Query         T0623 3NKH, , 220 residues
Match_columns 220
No_of_seqs    108 out of 7094
Neff          9.9 
Searched_HMMs 15564
Date          Thu Jul 22 15:10:53 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0623.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/scop70_1.75_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/scop70search/T0623.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d1a0pa2 d.163.1.1 (A:111-292)  100.0 1.9E-32 1.2E-36  206.3  10.6  179    1-211     2-181 (182)
  2 d1a0pa2 d.163.1.1 (A:111-292)  100.0   1E-28 6.6E-33  184.5  11.2  179    1-211     2-181 (182)
  3 d1aiha_ d.163.1.1 (A:) Integra  99.9 4.2E-27 2.7E-31  175.1  11.7  156    1-212     6-161 (170)
  4 d1f44a2 d.163.1.1 (A:130-343)   99.9 1.1E-25   7E-30  166.9  13.8  191    2-216     8-212 (214)
  5 d1ae9a_ d.163.1.1 (A:) Integra  99.9 1.9E-22 1.2E-26  147.9   5.7  164    1-202     3-169 (179)
  6 d1a41a_ d.163.1.2 (A:) Eukaryo  97.1  0.0012 7.7E-08   38.4   7.5  131   32-202    36-197 (230)
  7 d1k4ta2 d.163.1.2 (A:431-640,A  91.9    0.36 2.3E-05   23.9   7.0  122   32-190    44-203 (263)
  8 d1dzfa2 d.78.1.1 (A:144-215) E  47.3     4.4 0.00028   17.6   1.6   45    2-55     13-57  (72)
  9 d1dzfa2 d.78.1.1 (A:144-215) E  44.7     5.1 0.00033   17.2   1.6   46    2-56     13-58  (72)
 10 d1hmja_ d.78.1.1 (A:) RNA poly  40.0     6.1 0.00039   16.8   1.4   45    2-55      6-50  (68)
 11 d1eika_ d.78.1.1 (A:) RNA poly  35.7     5.6 0.00036   17.0   0.7   45    2-55     17-61  (77)
 12 d1j09a1 a.97.1.1 (A:306-468) C  30.5      15 0.00099   14.4   2.7   55  138-197   102-156 (163)
 13 d1j09a1 a.97.1.1 (A:306-468) C  26.6      18  0.0012   14.0   2.7   49  138-188   102-150 (163)
 14 d1uoua1 a.46.2.1 (A:33-100) Th  23.0      21  0.0014   13.6   3.8   45    2-55     17-61  (68)

No 1  
>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=99.97  E-value=1.9e-32  Score=206.34  Aligned_cols=179  Identities=22%  Similarity=0.332  Sum_probs=148.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             98888999999986310111001002467899999999998617666888417532310247807872101023323465
Q T0623             1 YLELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDFDNKSLNINGTIHWFHDESGG   80 (220)
Q Consensus         1 yl~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~~~~~~i~i~~~~~~~~~~~~~   80 (220)
                      +||.+|++++++.++.....         ..+..+++.+++.||||++|+++|+|+||+++++.+.|..           
T Consensus         2 ~lt~eE~~~ll~~~~~~~~~---------~~r~~~~~~l~~~tG~R~~Ei~~L~~~~i~~~~~~i~i~~-----------   61 (182)
T d1a0pa2           2 DLSEAQVERLLQAPLIDQPL---------ELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIG-----------   61 (182)
T ss_dssp             CCCHHHHHHHHHCSCTTSHH---------HHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEEEEEC-----------
T ss_pred             CCCHHHHHHHHHHHCCCCCH---------HHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCCCCC-----------
T ss_conf             98889999999862347814---------5789999999997124611021111121111100111001-----------


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCC-C
Q ss_conf             201246668761102566089999999998764221002455678870671233333230134555555565338865-4
Q T0623            81 FGVKDTTKTESSYRTIGLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDK-E  159 (220)
Q Consensus        81 ~~~~~~~k~~~~~R~vpi~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~~-~  159 (220)
                             |+.+ .|.||+++.+.+.+.+|+........   .....+++|.+..|++++.+++++.++++++.+|++. .
T Consensus        62 -------k~~k-~r~ipi~~~~~~~l~~~~~~~~~~~~---~~~~~~~lf~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~  130 (182)
T d1a0pa2          62 -------KGNK-ERLVPLGEEAVYWLETYLEHGRPWLL---NGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEK  130 (182)
T ss_dssp             -------SSSC-EEEEECCHHHHHHHHHHHHHTHHHHH---TTCCCCBSSBCTTSSBCCHHHHHHHHHHHHHHTTCCGGG
T ss_pred             -------CCCC-CCCCCCHHHHHHHHHHHHHHHHHHHH---CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             -------3433-21110001235778877764102210---023331000011111111100000012333211100135


Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHH
Q ss_conf             4202455565434664389989999985899878999984123788999999
Q T0623           160 VSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHVTEQMDKDMM  211 (220)
Q Consensus       160 ~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~~~~~~~~~~~  211 (220)
                      +++|+||||+||.++++|+|+..||+++||+|++||+ +|+|++++..++++
T Consensus       131 ~t~H~lRht~at~~~~~G~~~~~i~~~~GH~~~~~t~-~Y~~~~~~~~~~~~  181 (182)
T d1a0pa2         131 LSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQ-IYTHVATERLRQLH  181 (182)
T ss_dssp             CCHHHHHHHHHHHHHHHCSSCGGGSSCC--CCCCHHH-HHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHCCCCCHHHHHHHHCCCCHHHHH-HHHCCCHHHHHHHH
T ss_conf             4411133530121101688989999985889889999-98628988999981


No 2  
>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=99.96  E-value=1e-28  Score=184.50  Aligned_cols=179  Identities=22%  Similarity=0.333  Sum_probs=134.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             98888999999986310111001002467899999999998617666888417532310247807872101023323465
Q T0623             1 YLELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDFDNKSLNINGTIHWFHDESGG   80 (220)
Q Consensus         1 yl~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~~~~~~i~i~~~~~~~~~~~~~   80 (220)
                      +||.||+++|++.......         ..++..+++.++++||+|++|+++|+|+||+++++.+.+.+.          
T Consensus         2 ~Lt~eei~~ll~~~~~~~~---------~~lRd~~l~~l~~~tG~R~~ei~~L~~~~i~~~~~~i~~~~~----------   62 (182)
T d1a0pa2           2 DLSEAQVERLLQAPLIDQP---------LELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGK----------   62 (182)
T ss_dssp             CCCHHHHHHHHHCSCTTSH---------HHHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEEEEECS----------
T ss_pred             CCCHHHHHHHHHCCCCCCC---------HHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCEEEEEECC----------
T ss_conf             8999999999827463881---------879999999999996776477420214141144328998368----------


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCC-CC
Q ss_conf             20124666876110256608999999999876422100245567887067123333323013455555556533886-54
Q T0623            81 FGVKDTTKTESSYRTIGLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGID-KE  159 (220)
Q Consensus        81 ~~~~~~~k~~~~~R~vpi~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~-~~  159 (220)
                              +. ..|.++........+...+.......   .......+.+....+.+++..++++.++++++.+|++ ++
T Consensus        63 --------~~-k~r~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  130 (182)
T d1a0pa2          63 --------GN-KERLVPLGEEAVYWLETYLEHGRPWL---LNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEK  130 (182)
T ss_dssp             --------SS-CEEEEECCHHHHHHHHHHHHHTHHHH---HTTCCCCBSSBCTTSSBCCHHHHHHHHHHHHHHTTCCGGG
T ss_pred             --------CC-EEEEEEECCHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             --------98-01257520013355666553112300---1234565421023577366899999999999984998578


Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHH
Q ss_conf             4202455565434664389989999985899878999984123788999999
Q T0623           160 VSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHVTEQMDKDMM  211 (220)
Q Consensus       160 ~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~~~~~~~~~~~  211 (220)
                      ++||+||||+||.|+++|+|+..|++++||+|++||+ +|.|++.+..+++.
T Consensus       131 ~t~H~~Rht~at~l~~~G~~~~~I~~~lGH~s~~tt~-~Y~~~~~e~~re~~  181 (182)
T d1a0pa2         131 LSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQ-IYTHVATERLRQLH  181 (182)
T ss_dssp             CCHHHHHHHHHHHHHHHCSSCGGGSSCC--CCCCHHH-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHCCCHHHHHHHH
T ss_conf             3614146589996556499999999995899889999-87687999999860


No 3  
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]}
Probab=99.94  E-value=4.2e-27  Score=175.14  Aligned_cols=156  Identities=19%  Similarity=0.311  Sum_probs=113.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             98888999999986310111001002467899999999998617666888417532310247807872101023323465
Q T0623             1 YLELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDFDNKSLNINGTIHWFHDESGG   80 (220)
Q Consensus         1 yl~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~~~~~~i~i~~~~~~~~~~~~~   80 (220)
                      |||.+|++++++.+......           ...+++.++++||||++|+++|+|+||+++...  +             
T Consensus         6 ~Lt~eEi~~l~~~~~~~~~~-----------~~~~~i~l~~~tG~R~~E~~~L~~~dI~~~~~~--~-------------   59 (170)
T d1aiha_           6 FLYERDIYRLLAECDNSRNP-----------DLGLIVRICLATGARWSEAETLTQSQVMPYKIT--F-------------   59 (170)
T ss_dssp             CCCHHHHHHHHHHHTTSSST-----------THHHHHHHHHHHCCCHHHHHTCBTTTEETTEEE--E-------------
T ss_pred             CCCHHHHHHHHHHHHHCCCH-----------HHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCEE--E-------------
T ss_conf             89999999999986365896-----------699999999997776112444331024421102--1-------------


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCC
Q ss_conf             20124666876110256608999999999876422100245567887067123333323013455555556533886544
Q T0623            81 FGVKDTTKTESSYRTIGLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDKEV  160 (220)
Q Consensus        81 ~~~~~~~k~~~~~R~vpi~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~~~~  160 (220)
                          ..+|+++ .|.||+++.+.++|..+                .+.+|.      .....+...+  ....+++++++
T Consensus        60 ----~~~K~~~-~r~ipl~~~~~~~l~~~----------------~~~~~~------~~~~~~~~~~--~~~~~~~~~~~  110 (170)
T d1aiha_          60 ----TNTKSKK-NRTVPISDELFDMLPKK----------------RGRLFN------DAYESFENAV--LRAEIELPKGQ  110 (170)
T ss_dssp             ----ESSSSSC-EEEEECCHHHHHHSCCC----------------SSBSSC------CCHHHHHHHH--HHTTCCCCTTC
T ss_pred             ----CCCCCCC-HHHHHHHHHHHHHHHHH----------------HCCCCC------CCHHHHHHHH--HHHHHCCCCCC
T ss_conf             ----1444430-05776699999998751----------------001101------1112443345--66650257761


Q ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             2024555654346643899899999858998789999841237889999999
Q T0623           161 SSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHVTEQMDKDMMN  212 (220)
Q Consensus       161 ~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~~~~~~~~~~~~  212 (220)
                      +||+|||||||.|+++|+|+..|++++||+|++||. +|+|++++..+++++
T Consensus       111 ~~H~lRht~at~l~~~g~~~~~i~~~lGH~~~~~t~-~Y~~~~~~~~~~a~~  161 (170)
T d1aiha_         111 LTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTM-RYAHFAPSHLESAVK  161 (170)
T ss_dssp             TTTHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHG-GGGGGSCCCTTHHHH
T ss_pred             EEEECHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHH-HHHCCCHHHHHHHHH
T ss_conf             011104655145521698999999980899989999-887679999999998


No 4  
>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]}
Probab=99.93  E-value=1.1e-25  Score=166.87  Aligned_cols=191  Identities=17%  Similarity=0.149  Sum_probs=129.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCCC-EEEEEEECCCCCCCCC
Q ss_conf             888899999998631011100100246789999999999861766688841753231024780-7872101023323465
Q T0623             2 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDFDNKS-LNINGTIHWFHDESGG   80 (220)
Q Consensus         2 l~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~~~~~~-i~i~~~~~~~~~~~~~   80 (220)
                      ++.+|++.+...++...        ....++..+++.++++||||++|+++|+|+||++..+. ..+..           
T Consensus         8 ~~~~e~~~~~~~~~~~~--------~~~~~R~~ali~l~~~tGlR~~Ei~~L~~~di~~~~~~~~~i~i-----------   68 (214)
T d1f44a2           8 FERTDFDQVRSLMENSD--------RCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHI-----------   68 (214)
T ss_dssp             CCHHHHHHHHHHHTTCC--------CHHHHHHHHHHHHHHHHCCCHHHHHHCBGGGEEECGGGCEEEEE-----------
T ss_pred             CCHHHHHHHHHHHHCCC--------CHHHHHHHHHHHHHHHHCCCHHHHHHCCCCEEECCCCCCEEEEE-----------
T ss_conf             99999999999986247--------22638999999999998107777875123112023331036666-----------


Q ss_pred             CCCCCCCCC--CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC---CCCCCCCEEEECCCCCCCCCHHHHHHHHHH---HH
Q ss_conf             201246668--7611025660899999999987642210024---556788706712333332301345555555---65
Q T0623            81 FGVKDTTKT--ESSYRTIGLSSRSCEILKKAILENKKDSKWN---DGYLNRNFVFTNHKGNPMQTERFNKILREA---AK  152 (220)
Q Consensus        81 ~~~~~~~k~--~~~~R~vpi~~~~~~~L~~~~~~~~~~~~~~---~~~~~~~~if~~~~g~~l~~~~i~~~l~~~---~~  152 (220)
                          ...|+  ....+.+++++.....+..++..........   .........|....+.+++.+.++..++..   .+
T Consensus        69 ----~~~k~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (214)
T d1f44a2          69 ----GRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIY  144 (214)
T ss_dssp             ----CC--------CEEEECCHHHHHHHHHHHHHHCGGGSTTSBSSCCBCTTSCBCCCSSCCCCHHHHHHHHHHHHHHHH
T ss_pred             ----EECCCCCCCEECCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             ----3024564330010245366888775445542333232213321100124445643333443323333222322222


Q ss_pred             ----HCCC-CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             ----3388-654420245556543466438998999998589987899998412378899999999987
Q T0623           153 ----DVGI-DKEVSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHVTEQMDKDMMNKLEQ  216 (220)
Q Consensus       153 ----~~gi-~~~~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~~~~~~~~~~~~~~~~  216 (220)
                          .+|. ..+++||+||||+||.|+++|+|+..||+++||+|++||. +|.+..+....++++.|++
T Consensus       145 ~~~~~~~~~~~~~t~HslRht~at~l~~~G~~~~~i~~~~GH~s~~~~~-~Y~~~~~~~~~~~~~~l~~  212 (214)
T d1f44a2         145 GAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVM-NFIRNLDSETGAMVRLLED  212 (214)
T ss_dssp             CSCCTTCCTTSSCCTTHHHHHHHHHHHHTTCCHHHHHHHHTCCCHHHHH-HHTTTCCSCCCHHHHHHTT
T ss_pred             CCCCCCCCCCCCCCHHHHHCCCCHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHCCHHHHHHHHHHHHC
T ss_conf             2222011356678666641330027977799999999996899989999-9860334779999998862


No 5  
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]}
Probab=99.85  E-value=1.9e-22  Score=147.93  Aligned_cols=164  Identities=16%  Similarity=0.177  Sum_probs=108.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             98888999999986310111001002467899999999998617666888417532310247807872101023323465
Q T0623             1 YLELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDFDNKSLNINGTIHWFHDESGG   80 (220)
Q Consensus         1 yl~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~~~~~~i~i~~~~~~~~~~~~~   80 (220)
                      .||.||++++++.++....            .+..++.++++||||++|+++|+|+||+.+...+...            
T Consensus         3 ~lt~ee~~~l~~~~~~~~~------------~~~~~~~l~~~tG~R~~El~~L~~~di~~~~~~i~~~------------   58 (179)
T d1ae9a_           3 RLTADEYLKIYQAAESSPC------------WLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQS------------   58 (179)
T ss_dssp             CCCHHHHHHHHHHGGGSCH------------HHHHHHHHHHHHCCCHHHHHHCBGGGEETTEEEEECT------------
T ss_pred             CCCHHHHHHHHHHHHHCCH------------HHHHHHHHHHHHCCCCCCCCCCCEEEEEECCEEEEEC------------
T ss_conf             8999999999998756889------------9999999999967998764666202663011146411------------


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCC---
Q ss_conf             20124666876110256608999999999876422100245567887067123333323013455555556533886---
Q T0623            81 FGVKDTTKTESSYRTIGLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGID---  157 (220)
Q Consensus        81 ~~~~~~~k~~~~~R~vpi~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~---  157 (220)
                             |++. .+.+|+.+.....+..+........    ........+....+.+++...++..+....+.++..   
T Consensus        59 -------K~~~-~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (179)
T d1ae9a_          59 -------KTGV-KIAIPTALHIDALGISMKETLDKCK----EILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEG  126 (179)
T ss_dssp             -------TTCC-EEEEETTCEEGGGTEEHHHHHHHHH----HHTCCSBSSCCTTSCCCCHHHHHHHHHHHHHHHTCCCSS
T ss_pred             -------CCCC-CCCCCCCHHHHHHHHHHHHHHHHHC----CCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCC
T ss_conf             -------3333-2346674156778877655443311----357765213330477633453034666665311344332


Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             544202455565434664389989999985899878999984123
Q T0623           158 KEVSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHV  202 (220)
Q Consensus       158 ~~~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~~  202 (220)
                      ..+++|++||+ ++.++++|+|+..||+++||+|++||. +|.+.
T Consensus       127 ~~~~~h~lR~~-~t~~~~~g~~~~~i~~~lGH~s~~~t~-~Y~~~  169 (179)
T d1ae9a_         127 DPPTFHELRSL-SARLYEKQISDKFAQHLLGHKSDTMAS-QFRDD  169 (179)
T ss_dssp             SCCCTTHHHHH-HHHHHHHHTCHHHHHHHHTC---------CEEC
T ss_pred             CCCHHHHHHHH-HHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHC
T ss_conf             31037788888-889998499999999995899999999-98736


No 6  
>d1a41a_ d.163.1.2 (A:) Eukaryotic DNA topoisomerase I, catalytic core {Vaccinia virus [TaxId: 10245]}
Probab=97.09  E-value=0.0012  Score=38.38  Aligned_cols=131  Identities=17%  Similarity=0.247  Sum_probs=75.9

Q ss_pred             HHHHHHHHHHHCCCCHH-H----------HHCCCHHHCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCC-CCCCH
Q ss_conf             99999999986176668-8----------841753231024780787210102332346520124666876110-25660
Q T0623            32 FVALMTEFQALNGMRIG-E----------MLAIQNEDIDFDNKSLNINGTIHWFHDESGGFGVKDTTKTESSYR-TIGLS   99 (220)
Q Consensus        32 ~~~~~~~~~~~tGlR~~-E----------l~~L~~~di~~~~~~i~i~~~~~~~~~~~~~~~~~~~~k~~~~~R-~vpi~   99 (220)
                      .+++++.++-.+.+|+| |          +..|+..+|.++.+.+.+.  .              .+|.+..+. .+.-+
T Consensus        36 vlA~vv~Lld~~~iRvGne~Ya~~n~SyGltTLr~~Hv~i~~~~i~f~--F--------------~GKsGv~~~~~i~~d   99 (230)
T d1a41a_          36 QLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDEIVIK--F--------------VGKDKVSHEFVVHKS   99 (230)
T ss_dssp             HHHHHHHHHHCCC---------CCHHHHHHHTCBGGGEEEETTEEEEC--E--------------EETTTEEECCEEETT
T ss_pred             HHHHHHHHHHHHCEECCCHHHHHHCCCCCEEEEEHHHEEEECCEEEEE--E--------------ECCCCCEEEEEEECC
T ss_conf             999999999973651688656762598351220131067718926998--7--------------558773489988337


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHC---
Q ss_conf             89999999998764221002455678870671233333230134555555565338865442024555654346643---
Q T0623           100 SRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDKEVSSHILRHSHISLLSQQ---  176 (220)
Q Consensus       100 ~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~~~~~~H~lRht~at~l~~~---  176 (220)
                      +.+...+.......          ....++|.     .++...++..++..        .+|+..||-+.||.++..   
T Consensus       100 ~~l~~~l~~~~~~~----------~~~~~lf~-----~v~~~~vn~yl~~~--------~~taKdFRTw~at~~~~~~l~  156 (230)
T d1a41a_         100 NRLYKPLLKLTDDS----------SPEEFLFN-----KLSERKVYECIKQF--------GIRIKDLRTYGVNYTFLYNFW  156 (230)
T ss_dssp             SSSHHHHHHHCCTT----------CTTSBSST-----TCCHHHHHHHHHHT--------TCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCC----------CCCCCCCC-----CCCCHHHHHHHHHC--------CCCHHHHHHHCHHHHHHHHHH
T ss_conf             89999999998666----------95200000-----25633778888873--------760999998652899999998


Q ss_pred             -----CC-----------CHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             -----89-----------989999985899878999984123
Q T0623           177 -----GV-----------SLKAIMDRVGHSDHRTTLSIYSHV  202 (220)
Q Consensus       177 -----G~-----------~~~~i~~~lGH~s~~~t~~~Y~~~  202 (220)
                           ..           -+..+++.|||+ |+++-+.|+|-
T Consensus       157 ~~~~~~~~~~~~kk~i~~~i~~vA~~LgNT-paV~rksYI~P  197 (230)
T d1a41a_         157 TNVKSISPLPSPKKLIALTIKQTAEVVGHT-PSISKRAYMAT  197 (230)
T ss_dssp             HHHHHSSSCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHH
T ss_pred             HCCCCCCCHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHCCCH
T ss_conf             506877877788999999999999995897-66678865799


No 7  
>d1k4ta2 d.163.1.2 (A:431-640,A:713-765) Eukaryotic DNA topoisomerase I, catalytic core {Human (Homo sapiens) [TaxId: 9606]}
Probab=91.90  E-value=0.36  Score=23.93  Aligned_cols=122  Identities=16%  Similarity=0.220  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHCCCCHH------H------HHCCCHHHCCCCC------CCEEEEEEECCCCCCCCCCCCCCCCCCCC-C
Q ss_conf             99999999986176668------8------8417532310247------80787210102332346520124666876-1
Q T0623            32 FVALMTEFQALNGMRIG------E------MLAIQNEDIDFDN------KSLNINGTIHWFHDESGGFGVKDTTKTES-S   92 (220)
Q Consensus        32 ~~~~~~~~~~~tGlR~~------E------l~~L~~~di~~~~------~~i~i~~~~~~~~~~~~~~~~~~~~k~~~-~   92 (220)
                      ..++++.++-.+.+|+|      |      ++.|+..+|.+..      +.+.+.                -.+|.+. -
T Consensus        44 ~lA~al~LiD~~~lRvGneky~~en~dT~G~tTLr~eHv~l~~~~~~~~~~i~~~----------------F~GK~gvr~  107 (263)
T d1k4ta2          44 QRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFD----------------FLGKDSIRY  107 (263)
T ss_dssp             HHHHHHHHHHHSCCCCCCCCCTTTSCCCCCGGGCBGGGEEEEEEETTEEEEEEEE----------------EECGGGCEE
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHHEEECCCCCCCCCEEEEE----------------EECCCCEEE
T ss_conf             9999999999737316880013235897602002221157614656778558999----------------744776389


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf             10256608999999999876422100245567887067123333323013455555556533886544202455565434
Q T0623            93 YRTIGLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDKEVSSHILRHSHISL  172 (220)
Q Consensus        93 ~R~vpi~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~~~~~~H~lRht~at~  172 (220)
                      ...|++++.+...|+......          .+.+.+|     ..++...+|..++.+    +  ..+|+..||=+.||.
T Consensus       108 ~~~v~~~~~v~~~l~~~~~~k----------~~~d~LF-----~~i~s~~vN~yLk~~----~--~g~TaKdFRTw~As~  166 (263)
T d1k4ta2         108 YNKVPVEKRVFKNLQLFMENK----------QPEDDLF-----DRLNTGILNKHLQDL----M--EGLTAKVFRTYNASI  166 (263)
T ss_dssp             EEEEECCHHHHHHHHHHTTTC----------CTTSBSS-----TTCCHHHHHHHHHHH----S--TTCCTTHHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHHCC----------CCCHHHC-----CCCCHHHHHHHHHHH----C--CCCCEEECCCCCHHH
T ss_conf             999835889999999998766----------9821111-----668889999999996----6--997213021344699


Q ss_pred             HH-----HCCCC---H-----------HHHHHHHCCC
Q ss_conf             66-----43899---8-----------9999985899
Q T0623           173 LS-----QQGVS---L-----------KAIMDRVGHS  190 (220)
Q Consensus       173 l~-----~~G~~---~-----------~~i~~~lGH~  190 (220)
                      ++     +.+.+   .           ..|+-+++|.
T Consensus       167 ~~~~~L~~~~~~~~~~~~k~~~~n~Anr~VA~lcnHq  203 (263)
T d1k4ta2         167 TLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ  203 (263)
T ss_dssp             HHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHHHTTCB
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999998379998679999999999999999982887


No 8  
>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=47.31  E-value=4.4  Score=17.60  Aligned_cols=45  Identities=18%  Similarity=0.269  Sum_probs=26.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCH
Q ss_conf             888899999998631011100100246789999999999861766688841753
Q T0623             2 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQN   55 (220)
Q Consensus         2 l~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~   55 (220)
                      |+.+|.+++++...........-...+     .+    +.+.|+|+|+++.+..
T Consensus        13 l~~eE~~~il~~y~i~~~qLP~I~~~D-----Pv----a~~~g~~~GdvikI~R   57 (72)
T d1dzfa2          13 LSSDEKRELLKRYRLKESQLPRIQRAD-----PV----ALYLGLKRGEVVKIIR   57 (72)
T ss_dssp             CCHHHHHHHHHHTTCCGGGSCEECTTC-----HH----HHHHTCCTTCEEEEEC
T ss_pred             CCHHHHHHHHHHHCCCHHHCCEECCCC-----HH----HHHCCCCCCCEEEEEE
T ss_conf             599999999999598975799543639-----73----5611888897899997


No 9  
>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} SCOP: d1eika_ d1hmja_
Probab=44.71  E-value=5.1  Score=17.22  Aligned_cols=46  Identities=17%  Similarity=0.272  Sum_probs=26.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHH
Q ss_conf             8888999999986310111001002467899999999998617666888417532
Q T0623             2 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNE   56 (220)
Q Consensus         2 l~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~   56 (220)
                      |+.+|.+++++..+........-.+.+     .+    ..+.|+++|+++.+...
T Consensus        13 l~~eE~~~~l~~y~i~~~qLP~I~~~D-----Pv----a~~~g~k~GdvikI~R~   58 (72)
T d1dzfa2          13 LSSDEKRELLKRYRLKESQLPRIQRAD-----PV----ALYLGLKRGEVVKIIRK   58 (72)
T ss_dssp             CCHHHHHHHHHHTTCCGGGSCEECTTC-----HH----HHHHTCCTTCEEEEECT
T ss_pred             CCHHHHHHHHHHHCCCHHHCCEECCCC-----HH----HHHHCCCCCCEEEEEEC
T ss_conf             897899999987088968796631478-----30----43007998987889847


No 10 
>d1hmja_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanococcus jannaschii [TaxId: 2190]}
Probab=40.05  E-value=6.1  Score=16.77  Aligned_cols=45  Identities=20%  Similarity=0.278  Sum_probs=26.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCH
Q ss_conf             888899999998631011100100246789999999999861766688841753
Q T0623             2 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQN   55 (220)
Q Consensus         2 l~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~   55 (220)
                      |+.+|.+.+++...........-..     .+.+.    .+.|+++|+++.+..
T Consensus         6 l~~eE~~~ll~~y~i~~~qLP~I~~-----~DPva----~~~g~k~GdvvkI~R   50 (68)
T d1hmja_           6 VPKEEVEEILKRYNIKIQQLPKIYE-----DDPVI----QEIGAKEGDVVRVIR   50 (68)
T ss_pred             CCHHHHHHHHHHHCCCHHHCCCCCC-----CCHHH----HHHCCCCCCEEEEEE
T ss_conf             7999999999992989889991225-----19878----981999995899997


No 11 
>d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}
Probab=35.73  E-value=5.6  Score=17.00  Aligned_cols=45  Identities=13%  Similarity=0.296  Sum_probs=26.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCH
Q ss_conf             888899999998631011100100246789999999999861766688841753
Q T0623             2 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQN   55 (220)
Q Consensus         2 l~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~   55 (220)
                      |+.+|.+++++...........-...     +.+    +.+.|+++|+++.+.+
T Consensus        17 l~~ee~~~~l~~~~i~~~qLP~I~~~-----DPv----a~~~g~k~GdvvkI~R   61 (77)
T d1eika_          17 LNESEAKRVLKELDAHPEQLPKIKTT-----DPV----AKAIGAKRGDIVKIIR   61 (77)
T ss_dssp             ECHHHHHHHHHHTTCCTTTSCCCBTT-----SHH----HHGGGCCTTCEEEEEE
T ss_pred             CCHHHHHHHHHHHCCCHHHCCEECCC-----CHH----HHHHCCCCCCEEEEEE
T ss_conf             69999999999856998789940362-----972----4510786885799997


No 12 
>d1j09a1 a.97.1.1 (A:306-468) C-terminal domain of glutamyl-tRNA synthetase (GluRS) {Thermus thermophilus [TaxId: 274]}
Probab=30.45  E-value=15  Score=14.44  Aligned_cols=55  Identities=20%  Similarity=0.222  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf             230134555555565338865442024555654346643899899999858998789999
Q T0623           138 MQTERFNKILREAAKDVGIDKEVSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLS  197 (220)
Q Consensus       138 l~~~~i~~~l~~~~~~~gi~~~~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~  197 (220)
                      .+..++...++.+++..|+..+--++.+|-.  ..--..|.++..++..+|   .+.|.+
T Consensus       102 ~~~~~i~~~ik~~~~~~~~k~k~l~~plR~a--ltG~~~GP~i~~i~~llG---ke~~l~  156 (163)
T d1j09a1         102 WTEAALEALLRGFAAEKGVKLGQVAQPLRAA--LTGSLETPGLFEILALLG---KERALR  156 (163)
T ss_dssp             CSHHHHHHHHHHHHHHHTSCHHHHHHHHHHH--HHSCSCCSCHHHHHHHTC---HHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHCCCHHHHHHHHHHH--HHCCCCCCCHHHHHHHHC---HHHHHH
T ss_conf             7857799999999986078667889888887--726777887999999957---689999


No 13 
>d1j09a1 a.97.1.1 (A:306-468) C-terminal domain of glutamyl-tRNA synthetase (GluRS) {Thermus thermophilus [TaxId: 274]}
Probab=26.63  E-value=18  Score=14.04  Aligned_cols=49  Identities=20%  Similarity=0.213  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             230134555555565338865442024555654346643899899999858
Q T0623           138 MQTERFNKILREAAKDVGIDKEVSSHILRHSHISLLSQQGVSLKAIMDRVG  188 (220)
Q Consensus       138 l~~~~i~~~l~~~~~~~gi~~~~~~H~lRht~at~l~~~G~~~~~i~~~lG  188 (220)
                      .+..++...++.+++..|+..+--++.+|-.  ..-...|.++..++.++|
T Consensus       102 ~~~~~i~~~i~~~~~~~~ik~~~v~~plR~a--ltG~~~gP~l~~~i~llG  150 (163)
T d1j09a1         102 WTEAALEALLRGFAAEKGVKLGQVAQPLRAA--LTGSLETPGLFEILALLG  150 (163)
T ss_dssp             CSHHHHHHHHHHHHHHHTSCHHHHHHHHHHH--HHSCSCCSCHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCHHHH--HCCCCCCCCHHHHHHHHC
T ss_conf             2288898899999998087733343405754--148998979999999928


No 14 
>d1uoua1 a.46.2.1 (A:33-100) Thymidine phosphorylase {Human (Homo sapiens) [TaxId: 9606]}
Probab=22.98  E-value=21  Score=13.63  Aligned_cols=45  Identities=16%  Similarity=0.205  Sum_probs=26.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCH
Q ss_conf             888899999998631011100100246789999999999861766688841753
Q T0623             2 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQN   55 (220)
Q Consensus         2 l~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~   55 (220)
                      |+.+|++.+++.+-.-.-..         .....++.-+..-|+-..|+.++..
T Consensus        17 Ls~~E~~~~~~~i~~g~~s~---------~qi~afL~al~~kG~t~~Ei~~~t~   61 (68)
T d1uoua1          17 LSEADIRGFVAAVVNGSAQG---------AQIGAMLMAIRLRGMDLEETSVLTQ   61 (68)
T ss_dssp             CCHHHHHHHHHHHHHTCSCH---------HHHHHHHHHHHHHCCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCH---------HHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             99999999999998499889---------9999999999982999999999999


Done!