCBCCC-----------------CCSBCCBC----------CBCSBC---------
T ss_pred             CCCCEEEEEEECCCCCEECCCCEEEEEEECCCCCEEECCCCCCEEEEECCCEEEEEECCCCEEEEEECCCCEEECCCCEE
T ss_conf             99874899997587405647856899997684474666898151467328826899379970332444782565279849


Q ss_pred             EEEEECCEEHH
Q ss_conf             99981122076
Q gi|254780614|r   80 TVLSETILPMD   90 (135)
Q Consensus        80 ~Il~~~a~~~~   90 (135)
                      +|++++|+++|
T Consensus       113 ~Ila~~a~~~E  123 (123)
T 2w6j_H          113 QLLAEEAVTLD  123 (123)
T ss_dssp             CEEBSSBCCSS
T ss_pred             EEEEEEEEEHH
T ss_conf             99871026643


No 7  
>>2ck3_H ATP synthase delta chain; ATP phosphorylase, ATP phosphorylase (H+ transporting), F1FO ATP synthase, F1-ATPase, hydrolase, ATP synthesis; HET: ANP ADP; 1.9A {Bos taurus} (H:1-100)
Probab=99.88  E-value=3e-24  Score=171.74  Aligned_cols=88  Identities=23%  Similarity=0.480  Sum_probs=82.8

Q ss_pred             CCCCEEEEEEECCCCEEECC-EEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEEEECCCCEEEEE-CCEE
Q ss_conf             84440269998488637522-131999960573357768980026670688079962688403542267569994-9969
Q gi|254780614|r    2 SLVNDLHFELVSPEKCVFSG-EVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHRYVVIGGICDIV-PSHC   79 (135)
Q Consensus         2 ~M~~~~~l~ivtP~~~i~~~-~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~~~V~gG~~~v~-~~~v   79 (135)
                      .||++|+|+|+||++.+|++ +|++|++||.+|+|||||||+|+++.|.||+++|+.+|++++.|+|+|||++|. +|.|
T Consensus        11 ~m~~~~~l~IvtP~~~~~~~~~v~~v~~~~~~G~~gIL~~H~p~it~L~~G~i~i~~~~~~~~~~~v~gG~~~v~~~n~v   90 (100)
T 2ck3_H           11 AGPGQMSFTFASPTQVFFNSANVRQVDVPTQTGAFGILAAHVPTLQVLRPGLVVVHAEDGTTSKYFVSSGSVTVNADSSV   90 (100)
T ss_dssp             ------CCCEECSSCEEEC-----CCBCCC-----------------CCSBCCBC----------CBCSBC---------
T ss_pred             CCCCEEEEEEECCCCEEECCCCEEEEEEECCCCCEEECCCCCCEEEEECCCEEEEEECCCCEEEEEECCCCEEECCCCEE
T ss_conf             99986899998698005678857999986685365676898252576128868999379970333543782576379969


Q ss_pred             EEEEECCEEH
Q ss_conf             9998112207
Q gi|254780614|r   80 TVLSETILPM   89 (135)
Q Consensus        80 ~Il~~~a~~~   89 (135)
                      +|++++|++.
T Consensus        91 ~Il~~~a~~i  100 (100)
T 2ck3_H           91 QLLAEEAVTL  100 (100)
T ss_dssp             CEEBSSBCCS
T ss_pred             EEEEEEEEEH
T ss_conf             9987213763


No 8  
>>3hqx_A UPF0345 protein aciad0356; DUF1255,PF06865,PSI2,MCSG, structural genomics, protein structure initiative, midwest center for structural genomics; 1.66A {Acinetobacter SP} (A:)
Probab=88.75  E-value=1.8  Score=23.15  Aligned_cols=82  Identities=20%  Similarity=0.182  Sum_probs=62.5

Q ss_pred             CCCCCEEEEEEECCCCEEECCEEEEEEEEECCCE---EEE-CCC--------CCEEEEECCCCEEEEEECCC-CEEEEEC
Q ss_conf             9844402699984886375221319999605733---577-689--------80026670688079962688-4035422
Q gi|254780614|r    1 MSLVNDLHFELVSPEKCVFSGEVQSVVLPSELGD---ITV-LVG--------HAPVLTTIKSGIVTISLSCE-EIHRYVV   67 (135)
Q Consensus         1 m~M~~~~~l~ivtP~~~i~~~~v~~v~~p~~~G~---~gI-Lp~--------H~p~i~~L~~G~i~i~~~~~-~~~~~~V   67 (135)
                      |+|+.-=.+.|+.--.+.|+|.|.+..+-..||.   +|| +|+        ++|=+..+..|.+.++.++. +|+ -+-
T Consensus         4 ~~m~~f~nVsv~kkaNvYFDGkv~S~~~~~~dG~~kTlGVm~pGe~~Y~F~T~~~E~MevvsG~l~VkLpg~~ew~-~~~   82 (111)
T 3hqx_A            4 XSSAQFDHVTVIKKSNVYFGGLCISHTVQFEDGTKKTLGVILPTEQPLTFETHVPERXEIISGECRVKIADSTESE-LFR   82 (111)
T ss_dssp             --CCCCCSCEECSSCEEETTTTEEEEEEECTTSCEEEEEEECCCSSCEEEECSSCEEEEEEESEEEEEETTCSSCE-EEE
T ss_pred             CCHHHCCCEEEEEEEEEEECCEEEEEEEECCCCCEEEEEEEECCCCEEEECCCCCEEEEEEEEEEEEECCCCCCCE-EEC
T ss_conf             5874647789999947789887899999918999888999915751278759996899999618999989986557-957


Q ss_pred             CCCEEEEECC-EEEEEE
Q ss_conf             6756999499-699998
Q gi|254780614|r   68 IGGICDIVPS-HCTVLS   83 (135)
Q Consensus        68 ~gG~~~v~~~-~v~Il~   83 (135)
                      .|-..+|-.| +-.|-+
T Consensus        83 aGesF~VpanssF~i~v   99 (111)
T 3hqx_A           83 AGQSFYVPGNSLFKIET   99 (111)
T ss_dssp             TTCEEEECTTCEEEEEC
T ss_pred             CCCEEEECCCCEEEEEE
T ss_conf             99758968999899998


No 9  
>>3eo6_A Protein of unknown function (DUF1255); AFE_2634, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 0.97A {Acidithiobacillus ferrooxidans ATCC23270} (A:)
Probab=50.59  E-value=18  Score=16.91  Aligned_cols=69  Identities=14%  Similarity=0.136  Sum_probs=53.7

Q ss_pred             EEEEECCCCEEECCEEEEEEEEECCCE---EEEC-CC------CCEEEEECCCCEEEEEECCCC-EEEEECCCCEEEEEC
Q ss_conf             699984886375221319999605733---5776-89------800266706880799626884-035422675699949
Q gi|254780614|r    8 HFELVSPEKCVFSGEVQSVVLPSELGD---ITVL-VG------HAPVLTTIKSGIVTISLSCEE-IHRYVVIGGICDIVP   76 (135)
Q Consensus         8 ~l~ivtP~~~i~~~~v~~v~~p~~~G~---~gIL-p~------H~p~i~~L~~G~i~i~~~~~~-~~~~~V~gG~~~v~~   76 (135)
                      .+.++.--.+.|+|.|.+..+-..+|.   +||+ ||      ++|=+..+..|.+.++.++.. |+ -+-.|-..+|-.
T Consensus        10 nVtv~kkaNvYFdGkV~S~~~~~~dG~~kTlGVm~pGeY~F~T~~~E~MevvsG~l~V~Lpg~~ew~-~~~aG~sF~Vpa   88 (106)
T 3eo6_A           10 ATALGKSSRISLDGRRSERSVILADGSXHSLTLLHPGVYTLSSEVAETIRVLSGXAYYHAEGANDVQ-ELHAGDSXVIPA   88 (106)
T ss_dssp             EEEEESCCEEETTTTEEEEEEEETTSCEEEEEEECSEEEEECCSSCEEEEEEEEEEEEECTTCSSCE-EEETTCEEEECS
T ss_pred             CEEEEEEEEEEECCEEEEEEEECCCCCEEEEEEEECCEEEECCCCCEEEEEEEEEEEEECCCCCCCE-EECCCCEEEECC
T ss_conf             5078678779999858999999089986689999620688759994899998518999989985427-946998799789


Q ss_pred             C
Q ss_conf             9
Q gi|254780614|r   77 S   77 (135)
Q Consensus        77 ~   77 (135)
                      |
T Consensus        89 n   89 (106)
T 3eo6_A           89 N   89 (106)
T ss_dssp             S
T ss_pred             C
T ss_conf             9


No 10 
>>1vq8_E 50S ribosomal protein L6P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} (E:1-79)
Probab=41.16  E-value=25  Score=16.00  Aligned_cols=57  Identities=14%  Similarity=0.168  Sum_probs=47.1

Q ss_pred             EEEEECCCCEEECCEEEEEEEEECCCEEEECCCCCEEEEECCCCEEEEEECCCCEEE
Q ss_conf             699984886375221319999605733577689800266706880799626884035
Q gi|254780614|r    8 HFELVSPEKCVFSGEVQSVVLPSELGDITVLVGHAPVLTTIKSGIVTISLSCEEIHR   64 (135)
Q Consensus         8 ~l~ivtP~~~i~~~~v~~v~~p~~~G~~gILp~H~p~i~~L~~G~i~i~~~~~~~~~   64 (135)
                      +..|--|+++=.+-+-..|++.|..|++..-=.|.+.-..+..+.+.+...++..+.
T Consensus         3 ripI~IP~~V~v~i~~~~i~vkGp~G~l~~~~~~~~v~i~~~~~~i~v~~~~~~k~~   59 (79)
T 1vq8_E            3 RVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKT   59 (79)
T ss_dssp             EEEEECCTTCEEEEETTEEEEEETTEEEEEECCCTTCEEEEETTEEEEECSCCSHHH
T ss_pred             CCCEECCCCCEEEEECCEEEEECCCEEEEEEECCCCEEEEECCCEEEEECCCCCCHH
T ss_conf             665618999789997999999848989999914885799983988998427664236


No 11 
>>1u8s_A Glycine cleavage system transcriptional repressor, putative; structural genomics, protein structure initiative (PSI), domain swapping; 2.45A {Vibrio cholerae} (A:1-86)
Probab=26.65  E-value=29  Score=15.59  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=12.4

Q ss_pred             CCCCCEEEEEEECCCCE
Q ss_conf             98444026999848863
Q gi|254780614|r    1 MSLVNDLHFELVSPEKC   17 (135)
Q Consensus         1 m~M~~~~~l~ivtP~~~   17 (135)
                      |+|.+++-++++.|++.
T Consensus         1 Ms~~~~~vitv~g~Drp   17 (86)
T 1u8s_A            1 MSLTQHLVITAVGTDRP   17 (86)
T ss_dssp             -CCCEEEEEEEEEECCT
T ss_pred             CCCCEEEEEEEEECCCC
T ss_conf             99741899999926988


Done!