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!