Query         gi|255764498|ref|YP_003065000.2| site-specific tyrosine recombinase XerD [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 300
No_of_seqs    163 out of 12975
Neff          9.6 
Searched_HMMs 13730
Date          Wed Jun  1 09:44:24 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764498.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-35 7.8E-40  224.2   4.7  180   98-285     1-181 (182)
  2 d1aiha_ d.163.1.1 (A:) Integra 100.0 1.1E-31 7.8E-36  201.0   5.0  166   96-294     3-168 (170)
  3 d1f44a2 d.163.1.1 (A:130-343)   99.9 2.1E-28 1.5E-32  181.8   7.8  176   96-279     4-201 (214)
  4 d1ae9a_ d.163.1.1 (A:) Integra  99.9 7.6E-25 5.5E-29  161.1   2.3  166   98-276     2-169 (179)
  5 d1a0pa1 a.60.9.1 (A:3-100) Rec  99.7 2.1E-18 1.5E-22  123.6   4.5   86    2-87     13-98  (98)
  6 d1f44a1 a.60.9.1 (A:20-129) Cr  99.4 1.1E-13 7.8E-18   96.3   7.9   75    1-75     11-85  (110)
  7 d1a41a_ d.163.1.2 (A:) Eukaryo  97.2 0.00051 3.7E-08   40.0   6.5  124  130-275    38-196 (230)
  8 d1k4ta2 d.163.1.2 (A:431-640,A  96.6  0.0045 3.3E-07   34.5   7.5  117  130-265    46-203 (263)
  9 d1a0pa1 a.60.9.1 (A:3-100) Rec  94.5   0.032 2.4E-06   29.5   5.2   38   40-77      4-42  (98)
 10 d1p4ea2 d.163.1.1 (A:136-422)   91.7     0.3 2.2E-05   23.9   6.6  146  129-277    43-212 (287)
 11 d1f44a1 a.60.9.1 (A:20-129) Cr  82.2   0.074 5.4E-06   27.4  -1.2   37   42-78      5-42  (110)
 12 d1dzfa2 d.78.1.1 (A:144-215) E  26.3      15  0.0011   14.0   1.9   49   98-153    11-59  (72)
 13 d1eika_ d.78.1.1 (A:) RNA poly  20.5      21  0.0015   13.2   1.7   49   98-153    15-63  (77)
 14 d1hmja_ d.78.1.1 (A:) RNA poly  20.5      19  0.0014   13.4   1.4   49   98-153     4-52  (68)

No 1  
>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=100.00  E-value=1.1e-35  Score=224.22  Aligned_cols=180  Identities=43%  Similarity=0.642  Sum_probs=147.2

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf             23320246999986432001256102776543110001221001343334320000011110001112221111100001
Q gi|255764498|r   98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSP  177 (300)
Q Consensus        98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k~R~ipi~~  177 (300)
                      +.||+||+++|+++...       .....+||+++|.++++||||++|+++|+|+||+++++.+.+.+|++|.|.++.+.
T Consensus         1 k~Lt~eei~~ll~~~~~-------~~~~~lRd~~l~~l~~~tG~R~~ei~~L~~~~i~~~~~~i~~~~~~~k~r~~~~~~   73 (182)
T d1a0pa2           1 KDLSEAQVERLLQAPLI-------DQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGE   73 (182)
T ss_dssp             CCCCHHHHHHHHHCSCT-------TSHHHHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEEEEECSSSCEEEEECCH
T ss_pred             CCCCHHHHHHHHHCCCC-------CCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCEEEEEECCCCEEEEEEECC
T ss_conf             98999999999827463-------88187999999999999677647742021414114432899836898012575200


Q ss_pred             HHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHH
Q ss_conf             24788753232100124-67775200123332222211111110123442014667642598858899999998588888
Q gi|255764498|r  178 SALHALQMYKKTCSSMK-MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLR  256 (300)
Q Consensus       178 ~~~~~l~~y~~~~~~~~-~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~  256 (300)
                      .....+..++....... ......++++ ..++.+++.++++..++++++.+|++.++++||+|||||||.|+++|+|+.
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~t~H~~Rht~at~l~~~G~~~~  152 (182)
T d1a0pa2          74 EAVYWLETYLEHGRPWLLNGVSIDVLFP-SQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLR  152 (182)
T ss_dssp             HHHHHHHHHHHHTHHHHHTTCCCCBSSB-CTTSSBCCHHHHHHHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHCSSCG
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCHH
T ss_conf             1335566655311230012345654210-235773668999999999999849985783614146589996556499999


Q ss_pred             HHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             99998558998998999645999999999
Q gi|255764498|r  257 TIQILLGHTDISTTQIYTHLLPDKLQKLV  285 (300)
Q Consensus       257 ~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~  285 (300)
                      .|+++|||+|++||++|++++.+++++++
T Consensus       153 ~I~~~lGH~s~~tt~~Y~~~~~e~~re~~  181 (182)
T d1a0pa2         153 VVQMLLGHSDLSTTQIYTHVATERLRQLH  181 (182)
T ss_dssp             GGSSCC--CCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999589988999987687999999860


No 2  
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]}
Probab=99.97  E-value=1.1e-31  Score=200.97  Aligned_cols=166  Identities=28%  Similarity=0.408  Sum_probs=125.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHH
Q ss_conf             12233202469999864320012561027765431100012210013433343200000111100011122211111000
Q gi|255764498|r   96 LPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVIL  175 (300)
Q Consensus        96 ~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k~R~ipi  175 (300)
                      ...+|+++|+.+|++++.... .        ...++++.++++||||++|+++|+|+||+++. ...+.+|++++|.|||
T Consensus         3 ~~~~Lt~eEi~~l~~~~~~~~-~--------~~~~~~i~l~~~tG~R~~E~~~L~~~dI~~~~-~~~~~~K~~~~r~ipl   72 (170)
T d1aiha_           3 ELAFLYERDIYRLLAECDNSR-N--------PDLGLIVRICLATGARWSEAETLTQSQVMPYK-ITFTNTKSKKNRTVPI   72 (170)
T ss_dssp             CCCCCCHHHHHHHHHHHTTSS-S--------TTHHHHHHHHHHHCCCHHHHHTCBTTTEETTE-EEEESSSSSCEEEEEC
T ss_pred             CCCCCCHHHHHHHHHHHHHCC-C--------HHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCC-EEECCCCCCCHHHHHH
T ss_conf             466899999999999863658-9--------66999999999977761124443310244211-0211444430057766


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCH
Q ss_conf             01247887532321001246777520012333222221111111012344201466764259885889999999858888
Q gi|255764498|r  176 SPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADL  255 (300)
Q Consensus       176 ~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~  255 (300)
                      ++.+.++|..+            ..++|+...       ..+...+  .....++. ++++||+|||||||.|+++|+|+
T Consensus        73 ~~~~~~~l~~~------------~~~~~~~~~-------~~~~~~~--~~~~~~~~-~~~~~H~lRht~at~l~~~g~~~  130 (170)
T d1aiha_          73 SDELFDMLPKK------------RGRLFNDAY-------ESFENAV--LRAEIELP-KGQLTHVLRHTFASHFMMNGGNI  130 (170)
T ss_dssp             CHHHHHHSCCC------------SSBSSCCCH-------HHHHHHH--HHTTCCCC-TTCTTTHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHH------------HCCCCCCCH-------HHHHHHH--HHHHHCCC-CCCEEEECHHHHHHHHHCCCCCH
T ss_conf             99999998751------------001101111-------2443345--66650257-76101110465514552169899


Q ss_pred             HHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHC
Q ss_conf             899998558998998999645999999999982801110
Q gi|255764498|r  256 RTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKK  294 (300)
Q Consensus       256 ~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~~  294 (300)
                      ..|+++|||+|++||++|+|++++.+++++ +.||++.+
T Consensus       131 ~~i~~~lGH~~~~~t~~Y~~~~~~~~~~a~-~~~p~~~~  168 (170)
T d1aiha_         131 LVLKEILGHSTIEMTMRYAHFAPSHLESAV-KFNPLSNP  168 (170)
T ss_dssp             HHHHHHHTCSSHHHHGGGGGGSCCCTTHHH-HHSTTTSC
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-HHCCCCCC
T ss_conf             999998089998999988767999999999-86857687


No 3  
>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]}
Probab=99.95  E-value=2.1e-28  Score=181.79  Aligned_cols=176  Identities=15%  Similarity=0.187  Sum_probs=126.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHC---CCC-CCCC---C
Q ss_conf             12233202469999864320012561027765431100012210013433343200000111100---011-1222---1
Q gi|255764498|r   96 LPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERT---MII-QGKG---N  168 (300)
Q Consensus        96 ~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~---i~v-~~K~---~  168 (300)
                      .+.+++.+|++++...+..      ......+||++++.++|.||||++|+++|+|+||++.++.   +.+ .+|+   .
T Consensus         4 ~~~~~~~~e~~~~~~~~~~------~~~~~~~R~~ali~l~~~tGlR~~Ei~~L~~~di~~~~~~~~~i~i~~~k~~~~~   77 (214)
T d1f44a2           4 QALAFERTDFDQVRSLMEN------SDRCQDIRNLAFLGIAYNTLLRIAEIARIRVKDISRTDGGRMLIHIGRTKTLVST   77 (214)
T ss_dssp             CCCCCCHHHHHHHHHHHTT------CCCHHHHHHHHHHHHHHHHCCCHHHHHHCBGGGEEECGGGCEEEEECC-------
T ss_pred             CCCCCCHHHHHHHHHHHHC------CCCHHHHHHHHHHHHHHHHCCCHHHHHHCCCCEEECCCCCCEEEEEEECCCCCCC
T ss_conf             4677999999999999862------4722638999999999998107777875123112023331036666302456433


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--------CCCCCCCCCCCCH-------HHHHHHCCCCCC
Q ss_conf             1111000012478875323210012467775200123332--------2222111111101-------234420146676
Q gi|255764498|r  169 KERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTK--------TGHLSRQVFARDL-------KALAARAGIQKK  233 (300)
Q Consensus       169 k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~--------~~~~s~~~~~~~~-------~~~~~~~gi~~~  233 (300)
                      +.+.+++++.....|..++........+  ..++|.....        +.+++.+.+...+       +.....+|....
T Consensus        78 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (214)
T d1f44a2          78 AGVEKALSLGVTKLVERWISVSGVADDP--NNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYL  155 (214)
T ss_dssp             -CEEEECCHHHHHHHHHHHHHHCGGGST--TSBSSCCBCTTSCBCCCSSCCCCHHHHHHHHHHHHHHHHCSCCTTCCTTS
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCCCC--CHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             0010245366888775445542333232--21332110012444564333344332333322232222222220113566


Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHH
Q ss_conf             4259885889999999858888899998558998998999645999
Q gi|255764498|r  234 NISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPD  279 (300)
Q Consensus       234 ~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~  279 (300)
                      +++||+|||||||.|+++|+|+..||+++||+|++||++|++..+.
T Consensus       156 ~~t~HslRht~at~l~~~G~~~~~i~~~~GH~s~~~~~~Y~~~~~~  201 (214)
T d1f44a2         156 AWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNFIRNLDS  201 (214)
T ss_dssp             SCCTTHHHHHHHHHHHHTTCCHHHHHHHHTCCCHHHHHHHTTTCCS
T ss_pred             CCCHHHHHCCCCHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHH
T ss_conf             7866664133002797779999999999689998999998603347


No 4  
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]}
Probab=99.89  E-value=7.6e-25  Score=161.13  Aligned_cols=166  Identities=19%  Similarity=0.122  Sum_probs=118.4

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf             23320246999986432001256102776543110001221001343334320000011110001112221111100001
Q gi|255764498|r   98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSP  177 (300)
Q Consensus        98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k~R~ipi~~  177 (300)
                      ++||.||+.++++++.....        .+  .+++.+++.||||++|+++|+|+||+.+...+. ..|+++.+.+|+.+
T Consensus         2 ~~lt~ee~~~l~~~~~~~~~--------~~--~~~~~l~~~tG~R~~El~~L~~~di~~~~~~i~-~~K~~~~~~~~~~~   70 (179)
T d1ae9a_           2 SRLTADEYLKIYQAAESSPC--------WL--RLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVE-QSKTGVKIAIPTAL   70 (179)
T ss_dssp             CCCCHHHHHHHHHHGGGSCH--------HH--HHHHHHHHHHCCCHHHHHHCBGGGEETTEEEEE-CTTTCCEEEEETTC
T ss_pred             CCCCHHHHHHHHHHHHHCCH--------HH--HHHHHHHHHHCCCCCCCCCCCEEEEEECCEEEE-ECCCCCCCCCCCCH
T ss_conf             98999999999998756889--------99--999999999679987646662026630111464-11333323466741


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCC--CCCCCHHHHHHHHHHHHHHCCCCH
Q ss_conf             247887532321001246777520012333222221111111012344201466--764259885889999999858888
Q gi|255764498|r  178 SALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQ--KKNISPHIIRHAFASHLLEGGADL  255 (300)
Q Consensus       178 ~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~--~~~~t~H~lRht~at~l~~~G~~~  255 (300)
                      .....+..+..............+++ ....+.+++...+...+..+.+.+++.  ...+++|++||+ ||.++++|+|+
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lR~~-~t~~~~~g~~~  148 (179)
T d1ae9a_          71 HIDALGISMKETLDKCKEILGGETII-ASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSL-SARLYEKQISD  148 (179)
T ss_dssp             EEGGGTEEHHHHHHHHHHHTCCSBSS-CCTTSCCCCHHHHHHHHHHHHHHHTCCCSSSCCCTTHHHHH-HHHHHHHHTCH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCEE-EEECCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHH-HHHHHHCCCCH
T ss_conf             56778877655443311357765213-33047763345303466666531134433231037788888-88999849999


Q ss_pred             HHHHHHHCCCCHHHHHHHHHC
Q ss_conf             899998558998998999645
Q gi|255764498|r  256 RTIQILLGHTDISTTQIYTHL  276 (300)
Q Consensus       256 ~~v~~~lGH~s~~tT~~Y~~~  276 (300)
                      ..||.+|||+|++||++|.+.
T Consensus       149 ~~i~~~lGH~s~~~t~~Y~~~  169 (179)
T d1ae9a_         149 KFAQHLLGHKSDTMASQFRDD  169 (179)
T ss_dssp             HHHHHHHTC--------CEEC
T ss_pred             HHHHHHHCCCCHHHHHHHHHC
T ss_conf             999999589999999998736


No 5  
>d1a0pa1 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=99.71  E-value=2.1e-18  Score=123.64  Aligned_cols=86  Identities=30%  Similarity=0.522  Sum_probs=81.8

Q ss_pred             CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             64664138999999999999999997544998688999999999999997799843532210112334321000122222
Q gi|255764498|r    2 MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKD   81 (300)
Q Consensus         2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~   81 (300)
                      |..|||+|++|+++|..+++.|..||...++++.+++..++..|+.++.++|++++|+++++++|++||+|+..+|+++.
T Consensus        13 l~~erg~S~~Ti~aY~~dl~~f~~~l~~~~~~~~~i~~~~i~~yl~~l~~~g~s~~Ti~r~lsalr~ff~~l~~~~~i~~   92 (98)
T d1a0pa1          13 LWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSARLLSAVRRLFQYLYREKFRED   92 (98)
T ss_dssp             HHHTTCSCHHHHHHHHHHHHHHHHHHHHTSCCTTTCCHHHHHHHHHSCC-------CHHHHHHHHHHHHHHHHHTTSSSS
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99884959999999999999999988761644111558999999999985245510599999999999999999789376


Q ss_pred             CCCCCC
Q ss_conf             212222
Q gi|255764498|r   82 NPSDTL   87 (300)
Q Consensus        82 np~~~i   87 (300)
                      ||+..|
T Consensus        93 nP~~~i   98 (98)
T d1a0pa1          93 DPSAHL   98 (98)
T ss_dssp             CTTSCC
T ss_pred             CCCCCC
T ss_conf             833419


No 6  
>d1f44a1 a.60.9.1 (A:20-129) Cre recombinase {Bacteriophage P1 [TaxId: 10678]}
Probab=99.45  E-value=1.1e-13  Score=96.27  Aligned_cols=75  Identities=13%  Similarity=0.102  Sum_probs=70.8

Q ss_pred             CCHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             964664138999999999999999997544998688999999999999997799843532210112334321000
Q gi|255764498|r    1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCY   75 (300)
Q Consensus         1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~   75 (300)
                      ||..|+++|+||+++|..+|+.|..||...+.++.+++.+++..|+.++...|++++|+++++++|+.|++++..
T Consensus        11 ~l~~~~~~S~nT~~aY~~dl~~f~~w~~~~~~~~l~~~~~~v~~yl~~l~~~g~s~sTi~R~lsair~f~r~~g~   85 (110)
T d1f44a1          11 MFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQQHLGQLNMLHRRSGL   85 (110)
T ss_dssp             CCSCGGGSCHHHHHHHHHHHHHHHHHHHHTTCCTTTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             999986538989999999999999988651123462345378999999986388840899999999999998699


No 7  
>d1a41a_ d.163.1.2 (A:) Eukaryotic DNA topoisomerase I, catalytic core {Vaccinia virus [TaxId: 10245]}
Probab=97.17  E-value=0.00051  Score=39.99  Aligned_cols=124  Identities=17%  Similarity=0.229  Sum_probs=74.4

Q ss_pred             HHCCCHHHHHCCCCCC-----------CCCCCHHHHHHHHHCCCC--CCCCCCCCCCHH--HHHHHHHHHHHHHHHCCCC
Q ss_conf             1100012210013433-----------343200000111100011--122211111000--0124788753232100124
Q gi|255764498|r  130 FLLIELLYATGMRVSE-----------LVTLSAHTLNLTERTMII--QGKGNKERLVIL--SPSALHALQMYKKTCSSMK  194 (300)
Q Consensus       130 ~~il~ll~~tGlR~~E-----------i~~L~~~di~~~~~~i~v--~~K~~k~R~ipi--~~~~~~~l~~y~~~~~~~~  194 (300)
                      .+++.|+-.|.+|+|-           ++.|+..+|.+.++.+.+  .||.|+.+.+-+  ++.+...|....+      
T Consensus        38 A~vv~Lld~~~iRvGne~Ya~~n~SyGltTLr~~Hv~i~~~~i~f~F~GKsGv~~~~~i~~d~~l~~~l~~~~~------  111 (230)
T d1a41a_          38 AVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDEIVIKFVGKDKVSHEFVVHKSNRLYKPLLKLTD------  111 (230)
T ss_dssp             HHHHHHHHCCC---------CCHHHHHHHTCBGGGEEEETTEEEECEEETTTEEECCEEETTSSSHHHHHHHCC------
T ss_pred             HHHHHHHHHHCEECCCHHHHHHCCCCCEEEEEHHHEEEECCEEEEEEECCCCCEEEEEEECCHHHHHHHHHHHH------
T ss_conf             99999999736516886567625983512201310677189269987558773489988337899999999986------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHH-----HC---CCC-----------H
Q ss_conf             6777520012333222221111111012344201466764259885889999999-----85---888-----------8
Q gi|255764498|r  195 MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLL-----EG---GAD-----------L  255 (300)
Q Consensus       195 ~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~-----~~---G~~-----------~  255 (300)
                      .++...++|..      ++...++..++    ..     .+|..+||=-.||..+     ..   ..+           +
T Consensus       112 ~~~~~~~lf~~------v~~~~vn~yl~----~~-----~~taKdFRTw~at~~~~~~l~~~~~~~~~~~~~kk~i~~~i  176 (230)
T d1a41a_         112 DSSPEEFLFNK------LSERKVYECIK----QF-----GIRIKDLRTYGVNYTFLYNFWTNVKSISPLPSPKKLIALTI  176 (230)
T ss_dssp             TTCTTSBSSTT------CCHHHHHHHHH----HT-----TCCHHHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHHH
T ss_pred             CCCCCCCCCCC------CCCHHHHHHHH----HC-----CCCHHHHHHHCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             66952000002------56337788888----73-----76099999865289999999850687787778899999999


Q ss_pred             HHHHHHHCCCCHHHHH-HHHH
Q ss_conf             8999985589989989-9964
Q gi|255764498|r  256 RTIQILLGHTDISTTQ-IYTH  275 (300)
Q Consensus       256 ~~v~~~lGH~s~~tT~-~Y~~  275 (300)
                      ..|++.|||+- ++.. -|+|
T Consensus       177 ~~vA~~LgNTp-aV~rksYI~  196 (230)
T d1a41a_         177 KQTAEVVGHTP-SISKRAYMA  196 (230)
T ss_dssp             HHHHHHHSSCC-CHHHHHHHH
T ss_pred             HHHHHHHCCCH-HHHHHHCCC
T ss_conf             99999958976-667886579


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=96.61  E-value=0.0045  Score=34.51  Aligned_cols=117  Identities=22%  Similarity=0.310  Sum_probs=72.7

Q ss_pred             HHCCCHHHHHCCCCC------C------CCCCCHHHHHHH------HHCCCC--CCCCCCC--CCCHHHHHHHHHHHHHH
Q ss_conf             110001221001343------3------343200000111------100011--1222111--11000012478875323
Q gi|255764498|r  130 FLLIELLYATGMRVS------E------LVTLSAHTLNLT------ERTMII--QGKGNKE--RLVILSPSALHALQMYK  187 (300)
Q Consensus       130 ~~il~ll~~tGlR~~------E------i~~L~~~di~~~------~~~i~v--~~K~~k~--R~ipi~~~~~~~l~~y~  187 (300)
                      .+++.|+-.+.+|+|      |      ++.|+..+|.+.      ++.+.+  .||.+..  ..|++++.+...|....
T Consensus        46 A~al~LiD~~~lRvGneky~~en~dT~G~tTLr~eHv~l~~~~~~~~~~i~~~F~GK~gvr~~~~v~~~~~v~~~l~~~~  125 (263)
T d1k4ta2          46 AVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFM  125 (263)
T ss_dssp             HHHHHHHHHSCCCCCCCCCTTTSCCCCCGGGCBGGGEEEEEEETTEEEEEEEEEECGGGCEEEEEEECCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHHEEECCCCCCCCCEEEEEEECCCCEEEEEEEECCHHHHHHHHHHH
T ss_conf             99999999737316880013235897602002221157614656778558999744776389999835889999999998


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHH-----HCCCC---H----
Q ss_conf             21001246777520012333222221111111012344201466764259885889999999-----85888---8----
Q gi|255764498|r  188 KTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLL-----EGGAD---L----  255 (300)
Q Consensus       188 ~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~-----~~G~~---~----  255 (300)
                      +..      .+...||      ..++...++..++.+    |   +++|...||=-.||.++     +.+.+   .    
T Consensus       126 ~~k------~~~d~LF------~~i~s~~vN~yLk~~----~---~g~TaKdFRTw~As~~~~~~L~~~~~~~~~~~~k~  186 (263)
T d1k4ta2         126 ENK------QPEDDLF------DRLNTGILNKHLQDL----M---EGLTAKVFRTYNASITLQQQLKELTAPDENIPAKI  186 (263)
T ss_dssp             TTC------CTTSBSS------TTCCHHHHHHHHHHH----S---TTCCTTHHHHHHHHHHHHHHHHHHCCTTCCHHHHH
T ss_pred             HCC------CCCHHHC------CCCCHHHHHHHHHHH----C---CCCCEEECCCCCHHHHHHHHHHHCCCCCCCHHHHH
T ss_conf             766------9821111------668889999999996----6---99721302134469999999983799986799999


Q ss_pred             -------HHHHHHHCCC
Q ss_conf             -------8999985589
Q gi|255764498|r  256 -------RTIQILLGHT  265 (300)
Q Consensus       256 -------~~v~~~lGH~  265 (300)
                             ..|+.+++|+
T Consensus       187 ~~~n~Anr~VA~lcnHq  203 (263)
T d1k4ta2         187 LSYNRANRAVAILCNHQ  203 (263)
T ss_dssp             HHHHHHHHHHHHHTTCB
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             99999999999982887


No 9  
>d1a0pa1 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [TaxId: 562]}
Probab=94.46  E-value=0.032  Score=29.51  Aligned_cols=38  Identities=13%  Similarity=0.247  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999-779984353221011233432100012
Q gi|255764498|r   40 NHLISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYEG   77 (300)
Q Consensus        40 ~~i~~~~~~l~-~~~~s~~T~~~~~~~l~~~~~~~~~~~   77 (300)
                      ..|+.|+.++. ++|+|++|+..+...|+.|+.|+...+
T Consensus         4 ~~ie~fl~~l~~erg~S~~Ti~aY~~dl~~f~~~l~~~~   42 (98)
T d1a0pa1           4 ARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRG   42 (98)
T ss_dssp             HHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999999998849599999999999999999887616


No 10 
>d1p4ea2 d.163.1.1 (A:136-422) Flp recombinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=91.70  E-value=0.3  Score=23.90  Aligned_cols=146  Identities=17%  Similarity=0.188  Sum_probs=72.4

Q ss_pred             HHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH-----CCCC---CCCCCCCCCC---HHHH--HHHHHHHHHHHHHCCCCC
Q ss_conf             3110001221001343334320000011110-----0011---1222111110---0001--247887532321001246
Q gi|255764498|r  129 IFLLIELLYATGMRVSELVTLSAHTLNLTER-----TMII---QGKGNKERLV---ILSP--SALHALQMYKKTCSSMKM  195 (300)
Q Consensus       129 ~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~-----~i~v---~~K~~k~R~i---pi~~--~~~~~l~~y~~~~~~~~~  195 (300)
                      ...|+.+-+.-+||.+++.++..+-+.+-..     .+++   .+|++++|.|   |+..  +..-.|.+|+....+...
T Consensus        43 y~~lll~tf~NCcR~sDLkN~DP~tFeiv~nk~lG~ilra~V~eTKTr~~R~IyFfPv~g~~DpllaL~~~l~~~~P~~K  122 (287)
T d1p4ea2          43 YQFLFLATFINCGRFSDIKNVDPKSFKLVQNKYLGVIIQCLVTETKTSVSRHIYFFSARGRIDPLVYLDEFLRNSEPVLK  122 (287)
T ss_dssp             HHHHHHHHHHHTCCHHHHHTBCGGGCEEEEETTTEEEEEEEECSCTTSCCEEEEECCCSSSCCHHHHHHHHHTTCCCEEC
T ss_pred             HHHHHHHHHHHHHCHHHCCCCCCCCEEEECCCCHHHHHEEEEECCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             99999999983411010145893324651453022252024303556653149997458987636889999873488654


Q ss_pred             CC--CCCCCCCCCCCCCCCCCC----CCCCCHHHHHHH--CCCCCCCCCHHHHHHHHHHHHHHCCCCHHH--HHHHHCCC
Q ss_conf             77--752001233322222111----111101234420--146676425988588999999985888889--99985589
Q gi|255764498|r  196 TG--NDLWLFPSSTKTGHLSRQ----VFARDLKALAAR--AGIQKKNISPHIIRHAFASHLLEGGADLRT--IQILLGHT  265 (300)
Q Consensus       196 ~~--~~~~lf~~~~~~~~~s~~----~~~~~~~~~~~~--~gi~~~~~t~H~lRht~at~l~~~G~~~~~--v~~~lGH~  265 (300)
                      .-  ...  -.+.....++-+.    +..+.+.+....  .+|... --.|--||-.+|-|-.++.+..+  +..+.+-.
T Consensus       123 ~~sRts~--~~s~~q~~Qllrdsl~~~YdrF~~k~~~~~iF~I~~G-PKSHlGRHLM~SyLs~~~~~~~~s~~GNWs~~r  199 (287)
T d1p4ea2         123 RVNRTGN--SSSNKQEYQLLKDNLVRSYNKALKKNAPYPIFAIKNG-PKSHIGRHLMTSFLSMKGLTELTNVVGNFSDKR  199 (287)
T ss_dssp             CCCBSCC--CCSSSCSEESSCTTHHHHHHHHHHHTCSSGGGGSTTC-CSSTHHHHHHHHHHHHTTCHHHHHHHHTCCCC-
T ss_pred             CCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCC-CHHHHHHHHHHHHHHHCCCCCEECCCCCCHHHH
T ss_conf             3444456--6312678998898888889999973788863405789-677887899998852056775001456620235


Q ss_pred             CHHHH-HHHHHCC
Q ss_conf             98998-9996459
Q gi|255764498|r  266 DISTT-QIYTHLL  277 (300)
Q Consensus       266 s~~tT-~~Y~~~~  277 (300)
                      .-.+. ..|+|..
T Consensus       200 eS~vAr~~Y~H~~  212 (287)
T d1p4ea2         200 ASAVARTTYTHQI  212 (287)
T ss_dssp             -----------CC
T ss_pred             HHHHHHHHCCCCC
T ss_conf             6666653024344


No 11 
>d1f44a1 a.60.9.1 (A:20-129) Cre recombinase {Bacteriophage P1 [TaxId: 10678]}
Probab=82.18  E-value=0.074  Score=27.43  Aligned_cols=37  Identities=8%  Similarity=0.135  Sum_probs=30.0

Q ss_pred             HHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             999999999-7799843532210112334321000122
Q gi|255764498|r   42 LISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYEGL   78 (300)
Q Consensus        42 i~~~~~~l~-~~~~s~~T~~~~~~~l~~~~~~~~~~~~   78 (300)
                      .+.|++++. ++++|++|++.+.+.++.|+.||...+.
T Consensus         5 ~~~~~~~l~~~~~~S~nT~~aY~~dl~~f~~w~~~~~~   42 (110)
T d1f44a1           5 RKNLMDMFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNR   42 (110)
T ss_dssp             HHHHHSCCSCGGGSCHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999998653898999999999999998865112


No 12 
>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=26.28  E-value=15  Score=13.95  Aligned_cols=49  Identities=16%  Similarity=0.201  Sum_probs=28.6

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHH
Q ss_conf             23320246999986432001256102776543110001221001343334320000
Q gi|255764498|r   98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHT  153 (300)
Q Consensus        98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~d  153 (300)
                      ..++++|...+++....... +.+.-.  .-|- +   .-+.|+++|+++.+....
T Consensus        11 ~~l~~eE~~~il~~y~i~~~-qLP~I~--~~DP-v---a~~~g~~~GdvikI~R~s   59 (72)
T d1dzfa2          11 IRLSSDEKRELLKRYRLKES-QLPRIQ--RADP-V---ALYLGLKRGEVVKIIRKS   59 (72)
T ss_dssp             EECCHHHHHHHHHHTTCCGG-GSCEEC--TTCH-H---HHHHTCCTTCEEEEECTT
T ss_pred             EECCHHHHHHHHHHHCCCHH-HCCEEC--CCCH-H---HHHCCCCCCCEEEEEECC
T ss_conf             88599999999999598975-799543--6397-3---561188889789999758


No 13 
>d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}
Probab=20.47  E-value=21  Score=13.20  Aligned_cols=49  Identities=14%  Similarity=0.178  Sum_probs=28.4

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHH
Q ss_conf             23320246999986432001256102776543110001221001343334320000
Q gi|255764498|r   98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHT  153 (300)
Q Consensus        98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~d  153 (300)
                      ..++++|...+++....... ..+.-.  .-|- +   .-+.|+++|+++.+....
T Consensus        15 ~il~~ee~~~~l~~~~i~~~-qLP~I~--~~DP-v---a~~~g~k~GdvvkI~R~S   63 (77)
T d1eika_          15 VILNESEAKRVLKELDAHPE-QLPKIK--TTDP-V---AKAIGAKRGDIVKIIRKS   63 (77)
T ss_dssp             EEECHHHHHHHHHHTTCCTT-TSCCCB--TTSH-H---HHGGGCCTTCEEEEEEEE
T ss_pred             EECCHHHHHHHHHHHCCCHH-HCCEEC--CCCH-H---HHHHCCCCCCEEEEEECC
T ss_conf             98699999999998569987-899403--6297-2---451078688579999758


No 14 
>d1hmja_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanococcus jannaschii [TaxId: 2190]}
Probab=20.45  E-value=19  Score=13.40  Aligned_cols=49  Identities=12%  Similarity=0.243  Sum_probs=27.6

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHH
Q ss_conf             23320246999986432001256102776543110001221001343334320000
Q gi|255764498|r   98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHT  153 (300)
Q Consensus        98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~d  153 (300)
                      ..++++|...+++....... +.+.-  ...|-+    .-+.|+++|+++.+....
T Consensus         4 ~il~~eE~~~ll~~y~i~~~-qLP~I--~~~DPv----a~~~g~k~GdvvkI~R~S   52 (68)
T d1hmja_           4 EIVPKEEVEEILKRYNIKIQ-QLPKI--YEDDPV----IQEIGAKEGDVVRVIRKS   52 (68)
T ss_pred             EECCHHHHHHHHHHHCCCHH-HCCCC--CCCCHH----HHHHCCCCCCEEEEEECC
T ss_conf             78799999999999298988-99912--251987----898199999589999758


Done!