Query         gi|254780882|ref|YP_003065295.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 328
No_of_seqs    176 out of 10042
Neff          8.9 
Searched_HMMs 13730
Date          Wed Jun  1 10:50:18 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780882.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 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 1.1E-33 8.4E-38  226.8   4.4  176  127-307     1-178 (182)
  2 d1aiha_ d.163.1.1 (A:) Integra 100.0 1.2E-30 8.9E-35  207.9   4.7  164  126-322     4-167 (170)
  3 d1f44a2 d.163.1.1 (A:130-343)   99.9 7.3E-28 5.3E-32  190.5   6.2  185  125-316     4-212 (214)
  4 d1ae9a_ d.163.1.1 (A:) Integra  99.9 1.1E-24 7.8E-29  170.7   4.2  165  127-301     2-169 (179)
  5 d1a0pa1 a.60.9.1 (A:3-100) Rec  99.8 6.7E-19 4.9E-23  134.5   7.5   95   16-116     4-98  (98)
  6 d1f44a1 a.60.9.1 (A:20-129) Cr  99.4 1.7E-13 1.2E-17  100.8   5.4   84   16-105     3-86  (110)
  7 d1a41a_ d.163.1.2 (A:) Eukaryo  96.9  0.0011 8.2E-08   39.4   6.0  122  159-300    40-196 (230)
  8 d1k4ta2 d.163.1.2 (A:431-640,A  95.9  0.0048 3.5E-07   35.5   4.6  101  173-290    74-203 (263)
  9 d1a0pa1 a.60.9.1 (A:3-100) Rec  92.1   0.043 3.2E-06   29.5   2.7   40   68-107     3-43  (98)
 10 d2e1za1 c.55.1.2 (A:4-192) Pro  35.1      11 0.00077   14.6   3.8   24  248-272   158-181 (189)

No 1  
>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=99.97  E-value=1.1e-33  Score=226.77  Aligned_cols=176  Identities=36%  Similarity=0.490  Sum_probs=146.1

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCC
Q ss_conf             11111015678776531013567757753201222100112332222211222223323220332378531000112210
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSV  206 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~  206 (328)
                      +.||.+|+.++++++..     ....++||++||.++++||||++|+++|+|+||+++.+.+.+.+|+.|.|.++.....
T Consensus         1 k~Lt~eei~~ll~~~~~-----~~~~~lRd~~l~~l~~~tG~R~~ei~~L~~~~i~~~~~~i~~~~~~~k~r~~~~~~~~   75 (182)
T d1a0pa2           1 KDLSEAQVERLLQAPLI-----DQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEA   75 (182)
T ss_dssp             CCCCHHHHHHHHHCSCT-----TSHHHHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEEEEECSSSCEEEEECCHHH
T ss_pred             CCCCHHHHHHHHHCCCC-----CCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCEEEEEECCCCEEEEEEECCHH
T ss_conf             98999999999827463-----8818799999999999967764774202141411443289983689801257520013


Q ss_pred             HHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf             023432211100123-446655432111122111000123567899976869-998805417999999998489988999
Q gi|254780882|r  207 RKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFATHLLSNGGDLRSIQ  284 (328)
Q Consensus       207 ~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt~ll~~G~~~~~v~  284 (328)
                      ...+..++....... ......+++++..+.+++.+++++.++++++.+|++ .+++||+|||||||.|+++|+|+.+|+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~t~H~~Rht~at~l~~~G~~~~~I~  155 (182)
T d1a0pa2          76 VYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQ  155 (182)
T ss_dssp             HHHHHHHHHHTHHHHHTTCCCCBSSBCTTSSBCCHHHHHHHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHCSSCGGGS
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHH
T ss_conf             35566655311230012345654210235773668999999999999849985783614146589996556499999999


Q ss_pred             HHHCCCCHHHHHHHHHHCHHHHH
Q ss_conf             98378887897999961989999
Q gi|254780882|r  285 SILGHFRLSTTQIYTNVNSKNGG  307 (328)
Q Consensus       285 ~~lGH~s~~tT~~Y~h~~~~~~~  307 (328)
                      ++|||+|++||++|+|++.++.+
T Consensus       156 ~~lGH~s~~tt~~Y~~~~~e~~r  178 (182)
T d1a0pa2         156 MLLGHSDLSTTQIYTHVATERLR  178 (182)
T ss_dssp             SCC--CCCCHHHHHHHHHHHHHH
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHH
T ss_conf             99589988999987687999999


No 2  
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]}
Probab=99.96  E-value=1.2e-30  Score=207.85  Aligned_cols=164  Identities=24%  Similarity=0.291  Sum_probs=123.8

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCC
Q ss_conf             11111101567877653101356775775320122210011233222221122222332322033237853100011221
Q gi|254780882|r  126 PRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPS  205 (328)
Q Consensus       126 p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~  205 (328)
                      ..+||.+|+.++++++.....+       ..++++.+++.||||+||+++|+|+||+++.. ..+.+|++++|.|||++.
T Consensus         4 ~~~Lt~eEi~~l~~~~~~~~~~-------~~~~~i~l~~~tG~R~~E~~~L~~~dI~~~~~-~~~~~K~~~~r~ipl~~~   75 (170)
T d1aiha_           4 LAFLYERDIYRLLAECDNSRNP-------DLGLIVRICLATGARWSEAETLTQSQVMPYKI-TFTNTKSKKNRTVPISDE   75 (170)
T ss_dssp             CCCCCHHHHHHHHHHHTTSSST-------THHHHHHHHHHHCCCHHHHHTCBTTTEETTEE-EEESSSSSCEEEEECCHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCH-------HHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCE-EECCCCCCCHHHHHHHHH
T ss_conf             6689999999999986365896-------69999999999777611244433102442110-211444430057766999


Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
Q ss_conf             00234322111001234466554321111221110001235678999768699988054179999999984899889999
Q gi|254780882|r  206 VRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQS  285 (328)
Q Consensus       206 ~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~  285 (328)
                      +.+.|..+            .+++|...        .............+++++++||+|||||||.|+++|+|+.+|++
T Consensus        76 ~~~~l~~~------------~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~~g~~~~~i~~  135 (170)
T d1aiha_          76 LFDMLPKK------------RGRLFNDA--------YESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKE  135 (170)
T ss_dssp             HHHHSCCC------------SSBSSCCC--------HHHHHHHHHHTTCCCCTTCTTTHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHH------------HCCCCCCC--------HHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHCCCCCHHHHHH
T ss_conf             99998751------------00110111--------12443345666502577610111046551455216989999999


Q ss_pred             HHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHH
Q ss_conf             8378887897999961989999999999998173000
Q gi|254780882|r  286 ILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSIT  322 (328)
Q Consensus       286 ~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~  322 (328)
                      +|||+|++||++|+|+++++.    ++++ +.||+..
T Consensus       136 ~lGH~~~~~t~~Y~~~~~~~~----~~a~-~~~p~~~  167 (170)
T d1aiha_         136 ILGHSTIEMTMRYAHFAPSHL----ESAV-KFNPLSN  167 (170)
T ss_dssp             HHTCSSHHHHGGGGGGSCCCT----THHH-HHSTTTS
T ss_pred             HHCCCCHHHHHHHHCCCHHHH----HHHH-HHCCCCC
T ss_conf             808999899998876799999----9999-8685768


No 3  
>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]}
Probab=99.94  E-value=7.3e-28  Score=190.50  Aligned_cols=185  Identities=16%  Similarity=0.117  Sum_probs=131.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---EEEC-CC---CCCC
Q ss_conf             111111101567877653101356775775320122210011233222221122222332322---0332-37---8531
Q gi|254780882|r  125 LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQST---LRIQ-GK---GDKI  197 (328)
Q Consensus       125 ~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~---i~v~-gK---g~K~  197 (328)
                      .+.+++.+|+..+...+.    ......++||++|+.|+|.||||++|+++|+|+||++..+.   +.+. +|   +.+.
T Consensus         4 ~~~~~~~~e~~~~~~~~~----~~~~~~~~R~~ali~l~~~tGlR~~Ei~~L~~~di~~~~~~~~~i~i~~~k~~~~~~~   79 (214)
T d1f44a2           4 QALAFERTDFDQVRSLME----NSDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAG   79 (214)
T ss_dssp             CCCCCCHHHHHHHHHHHT----TCCCHHHHHHHHHHHHHHHHCCCHHHHHHCBGGGEEECGGGCEEEEECC--------C
T ss_pred             CCCCCCHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHHHHCCCHHHHHHCCCCEEECCCCCCEEEEEEECCCCCCCEE
T ss_conf             467799999999999986----2472263899999999999810777787512311202333103666630245643300


Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC---------CCCCCCCCCCHHHHHHHH---HHHC----CC-CCCC
Q ss_conf             00011221002343221110012344665543211---------112211100012356789---9976----86-9998
Q gi|254780882|r  198 RIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRG---------IRGKPLNPGVFQRYIRQL---RRYL----GL-PLST  260 (328)
Q Consensus       198 R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~---------~~g~~ls~~~i~~~~~~~---~~~~----gi-~~~~  260 (328)
                      +.+++++.....+..++..+....  ...+++|..         ..+.+++.+.+...++..   .+.+    |. ..++
T Consensus        80 ~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (214)
T d1f44a2          80 VEKALSLGVTKLVERWISVSGVAD--DPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAW  157 (214)
T ss_dssp             EEEECCHHHHHHHHHHHHHHCGGG--STTSBSSCCBCTTSCBCCCSSCCCCHHHHHHHHHHHHHHHHCSCCTTCCTTSSC
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCC--CCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             102453668887754455423332--322133211001244456433334433233332223222222222011356678


Q ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHH
Q ss_conf             80541799999999848998899998378887897999961989999999999998
Q gi|254780882|r  261 TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQ  316 (328)
Q Consensus       261 spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~  316 (328)
                      |||+|||||||.|+++|+|+..||++|||+|++||++|++..++ ...++.++.++
T Consensus       158 t~HslRht~at~l~~~G~~~~~i~~~~GH~s~~~~~~Y~~~~~~-~~~~~~~~l~~  212 (214)
T d1f44a2         158 SGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNFIRNLDS-ETGAMVRLLED  212 (214)
T ss_dssp             CTTHHHHHHHHHHHHTTCCHHHHHHHHTCCCHHHHHHHTTTCCS-CCCHHHHHHTT
T ss_pred             CHHHHHCCCCHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHH-HHHHHHHHHHC
T ss_conf             66664133002797779999999999689998999998603347-79999998862


No 4  
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]}
Probab=99.89  E-value=1.1e-24  Score=170.74  Aligned_cols=165  Identities=18%  Similarity=0.201  Sum_probs=128.3

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCC
Q ss_conf             11111015678776531013567757753201222100112332222211222223323220332378531000112210
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSV  206 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~  206 (328)
                      +.||.||+.++++++....+    +.    ++++.|++.||||++|+++|+|+||+.+...+ ..+|+++.+.+|+.+..
T Consensus         2 ~~lt~ee~~~l~~~~~~~~~----~~----~~~~~l~~~tG~R~~El~~L~~~di~~~~~~i-~~~K~~~~~~~~~~~~~   72 (179)
T d1ae9a_           2 SRLTADEYLKIYQAAESSPC----WL----RLAMELAVVTGQRVGDLCEMKWSDIVDGYLYV-EQSKTGVKIAIPTALHI   72 (179)
T ss_dssp             CCCCHHHHHHHHHHGGGSCH----HH----HHHHHHHHHHCCCHHHHHHCBGGGEETTEEEE-ECTTTCCEEEEETTCEE
T ss_pred             CCCCHHHHHHHHHHHHHCCH----HH----HHHHHHHHHHCCCCCCCCCCCEEEEEECCEEE-EECCCCCCCCCCCCHHH
T ss_conf             98999999999998756889----99----99999999967998764666202663011146-41133332346674156


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC---CCCCCCCCHHHHHHHHHHCCCCHHHH
Q ss_conf             023432211100123446655432111122111000123567899976869---99880541799999999848998899
Q gi|254780882|r  207 RKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP---LSTTAHTLRHSFATHLLSNGGDLRSI  283 (328)
Q Consensus       207 ~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~---~~~spH~lRHtfAt~ll~~G~~~~~v  283 (328)
                      ...+..+...............++.+..|.+++...+.+.+....+.++..   ...++|++||+ ||.++++|+|+..|
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lR~~-~t~~~~~g~~~~~i  151 (179)
T d1ae9a_          73 DALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSL-SARLYEKQISDKFA  151 (179)
T ss_dssp             GGGTEEHHHHHHHHHHHTCCSBSSCCTTSCCCCHHHHHHHHHHHHHHHTCCCSSSCCCTTHHHHH-HHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHH-HHHHHHCCCCHHHH
T ss_conf             77887765544331135776521333047763345303466666531134433231037788888-88999849999999


Q ss_pred             HHHHCCCCHHHHHHHHHH
Q ss_conf             998378887897999961
Q gi|254780882|r  284 QSILGHFRLSTTQIYTNV  301 (328)
Q Consensus       284 ~~~lGH~s~~tT~~Y~h~  301 (328)
                      |.+|||+|++||++|.+.
T Consensus       152 ~~~lGH~s~~~t~~Y~~~  169 (179)
T d1ae9a_         152 QHLLGHKSDTMASQFRDD  169 (179)
T ss_dssp             HHHHTC--------CEEC
T ss_pred             HHHHCCCCHHHHHHHHHC
T ss_conf             999589999999998736


No 5  
>d1a0pa1 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=99.76  E-value=6.7e-19  Score=134.51  Aligned_cols=95  Identities=20%  Similarity=0.340  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999862548899999999999999999851214788789689899999999999986121013321123444
Q gi|254780882|r   16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGI   95 (328)
Q Consensus        16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~l   95 (328)
                      +.+++||+++..|||+||+|+++|+.++..|..||....      .++.+++..+|..|+.++.++|++++|+++++++|
T Consensus         4 ~~ie~fl~~l~~erg~S~~Ti~aY~~dl~~f~~~l~~~~------~~~~~i~~~~i~~yl~~l~~~g~s~~Ti~r~lsal   77 (98)
T d1a0pa1           4 ARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRG------LTLATAQSDDLQALLAERLEGGYKATSSARLLSAV   77 (98)
T ss_dssp             HHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHTS------CCTTTCCHHHHHHHHHSCC-------CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC------CCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             999999999998849599999999999999999887616------44111558999999999985245510599999999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCC
Q ss_conf             222233321012322222222
Q gi|254780882|r   96 KSFLKYLKKRKITTESNILNM  116 (328)
Q Consensus        96 r~f~~~~~~~~~i~~np~~~i  116 (328)
                      |+||+||..+|+++.||+..|
T Consensus        78 r~ff~~l~~~~~i~~nP~~~i   98 (98)
T d1a0pa1          78 RRLFQYLYREKFREDDPSAHL   98 (98)
T ss_dssp             HHHHHHHHHTTSSSSCTTSCC
T ss_pred             HHHHHHHHHCCCCCCCCCCCC
T ss_conf             999999999789376833419


No 6  
>d1f44a1 a.60.9.1 (A:20-129) Cre recombinase {Bacteriophage P1 [TaxId: 10678]}
Probab=99.39  E-value=1.7e-13  Score=100.82  Aligned_cols=84  Identities=8%  Similarity=0.143  Sum_probs=73.9

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999862548899999999999999999851214788789689899999999999986121013321123444
Q gi|254780882|r   16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGI   95 (328)
Q Consensus        16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~l   95 (328)
                      ++.++|+++++.++++|+||+++|..||+.|..||.....      ++-.++..+|..|+.++...|++++|+++++++|
T Consensus         3 ~~~~~~~~~l~~~~~~S~nT~~aY~~dl~~f~~w~~~~~~------~~l~~~~~~v~~yl~~l~~~g~s~sTi~R~lsai   76 (110)
T d1f44a1           3 EVRKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNR------KWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQL   76 (110)
T ss_dssp             TTHHHHHSCCSCGGGSCHHHHHHHHHHHHHHHHHHHHTTC------CTTTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC------CCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             8999999999998653898999999999999998865112------3462345378999999986388840899999999


Q ss_pred             HHHHHHHHHH
Q ss_conf             2222333210
Q gi|254780882|r   96 KSFLKYLKKR  105 (328)
Q Consensus        96 r~f~~~~~~~  105 (328)
                      ++|++|+...
T Consensus        77 r~f~r~~g~~   86 (110)
T d1f44a1          77 NMLHRRSGLP   86 (110)
T ss_dssp             HHHHHHTTCC
T ss_pred             HHHHHHCCCC
T ss_conf             9999986999


No 7  
>d1a41a_ d.163.1.2 (A:) Eukaryotic DNA topoisomerase I, catalytic core {Vaccinia virus [TaxId: 10245]}
Probab=96.87  E-value=0.0011  Score=39.40  Aligned_cols=122  Identities=16%  Similarity=0.188  Sum_probs=72.7

Q ss_pred             CCCCCCCCCCCCCC-----------CCCCCCCCCCCCCCCEEE--CCCCCCCCCCCC--CCCCHHHHHHHHHHHCCCCCC
Q ss_conf             22210011233222-----------221122222332322033--237853100011--221002343221110012344
Q gi|254780882|r  159 ILYLLYGCGLRISE-----------ALSLTPQNIMDDQSTLRI--QGKGDKIRIVPL--LPSVRKAILEYYDLCPFDLNL  223 (328)
Q Consensus       159 i~~ll~~TGlR~~E-----------l~~L~~~did~~~~~i~v--~gKg~K~R~Vpi--~~~~~~~l~~yl~~~~~~~~~  223 (328)
                      ++.|+-.|.+|+|-           ++.|+.+||....+.+.+  .||+|+++.+-+  .+.+...+....+      ..
T Consensus        40 vv~Lld~~~iRvGne~Ya~~n~SyGltTLr~~Hv~i~~~~i~f~F~GKsGv~~~~~i~~d~~l~~~l~~~~~------~~  113 (230)
T d1a41a_          40 FMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDEIVIKFVGKDKVSHEFVVHKSNRLYKPLLKLTD------DS  113 (230)
T ss_dssp             HHHHHHCCC---------CCHHHHHHHTCBGGGEEEETTEEEECEEETTTEEECCEEETTSSSHHHHHHHCC------TT
T ss_pred             HHHHHHHHCEECCCHHHHHHCCCCCEEEEEHHHEEEECCEEEEEEECCCCCEEEEEEECCHHHHHHHHHHHH------CC
T ss_conf             999999736516886567625983512201310677189269987558773489988337899999999986------66


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH-----H---CCCC-----------HHHHH
Q ss_conf             665543211112211100012356789997686999880541799999999-----8---4899-----------88999
Q gi|254780882|r  224 NIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLL-----S---NGGD-----------LRSIQ  284 (328)
Q Consensus       224 ~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll-----~---~G~~-----------~~~v~  284 (328)
                      .++.++|.     .++...++.+++    ..    .+|+.+||-..||.++     .   ...+           +..|+
T Consensus       114 ~~~~~lf~-----~v~~~~vn~yl~----~~----~~taKdFRTw~at~~~~~~l~~~~~~~~~~~~~kk~i~~~i~~vA  180 (230)
T d1a41a_         114 SPEEFLFN-----KLSERKVYECIK----QF----GIRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTIKQTA  180 (230)
T ss_dssp             CTTSBSST-----TCCHHHHHHHHH----HT----TCCHHHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCC-----CCCCHHHHHHHH----HC----CCCHHHHHHHCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             95200000-----256337788888----73----760999998652899999998506877877788999999999999


Q ss_pred             HHHCCCCHHHH-HHHHH
Q ss_conf             98378887897-99996
Q gi|254780882|r  285 SILGHFRLSTT-QIYTN  300 (328)
Q Consensus       285 ~~lGH~s~~tT-~~Y~h  300 (328)
                      +.|||+ ++++ .-|.|
T Consensus       181 ~~LgNT-paV~rksYI~  196 (230)
T d1a41a_         181 EVVGHT-PSISKRAYMA  196 (230)
T ss_dssp             HHHSSC-CCHHHHHHHH
T ss_pred             HHHCCC-HHHHHHHCCC
T ss_conf             995897-6667886579


No 8  
>d1k4ta2 d.163.1.2 (A:431-640,A:713-765) Eukaryotic DNA topoisomerase I, catalytic core {Human (Homo sapiens) [TaxId: 9606]}
Probab=95.91  E-value=0.0048  Score=35.50  Aligned_cols=101  Identities=22%  Similarity=0.197  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCC------CCCEEE--CCCCCCC--CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             221122222332------322033--2378531--000112210023432211100123446655432111122111000
Q gi|254780882|r  173 ALSLTPQNIMDD------QSTLRI--QGKGDKI--RIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGV  242 (328)
Q Consensus       173 l~~L~~~did~~------~~~i~v--~gKg~K~--R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~  242 (328)
                      ++.|+.+||.+.      .+.|.+  .||.|..  ..|++.+.+...|....+.      ..+++.||     .+++...
T Consensus        74 ~tTLr~eHv~l~~~~~~~~~~i~~~F~GK~gvr~~~~v~~~~~v~~~l~~~~~~------k~~~d~LF-----~~i~s~~  142 (263)
T d1k4ta2          74 CCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMEN------KQPEDDLF-----DRLNTGI  142 (263)
T ss_dssp             GGGCBGGGEEEEEEETTEEEEEEEEEECGGGCEEEEEEECCHHHHHHHHHHTTT------CCTTSBSS-----TTCCHHH
T ss_pred             EEECCHHHEEECCCCCCCCCEEEEEEECCCCEEEEEEEECCHHHHHHHHHHHHC------CCCCHHHC-----CCCCHHH
T ss_conf             200222115761465677855899974477638999983588999999999876------69821111-----6688899


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH-----HCCCC--------------HHHHHHHHCCC
Q ss_conf             12356789997686999880541799999999-----84899--------------88999983788
Q gi|254780882|r  243 FQRYIRQLRRYLGLPLSTTAHTLRHSFATHLL-----SNGGD--------------LRSIQSILGHF  290 (328)
Q Consensus       243 i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll-----~~G~~--------------~~~v~~~lGH~  290 (328)
                      ++.+    .+.+|  ..+|+.+||--.||.++     +.+.+              ...|+-+++|.
T Consensus       143 vN~y----Lk~~~--~g~TaKdFRTw~As~~~~~~L~~~~~~~~~~~~k~~~~n~Anr~VA~lcnHq  203 (263)
T d1k4ta2         143 LNKH----LQDLM--EGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ  203 (263)
T ss_dssp             HHHH----HHHHS--TTCCTTHHHHHHHHHHHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHHHTTCB
T ss_pred             HHHH----HHHHC--CCCCEEECCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999----99966--9972130213446999999998379998679999999999999999982887


No 9  
>d1a0pa1 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=92.07  E-value=0.043  Score=29.50  Aligned_cols=40  Identities=13%  Similarity=0.361  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999998-6121013321123444222233321012
Q gi|254780882|r   68 YTEIRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKKRKI  107 (328)
Q Consensus        68 ~~~i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~~~~  107 (328)
                      ...|..|+.++. ++|+|+.|+..|...|+.|++|+..++.
T Consensus         3 ~~~ie~fl~~l~~erg~S~~Ti~aY~~dl~~f~~~l~~~~~   43 (98)
T d1a0pa1           3 LARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRGL   43 (98)
T ss_dssp             HHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             89999999999988495999999999999999998876164


No 10 
>d2e1za1 c.55.1.2 (A:4-192) Propionate kinase {Salmonella typhimurium [TaxId: 90371]}
Probab=35.15  E-value=11  Score=14.59  Aligned_cols=24  Identities=17%  Similarity=0.224  Sum_probs=19.0

Q ss_pred             HHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             7899976869998805417999999
Q gi|254780882|r  248 RQLRRYLGLPLSTTAHTLRHSFATH  272 (328)
Q Consensus       248 ~~~~~~~gi~~~~spH~lRHtfAt~  272 (328)
                      ..+.++.|+ .++.+|.+=|-+.+.
T Consensus       158 ~~~~~~~gI-RRYGFHGlS~~yva~  181 (189)
T d2e1za1         158 WEYFSSLGV-RRYGFHGTSHRYVSR  181 (189)
T ss_dssp             HHHHHTTCC-SCCCSCHHHHHHHHH
T ss_pred             HHHHHHCCC-EEECHHHHHHHHHHH
T ss_conf             999986596-062230772999999


Done!