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 39220
Date          Mon May 30 00:45:23 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780882.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02224 recomb_XerC tyrosine 100.0       0       0  609.8  18.6  300   19-323     1-313 (313)
  2 TIGR02225 recomb_XerD tyrosine 100.0       0       0  598.6  18.9  293   19-321     1-305 (305)
  3 COG4974 XerD Site-specific rec 100.0       0       0  518.4  19.3  294   14-321     5-300 (300)
  4 PRK01287 xerC site-specific ty 100.0       0       0  501.2  22.0  299   13-326    22-329 (361)
  5 PRK00236 xerC site-specific ty 100.0       0       0  486.0  22.0  294   10-321     2-295 (295)
  6 PRK00283 xerD site-specific ty 100.0       0       0  475.2  21.7  291   16-321     4-296 (296)
  7 COG4973 XerC Site-specific rec 100.0       0       0  461.0  19.9  294   14-324     6-299 (299)
  8 cd00798 INT_XerDC XerD and Xer 100.0       0       0  446.2  20.1  281   18-308     1-282 (284)
  9 PRK05084 xerS site-specific ty 100.0       0       0  438.4  18.7  300   11-313    14-356 (360)
 10 cd01196 INT_VanD VanD integras 100.0       0       0  395.7  16.7  260   21-314     1-261 (263)
 11 cd01187 INT_SG4 INT_SG4, DNA b 100.0       0       0  390.7  18.2  284   14-312     1-298 (299)
 12 PRK02436 xerD site-specific ty 100.0       0       0  391.6  15.1  247   18-300     1-247 (247)
 13 cd01185 INT_Tn4399 Tn4399 and  100.0       0       0  383.7  19.9  284    8-312     9-298 (299)
 14 cd01190 INT_SG5 INT_SG5, DNA b 100.0       0       0  376.5  15.2  247   61-319     3-260 (260)
 15 TIGR02249 integrase_gron integ 100.0       0       0  379.5  11.2  253   29-302    12-306 (320)
 16 cd01193 INT_IntI IntI (E2) int 100.0       0       0  358.1  12.7  229   60-301     4-242 (242)
 17 PRK09870 tyrosine recombinase; 100.0       0       0  338.5  11.1  195  118-323     2-197 (200)
 18 PRK09871 tyrosine recombinase; 100.0       0       0  324.9  10.3  189  127-325     5-194 (198)
 19 cd00799 INT_Cre Cre recombinas 100.0       0       0  314.9  15.5  258   33-306     1-280 (287)
 20 cd00801 INT_P4 Bacteriophage P 100.0 2.8E-45       0  302.5  18.1  275   10-311    69-353 (357)
 21 cd00796 INT_Rci Rci recombinas 100.0 1.4E-45       0  305.5  11.2  202   87-308     1-205 (206)
 22 cd01198 INT_ASSRA_C Archaeal s 100.0 4.6E-44       0  294.6   9.7  176  128-321     1-185 (186)
 23 cd01188 INT_pAE1 pAE1 and rela 100.0 8.5E-44       0  292.9  10.4  177  125-309     1-182 (188)
 24 cd01197 INT_FimBE_C FimB and F 100.0 1.3E-43       0  291.7   9.7  174  127-307     3-177 (180)
 25 cd01186 INT_SG3_C INT_SG3, DNA 100.0 1.9E-39 4.8E-44  265.7  10.4  169  130-317     8-178 (180)
 26 cd01194 INT_Tn554A_C Tn544A an 100.0 1.3E-39 3.2E-44  266.9   8.8  170  129-311     1-185 (186)
 27 cd01183 INT_SG1_C INT_SG1, DNA 100.0 5.5E-40 1.4E-44  269.1   6.7  172  128-300     1-196 (196)
 28 cd01199 INT_Tn1545_C Tn1545-re 100.0 5.4E-38 1.4E-42  256.7   9.9  179  128-312     1-204 (205)
 29 cd01192 INT_P22_C P22-like int 100.0 1.9E-37 4.7E-42  253.3   9.3  167  126-313     4-173 (177)
 30 pfam00589 Phage_integrase Phag 100.0 1.1E-37 2.8E-42  254.7   7.9  169  127-305     1-170 (170)
 31 cd01189 INT_phiLC3_C phiLC3 ph 100.0 4.4E-37 1.1E-41  250.9   6.9  171  127-305     1-190 (191)
 32 cd01195 INT_Tn544B_C Tn544B an 100.0 1.6E-36 4.2E-41  247.4   8.8  175  127-309     1-194 (195)
 33 cd00397 DNA_BRE_C DNA breaking 100.0 4.8E-33 1.2E-37  225.7   8.1  159  133-300     1-164 (164)
 34 cd01191 INT_phiCTX_C phiCTX ph 100.0 2.1E-32 5.3E-37  221.8   8.2  166  126-301     1-195 (196)
 35 PRK09692 integrase; Provisiona 100.0 3.3E-30 8.4E-35  208.0  17.2  280   12-317   105-392 (413)
 36 cd00797 HP1_INT_C Phage HP1 in 100.0 4.1E-32   1E-36  219.9   7.3  154  132-311     1-155 (158)
 37 cd01184 INT_SG2_C INT_SG2, DNA 100.0 1.7E-32 4.2E-37  222.4   5.0  163  129-300     1-181 (181)
 38 cd00800 INT_Lambda_C Lambda in 100.0 6.6E-31 1.7E-35  212.4   6.8  155  127-301     2-161 (162)
 39 cd01182 INT_REC_C DNA breaking  99.9 3.9E-27 9.8E-32  188.8   6.8  146  153-300    14-162 (162)
 40 COG0582 XerC Integrase [DNA re  99.9 4.1E-22 1.1E-26  157.4  18.1  208   84-312    84-301 (309)
 41 pfam02899 Phage_integr_N Phage  99.6 7.6E-16 1.9E-20  118.3   8.8   83   18-106     1-83  (83)
 42 PHA00730 int integrase          98.6   1E-06 2.6E-11   61.3  11.8  198   43-301    98-303 (322)
 43 COG4342 Uncharacterized protei  98.5 9.6E-07 2.4E-11   61.4   7.8  205   68-302    57-268 (291)
 44 pfam11917 DUF3435 Protein of u  97.8 3.8E-05 9.7E-10   51.4   4.8   64  235-299   170-235 (414)
 45 pfam01028 Topoisom_I Eukaryoti  96.9  0.0023 5.8E-08   40.3   5.3  115  173-300    84-224 (244)
 46 cd00659 Topo_IB_C DNA topoisom  96.9 0.00074 1.9E-08   43.4   2.6  114  173-300    71-207 (218)
 47 cd01190 INT_SG5 INT_SG5, DNA b  96.2   0.018 4.7E-07   34.7   6.3   62   16-77     11-86  (260)
 48 cd01193 INT_IntI IntI (E2) int  95.6   0.034 8.8E-07   33.0   5.7   71    5-78      5-83  (242)
 49 cd01185 INT_Tn4399 Tn4399 and   95.0   0.067 1.7E-06   31.2   5.6   39   16-54     69-107 (299)
 50 PRK01287 xerC site-specific ty  94.9   0.028 7.2E-07   33.5   3.5   39   69-107    25-63  (361)
 51 PRK05084 xerS site-specific ty  94.6   0.037 9.4E-07   32.8   3.5   41   68-108    18-58  (360)
 52 PRK00283 xerD site-specific ty  93.8   0.073 1.9E-06   30.9   3.5   38   16-54     51-88  (296)
 53 PRK00236 xerC site-specific ty  92.9    0.12 3.1E-06   29.5   3.5   37   16-53     56-92  (295)
 54 COG4688 Uncharacterized protei  92.1    0.22 5.7E-06   27.9   4.0   66  246-311   432-499 (665)
 55 pfam02899 Phage_integr_N Phage  91.3    0.59 1.5E-05   25.3   5.4   34   71-104     1-35  (83)
 56 TIGR01108 oadA oxaloacetate de  73.5     3.2 8.1E-05   20.7   2.7   91  207-299   146-245 (616)
 57 smart00435 TOPEUc DNA Topoisom  59.5     5.2 0.00013   19.4   1.6   92  164-272   124-231 (391)
 58 TIGR01983 UbiG ubiquinone bios  49.4      15 0.00038   16.5   2.5   11  278-288   229-239 (275)
 59 PRK11582 flagella biosynthesis  48.4      19 0.00048   15.9   6.7   68   33-107    58-126 (179)
 60 pfam08849 DUF1819 Putative inn  47.4      19  0.0005   15.8   4.1   20  128-147   116-135 (191)
 61 TIGR00802 nico transition meta  43.3      15 0.00039   16.5   1.8   26  146-178   151-176 (290)
 62 TIGR00016 ackA acetate kinase;  39.8      12 0.00031   17.0   0.9   14  169-182   204-217 (416)
 63 COG0282 ackA Acetate kinase [E  39.4      16 0.00042   16.3   1.5   13  169-181   188-200 (396)
 64 cd00569 HTH_Hin_like Helix-tur  36.2      29 0.00074   14.7   3.2   32  257-290     3-34  (42)
 65 COG4565 CitB Response regulato  35.9      29 0.00075   14.7   4.8   20  279-299   175-194 (224)
 66 TIGR01304 IMP_DH_rel_2 IMP deh  34.4      17 0.00042   16.2   0.9   24  260-284   140-163 (376)
 67 pfam05202 Flp_C Recombinase Fl  34.1      31  0.0008   14.5   3.7  132  167-302    53-211 (244)
 68 KOG0440 consensus               31.1      26 0.00066   15.0   1.4   81  162-254    99-182 (243)
 69 TIGR01822 2am3keto_CoA 2-amino  29.6      37 0.00095   14.0   2.5   34  245-278   305-348 (395)
 70 pfam07506 RepB RepB plasmid pa  29.1      38 0.00097   14.0   3.3   19   74-92     13-31  (185)
 71 PRK10046 dpiA two-component re  29.0      38 0.00097   14.0   4.6   44  255-300   154-199 (225)
 72 pfam04852 DUF640 Protein of un  27.6      40   0.001   13.8   4.2   39   40-82     25-63  (133)
 73 TIGR02810 agaZ_gatZ D-tagatose  27.2      39   0.001   13.9   1.8   35  276-317   383-425 (430)
 74 PRK02615 thiamine-phosphate py  26.4      42  0.0011   13.7   3.7   67  225-297   263-334 (345)
 75 PRK00043 thiE thiamine-phospha  25.8      44  0.0011   13.6   4.9   65  226-295   129-198 (210)
 76 TIGR02057 PAPS_reductase phosp  25.3      34 0.00088   14.2   1.2   46  163-217   144-192 (239)
 77 TIGR01262 maiA maleylacetoacet  24.5      46  0.0012   13.4   3.0   37  245-288   115-151 (218)
 78 pfam09968 DUF2202 Uncharacteri  23.9      47  0.0012   13.4   3.5   16  128-143    65-80  (162)
 79 PRK02249 DNA primase large sub  22.7      50  0.0013   13.2   4.9   51  241-296   223-276 (333)

No 1  
>TIGR02224 recomb_XerC tyrosine recombinase XerC; InterPro: IPR011931    The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This entry represents XerC, which is closely related to the other chromosomal protein XerD (IPR011932 from INTERPRO). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. XerC and XerD interact with cell division protein FtsK .; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=100.00  E-value=0  Score=609.80  Aligned_cols=300  Identities=35%  Similarity=0.565  Sum_probs=278.0

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC---CCCCCCCCHHHCCHHHHHHHHHHHHH--HHHHHHHHHHHHH
Q ss_conf             999999998625488999999999999999998512---14788789689899999999999986--1210133211234
Q gi|254780882|r   19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYT---EEKITIQTIRQLSYTEIRAFISKRRT--QKIGDRSLKRSLS   93 (328)
Q Consensus        19 e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~---~~~~~~~~~~~i~~~~i~~~l~~l~~--~~~s~~T~~~~ls   93 (328)
                      ++||+||+.||++|++|+++|+.||+.|..|+..+.   ...+ +.++.+++..+|+.|+..+..  +|+|++|++|.||
T Consensus         1 ~~fl~yL~~er~~S~hT~~aY~~DL~~f~~fl~~~~~~~~~~~-~~~~~~~~~~d~R~~la~l~~~~~g~s~rS~~R~LS   79 (313)
T TIGR02224         1 EAFLEYLRVERNYSPHTLRAYRRDLEAFLEFLEEHKQEEGGPL-LASLAEVTAADLRSFLAELHAKERGLSRRSLARKLS   79 (313)
T ss_pred             CHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHH-HCCHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             8678999988500089999999999999999999877520111-015762488999999999984657876768999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             44222233321012322222222222222121111111015678776531013567757753201222100112332222
Q gi|254780882|r   94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA  173 (328)
Q Consensus        94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El  173 (328)
                      +||+||+||+++++++.||+..|+.||.++++|++|+++|+..+++...........|.++||+|||+|||.||||+||+
T Consensus        80 alRsFy~~L~~~~~~~~nPa~~~~~PK~~~~LP~~L~~~~~~~ll~~~~~~~~~~~~~~~~RDrA~lEllYssGlRvSEl  159 (313)
T TIGR02224        80 ALRSFYRFLLRRGLIDANPAAGVRAPKKPKKLPKFLSEDEMEALLDAPEEDAEDREDWLALRDRAILELLYSSGLRVSEL  159 (313)
T ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999987287402238872267544679988898999999601234666677789998999999998746899998


Q ss_pred             CCCCCC-CCCCCC--CCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCC-----CCCCCCCCCCCCCCCCHHH
Q ss_conf             211222-223323--22033237853100011221002343221110012344665-----5432111122111000123
Q gi|254780882|r  174 LSLTPQ-NIMDDQ--STLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQ-----LPLFRGIRGKPLNPGVFQR  245 (328)
Q Consensus       174 ~~L~~~-did~~~--~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~-----~~lF~~~~g~~ls~~~i~~  245 (328)
                      ++|+++ |||++.  ++|+|+|||+|||+||+++.+.++|.+|++.++........     ++||+|.+|+||++++|++
T Consensus       160 ~~L~~~~D~d~~~~~~~vrV~GKG~KeR~VP~G~~A~~al~~YL~~~r~~~~~~~~~~~~~~~LF~~~~G~rL~~R~v~~  239 (313)
T TIGR02224       160 VGLDLSEDLDLDFSLGLVRVRGKGNKERIVPFGSYARDALQAYLEERREPLLAKEPPAQDHDALFLNRRGGRLTPRGVRY  239 (313)
T ss_pred             HCCCCCCCCCCHHCCCEEEEEECCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             24771336473221476777414881353031489999999998644721145667777522300178887257778999


Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHC
Q ss_conf             567899976869998805417999999998489988999983788878979999619899999999999981730001
Q gi|254780882|r  246 YIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQ  323 (328)
Q Consensus       246 ~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~  323 (328)
                      +++++..++|++.++|||+||||||||||++|+|+++|||||||+|++|||||||||.++.    +++|++||||++|
T Consensus       240 ~l~~~~~~~~l~~~~hPH~LRHSFATHLL~~gaDLRaVQELLGH~SLSTTQiYTHv~~~~L----~~~Y~~AHPRA~k  313 (313)
T TIGR02224       240 RLQQLVAKAGLPKHVHPHALRHSFATHLLENGADLRAVQELLGHASLSTTQIYTHVDFQHL----AKVYDKAHPRAKK  313 (313)
T ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH----HHHHHHHCCCCCC
T ss_conf             9999998568888678753113179999746883558989744464356679888409999----9999973777779


No 2  
>TIGR02225 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011932   Proteins in this entry are part of the wider so-called "phage" integrase fmaily which describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci.   This entry represents the chromosomally-encoded polypeptide XerD, which is closely related to, and interacts with, another chromosomally-encoded polypeptide, XerC (IPR011931 from INTERPRO). These proteins are site-specific tyrosine recombinases, which act by catalyzing the cutting and rejoining of the recombining DNA molecules . They form a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids.   XerD is composed of two domains, an N-terminal alpha-helical domain, and a C-terminal domain composed mostly of alpha helices, with a three-stranded antiprallel beta sheet along one edge . The active site is found at the extreme C-terminal end of the polypeptide. Most of the C-terminal domain is structurally homologous to that of other "phage" integrases, but the active site regions of these enzymes are stucturally distinct.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=100.00  E-value=0  Score=598.55  Aligned_cols=293  Identities=32%  Similarity=0.515  Sum_probs=272.0

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999862548899999999999999999851214788789689899999999999986121013321123444222
Q gi|254780882|r   19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSF   98 (328)
Q Consensus        19 e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f   98 (328)
                      ++||+++..|||+|+||+.+|++||..|..|+....    .. .+.+++..+|.+|+.++.++|.|++|++|.||+||+|
T Consensus         1 ~~Fl~~L~~E~GLs~NT~~aYrrDL~~f~~~L~~~~----~g-~~~~~~~~~i~~fl~~l~~~g~~~~S~AR~lsalR~F   75 (305)
T TIGR02225         1 DDFLDYLWVERGLSQNTLEAYRRDLEKFLEYLEESE----RG-DLAEVDRGDIEDFLAELKEAGLSARSIARALSALRSF   75 (305)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----CC-CHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             948899999863538889999999999999862224----78-7641687899999999986687700288999999999


Q ss_pred             HHHHHHHCCCCCCCCCC-CCCCCCCCCCCCCCCCCHHHHHHHHH-HHCCCCC-CCHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             23332101232222222-22222221211111110156787765-3101356-775775320122210011233222221
Q gi|254780882|r   99 LKYLKKRKITTESNILN-MRNLKKSNSLPRALNEKQALTLVDNV-LLHTSHE-TKWIDARNSAILYLLYGCGLRISEALS  175 (328)
Q Consensus        99 ~~~~~~~~~i~~np~~~-i~~~k~~~~~p~~lt~~e~~~ll~~~-~~~~~~~-~~~~~~Rd~~i~~ll~~TGlR~~El~~  175 (328)
                      |+||..+++++.||+.. |+.||..+++|++||++||.+||+++ ....+.. ... .+||+||+++||+||||+||+|+
T Consensus        76 y~fL~~e~~~~~dP~~~~~~~PK~~~~LP~vLt~~EV~~LL~~p~~~~~~~g~kr~-~lRDrAmLElLYATGlRVSELv~  154 (305)
T TIGR02225        76 YRFLLREGLREDDPSALRIETPKVARKLPKVLTVEEVEALLAAPIDVDTPLGGKRP-ALRDRAMLELLYATGLRVSELVG  154 (305)
T ss_pred             HHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCH-HHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             99998688745573366420342245788837989999998500246776767640-16547999999864883553305


Q ss_pred             CCCCCCCCCCCC-EE-ECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCC--CCCC---CCCCCC-CCCCCCCCHHHH
Q ss_conf             122222332322-03-32378531000112210023432211100123-446--6554---321111-221110001235
Q gi|254780882|r  176 LTPQNIMDDQST-LR-IQGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLN--IQLP---LFRGIR-GKPLNPGVFQRY  246 (328)
Q Consensus       176 L~~~did~~~~~-i~-v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~--~~~~---lF~~~~-g~~ls~~~i~~~  246 (328)
                      |+.+||+++.++ |. |.|||+|||.|||++.+++.|..|++.+|... ..+  ..++   ||+|.+ |++||+++|+++
T Consensus       155 L~~~d~~l~~g~~~~~v~GKG~KERlVP~G~~A~~~l~~Yl~~~R~~~~~~~~~~~d~~~~LFln~~~G~~lsRQ~~W~~  234 (305)
T TIGR02225       155 LRLEDVNLDEGVKVRKVRGKGSKERLVPLGEEAIEALERYLKEARPLLLKKKKKSSDAKSALFLNRREGGPLSRQGFWKI  234 (305)
T ss_pred             CCHHHHHCCCCEEEEEEEECCCCEEECCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             61665200277379998616884120220289999999999874067641778887554311246888888788999999


Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH
Q ss_conf             678999768699988054179999999984899889999837888789799996198999999999999817300
Q gi|254780882|r  247 IRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI  321 (328)
Q Consensus       247 ~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~  321 (328)
                      ++++++++||.++||||.|||+||||||++|+|+++||+||||+||+||||||||+    ++.|+++|.++|||+
T Consensus       235 ~K~~A~~aGI~k~isPHtLRHSFATHLLenGADLR~VQeLLGHadisTTQIYTHV~----~~~L~~~~~~~HPRa  305 (305)
T TIGR02225       235 LKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVA----RERLKEVHKKHHPRA  305 (305)
T ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH----HHHHHHHHHHHCCCC
T ss_conf             99999981889899975104679999873688276887774322147889999987----999999999628899


No 3  
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=518.43  Aligned_cols=294  Identities=33%  Similarity=0.505  Sum_probs=273.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998625488999999999999999998512147887896898999999999999861210133211234
Q gi|254780882|r   14 LLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLS   93 (328)
Q Consensus        14 l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls   93 (328)
                      ....+++||+++..|||+|.||+.+|+.||..|..|+...     ++..+.+++..++..|+.++.++|+|++|++|.+|
T Consensus         5 ~~~~i~~fL~~l~~Er~ls~nTl~sYrrDL~~f~~~L~~~-----~~~~l~~~~~~di~~yl~~l~~~g~s~~S~aR~ls   79 (300)
T COG4974           5 DEALIEQFLEYLWIERGLSANTLSSYRRDLEDFREWLEER-----GITDLADATEADIREYLTELAEQGLSATSIARALS   79 (300)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             7899999999999975432644999999999999998762-----79884546899999999999857867224889999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             44222233321012322222222222222121111111015678776531013567757753201222100112332222
Q gi|254780882|r   94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA  173 (328)
Q Consensus        94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El  173 (328)
                      ++|+||.|+..++++..||+..+..||.++++|++|+++|+..+++     .++.....++||+||++|||+||||+||+
T Consensus        80 alR~fy~fl~~E~~~~~dP~~~l~~PK~~~~LPk~Ls~~eve~Ll~-----~~~~~~p~~LRdrAmlELLYATGlRVSEl  154 (300)
T COG4974          80 ALRSFYQFLIREGLREDDPTRLLDSPKLPKRLPKFLSEEEVEALLE-----APDEDTPLGLRDRAMLELLYATGLRVSEL  154 (300)
T ss_pred             HHHHHHHHHHHCCCCCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHH-----CCCCCCCHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             9999999999779853382444247877776776259999999981-----88889807579999999999827759998


Q ss_pred             CCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC-CC-CCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             21122222332322033237853100011221002343221110012344-66-55432111122111000123567899
Q gi|254780882|r  174 LSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNL-NI-QLPLFRGIRGKPLNPGVFQRYIRQLR  251 (328)
Q Consensus       174 ~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~-~~-~~~lF~~~~g~~ls~~~i~~~~~~~~  251 (328)
                      ++|+..||++..+.+.|+|||+|+|+||+++.+...|..|+...|..... .. .++||+|.+|++||+++|++.++.+.
T Consensus       155 v~L~l~dv~~~~~~v~V~GKG~KeR~VP~g~~A~~~l~~Yl~~~R~~l~~~~~~~~~LF~n~~g~~ltrq~~w~~lk~~a  234 (300)
T COG4974         155 VGLTLSDVDLRQGVVRVRGKGNKERLVPFGEEAVEALEKYLEEARPKLLKGKSSTDALFPNQRGGGLTRQGFWKRLKDYA  234 (300)
T ss_pred             HCCCHHHHCCCCCEEEEECCCCCEEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             56757651324686899715882555213399999999999986598842578898564548999877999999999999


Q ss_pred             HHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH
Q ss_conf             9768699988054179999999984899889999837888789799996198999999999999817300
Q gi|254780882|r  252 RYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI  321 (328)
Q Consensus       252 ~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~  321 (328)
                      ..+|+.+.+|||.|||+|||+|+++|+|+++||++|||+|++||||||||+    .+.|+++|.++|||+
T Consensus       235 ~~Agi~~~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTTQIYTHV~----~e~L~~~~~~~HPra  300 (300)
T COG4974         235 ERAGIDKKISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVT----KERLRDLYAQHHPRA  300 (300)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHH----HHHHHHHHHHHCCCC
T ss_conf             981888786813657889999986785399999984866501557879988----999999999738999


No 4  
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=100.00  E-value=0  Score=501.25  Aligned_cols=299  Identities=25%  Similarity=0.361  Sum_probs=269.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHH------HHHHHH
Q ss_conf             99999999999999862548899999999999999999851214788789689899999999999986------121013
Q gi|254780882|r   13 ELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRT------QKIGDR   86 (328)
Q Consensus        13 ~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~------~~~s~~   86 (328)
                      .+...+++|++||+ +||+|++|+++|+.+|+.|+.||...     ++..+.+++..++..|..++..      .++|++
T Consensus        22 ~~~~ll~~Fl~yL~-er~~S~~Ti~aY~~dL~~F~~fl~~~-----g~~~~~~vt~~~l~~y~~~L~~~r~~~g~~ls~~   95 (361)
T PRK01287         22 SLYALLLRFVEWLQ-ERNWSERTLKVQTHHTYHFILWCEER-----GLYYAADVTRPVLERYQRYLYQYRKTNGEPLSQG   95 (361)
T ss_pred             HHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHHHHCCCCCCCHH
T ss_conf             79999999999999-83998999999999999999999984-----8999375899999999999998654068877999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC
Q ss_conf             32112344422223332101232222222222222212111-11110156787765310135677577532012221001
Q gi|254780882|r   87 SLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPR-ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYG  165 (328)
Q Consensus        87 T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~-~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~  165 (328)
                      |+++++++||+||+|+++++++..||+..|..||.++++|+ +++.+|+.++++++     +...+.+.||+||+.|||.
T Consensus        96 T~~r~LsalrsFf~~l~~~~~i~~nP~~~i~~PK~~k~lP~~~Ls~~Ev~~LL~~~-----~~~~~~g~RDrAil~LLy~  170 (361)
T PRK01287         96 TQRTQLTPLRVWFKWLTKQNLILYNPAADIELPKLEKRLPRYILSIDETEAILAAP-----DPTTLQGLRDRALLELLWS  170 (361)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCC-----CCCCCHHHHHHHHHHHHHH
T ss_conf             99999999999999999879935375876327776555777679999999998474-----5588065999999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             1233222221122222332322033-2378531000112210023432211100123-4466554321111221110001
Q gi|254780882|r  166 CGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVF  243 (328)
Q Consensus       166 TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i  243 (328)
                      ||||+||+++|+|+|||++.+.+.| .|||+|+|+|||++.+..+|.+|++..+... .....++||++.+|++|+++++
T Consensus       171 tGLRvsEl~~L~~~DId~~~~~i~v~~GKG~KeR~VPl~~~~~~~L~~Yl~~~r~~~~~~~~~~~lFvs~~G~~ls~~~v  250 (361)
T PRK01287        171 TGIRRSELARLDLYDVDGSRKTVTVRQGKGNKDRVVPLGERALVWLQRYLQQVRPQLIVNPDSGALFVAMDGDGLQRNGI  250 (361)
T ss_pred             HCCHHHHHHHCCCCCCCCCCCEEEEECCCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCCCHHHH
T ss_conf             37779888716664667888838873488874002027699999999999986176412788775212889995878999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHC
Q ss_conf             23567899976869998805417999999998489988999983788878979999619899999999999981730001
Q gi|254780882|r  244 QRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQ  323 (328)
Q Consensus       244 ~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~  323 (328)
                      +++++++++.+|+++.++||+|||||||+|+++|+|+.+||++|||+|++||||||||+.++    |+++|+++||+..+
T Consensus       251 ~~~vk~~~~~agi~k~~~pH~LRHTfAT~lL~~GadL~~VQelLGHasi~TTqiYtHv~~~~----l~~v~~~~HP~~~~  326 (361)
T PRK01287        251 TNLVGRYIRAAGIEKKGACHLFRHAMATQMLENGADLRWIQAMLGHASLETTQIYTQVSIRH----LQAVHASTHPAEQM  326 (361)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHH----HHHHHHHHCCCCCC
T ss_conf             99999999980899999821059999999998699999999986899778999998479999----99999981998889


Q ss_pred             CCC
Q ss_conf             223
Q gi|254780882|r  324 KDK  326 (328)
Q Consensus       324 ~~~  326 (328)
                      ..+
T Consensus       327 ~~~  329 (361)
T PRK01287        327 ADE  329 (361)
T ss_pred             CCC
T ss_conf             863


No 5  
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=100.00  E-value=0  Score=485.95  Aligned_cols=294  Identities=40%  Similarity=0.620  Sum_probs=271.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             49899999999999999862548899999999999999999851214788789689899999999999986121013321
Q gi|254780882|r   10 VSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLK   89 (328)
Q Consensus        10 ~~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~   89 (328)
                      .+.+|.+++++||+|++.++|+||+|+++|+.+++.|+.||...     +..++.+++..+|..|+.++..+|+|++|++
T Consensus         2 ~~~~~~~~i~~fl~~l~~~r~lS~~Ti~~Y~~~l~~f~~~~~~~-----~~~~l~~i~~~~i~~~~~~l~~~g~s~~Ti~   76 (295)
T PRK00236          2 ADADLPAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEV-----GLADLQQLDLADLRAFLARLRRQGLSARSLA   76 (295)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf             80778999999999999885907999999999999999999875-----9999476999999999999987699999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC
Q ss_conf             12344422223332101232222222222222212111111101567877653101356775775320122210011233
Q gi|254780882|r   90 RSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLR  169 (328)
Q Consensus        90 ~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR  169 (328)
                      +++++|++||+||+.+++++.||+..|+.||..++.|++++.+|+.++++....      ...+.||++|+.|||.||||
T Consensus        77 ~~l~~lr~~~~~a~~~~~i~~nP~~~i~~~k~~~~~~~~lt~~e~~~ll~~~~~------~~~~~Rd~~i~~ll~~tGlR  150 (295)
T PRK00236         77 RRLSALRSFYRWLVRRGLLKANPAAGLRAPKAPKRLPKPLDVDQAKRLLDADAD------DPLALRDRAILELLYGSGLR  150 (295)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCC------CCHHHHHHHHHHHHHHHCCC
T ss_conf             999999999998876286145778751277766568850018999999971325------80658999999999981978


Q ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             22222112222233232203323785310001122100234322111001234466554321111221110001235678
Q gi|254780882|r  170 ISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQ  249 (328)
Q Consensus       170 ~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~  249 (328)
                      +||+++|+|+|||++.++|+|.|||+|+|+|||++.+.+.|..|++.++.   ...+++||++.+|++++++++++.|++
T Consensus       151 ~~E~~~L~~~did~~~~~i~i~~Kg~K~R~Vpl~~~~~~~L~~yl~~~~~---~~~~~~lF~~~~g~~l~~~~i~~~~~~  227 (295)
T PRK00236        151 LSELVGLDIDDLDLASGTVRVLGKGNKERTVPVGSAALEALEAYLARPLA---EEDDDALFLGARGGRLSPRVVQRRVKK  227 (295)
T ss_pred             HHHHCCCCHHHCCCCCCEEEEECCCCEEEEEECCHHHHHHHHHHHHHCCC---CCCCCEEEECCCCCCCCHHHHHHHHHH
T ss_conf             33120563977277789898817898168986599999999999996776---789983775689995878899999999


Q ss_pred             HHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH
Q ss_conf             999768699988054179999999984899889999837888789799996198999999999999817300
Q gi|254780882|r  250 LRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI  321 (328)
Q Consensus       250 ~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~  321 (328)
                      +++++|++.+++||+|||||||+|+++|+|+.+||++|||+|++||++|+|++.++    |+++|+++|||+
T Consensus       228 ~~~~~gi~~~~~~H~lRHt~At~l~~~G~~l~~vq~~LGHssi~tT~~Y~h~~~~~----l~~~~~~~~p~~  295 (295)
T PRK00236        228 LRKKAGLPEHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQH----LAEVYDAAHPRA  295 (295)
T ss_pred             HHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHH----HHHHHHHHCCCC
T ss_conf             99985999999899788999999998799999999881899889999988689999----999999878399


No 6  
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=100.00  E-value=0  Score=475.22  Aligned_cols=291  Identities=33%  Similarity=0.478  Sum_probs=267.2

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 ~~i~~fl~~L~~erg~S~~Ti~~Y~~~l~~f~~~l~~~~------~~~~~it~~~i~~y~~~L~~~~~s~~Tin~~l~~l   77 (296)
T PRK00283          4 ALIEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG------LSLAEATRDDLQAFLAELAEGGYKATSSARRLSAL   77 (296)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC------CCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             999999999999879079999999999999999998759------99477999999999999987799999999999999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             22223332101232222222222222212111111101567877653101356775775320122210011233222221
Q gi|254780882|r   96 KSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALS  175 (328)
Q Consensus        96 r~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~  175 (328)
                      ++||+||+.+++++.||+..|+.||.+++.|++++.+|+.++++++..     ....+.||++|+.+||.||||+||+++
T Consensus        78 r~~~~~a~~~~~i~~np~~~i~~~k~~~~~~~~lt~eei~~ll~~~~~-----~~~~~~Rd~ail~ll~~tGlR~~El~~  152 (296)
T PRK00283         78 RRFFQFLLREGLREDDPTALLDSPKLPRRLPKTLSEAQVEALLDAPDI-----DTPLGLRDRAMLELLYATGLRVSELVG  152 (296)
T ss_pred             HHHHHHHHHCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCC-----CCHHHHHHHHHHHHHHHHCCCHHHHCC
T ss_conf             974799987074334878636677888889741437899998732377-----865768999999999983876120217


Q ss_pred             CCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf             1222223323220332378531000112210023432211100123-446655432111122111000123567899976
Q gi|254780882|r  176 LTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYL  254 (328)
Q Consensus       176 L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~  254 (328)
                      |+|+|||++.+.|.|.|||+|+|+|||++.+.++|.+|+...+... ....+++||++.+|++++++++++.++++++.+
T Consensus       153 L~~~di~~~~~~i~v~~Kg~K~R~vpl~~~~~~~l~~yl~~~r~~~~~~~~~~~lF~~~~g~~l~~~~~~~~~~~~~~~a  232 (296)
T PRK00283        153 LTLDDVSLRQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGRPALLGGRSSDALFPSARGGQLTRQTFWHRIKHYAKRA  232 (296)
T ss_pred             CCHHHCCCCCCCEEEECCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             85999235779557717898036997088999999999998657751489997475428898467999999999999980


Q ss_pred             CCC-CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH
Q ss_conf             869-9988054179999999984899889999837888789799996198999999999999817300
Q gi|254780882|r  255 GLP-LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI  321 (328)
Q Consensus       255 gi~-~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~  321 (328)
                      |++ .++|||+|||||||+|+++|+|+.+||++|||+|++||++|+|+++++.    +++|++|||++
T Consensus       233 gi~~~~~tpH~lRHt~at~ll~~G~~l~~i~~~LGHssi~TT~~Y~h~~~~~l----~~~~~~~~p~~  296 (296)
T PRK00283        233 GIDPKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERL----KELHAQHHPRA  296 (296)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHH----HHHHHHHCCCC
T ss_conf             89999889987879999999987989999998828998899999886899999----99999868499


No 7  
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=461.02  Aligned_cols=294  Identities=32%  Similarity=0.518  Sum_probs=274.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998625488999999999999999998512147887896898999999999999861210133211234
Q gi|254780882|r   14 LLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLS   93 (328)
Q Consensus        14 l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls   93 (328)
                      +...+++|++|+..||++|++|+.+|+.+|...+.+....     ++.+|..+++.+++.++.....+|++++++.+++|
T Consensus         6 ~~~~~~~yl~~L~~Er~lS~hTl~~Y~rqL~~l~~~~~q~-----~~~~w~~ld~~~vr~~~a~~~~~Gl~a~SlA~rLS   80 (299)
T COG4973           6 MAADLDAYLRYLRVERQLSPHTLANYRRQLEALIALLAQM-----GLGSWQQLDPADVRAFVARSHRRGLSARSLARRLS   80 (299)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             6788999999999861468888999999999999999972-----76566656999999999998318855778999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             44222233321012322222222222222121111111015678776531013567757753201222100112332222
Q gi|254780882|r   94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA  173 (328)
Q Consensus        94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El  173 (328)
                      ++|+||.|++++|.+..||+.+|+.||.++++|+.++.||+.++++ +     +....++.||+||+++||.+|+|.||+
T Consensus        81 a~R~f~~wLv~~g~l~~nPa~GvsaPK~~r~LPk~ld~d~~~~ll~-~-----d~~dPlavRDrAllElmY~sGLRLSEL  154 (299)
T COG4973          81 ALRSFYDWLVKQGELKANPAKGVSAPKQPRHLPKNLDVDEANRLLD-I-----DGDDPLAVRDRALLELMYGSGLRLSEL  154 (299)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHC-C-----CCCCCHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             9999999998727646686456889887443777689999999966-7-----899933478999999998437008988


Q ss_pred             CCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             21122222332322033237853100011221002343221110012344665543211112211100012356789997
Q gi|254780882|r  174 LSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRY  253 (328)
Q Consensus       174 ~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~  253 (328)
                      ++|+++|||++.+.++|.|||+|+|.||++..+.++|..|+..+..  ....++.||++..|++||.+.|.+.+..+..+
T Consensus       155 vgLd~~~vdl~~geV~V~GKGnKeR~vP~g~~A~~al~~WL~lR~~--~a~~d~AlF~s~~G~Ris~R~iQkR~~~wgik  232 (299)
T COG4973         155 VGLDLKHVDLDEGEVRVMGKGNKERRVPVGRKAVEALEHWLALRGL--FASEDDALFLSRLGKRISARAIQKRLAQWGIK  232 (299)
T ss_pred             HCCCCCCCCCCCCEEEEECCCCCEEECCCHHHHHHHHHHHHHHHHC--CCCCCCEEEECCCCCCCCHHHHHHHHHHHHHH
T ss_conf             4788444545542589962787346535217799999999865510--37987605310368816488999999999986


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHCC
Q ss_conf             68699988054179999999984899889999837888789799996198999999999999817300012
Q gi|254780882|r  254 LGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQK  324 (328)
Q Consensus       254 ~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~~  324 (328)
                      .|+..+++||.|||+|||+|+|+..|++.||++|||+|++|||||||+|-++    |.++||.+|||+|||
T Consensus       233 qg~~~HvhPH~LRHSFAtHmLesSgDLRaVQELLGHanlsTTQIYThLDFQH----LA~vYD~AHPRAkrk  299 (299)
T COG4973         233 QGLNSHVHPHKLRHSFATHMLESSGDLRAVQELLGHANLSTTQIYTHLDFQH----LASVYDAAHPRAKRK  299 (299)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHCCHHH----HHHHHHHHCCCCCCC
T ss_conf             0322138768777788999987035489999985646512444323236899----999986317411269


No 8  
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily.  In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequen
Probab=100.00  E-value=0  Score=446.21  Aligned_cols=281  Identities=35%  Similarity=0.506  Sum_probs=258.3

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999986254889999999999999999985121478878968989999999999998612101332112344422
Q gi|254780882|r   18 RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKS   97 (328)
Q Consensus        18 ~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~   97 (328)
                      +|+|++||..+||+||+|+++|+.+++.|..||...     +...+.+++..+|..|+.++.+.++|++|+++++++|++
T Consensus         1 i~~fl~~l~~~r~lS~~T~~~Y~~~l~~f~~~~~~~-----~~~~~~~i~~~~i~~~~~~L~~~~~s~~Ti~~~~~~l~~   75 (284)
T cd00798           1 IERFLDYLAVERGLSENTLAAYRRDLERFLEFLEER-----GILFPADVTPDDIRRFLAELKDQGLSARSIARKLSALRS   75 (284)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             978999999985907999999999999999999982-----999948799999999999998769999999999999999


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             22333210123222222222222221211111110156787765310135677577532012221001123322222112
Q gi|254780882|r   98 FLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLT  177 (328)
Q Consensus        98 f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~  177 (328)
                      ||+||+++++++.||+..++.|+..+..|++++.+|+.++++++.     .....+.||++|+.+++.||||++|+++|+
T Consensus        76 ~~~~~~~~~~i~~np~~~i~~~k~~~~~~~~l~~~ei~~ll~~~~-----~~~~~~~Rd~~i~~ll~~tGlR~~E~~~L~  150 (284)
T cd00798          76 FFKFLLREGLILANPAELIEPPKLKRSLPKVLTIEEVERLLAAPD-----GDTPLGLRDRALLELLYSTGLRVSELVGLK  150 (284)
T ss_pred             HHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHC-----CCCHHHHHHHHHHHHHHHHCCCHHHHHCCC
T ss_conf             999998658765682320257886877888679999899998632-----377677999999999999679924461696


Q ss_pred             CCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             22223323220332378531000112210023432211100123-44665543211112211100012356789997686
Q gi|254780882|r  178 PQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGL  256 (328)
Q Consensus       178 ~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi  256 (328)
                      |+|||++.+++.|.|||+|+|+|||++.+.++|..|+..++... .....+++|++.+|++++++++++.++++++++|+
T Consensus       151 ~~did~~~~~i~v~~K~~k~r~vpl~~~~~~~l~~~~~~~~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~g~  230 (284)
T cd00798         151 LSDVDLSRGLIRVRGKGNKERIVPLGETAVEALQRYLEVRRPLLLKVGDSDALFLNQRGKRLSRRGVWKILKEYARRAGI  230 (284)
T ss_pred             HHHCCCCCCEEEEECCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             99947667779996479944788649999999999999833420367877633223689826579999999999999099


Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHH
Q ss_conf             9998805417999999998489988999983788878979999619899999
Q gi|254780882|r  257 PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGD  308 (328)
Q Consensus       257 ~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~  308 (328)
                      +.+++||+|||||||+|+++|+|+..||++|||+|++||++|+|++.++.++
T Consensus       231 ~~~~~~H~lRHt~at~l~~~g~~~~~i~~~lGH~s~~tT~~Y~h~~~~~l~e  282 (284)
T cd00798         231 EKKISPHTLRHSFATHLLENGADLRAVQELLGHASLATTQIYTHVSFEHLKE  282 (284)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf             9999914659999999998789999999880798799999877779999985


No 9  
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=100.00  E-value=0  Score=438.39  Aligned_cols=300  Identities=22%  Similarity=0.315  Sum_probs=251.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC------CCCCCCCHHHCCHHHHHHHHHHHHH----
Q ss_conf             989999999999999986254889999999999999999985121------4788789689899999999999986----
Q gi|254780882|r   11 SFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTE------EKITIQTIRQLSYTEIRAFISKRRT----   80 (328)
Q Consensus        11 ~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~------~~~~~~~~~~i~~~~i~~~l~~l~~----   80 (328)
                      ..+|+..+++|++++. ++++||+|+.+|..||+.|+.|+.....      ..+++..+.+++..||..|+.||..    
T Consensus        14 ~~~~P~~i~ey~~~~~-~~~~Sp~Ti~~Y~~DL~~F~~fL~~~~~~~~~~~~~i~~~~l~~l~~~di~~y~~~L~~~~~~   92 (360)
T PRK05084         14 KAEMPWYVLEYYQSKL-ATPYSPTTLYEYLTEYRRFFNWLIDEGLTVATKIKDIPLSTLENLTKKDVELFILYLRERPSL   92 (360)
T ss_pred             HHHCHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHHHCCCC
T ss_conf             8867099999999886-059898999999999999999998649875556332778999756699999999999852223


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCCCCCCCCCCCCCCCC--------CCCCCCCCHHHHHHH
Q ss_conf             ------12101332112344422223332101-------232222222222222212--------111111101567877
Q gi|254780882|r   81 ------QKIGDRSLKRSLSGIKSFLKYLKKRK-------ITTESNILNMRNLKKSNS--------LPRALNEKQALTLVD  139 (328)
Q Consensus        81 ------~~~s~~T~~~~ls~lr~f~~~~~~~~-------~i~~np~~~i~~~k~~~~--------~p~~lt~~e~~~ll~  139 (328)
                            .++|++|+||++++|++||+|+.+++       ++..||...+..|+....        .|+.++.+|+..+++
T Consensus        93 ~~~~~~~~~s~~tinRklsaLrsFfkyL~~~~~~~~~~~y~~~n~~~~i~~~k~~~~~~~r~~~~~~~~l~~~e~~~ll~  172 (360)
T PRK05084         93 NGHLTGEGVSQTTINRTLSALKSLFKYLTEETENEDGEPYFYRNVMKKISLKKKKETLAARAENLKQKLFLGDETVEFLD  172 (360)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCHHHHCCCCCCCCCCCCCCHHCCCCCCCHHHHHHHHH
T ss_conf             43212257678899999999999999999852022322133115265257776532122310000120055678999997


Q ss_pred             HHHHCCCCCCC--------HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHH
Q ss_conf             65310135677--------5775320122210011233222221122222332322033237853100011221002343
Q gi|254780882|r  140 NVLLHTSHETK--------WIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAIL  211 (328)
Q Consensus       140 ~~~~~~~~~~~--------~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~  211 (328)
                      .+.........        ....||+||+.|||.||||+||+++|+|+|||++.+.|.|.|||+|+|.||+++.+.++|.
T Consensus       173 ~i~~~~~~~l~~~~~~~~~~~~~RD~aIi~ll~~tGlRvsEl~~L~~~DId~~~~~i~V~~Kg~K~r~vpi~~~~~~~l~  252 (360)
T PRK05084        173 FIDNEYEQKLSNRALSSFKKNKERDLAIIALLLGSGIRVSELVNLDLKDLNLKQMTIDVTRKGGKRDSVPIAPFALPYLE  252 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEECCHHHHHHHH
T ss_conf             65244341202555443012367999999999985879999976979985878997999847984468877899999999


Q ss_pred             HHHHHHCCCCC-CCCCCCCCCCCCC---CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             22111001234-4665543211112---2111000123567899976869998805417999999998489988999983
Q gi|254780882|r  212 EYYDLCPFDLN-LNIQLPLFRGIRG---KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSIL  287 (328)
Q Consensus       212 ~yl~~~~~~~~-~~~~~~lF~~~~g---~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~l  287 (328)
                      +|++.+..... ....+++|++..|   ++++.++|.+++++++..+|+  ++|||+|||||||+|+++|+|+..||++|
T Consensus       253 ~yl~~r~~~~~~~~~~~~lF~~~~~~~~~rls~~~i~~~v~k~~~~~~~--~itpH~LRHtfAT~Ll~~G~dl~~vq~lL  330 (360)
T PRK05084        253 EYLKIRAQRYKAEKNDTALFLTKYRGKPNRISASAIEKMVAKYSEAFGV--RVTPHKLRHTLATRLYDATKDQVLVADQL  330 (360)
T ss_pred             HHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             9999708743577888815764689988822499999999999986799--97841329999999998799999999985


Q ss_pred             CCCCHHHHHHHHHHCHHHHHHHHHHH
Q ss_conf             78887897999961989999999999
Q gi|254780882|r  288 GHFRLSTTQIYTNVNSKNGGDWMMEI  313 (328)
Q Consensus       288 GH~s~~tT~~Y~h~~~~~~~~~l~~~  313 (328)
                      ||+|++||++|+|++.++.++++.++
T Consensus       331 GH~si~TT~iYthv~~~~~r~a~~~l  356 (360)
T PRK05084        331 GHTSTQVTDLYTHIVNDEQKDALDKL  356 (360)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             89987999998868999999999863


No 10 
>cd01196 INT_VanD VanD integrase, IntD, and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases including those similar to IntD, a putative integrase-like protein, a component of the vanD glycopeptide resistance cluster in Enterococcus faecium BM4339. Members of this CD are predominantly bacterial in origin.
Probab=100.00  E-value=0  Score=395.73  Aligned_cols=260  Identities=18%  Similarity=0.287  Sum_probs=218.0

Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999986254889999999999999999985121478878968989999999999998612101332112344422223
Q gi|254780882|r   21 WLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLK  100 (328)
Q Consensus        21 ~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~  100 (328)
                      |.+||. ++|+|++|+++|..++.+|+  +.           ..+++..++.+|+.++.+ +++++|+|+++++|++||+
T Consensus         1 F~~yL~-e~g~S~~Ti~sY~~dl~~ff--~~-----------~~~i~~~~i~~y~~~L~~-~~~~~Tin~~lsalr~F~~   65 (263)
T cd01196           1 FEEYLY-KNNLSKNTVSSYLRTVVQYF--LN-----------GKELTKPNLLEYKGYLQE-NFKAQTVNLRLQGINKYLE   65 (263)
T ss_pred             CHHHHH-HCCCCHHHHHHHHHHHHHHH--CC-----------CCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHH
T ss_conf             958796-76978999999999999997--15-----------588999999999999996-8989999999999999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             33210123222222222222221211111110156787765310135677577532012221001123322222112222
Q gi|254780882|r  101 YLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQN  180 (328)
Q Consensus       101 ~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~d  180 (328)
                      |+..+++.    .. ...++....+|.+++.+|+..+++++....       ..||++|+.+||.||||+||+++|+++|
T Consensus        66 fl~~~~~~----~k-~~k~~~~~~l~~~l~~~e~~~l~~~~~~~~-------~~r~~~ii~lL~~tGlRvsEl~~L~~~d  133 (263)
T cd01196          66 FIGWHDLK----LK-FVKVQQKAFLENVISDADYKFLKTALKADG-------NEEWYFVVWFLAATGARVSELIHIKVEH  133 (263)
T ss_pred             HHHHCCCC----CC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-------CHHHHHHHHHHHHHCCHHHHHHCCCHHH
T ss_conf             96554786----55-678888899999899999999997631366-------7769999999998499999998368988


Q ss_pred             CCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CC
Q ss_conf             23323220332378531000112210023432211100123446655432111122111000123567899976869-99
Q gi|254780882|r  181 IMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP-LS  259 (328)
Q Consensus       181 id~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~-~~  259 (328)
                      |+++  .+.|.|||+|+|.|||++.+...+.+|++.+.     ..+++||++..|+|++++++++.++++++++|++ ..
T Consensus       134 i~~~--~~~i~~KG~K~R~v~i~~~~~~~l~~y~~~~~-----~~~~~lF~~~~g~~l~~~~i~~~~k~~~~~agi~~~~  206 (263)
T cd01196         134 VQTG--YADIYSKGGKIRRLYIPKNLRVEALKWLKELN-----LDSGYIFLNRFGKPITARGIAQQLKNYAAKYKMNPRV  206 (263)
T ss_pred             HCCC--CEEEEECCCCEEEEEECHHHHHHHHHHHHHCC-----CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             2668--64999559937887307999999999999728-----8657716699949888999999999999985999877


Q ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHH
Q ss_conf             8805417999999998489988999983788878979999619899999999999
Q gi|254780882|r  260 TTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIY  314 (328)
Q Consensus       260 ~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~  314 (328)
                      ++||+|||||||+|+++|+|+..||++|||+|++||++|+|++.++.++++.+++
T Consensus       207 ~~PH~lRHtfAt~ll~~g~dl~~vq~lLGH~si~TT~iY~~~~~~~~k~~~~k~~  261 (263)
T cd01196         207 VYPHSFRHLFAKNFLAKYNDLALLADLMGHESIETTRIYLRKTATEQQRIVDKIV  261 (263)
T ss_pred             CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHC
T ss_conf             8872269999999998699999999995899878999988079999999999870


No 11 
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases for which not much biochemical characterization is available.
Probab=100.00  E-value=0  Score=390.72  Aligned_cols=284  Identities=20%  Similarity=0.189  Sum_probs=237.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998625488999999999999999998512147887896898999999999999861210133211234
Q gi|254780882|r   14 LLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLS   93 (328)
Q Consensus        14 l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls   93 (328)
                      |.+++++||++.+. .|+|.+|   |..+|+.|..||....        ...++.+++..|+..  ..+.+++|++++++
T Consensus         1 l~~~i~~yl~~~r~-~G~~~~t---~~~~L~~F~~fl~~~~--------~~~~~~~~~~~w~~~--~~~~s~~t~~~rls   66 (299)
T cd01187           1 LRQALEEYIALRRA-LGYKYRT---PARLLRDFVRFLERHG--------AGFITTDLALRWAAS--PPSAQPATWAGRLG   66 (299)
T ss_pred             CHHHHHHHHHHHHH-CCCCHHH---HHHHHHHHHHHHHHCC--------CCCCCHHHHHHHHHH--CCCCCHHHHHHHHH
T ss_conf             96999999999998-7998156---8999999999998679--------988899999999987--79998899999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             44222233321012322222222222222121111111015678776531013567757753201222100112332222
Q gi|254780882|r   94 GIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA  173 (328)
Q Consensus        94 ~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El  173 (328)
                      +||+||+|+..+|++..||...+..|+..+..|.++|++|+.++++++.... ......+.|+++||.|||.||||+||+
T Consensus        67 ~lr~F~~~l~~~g~~~~~P~~~~~~~k~~~~~P~~lt~~Ei~~Ll~a~~~~~-~~~~~~~~~~~~l~~Lly~tGlR~sEl  145 (299)
T cd01187          67 VVRRFARHRRRADPRTEVPPADLFPRRPRRPTPYIYTDEEIQRLLAAALQLP-PTSGLRPWTYRTLFGLLAVTGLRLGEA  145 (299)
T ss_pred             HHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             9999999999869956690765457899999999999999999984110169-961057689999999999958889998


Q ss_pred             CCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHH---HHHHH
Q ss_conf             211222223323220332-37853100011221002343221110012344665543211112211100012---35678
Q gi|254780882|r  174 LSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQ---RYIRQ  249 (328)
Q Consensus       174 ~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~---~~~~~  249 (328)
                      ++|+++|||++++.|.|. |||+|+|+|||++.+.++|.+|++.++.......+++||++.+|++++..+..   ..++.
T Consensus       146 ~~L~~~Dvd~~~~~i~v~~gKg~K~R~Vpl~~~~~~~L~~yl~~r~~~~~~~~~~~lF~~~~g~~l~~~~~~~~~~~~r~  225 (299)
T cd01187         146 LRLRLSDVDLDSGILTVRDSKFGKSRLVPLHASTRAALRDYLARRDRLLPAPDSSAFFVSSRGGRLSYGGHRVFYALSRE  225 (299)
T ss_pred             HCCCCCCCCCCCCEEEEECCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHH
T ss_conf             03343305676784765418899707985669999999999998476426898986745899897877789999999999


Q ss_pred             HHHHCCC--CCCCCCCCCHHHHHHHHH----HCCCCHH----HHHHHHCCCCHHHHHHHHHHCHHHHHHHHHH
Q ss_conf             9997686--999880541799999999----8489988----9999837888789799996198999999999
Q gi|254780882|r  250 LRRYLGL--PLSTTAHTLRHSFATHLL----SNGGDLR----SIQSILGHFRLSTTQIYTNVNSKNGGDWMME  312 (328)
Q Consensus       250 ~~~~~gi--~~~~spH~lRHtfAt~ll----~~G~~~~----~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~  312 (328)
                      +....+.  ....+||+|||||||+++    ++|+|+.    +||++|||+|++||++|+|+++|..+++.++
T Consensus       226 ~~~~~~~~~~~~~~pH~LRHtfAt~~l~~~~~~G~di~~~L~~lq~~LGH~si~tT~~Y~h~~~e~l~~a~~r  298 (299)
T cd01187         226 IGLRGWAQRGRGPRLHDLRHRFAVTRLTRWYRAGADVERKLPVLATYLGHANITDTYWYLHASPELMELAARR  298 (299)
T ss_pred             HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHH
T ss_conf             9986066668999976571389999999998679973433999999748998688898880399999999850


No 12 
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed
Probab=100.00  E-value=0  Score=391.64  Aligned_cols=247  Identities=21%  Similarity=0.263  Sum_probs=208.8

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999986254889999999999999999985121478878968989999999999998612101332112344422
Q gi|254780882|r   18 RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKS   97 (328)
Q Consensus        18 ~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~   97 (328)
                      +++||+++..|||+|+||+++|+.||+.|..|+..            +++..++..|..++.  +++++|++|++++|++
T Consensus         1 l~~fl~~l~~ek~lS~nTi~aY~~DL~~F~~fl~~------------~i~~~~i~~y~~~L~--~~~~st~~Rklsslr~   66 (247)
T PRK02436          1 MKNYIEPFLASKALSVNSQKSYRYDLQQFCQLVGE------------RVNQTSLKLYQNSLA--NLKLSAQKRKLSAVNQ   66 (247)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH------------HCCHHHHHHHHHHHH--CCCHHHHHHHHHHHHH
T ss_conf             98899999998691499999999999999999873------------589999999999987--1679999999999999


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             22333210123222222222222221211111110156787765310135677577532012221001123322222112
Q gi|254780882|r   98 FLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLT  177 (328)
Q Consensus        98 f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~  177 (328)
                      ||+|+.++++++..+- ....|+.++..|..++..++..+++..          ...|+++|+.+||.||||+||+++|+
T Consensus        67 F~~fL~~~~~i~~~~~-~~~~~k~~~~~~~~~~~~~~~~~~~~~----------~~~~~r~i~~ll~~tGlRvSEl~~L~  135 (247)
T PRK02436         67 FLYFLYQKKYLDSFFK-LKETAKVMRSEKQQPEILDLSSFYQET----------PFPEGQLIALLILELGLTPSEIAGLK  135 (247)
T ss_pred             HHHHHHHCCCCCCCCC-HHCCCCCCCCCCCCCHHHHHHHHHCCC----------CCHHHHHHHHHHHHHCCHHHHHHCCC
T ss_conf             9999997687667520-420588988765413186799885646----------78568999999999694799997891


Q ss_pred             CCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             22223323220332378531000112210023432211100123446655432111122111000123567899976869
Q gi|254780882|r  178 PQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP  257 (328)
Q Consensus       178 ~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~  257 (328)
                      |+|||++.+.|.| |||+|+|.|||++.+.+.|..|++.        ...++| +.+|+|++++++++.++++++.+|++
T Consensus       136 ~~Did~~~~~i~v-~kg~k~R~Vpl~~~~~~~l~~y~~~--------~~~~l~-~~~g~~lsr~~~~~~lk~~~~~~g~~  205 (247)
T PRK02436        136 VADIDLDFQVLTI-EKAGGKRVLPLPEALLPFLEQILNG--------KEVYLF-EHKGKPYSRQWFFNQLKSFVNSIGYP  205 (247)
T ss_pred             HHHHCCCCCEEEE-ECCCEEEEEECCHHHHHHHHHHHHC--------CCCEEE-CCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             9991988787999-0799078754679999999998715--------865011-68999667999999999999974999


Q ss_pred             CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9988054179999999984899889999837888789799996
Q gi|254780882|r  258 LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTN  300 (328)
Q Consensus       258 ~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h  300 (328)
                       ++|||.|||||||+|+++|+|+.+||++|||+|++|||||++
T Consensus       206 -~vtPH~LRHsFAthlL~~Gadlr~vQeLLGH~sisTTqiY~k  247 (247)
T PRK02436        206 -GLTAQKLREQFILKQKEAGKSIYELARLLGLKTPVTLEKYYK  247 (247)
T ss_pred             -CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCC
T ss_conf             -998710099999999987999999998808998788553069


No 13 
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=100.00  E-value=0  Score=383.75  Aligned_cols=284  Identities=20%  Similarity=0.256  Sum_probs=237.4

Q ss_pred             HHCCHHHHHHHHHHHHHH-HHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHH-HHHHHH
Q ss_conf             314989999999999999-986254889999999999999999985121478878968989999999999998-612101
Q gi|254780882|r    8 EIVSFELLKERQNWLQNL-EIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRR-TQKIGD   85 (328)
Q Consensus         8 ~~~~~~l~~~~e~~L~~l-~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~-~~~~s~   85 (328)
                      +...-++++.+++|++.+ +.++++|++|+++|..+++.|..|+......  ....+.+++..+|.+|+.++. +.++|+
T Consensus         9 ~~~~~tf~~~~~~~~e~~~~~~k~~S~~Ti~~Y~~~l~~f~~Fl~~~~~~--~di~~~~i~~~~i~~f~~~L~~~k~~s~   86 (299)
T cd01185           9 KEMQQTFLAYFDKHNDERERVGKDKAQSTWKRYRTHLKNLREFIECTYKE--IDIALLELTREFILEFKLFLRKEKKLSR   86 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCCHHHCCHHHHHHHHHHHHHCCCCCH
T ss_conf             78899999999999999998677567999999999999999999982887--7788788479999999999987579888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC
Q ss_conf             33211234442222333210123222222222222221211111110156787765310135677577532012221001
Q gi|254780882|r   86 RSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYG  165 (328)
Q Consensus        86 ~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~  165 (328)
                      +|+++++++|++||+||++++++..||+..++.|+.++..|++|+.+|+.++++...    ........||.++|.+  .
T Consensus        87 ~Ti~~~l~~lr~~~~~a~~~~~i~~nP~~~i~~~k~~~~~~~~Lt~eEi~~ll~~~~----~~~~~~~~r~~~l~~~--~  160 (299)
T cd01185          87 NTAVHYLSWLKKLLKIAYRDKGLRDNPFAKFKCKKEEETDREYLTPDELQKLAETPC----KDPRLELVRRAFLFSC--F  160 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC----CCCCHHHHHHHHHHHH--H
T ss_conf             899999999999999999889921192965617888998999999999999982714----7874699999999998--8


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCC---EEE-CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1233222221122222332322---033-237853100011221002343221110012344665543211112211100
Q gi|254780882|r  166 CGLRISEALSLTPQNIMDDQST---LRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPG  241 (328)
Q Consensus       166 TGlR~~El~~L~~~did~~~~~---i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~  241 (328)
                      ||||+||+++|+|+||+++...   +.+ .+|+++.+.|||++.+.++|..|..        ...+++|+.     ++..
T Consensus       161 TGlR~~El~~L~~~dI~~~~~~~~~i~~~~~Kt~~~~~ipl~~~~~~~l~~~~~--------~~~~~lF~~-----~~~~  227 (299)
T cd01185         161 TGLRYSDIKKLTWEEIVEDSDGEKWIRKRRQKTKVEVYIPLLDEALQILGKYPD--------EKEGLVFPL-----LKNS  227 (299)
T ss_pred             HCCCHHHHHHCCHHHHHHCCCCEEEEEECCCCCCEEEEEECHHHHHHHHHHHHC--------CCCCCCCCC-----CCHH
T ss_conf             098899998396998213369648998516744224320015999999998522--------675440688-----8756


Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHH
Q ss_conf             01235678999768699988054179999999984899889999837888789799996198999999999
Q gi|254780882|r  242 VFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMME  312 (328)
Q Consensus       242 ~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~  312 (328)
                      .+++.++++++.+|+++++|||+|||||||+|+++|+|+.+||++|||+|++||++|+|++++++.+++.+
T Consensus       228 ~~~~~lk~~~~~agi~~~it~H~lRHTfAt~ll~~G~~l~~vq~~LGHssi~tT~~Y~hv~~e~~~e~~~k  298 (299)
T cd01185         228 NMNKPLKEWAKLAGIKKHITFHCARHTFATLQLLSGGPIETVSKMLGHTNIKTTQVYARVTDEKKSEDMNK  298 (299)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf             89999999999828899998114099999999987989999998818998899999987798899999963


No 14 
>cd01190 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases.
Probab=100.00  E-value=0  Score=376.54  Aligned_cols=247  Identities=26%  Similarity=0.374  Sum_probs=213.2

Q ss_pred             CCHHHCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             8968989999999999998-6121013321123444222233321012322---22222222222212111111101567
Q gi|254780882|r   61 QTIRQLSYTEIRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKKRKITTE---SNILNMRNLKKSNSLPRALNEKQALT  136 (328)
Q Consensus        61 ~~~~~i~~~~i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~---np~~~i~~~k~~~~~p~~lt~~e~~~  136 (328)
                      .++.+|+..+|.+|+.+|. ++|+|++|+|+++++|++||+||..++....   +|+..++..+..+..+.+++.+|+.+
T Consensus         3 l~l~dI~~~~i~~y~~~L~~~rg~s~~Tin~~l~~L~~f~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~l~~eei~~   82 (260)
T cd01190           3 LEIEDIDAPLILAFLDHLENDRGNSIRTRNARLAALHSFFRYAAREVPEHLPTIQRVLAIPMKRFKRPLVTYLTREEVQA   82 (260)
T ss_pred             CCHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
T ss_conf             87587999999999999998469999999999999999999999808401455371014887888999998899999999


Q ss_pred             HHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEECCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             87765310135677577532012221001123322222112222233232-20332378531000112210023432211
Q gi|254780882|r  137 LVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS-TLRIQGKGDKIRIVPLLPSVRKAILEYYD  215 (328)
Q Consensus       137 ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~-~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~  215 (328)
                      +++..     ....+.+.||++|+.+++.||||+||+++|+|+|||++.+ .+.+.|||+|+|.|||++.+.++|.+|++
T Consensus        83 ll~~~-----~~~~~~~~rd~~i~~ll~~tGlR~sEl~~L~~~did~~~~~~~~~~~K~~k~r~vpi~~~~~~~L~~~~~  157 (260)
T cd01190          83 LLAAP-----DRRTWSGRRDRAMLLFLYNTGARVSEATGLKVDDLQLDPPAQVRLIGKGRKERTVPLWRSTAAALRAWLR  157 (260)
T ss_pred             HHHCC-----CCCCCCCHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEEECCHHHHHHHHHHHH
T ss_conf             98186-----6567303689999999999575589786286976178998089996899804135468999999999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC------CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf             10012344665543211112211100012356789997686------999880541799999999848998899998378
Q gi|254780882|r  216 LCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGL------PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGH  289 (328)
Q Consensus       216 ~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi------~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH  289 (328)
                      .++.   ...+++||++..|++++..++.+.++++...+|.      .++++||+|||||||+|+++|+|+..||++|||
T Consensus       158 ~~~~---~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRHt~At~ll~~G~~l~~vq~~LGH  234 (260)
T cd01190         158 ERGL---HAEDEPLFVNRRGEPMTRFGVTYLLRKHAAKAAATAPTLATKRISPHVLRHTTAMHLLQSGVDIVVIALWLGH  234 (260)
T ss_pred             HCCC---CCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf             7544---6876615127899947868899999999999724164324677676713899999999879999999998689


Q ss_pred             CCHHHHHHHHHHCHHHHHHHHHHHHHHHCC
Q ss_conf             887897999961989999999999998173
Q gi|254780882|r  290 FRLSTTQIYTNVNSKNGGDWMMEIYDQTHP  319 (328)
Q Consensus       290 ~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~  319 (328)
                      +|++||++|+|++.++.    +++++++||
T Consensus       235 ~~i~tT~~Y~hv~~~~~----r~a~~k~~p  260 (260)
T cd01190         235 ASLETTNIYAEADLEMK----RRALAKATP  260 (260)
T ss_pred             CCHHHHHHHHCCCHHHH----HHHHHHHCC
T ss_conf             98899999984799999----999998691


No 15 
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946    Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=100.00  E-value=0  Score=379.55  Aligned_cols=253  Identities=32%  Similarity=0.448  Sum_probs=212.1

Q ss_pred             HCCCHHHHHHHHHHHHHHHHH--HHHCCCCCCCCCCHHHCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             254889999999999999999--985121478878968989999999999998-61210133211234442222333210
Q gi|254780882|r   29 RGLSKLTLQSYECDTRQFLIF--LAFYTEEKITIQTIRQLSYTEIRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKKR  105 (328)
Q Consensus        29 r~~s~~T~~~Y~~~l~~f~~~--~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~~  105 (328)
                      ++||..|+.+|-.-+++|+.|  -..       ..+++.+...+|++|+.+|. +.+.|++|.|..|++|.-||+-....
T Consensus        12 ~hYs~~T~~aY~~Wi~rfI~frG~~C-------~~hp~~~g~~eVeaFLs~LAv~~~Vs~sTQ~QAL~ALlFLY~~iL~~   84 (320)
T TIGR02249        12 RHYSKRTEEAYLHWIKRFIRFRGHNC-------LRHPSTLGDTEVEAFLSDLAVDGKVSASTQNQALAALLFLYKEILKL   84 (320)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCC-------CCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             88789999999999999998850510-------13853307567888856776425747657999999999999998468


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1232222222222222212111111101567877653-101356775775320122210011233222221122222332
Q gi|254780882|r  106 KITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVL-LHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDD  184 (328)
Q Consensus       106 ~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~-~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~  184 (328)
                      ++-.   ...+-.++.++++|-+||+||+.++++.+. ...           +++..|||+||||+.|++.|+++||||+
T Consensus        85 ~L~~---~~~~~Ra~~~~kLPvVLT~eEV~~~l~~l~eg~y-----------~L~a~LLYGsGMRlmE~LRLRikDiDF~  150 (320)
T TIGR02249        85 ELSL---MENFVRAKRPRKLPVVLTREEVARLLEHLEEGKY-----------RLIAKLLYGSGMRLMECLRLRIKDIDFD  150 (320)
T ss_pred             CCCC---HHHCCCCCCCCCCCEECCHHHHHHHHHHCCCCCH-----------HHHHHHHCCCHHHHHHHHHCCCCEEEEC
T ss_conf             8874---2222067888737733598899999842578613-----------1122231255158988875101103433


Q ss_pred             CCCEEEC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC--------------------------CCCCCCCCCC---
Q ss_conf             3220332-378531000112210023432211100123446--------------------------6554321111---
Q gi|254780882|r  185 QSTLRIQ-GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLN--------------------------IQLPLFRGIR---  234 (328)
Q Consensus       185 ~~~i~v~-gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~--------------------------~~~~lF~~~~---  234 (328)
                      .+.|.|+ |||+|.|.|||+.++.+-|+..++..+.-...+                          ..-||||+.+   
T Consensus       151 ~~~I~vr~GKG~KdR~v~Lp~~L~~~L~~q~~~~~~~h~~Dl~~~G~g~V~LP~AL~rKYPnA~~~~~WqylFPs~~~S~  230 (320)
T TIGR02249       151 YGEIRVRDGKGGKDRVVTLPKSLAPPLREQLERARALHEKDLLAEGYGGVYLPHALARKYPNASKEWGWQYLFPSARLSR  230 (320)
T ss_pred             CCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHCCCCCCCCCCCCEEECCCCCCCC
T ss_conf             76689973668988612681755799999999999999986405885301004554215787356678766537750155


Q ss_pred             ----CC----CCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHC
Q ss_conf             ----22----111000123567899976869998805417999999998489988999983788878979999619
Q gi|254780882|r  235 ----GK----PLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVN  302 (328)
Q Consensus       235 ----g~----~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~  302 (328)
                          |.    .|+..+|.+.++++..+|||+|.+|||+|||||||+||++|.||++||++|||+|++||||||||-
T Consensus       231 DPrsG~~~RHH~~e~~~QRav~~Av~~AGI~KpvTcHTLRHSFATHLLe~G~DIRTVQelLGHsDVkTTqIYTHVL  306 (320)
T TIGR02249       231 DPRSGRIRRHHIDEKTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVL  306 (320)
T ss_pred             CCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCEEEEEE
T ss_conf             7777852001067004328999999957898867887421224430565177367898861788422463453051


No 16 
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=100.00  E-value=0  Score=358.12  Aligned_cols=229  Identities=33%  Similarity=0.478  Sum_probs=203.8

Q ss_pred             CCCHHHCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             78968989999999999998612-10133211234442222333210123222222222222221211111110156787
Q gi|254780882|r   60 IQTIRQLSYTEIRAFISKRRTQK-IGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLV  138 (328)
Q Consensus        60 ~~~~~~i~~~~i~~~l~~l~~~~-~s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll  138 (328)
                      ..++++|+..||++|+.++..++ +|++|+|+++++|++||+|+...++   +|+..++.++.+++.|+++|.+|+.+++
T Consensus         4 ~k~~~~it~~dI~~y~~~L~~~~~~s~~Tin~~l~~l~~~~~~~~~~~~---~~~~~~~~~k~~~~~~~~lt~eEi~~ll   80 (242)
T cd01193           4 GRSPDELGEEDVRAFLTLLAVEGNVSASTQNQALSALLFFYRHTLKRDL---PWLQRIRRPRKPRKLPVVLSPEEVRRLL   80 (242)
T ss_pred             CCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCC---CHHHHCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             9895889999999999999984898999999999999999999987689---6566565578999899889999999999


Q ss_pred             HHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             7653101356775775320122210011233222221122222332322033-237853100011221002343221110
Q gi|254780882|r  139 DNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLC  217 (328)
Q Consensus       139 ~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~  217 (328)
                      +++.          +.|+++++.+++.||||+||+++|+|+|||+++++|.| .|||+|+|.|||++.+.++|.+|++..
T Consensus        81 ~~~~----------~~r~~~~~~ll~~tGlR~~El~~L~~~did~~~~~i~i~~~K~~k~R~vpl~~~~~~~l~~~l~~~  150 (242)
T cd01193          81 GALT----------GLKHRLILSLLYGCGLRLSECLRLRVKDIDFDRGQIRVRQGKGGKDRYVMLPEALLELLRAYWKRA  150 (242)
T ss_pred             HCCC----------CCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEECCHHHHHHHHHHHHHH
T ss_conf             7387----------767999999999828988889878663167675179986188996058875999999999999984


Q ss_pred             CCCCCCCCCCCCCCCCCC--------CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf             012344665543211112--------211100012356789997686999880541799999999848998899998378
Q gi|254780882|r  218 PFDLNLNIQLPLFRGIRG--------KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGH  289 (328)
Q Consensus       218 ~~~~~~~~~~~lF~~~~g--------~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH  289 (328)
                      +........+++|++.+|        .+++.+++++.++++++.+|++++++||+|||||||+|+++|+|+..||++|||
T Consensus       151 ~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~H~lRHT~at~ll~~G~~l~~v~~~lGH  230 (242)
T cd01193         151 RALGRERPWQWLFPSTRRSRDPVERRHHLSERTLQRALKKAVEQAGIDKRVTPHTLRHSFATHLLEAGYDIRTIQELLGH  230 (242)
T ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHCCC
T ss_conf             65300365210135667775755367767599999999999998499999886748999999999879999999988399


Q ss_pred             CCHHHHHHHHHH
Q ss_conf             887897999961
Q gi|254780882|r  290 FRLSTTQIYTNV  301 (328)
Q Consensus       290 ~s~~tT~~Y~h~  301 (328)
                      +|++|||+|+||
T Consensus       231 ~si~tT~~Y~Hv  242 (242)
T cd01193         231 SDLKTTMIYTHV  242 (242)
T ss_pred             CCHHHHHHHHCC
T ss_conf             888899870583


No 17 
>PRK09870 tyrosine recombinase; Provisional
Probab=100.00  E-value=0  Score=338.54  Aligned_cols=195  Identities=25%  Similarity=0.243  Sum_probs=174.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCC
Q ss_conf             22222121111111015678776531013567757753201222100112332222211222223323220332-37853
Q gi|254780882|r  118 NLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDK  196 (328)
Q Consensus       118 ~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K  196 (328)
                      ++|.+++.|++||.+|+.++++++..     . ..+.||++|+.+||.||||+||+++|+|+|||++++.+.|. +|+|+
T Consensus         2 k~K~~~k~~~~LT~~Ev~~lL~~~~~-----~-~~~~Rd~aii~ll~~tGlRvsEl~~L~~~DId~~~~~i~i~~~k~g~   75 (200)
T PRK09870          2 KNKADNKKRNFLTHSEIESLLKAANT-----G-PHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKGF   75 (200)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCC-----C-CHHHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCC
T ss_conf             98778888998899999999827799-----9-37589999999999968689999769598718779979999767897


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             10001122100234322111001234466554321111221110001235678999768699988054179999999984
Q gi|254780882|r  197 IRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSN  276 (328)
Q Consensus       197 ~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~  276 (328)
                      .|.+|+.+....+|.+|++.+... ....+++||+|.+|+|++++++++.++++++++|++.+++||+|||||||+|+++
T Consensus        76 ~~~~pl~~~~~~~l~~~l~~r~~~-~~~~~~~lF~s~~G~~ls~~~i~~~~~~~~~~agi~~~v~pH~LRHt~At~Ll~~  154 (200)
T PRK09870         76 STTHPLLNKEIQALKNWLSIRTSY-PHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANM  154 (200)
T ss_pred             EEEEECHHHHHHHHHHHHHHHHHC-CCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHC
T ss_conf             578876799999999999987524-5888871425799997779999999999999859997768760289999999986


Q ss_pred             CCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHC
Q ss_conf             89988999983788878979999619899999999999981730001
Q gi|254780882|r  277 GGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQ  323 (328)
Q Consensus       277 G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~  323 (328)
                      |+|+.+||++|||+|++|||+|+|++.+    .|+++|+++|||.++
T Consensus       155 G~di~~Iq~lLGHssi~TT~iYth~~~~----~l~~i~~~~hpr~~~  197 (200)
T PRK09870        155 GIDTRLIQDYLGHRNIRHTVWYTASNAG----RFYGIWDRARGRQRH  197 (200)
T ss_pred             CCCHHHHHHHHCCCCHHHHHHHHHCCHH----HHHHHHHHHCCCHHC
T ss_conf             9999999999489986689998817999----999999984973100


No 18 
>PRK09871 tyrosine recombinase; Provisional
Probab=100.00  E-value=0  Score=324.95  Aligned_cols=189  Identities=25%  Similarity=0.298  Sum_probs=169.6

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC-CCCCCCCCCCCCC
Q ss_conf             111110156787765310135677577532012221001123322222112222233232203323-7853100011221
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG-KGDKIRIVPLLPS  205 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~g-Kg~K~R~Vpi~~~  205 (328)
                      ++||.+|+.++++++..      ...+.||+||+.+||.||||+||+++|+|+|||++++.|.|.+ ||++.+++|+.+.
T Consensus         5 ryLt~~Ev~~Ll~a~~~------~~~~~Rd~aii~ll~~tGlR~sEl~~L~~~Did~~~~~i~i~~~k~g~~~~~pl~~~   78 (198)
T PRK09871          5 RYLTGKEVQAMMQAVCY------GATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFD   78 (198)
T ss_pred             CCCCHHHHHHHHHCCCC------CCCCHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEEECCHH
T ss_conf             76999999999844143------985448999999999978689999788887758779969999789974898748699


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        79 ~~~~l~~~~~~r~~~~~~~~~~~lF~s~~G~~ls~~~~~~~ik~~~~~aG~~~~~~pH~LRHTfAt~Ll~~G~dl~~Iq~  158 (198)
T PRK09871         79 EREAVERWTQERANWKGADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQD  158 (198)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf             99999999998777512677884143588994799999999999999849998889985579999999986999999999


Q ss_pred             HHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCHHCCC
Q ss_conf             8378887897999961989999999999998173000122
Q gi|254780882|r  286 ILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKD  325 (328)
Q Consensus       286 ~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~~~~~  325 (328)
                      +|||+|++||++|+|++.+    .|+++|+++||.+.+..
T Consensus       159 lLGHssi~TT~~Yth~~~~----~l~~~~~~~~p~~~~~~  194 (198)
T PRK09871        159 YLGHRNIRHTVRYTASNAA----RFAGLWERNNLINEKLK  194 (198)
T ss_pred             HHCCCCHHHHHHHHCCCHH----HHHHHHHHHCCCCCCCC
T ss_conf             9389977899998858999----99999999496100100


No 19 
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain.  Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.  The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites.  The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.
Probab=100.00  E-value=0  Score=314.87  Aligned_cols=258  Identities=19%  Similarity=0.199  Sum_probs=201.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             89999999999999999985121478878968989999999999998612101332112344422223332101232222
Q gi|254780882|r   33 KLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESN  112 (328)
Q Consensus        33 ~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~np  112 (328)
                      +||+++|.++++.|..||......     + ..++..+|..|+.++. ++++++|+++++++|++||.|+...+....+|
T Consensus         1 enT~~aY~~~l~~f~~wc~~~~~~-----~-~~~t~~~v~~yl~~L~-~~~~~~Ti~~~lsalr~~~~~~~~~~~~~~~~   73 (287)
T cd00799           1 DNTRKAYLSDWRRFAAWCQAHGRT-----P-LPASPETVTLYLTDLA-DSLAPSTISRRLSALSQLHRRSGLPSPADSPL   73 (287)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCC-----C-CCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCH
T ss_conf             905999999999999999974999-----7-8899999999999998-47787699999999999999970588654714


Q ss_pred             CCCC-C---CCC-CCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-
Q ss_conf             2222-2---222-221211111110156787765310135677577532012221001123322222112222233232-
Q gi|254780882|r  113 ILNM-R---NLK-KSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS-  186 (328)
Q Consensus       113 ~~~i-~---~~k-~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~-  186 (328)
                      +..+ +   .+. ..++.+.+++.+++.++++.+    +......++||++|+.++|.||||++|+++|+|+||+++.+ 
T Consensus        74 ~~~~~~~~~r~~~~~~~~~~~~~~~~l~~ll~~~----~~~~~~~~~Rd~ail~ll~~tGlR~~El~~L~~~di~~~~~~  149 (287)
T cd00799          74 VRLVLRGIRREEARPKRQALAILPEDLDKLRSLL----DESDTLRDLRDLALLLLGFAGLLRRSELVRLRWEDLTFTDGG  149 (287)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCC----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCC
T ss_conf             8887532112368876578989999999998625----557875879999999999986238999971839871857897


Q ss_pred             C--EEE-CCCCCCC------CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC------CCCCCCCCCHHHHHHHHH
Q ss_conf             2--033-2378531------000112210023432211100123446655432111------122111000123567899
Q gi|254780882|r  187 T--LRI-QGKGDKI------RIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI------RGKPLNPGVFQRYIRQLR  251 (328)
Q Consensus       187 ~--i~v-~gKg~K~------R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~------~g~~ls~~~i~~~~~~~~  251 (328)
                      .  |.+ .+|+++.      +.+|.......++..|+...     ....+++|++.      .+++++.+++++++++++
T Consensus       150 ~~~i~~~~~K~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~~lF~~~~~~~~~~~~~ls~~~v~~~~~~~~  224 (287)
T cd00799         150 GLLVTLRRSKTDQSGLGVLKLIPPLTTCPVRALERWLEAA-----RIPKGPLFRRIDRWGVLGPGALSDNSLNRILKRLA  224 (287)
T ss_pred             EEEEEECCCCEEECCCCCEEEECCCHHHHHHHHHHHHHHC-----CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             1799955874035487836750621589999999999872-----56766430244446775788787899999999999


Q ss_pred             HHCCCCC-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHH
Q ss_conf             9768699-988054179999999984899889999837888789799996198999
Q gi|254780882|r  252 RYLGLPL-STTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNG  306 (328)
Q Consensus       252 ~~~gi~~-~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~  306 (328)
                      +.+|++. .+|||+|||||||+|+++|+|+..||++|||+|++||++|.|..+.-.
T Consensus       225 ~~ag~~~~~~s~H~lRHt~At~ll~~G~~l~~Iq~~lGH~s~~tt~~Y~~~~d~~~  280 (287)
T cd00799         225 EAAGLRSGSWSGHSLRRGFATEAARAGYSLLEIMRQGRWRSPKMVSRYIRDADRFQ  280 (287)
T ss_pred             HHCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHC
T ss_conf             98599999989751389999999987999999999858999889999853713101


No 20 
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements.  They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=100.00  E-value=2.8e-45  Score=302.48  Aligned_cols=275  Identities=17%  Similarity=0.188  Sum_probs=214.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-HHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4989999999999999986254889999999999999-999985121478878968989999999999998612101332
Q gi|254780882|r   10 VSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQF-LIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSL   88 (328)
Q Consensus        10 ~~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f-~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~   88 (328)
                      ...++.+++++|++...  ...+++|.+.|+..++.. ..++        +..++.+|+..++..|+..+... .+++|+
T Consensus        69 ~~~T~~~~~e~~~~~~~--~~~~~~t~~~~~~~l~~~i~p~~--------g~~~l~~It~~~i~~~~~~l~~~-~~~~ta  137 (357)
T cd00801          69 AANTFAEVAEEWLAAKK--PRWSEKHARQWRRTLEKHVLPVL--------GKKPITEITARDLLDVLRRIEAR-GALETA  137 (357)
T ss_pred             HHCHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHHHHHHHH--------CCCCHHHCCHHHHHHHHHHHHHC-CCHHHH
T ss_conf             45549999999999731--02476899999999997758987--------78748991889999999999856-989999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC--CCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCC
Q ss_conf             112344422223332101232222222222222212--111111101567877653101356775775320122210011
Q gi|254780882|r   89 KRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNS--LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGC  166 (328)
Q Consensus        89 ~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~~~--~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~T  166 (328)
                      ++.++.|+++|+||+..++++.||+..++.++..+.  ..++++.+|+..+++++...... .     +...++.|++.|
T Consensus       138 ~~~~~~l~~~~~~A~~~~~i~~NP~~~i~~~~~~~~~~r~r~lt~ee~~~l~~~l~~~~~~-~-----~~~~~~~l~l~T  211 (357)
T cd00801         138 RRVRQRLKQVFRYAIARGLIEANPAADLRGADGAPKKQHDRALSPDELPEFLQALDAASGS-P-----VTRLALKLLLLT  211 (357)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC-H-----HHHHHHHHHHHH
T ss_conf             9999999999999998277443657654441067887766678999999999999857788-3-----799999999997


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEE---CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCC
Q ss_conf             233222221122222332322033---237853100011221002343221110012344665543211112--211100
Q gi|254780882|r  167 GLRISEALSLTPQNIMDDQSTLRI---QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRG--KPLNPG  241 (328)
Q Consensus       167 GlR~~El~~L~~~did~~~~~i~v---~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g--~~ls~~  241 (328)
                      |||+||+++|+|+|||++.++++|   ..|+++.+.|||++.+.++|+.+...      ...+++||++..|  .+++..
T Consensus       212 G~R~gE~~~L~w~diD~~~~~~~Ip~~~tK~~~~~~vPL~~~~~~~L~~~~~~------~~~~~~vF~~~~~~~~~~~~~  285 (357)
T cd00801         212 GVRPGELRGARWSEIDLENALWTIPAERMKTRRPHRVPLSDQALALLEELREL------SGHSEYVFPSRRDRGKPLSEN  285 (357)
T ss_pred             CCCHHHHHCCCHHHEECCCCEEEEECCCCCCCCCEEEECCHHHHHHHHHHHHH------CCCCCEEECCCCCCCCCCCHH
T ss_conf             77888886387998777788489620236589936983989999999999886------499945825799999977489


Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHHC-HHHHHHHHH
Q ss_conf             0123567899976869998805417999999998489988999983788878979-999619-899999999
Q gi|254780882|r  242 VFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQ-IYTNVN-SKNGGDWMM  311 (328)
Q Consensus       242 ~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~-~Y~h~~-~~~~~~~l~  311 (328)
                      ++++.++    ++|...+++||+|||||||.|+++|+|+.+||++|||++.++|+ +|+|.+ .++.+++|+
T Consensus       286 ~~~~~~~----~~~~~~~~t~HdlRhT~aT~l~~~Gv~~~~i~~~LGH~~~~~t~~~Y~h~~y~~ekr~~l~  353 (357)
T cd00801         286 TLNKALK----RMGYLGEWTPHGLRRTARTWLNELGFPPDVIERQLAHVLGGKVRAAYNRADYLEERREAMQ  353 (357)
T ss_pred             HHHHHHH----HHCCCCCCEEECCHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999----9659999503248899999999859899999998489999818999617448999999999


No 21 
>cd00796 INT_Rci Rci recombinase, C-terminal catalytic domain.  Rci enzymes are found in IncI1 incompatibility group plasmids such as R64.  These recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The R64 Rci recombinase mediates site specific recombination at the highly mobile DNA segments called shufflon located in the C-terminal region of the pilV gene, which determines the recipient specificity in liquid mating. This gene encodes a thin pilus component that recognizes recipient's receptors required for liquid mating. The recombination occurs between any of the seven inverted repeats that separate four DNA segments of the shufflon. The segments can be inverted independently or in groups, resulting in a complex DNA rearrangement. The catalytic domain of Rci is linked to a variable N-terminal domain, whose function is unknown.
Probab=100.00  E-value=1.4e-45  Score=305.49  Aligned_cols=202  Identities=19%  Similarity=0.255  Sum_probs=175.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCC
Q ss_conf             3211234442222333210--12322222222222222121111111015678776531013567757753201222100
Q gi|254780882|r   87 SLKRSLSGIKSFLKYLKKR--KITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLY  164 (328)
Q Consensus        87 T~~~~ls~lr~f~~~~~~~--~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~  164 (328)
                      |+|+++++|+++|+||+++  .++..||+.+|+.|+.++..+++++.+|+.++++++.....      ..+.++++.|++
T Consensus         1 Tinr~l~~L~~~f~~A~~~~~~~~~~NP~~~i~~pk~~~~r~r~lt~eE~~~ll~~~~~~~~------~~~~~~~~~l~~   74 (206)
T cd00796           1 TVRRELALLSHLFTVARKEWGLDVLTNPVELVRKPPVGKGRDRRLTEEEEERLLRAFGEEEG------SPRLPVIILLAL   74 (206)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC------CHHHHHHHHHHH
T ss_conf             98899999999999999978887677927748588999999887999999999996764545------766999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             11233222221122222332322033-23785310001122100234322111001234466554321111221110001
Q gi|254780882|r  165 GCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVF  243 (328)
Q Consensus       165 ~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i  243 (328)
                      +||||+||+++|+|+|||++.+.+.| .+|+++.|.|||++.+.++|..|...       ..++++|      |++..++
T Consensus        75 ~TG~R~~Ei~~L~~~did~~~~~i~i~~~K~~~~r~vpl~~~~~~~l~~~~~~-------~~~~~vf------~~~~~~~  141 (206)
T cd00796          75 ETAMRRGEILSLRWEQVDLKKRVAHLPDTKNGTSRDVPLSKRAVALLQMLPKV-------PDDGPVF------PITSDSV  141 (206)
T ss_pred             HHCCCHHHHHHCCCCCCCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHHHC-------CCCCCCC------CCCHHHH
T ss_conf             90998899942857334533584898636789656852889999999999861-------4777667------8861789


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHH
Q ss_conf             23567899976869998805417999999998489988999983788878979999619899999
Q gi|254780882|r  244 QRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGD  308 (328)
Q Consensus       244 ~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~  308 (328)
                      ++.|+++++++|++ +++||+|||||||.|+++|+|+.+||++|||+|++||++|+|+++|+..+
T Consensus       142 ~~~~~~~~~~~gi~-~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~t~~Y~h~~~e~L~~  205 (206)
T cd00796         142 DAAFRRAKERAGLE-DLHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSAEDLAE  205 (206)
T ss_pred             HHHHHHHHHHHCCC-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHC
T ss_conf             99999999982777-87532048999999998698999999985899999998846739988704


No 22 
>cd01198 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA), DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. Members of this CD are archael in origin. No biochemical characterization is available for the proteins of this subgroup at this point.
Probab=100.00  E-value=4.6e-44  Score=294.56  Aligned_cols=176  Identities=20%  Similarity=0.209  Sum_probs=146.3

Q ss_pred             CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCC-CCCCCCCCCC
Q ss_conf             111101567877653101356775775320122210011233222221122222332322033237853-1000112210
Q gi|254780882|r  128 ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDK-IRIVPLLPSV  206 (328)
Q Consensus       128 ~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K-~R~Vpi~~~~  206 (328)
                      +||.||+.++++++.          ..||+||+.+||.||||+||+++|+|+|||++.+++.|.++++| .+.++++...
T Consensus         1 iLt~eev~~li~~~~----------~~rdraii~lL~~TGlRvsEl~~L~~~DId~~~~~i~V~~~~~k~~~~~~~~~~~   70 (186)
T cd01198           1 LISVEAMRELIADIT----------HPLERAVIVGLAKTGIRRGELINLDRRDVNLDKPTLYLKPASNKRSNRTLFPDLE   70 (186)
T ss_pred             CCCHHHHHHHHHCCC----------CHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEECCCCCCCCEEECCCHHH
T ss_conf             989999999998379----------8799999999999587999997792877686578788527889866055583899


Q ss_pred             HHH-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-------CCCCCCCCHHHHHHHHHHCCC
Q ss_conf             023-432211100123446655432111122111000123567899976869-------998805417999999998489
Q gi|254780882|r  207 RKA-ILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP-------LSTTAHTLRHSFATHLLSNGG  278 (328)
Q Consensus       207 ~~~-l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~-------~~~spH~lRHtfAt~ll~~G~  278 (328)
                      .+. +..|+..+    .....+++|++.+|++++...++..++++++++|++       +++|||+|||||||+|+++|+
T Consensus        71 ~~~~~~~~~~~r----~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~vtPH~lRHtfAT~Ll~~G~  146 (186)
T cd01198          71 TELFRWLAIRPR----TTSPADALFIGTQDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRHFFTTWLRRRGG  146 (186)
T ss_pred             HHHHHHHHHHHH----HCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             999999998775----3589982676179997768689999999999977643212114675851638999999998699


Q ss_pred             CHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHCCCH
Q ss_conf             9889999837888789799996198999999999999817300
Q gi|254780882|r  279 DLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSI  321 (328)
Q Consensus       279 ~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~~~~~  321 (328)
                      |+.+||++|||+|++||++|+|++.+    .++++|+++|||.
T Consensus       147 dl~~vq~lLGHssi~tT~~Y~h~~~~----~l~e~y~k~~Pr~  185 (186)
T cd01198         147 DRGVVQELRGDSRDEAIDTYTHIWGD----ELREAYLKHIPSL  185 (186)
T ss_pred             CHHHHHHHHCCCCHHHHHHHHCCCHH----HHHHHHHHHCCCC
T ss_conf             99999999489988999999847999----9999999858899


No 23 
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain. This CD includes various bacterial integrases, including the predicted integrase of the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1.
Probab=100.00  E-value=8.5e-44  Score=292.87  Aligned_cols=177  Identities=30%  Similarity=0.382  Sum_probs=155.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCC
Q ss_conf             1111111015678776531013567757753201222100112332222211222223323220332-378531000112
Q gi|254780882|r  125 LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLL  203 (328)
Q Consensus       125 ~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~  203 (328)
                      +|++||+||+.++++++..     ....++||++||.++++||||+||+++|+|+|||++.++|.|. +||+|.|.||++
T Consensus         1 lpr~Ls~eEi~~Ll~a~~~-----~~~~~~Rd~ali~ll~~tGlR~~El~~L~~~Did~~~~~i~i~~~K~~k~r~vpl~   75 (188)
T cd01188           1 LPRALPWEDVERLLASCDR-----STPVGRRDYAILLLLARLGLRAGEVAALRLDDIDWRTGTIRVRQGKGGRVTRLPLP   75 (188)
T ss_pred             CCCCCCHHHHHHHHHCCCC-----CCCHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCH
T ss_conf             9699999999999957576-----88451799999999999881599998569835565689778863899853344684


Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCCCCCCCCC---CCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCC
Q ss_conf             2100234322111001234466554321111---22111000123567899976869-9988054179999999984899
Q gi|254780882|r  204 PSVRKAILEYYDLCPFDLNLNIQLPLFRGIR---GKPLNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFATHLLSNGGD  279 (328)
Q Consensus       204 ~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~---g~~ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt~ll~~G~~  279 (328)
                      +++.+.|.+|+...+..   ...+++|++.+   +.+.+..+++++++++++++|++ .+++||+|||||||+|+++|+|
T Consensus        76 ~~~~~~l~~~l~~~~~~---~~~~~lf~~~~~~~~~~~~~~~i~~~~~~~~~~ag~~~~~~~~H~lRHt~at~l~~~G~~  152 (188)
T cd01188          76 AEVGAALADYLRDGRPA---TDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAGAP  152 (188)
T ss_pred             HHHHHHHHHHHHHHCCC---CCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCC
T ss_conf             99999999999980767---887644350588888876699999999999998499889878761489999999996999


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHCHHHHHHH
Q ss_conf             889999837888789799996198999999
Q gi|254780882|r  280 LRSIQSILGHFRLSTTQIYTNVNSKNGGDW  309 (328)
Q Consensus       280 ~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~  309 (328)
                      +..||++|||+|++||++|+|++.|+.+++
T Consensus       153 l~~vq~~lGH~si~tT~~Y~h~~~e~lr~~  182 (188)
T cd01188         153 LKEIGDVLGHRSPDSTAIYAKVDVDALRAI  182 (188)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999999838998899999885699999866


No 24 
>cd01197 INT_FimBE_C FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI.
Probab=100.00  E-value=1.3e-43  Score=291.68  Aligned_cols=174  Identities=28%  Similarity=0.375  Sum_probs=156.4

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCC
Q ss_conf             11111015678776531013567757753201222100112332222211222223323220332-37853100011221
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPS  205 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~  205 (328)
                      ++||+||+.++++++...      ..+.||++||.+++.||||+||+++|+|+|||++++.+.|. .||++.+.+|+.+.
T Consensus         3 ~~Lt~eEi~~ll~~~~~~------~~~~Rd~~i~~ll~~tGlR~~El~~L~~~did~~~~~i~i~~~K~~~~~~~pl~~~   76 (180)
T cd01197           3 KYLTPSEVRSLLKAALDG------RYSARDYCLMLLMFRHGLRVSEACGLKLSDIDLESRQIYIRRLKGGFSTTHPLRDD   76 (180)
T ss_pred             CCCCHHHHHHHHHCCCCC------CCCHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEEEECCCCEEEECCCHH
T ss_conf             899999999999651507------64389999999999959529999518176561788848999704773036338289


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        77 ~~~~l~~~~~~~~~~-~~~~~~~lF~s~~g~~l~~~~i~~~~~~~~~~agl~~~~~~H~lRHt~At~l~~~G~~i~~Iq~  155 (180)
T cd01197          77 ELEALKNWLEIRAWK-GLPDSDWIFLSRRGGPLSRQQVYKLIRRLGAQAGLSIKVHPHMLRHACGYALANQGADTRLIQD  155 (180)
T ss_pred             HHHHHHHHHHHHHHC-CCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf             999999999986620-4775411222688884218889999999999828876678987789999999987999999999


Q ss_pred             HHCCCCHHHHHHHHHHCHHHHH
Q ss_conf             8378887897999961989999
Q gi|254780882|r  286 ILGHFRLSTTQIYTNVNSKNGG  307 (328)
Q Consensus       286 ~lGH~s~~tT~~Y~h~~~~~~~  307 (328)
                      +|||+|++||++|+|++.++..
T Consensus       156 ~LGH~~i~tT~~Yth~~~~~l~  177 (180)
T cd01197         156 YLGHRNIRHTVIYTASNAARFL  177 (180)
T ss_pred             HHCCCCHHHHHHHHHCCHHHHH
T ss_conf             8389987999999967999998


No 25 
>cd01186 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available.
Probab=100.00  E-value=1.9e-39  Score=265.74  Aligned_cols=169  Identities=22%  Similarity=0.336  Sum_probs=147.5

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHH
Q ss_conf             11015678776531013567757753201222100112332222211222223323220332378531000112210023
Q gi|254780882|r  130 NEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKA  209 (328)
Q Consensus       130 t~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~  209 (328)
                      ++||+.++++++....        .||++||.+++.||||+||+++|+|+||+.+.....+.+||+|.|.|||++.+.++
T Consensus         8 ~~eei~~i~~~l~~~~--------~Rd~~l~~l~~~TGlR~sEl~~Lk~~Di~~~~~i~i~~~K~~k~r~v~l~~~~~~~   79 (180)
T cd01186           8 DKEQIKAIKDYLKNHS--------ERNYLLFLIGINTGLRISDILALKVKDVRGDERISIKEKKTGKRKRIYLNPILKEE   79 (180)
T ss_pred             CHHHHHHHHHHHHCCC--------HHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCEEEEEECCCCCCCCCCCCHHHHHH
T ss_conf             9999999999987569--------88999999999839239999637648727998299997878844651188999999


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             43221110012344665543211112--2111000123567899976869998805417999999998489988999983
Q gi|254780882|r  210 ILEYYDLCPFDLNLNIQLPLFRGIRG--KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSIL  287 (328)
Q Consensus       210 l~~yl~~~~~~~~~~~~~~lF~~~~g--~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~l  287 (328)
                      |..|+...      ..++++|++.+|  .+++...+++.++++++.+|++ +++||+|||||||+|+++|+|+.+||++|
T Consensus        80 l~~y~~~~------~~~~~lF~s~~~~~~~is~~~~~~~~~~~~~~~gi~-~~~~H~lRHT~at~l~~~G~~l~~iq~~L  152 (180)
T cd01186          80 LLYYIKDL------EENEYLFQSRKGGNRPITRQQAYRILKKAAEQVGID-NIGTHTLRKTFGYHYYKQTKDIALLMEIF  152 (180)
T ss_pred             HHHHHHHC------CCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             99998843------877514323888998978999999999999980898-76676017899999999699999999993


Q ss_pred             CCCCHHHHHHHHHHCHHHHHHHHHHHHHHH
Q ss_conf             788878979999619899999999999981
Q gi|254780882|r  288 GHFRLSTTQIYTNVNSKNGGDWMMEIYDQT  317 (328)
Q Consensus       288 GH~s~~tT~~Y~h~~~~~~~~~l~~~~~~~  317 (328)
                      ||+|++||++|+|++.+..    ++++++|
T Consensus       153 GH~si~tT~~Y~~~~~e~~----~k~~~~~  178 (180)
T cd01186         153 NHSSPAITLRYIGINQDEI----DKQLDNF  178 (180)
T ss_pred             CCCCHHHHHHHHCCCHHHH----HHHHHHC
T ss_conf             8999899999858999999----9999737


No 26 
>cd01194 INT_Tn554A_C Tn544A and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. This CD includes various bacterial transposases similar to TnpA from transposon Tn554.
Probab=100.00  E-value=1.3e-39  Score=266.86  Aligned_cols=170  Identities=25%  Similarity=0.374  Sum_probs=147.0

Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC----------CCCCCCC
Q ss_conf             111015678776531013567757753201222100112332222211222223323220332----------3785310
Q gi|254780882|r  129 LNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ----------GKGDKIR  198 (328)
Q Consensus       129 lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~----------gKg~K~R  198 (328)
                      ||++|+.++++++.          ..||++||.+|+.||||+||+++|+|+|||++++.++|.          .|++++|
T Consensus         1 LT~~Ev~~ll~a~~----------~~Rd~~i~~ll~~TGlR~gE~~~L~~~Did~~~~~i~i~~~~~~~~~~~~K~~~~r   70 (186)
T cd01194           1 LTPSEVQRLINACG----------NLRDKFLFALLYETGLRIGEALGLRIEDIDLAENQIWLVPREDNANGARAKSGRER   70 (186)
T ss_pred             CCHHHHHHHHHHCC----------HHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEEECCCCCCCCCCCCCCEE
T ss_conf             99899999998154----------03899999999996989888970889872576998999854455555203688425


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC----CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             0011221002343221110012344665543211112----211100012356789997686999880541799999999
Q gi|254780882|r  199 IVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRG----KPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLL  274 (328)
Q Consensus       199 ~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g----~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll  274 (328)
                      .||+++.+.+.+.+|+...... .....+++|++..|    .|++..+++..++++++.+|+  +++||+|||||||+|+
T Consensus        71 ~vpi~~~l~~~~~~~~~~~~~~-~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~--~~~~H~lRHT~at~l~  147 (186)
T cd01194          71 RIPVSQYLIDLYVDYVTEIYYL-EELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGI--DFTPHMFRHTHATELI  147 (186)
T ss_pred             EEECCHHHHHHHHHHHHHHHHH-HCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCC--CCCCCCCHHHHHHHHH
T ss_conf             8877799999999999997633-215777445633577568877799999999999998499--8774575999999999


Q ss_pred             HCCCCHHHHHHHHCCCCHHHH-HHHHHHCHHHHHHHHH
Q ss_conf             848998899998378887897-9999619899999999
Q gi|254780882|r  275 SNGGDLRSIQSILGHFRLSTT-QIYTNVNSKNGGDWMM  311 (328)
Q Consensus       275 ~~G~~~~~v~~~lGH~s~~tT-~~Y~h~~~~~~~~~l~  311 (328)
                      ++|+|+..||++|||+|++|| ++|+|+++++.++++.
T Consensus       148 ~~G~~~~~v~~~lGH~~~~tT~~~Y~h~~~e~~~~~~~  185 (186)
T cd01194         148 RAGWSIEVVADRLGHAHVQTTLNTYGHLSEEDIRREFN  185 (186)
T ss_pred             HCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHC
T ss_conf             87999999999828998799999845689999999865


No 27 
>cd01183 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in proteobacteria. These proteins have not been biochemically characerised as yet.
Probab=100.00  E-value=5.5e-40  Score=269.10  Aligned_cols=172  Identities=29%  Similarity=0.331  Sum_probs=142.1

Q ss_pred             CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CEEE-CCCCCCCCCCCC
Q ss_conf             11110156787765310135677577532012221001123322222112222233232----2033-237853100011
Q gi|254780882|r  128 ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS----TLRI-QGKGDKIRIVPL  202 (328)
Q Consensus       128 ~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~----~i~v-~gKg~K~R~Vpi  202 (328)
                      .||.+|+.++++++.. .|+...+.+.||++||.|||.||||+||+++|+|+||+++.+    ++.| .|||+|+|+|||
T Consensus         1 ~lt~~~~~~~~~~~~~-~p~~~~~~~~Rd~ail~ll~~tGlR~sEl~~L~~~Di~~~~~~~~~~l~i~~gKg~k~R~vpl   79 (196)
T cd01183           1 ALTEDQWAFVIDTVAS-LPAQDPEHAARLLFLLALLYSTGLRISELAAATGPDLEAFVQGGGWWLYVPVGKGGKERRVPV   79 (196)
T ss_pred             CCCHHHHHHHHHHHHH-CCCCCCCHHHHHHHHHHHHHHHCCHHHHHHCCCHHHHCHHCCCCCEEEEEEECCCCCEEEECC
T ss_conf             9799999999999985-777897076999999999999666299998398887023116786059988588985003018


Q ss_pred             CCCCHHHHHHHHHHHCCCC--CCCCCCCCCCCC----CCCCCCCCCHHHHHHHHHHHCC-------------CCCCCCCC
Q ss_conf             2210023432211100123--446655432111----1221110001235678999768-------------69998805
Q gi|254780882|r  203 LPSVRKAILEYYDLCPFDL--NLNIQLPLFRGI----RGKPLNPGVFQRYIRQLRRYLG-------------LPLSTTAH  263 (328)
Q Consensus       203 ~~~~~~~l~~yl~~~~~~~--~~~~~~~lF~~~----~g~~ls~~~i~~~~~~~~~~~g-------------i~~~~spH  263 (328)
                      ++.+.+.|++|+..+....  ......++|++.    .|++++.++++..++++...++             ..+++|||
T Consensus        80 ~~~~~~~L~~yl~~r~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~v~~~~~~a~~~~~~~~~~~~~~~~~~~spH  159 (196)
T cd01183          80 SDELLAALARYRQARGLPPEPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAAADRLQADGFEEDAAQLRAASTH  159 (196)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCC
T ss_conf             89999999999998477655554667640103677766787519999999999999999997641217675103767883


Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             4179999999984899889999837888789799996
Q gi|254780882|r  264 TLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTN  300 (328)
Q Consensus       264 ~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h  300 (328)
                      +|||||||+|+++|+|+..||++|||+|++||++|+|
T Consensus       160 ~LRHt~At~ll~~G~~l~~Vq~~LGH~si~TT~~Y~H  196 (196)
T cd01183         160 WLRHTHASHDLAAGVPLEHVQDNLGHASIDTTSRYLH  196 (196)
T ss_pred             CCHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHCCC
T ss_conf             2589999999987999999998808998678734339


No 28 
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase.
Probab=100.00  E-value=5.4e-38  Score=256.67  Aligned_cols=179  Identities=26%  Similarity=0.381  Sum_probs=145.9

Q ss_pred             CCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC---------------
Q ss_conf             11110156787765310135677577532012221001123322222112222233232203323---------------
Q gi|254780882|r  128 ALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG---------------  192 (328)
Q Consensus       128 ~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~g---------------  192 (328)
                      +||.||+.++++++.....      ..|+++|+.+++.||||+||+++|+|+|||+++++|.|.+               
T Consensus         1 yLt~eEi~~ll~~~~~~~~------~~~~~~ii~ll~~TGlR~~Ei~~L~~~did~~~~~i~i~~~~~~~~~~~~~~~~~   74 (205)
T cd01199           1 YLEKNELKALLDVLNSYKN------NQLYADILEFLFLTGMRIGELLALQEKDIDFENKLINIDGTLDSHTGKEENGYKD   74 (205)
T ss_pred             CCCHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCCEEEEEEEEEEECCCCCCCEEC
T ss_conf             9398999999970514778------7699999999999773488897590988065589899977886412566662434


Q ss_pred             --CCC-CCCCCCCCCCCHHHHHHHHHHHCCCC---CCCCCCCCCCCCCCCCCCCCCH-HHHHHHHHHHCCCC--CCCCCC
Q ss_conf             --785-31000112210023432211100123---4466554321111221110001-23567899976869--998805
Q gi|254780882|r  193 --KGD-KIRIVPLLPSVRKAILEYYDLCPFDL---NLNIQLPLFRGIRGKPLNPGVF-QRYIRQLRRYLGLP--LSTTAH  263 (328)
Q Consensus       193 --Kg~-K~R~Vpi~~~~~~~l~~yl~~~~~~~---~~~~~~~lF~~~~g~~ls~~~i-~~~~~~~~~~~gi~--~~~spH  263 (328)
                        |+. ..|.|||++.+.++|.+|++......   .....+++|++..|.++....+ ...++++.+.+|.+  .+++||
T Consensus        75 ~~Kt~~~~R~vpl~~~~~~~l~~~~~~~~~~~~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H  154 (205)
T cd01199          75 TPKTKSSIRTISLSERAVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKGNPLDLGPINSKILSKFLKDLGSQSKKHVTTH  154 (205)
T ss_pred             CCCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             57788863686179999999999999714410354568776377616898476408999999999998575546775764


Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH-HHHHHHCHHHHHHHHHH
Q ss_conf             41799999999848998899998378887897-99996198999999999
Q gi|254780882|r  264 TLRHSFATHLLSNGGDLRSIQSILGHFRLSTT-QIYTNVNSKNGGDWMME  312 (328)
Q Consensus       264 ~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT-~~Y~h~~~~~~~~~l~~  312 (328)
                      +|||||||+|+++|+|+..||++|||+|++|| ++|+|++++.+++++.+
T Consensus       155 ~lRHT~at~l~~~G~~~~~v~~~lGHss~~tT~~iY~h~~~~~~~e~~~k  204 (205)
T cd01199         155 IFRHTHISFLAEEGVPLKAIMDRVGHSDGKTTLRIYSHVTEKMKDEIVKK  204 (205)
T ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHC
T ss_conf             55999999999869999999998679988999888661698999999960


No 29 
>cd01192 INT_P22_C P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1.
Probab=100.00  E-value=1.9e-37  Score=253.30  Aligned_cols=167  Identities=23%  Similarity=0.264  Sum_probs=143.8

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC---CCCCCCCCCCC
Q ss_conf             111111015678776531013567757753201222100112332222211222223323220332---37853100011
Q gi|254780882|r  126 PRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ---GKGDKIRIVPL  202 (328)
Q Consensus       126 p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~---gKg~K~R~Vpi  202 (328)
                      .++||++|+.++++++..         ..  +.++.+++.||||+||+++|+|+|||++++.++|.   +||++.|.||+
T Consensus         4 ~r~Lt~eE~~~ll~~~~~---------~~--r~~i~l~~~TG~R~~El~~L~~~did~~~~~i~i~~~~~K~~~~r~vpl   72 (177)
T cd01192           4 VRWLTPEEAERLIAELPP---------HL--KPAVLFALNTGLRRSEILGLEWSQVDLDNRVAWVRPATSKGGRAIRVPL   72 (177)
T ss_pred             CCCCCHHHHHHHHHHCCH---------HH--HHHHHHHHHHCCCHHHHHHCCCHHHHHHCCHHCCCCCCCCCCCEEECCC
T ss_conf             789999999999982898---------79--9999999997834999983878666630111011445688885442613


Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHH
Q ss_conf             22100234322111001234466554321111221110001235678999768699988054179999999984899889
Q gi|254780882|r  203 LPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRS  282 (328)
Q Consensus       203 ~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~  282 (328)
                      ++.+.++|..|...       ....++|++..|.+..  ...+.|+++++++|++ +++||+|||||||+|+++|+|+.+
T Consensus        73 ~~~~~~~l~~~~~~-------~~~~~vf~~~~~~~~~--~~~~~~~~~~~~agi~-~~~~H~lRHt~at~l~~~G~~~~~  142 (177)
T cd01192          73 NDEALQVLKRQKAG-------AHKPWVFAGAGGDPRI--DSKTAWRQALQRAGIS-DFRWHDLRHTWASWLVQSGVPLYV  142 (177)
T ss_pred             HHHHHHHHHHHHHC-------CCCCCEECCCCCCCCC--HHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHCCCCHHH
T ss_conf             09999999998723-------5775141158998510--1789999999973799-998688968899999996989999


Q ss_pred             HHHHHCCCCHHHHHHHHHHCHHHHHHHHHHH
Q ss_conf             9998378887897999961989999999999
Q gi|254780882|r  283 IQSILGHFRLSTTQIYTNVNSKNGGDWMMEI  313 (328)
Q Consensus       283 v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~~~  313 (328)
                      ||++|||+|++||++|+|++++..++++.++
T Consensus       143 i~~~lGH~~~~~T~~Y~h~~~~~~r~a~~~l  173 (177)
T cd01192         143 LQELLGHSSLQMVRRYAHLSPEHLRAAARAL  173 (177)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9999589989999998866999999999998


No 30 
>pfam00589 Phage_integrase Phage integrase family. Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.
Probab=100.00  E-value=1.1e-37  Score=254.72  Aligned_cols=169  Identities=38%  Similarity=0.464  Sum_probs=152.6

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCC
Q ss_conf             11111015678776531013567757753201222100112332222211222223323220332-37853100011221
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPS  205 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~  205 (328)
                      ++||++|+.++++++..       ..++||++||.+++.||||++|+++|+|+||+++.+.++|. +|+++.|.+|+++.
T Consensus         1 ~~lt~~e~~~ll~~~~~-------~~~lR~~~l~~l~~~tG~R~~El~~L~~~di~~~~~~i~i~~~K~~~~r~i~i~~~   73 (170)
T pfam00589         1 RRLTEDEVERLLAALEE-------PLNIRDRALVELLLLTGLRISELLSLRWSDIDLDNGTIRIPQTKTRKSRTVPLSDA   73 (170)
T ss_pred             CCCCHHHHHHHHHHHCC-------CCCHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCEEEEECCCCCCCCEECCCCHH
T ss_conf             98999999999986463-------45977999999999968698889742130046765178730441133100146777


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        74 ~~~~l~~~~~~~~~---~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~s~Hs~Rht~at~l~~~g~~~~~v~~  150 (170)
T pfam00589        74 ALEALKEWLGDRKE---AEESEFLFVSRRGKPLSRSTVNRAFRRAGKRAGIEKDLTPHDLRHTFATHLAENGVPLRVIQK  150 (170)
T ss_pred             HHHHHHHHHHHHCC---CCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf             99999999997314---677761432016885531346788888888607787678788848999999996999999999


Q ss_pred             HHCCCCHHHHHHHHHHCHHH
Q ss_conf             83788878979999619899
Q gi|254780882|r  286 ILGHFRLSTTQIYTNVNSKN  305 (328)
Q Consensus       286 ~lGH~s~~tT~~Y~h~~~~~  305 (328)
                      +|||+|++||++|+|+++|+
T Consensus       151 ~lGH~~~~tT~~Y~~~~~~~  170 (170)
T pfam00589       151 LLGHSSISMTMRYTHVAAER  170 (170)
T ss_pred             HHCCCCHHHHHHHCCCCCCC
T ss_conf             96899989999820838559


No 31 
>cd01189 INT_phiLC3_C phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus phage phiLC3, TPW22, Tuc2009, BK5-T, A2,  bIL285, bIL286, bIL311, ul36 and phi g1e; Staphylococcus aureus phage phi13 and phi42; Oenococcus oeni phage fOg44; Streptococcus thermophilus phage O1205 and Sfi21; and Streptococcus pyogenes phage T12 and T270.
Probab=100.00  E-value=4.4e-37  Score=250.93  Aligned_cols=171  Identities=27%  Similarity=0.374  Sum_probs=146.3

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC--------------C
Q ss_conf             11111015678776531013567757753201222100112332222211222223323220332--------------3
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ--------------G  192 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~--------------g  192 (328)
                      ++||++|+.++++++....       ..|++++|.+++.||||++|+++|+|+|||++++.+.|.              .
T Consensus         1 ~yLt~~Ei~~ll~~~~~~~-------~~~~~~~~~l~~~tGlR~~Ei~~L~~~did~~~~~i~v~~~~~~~~~~~~~~~~   73 (191)
T cd01189           1 KFLTKEELKKLLEYLKKHE-------NSFSKLLILLLAYTGLRIGEALALTWSDIDFENNTITINKTWDYKTGGYIFKPP   73 (191)
T ss_pred             CCCCHHHHHHHHHHHHHCC-------CHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEECCEEECCCCEEECCC
T ss_conf             9899999999999875668-------978999999999978149999728999946555858984101211353033577


Q ss_pred             CCCC-CCCCCCCCCCHHHHHHHHHHHCCC---CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHH
Q ss_conf             7853-100011221002343221110012---344665543211112211100012356789997686999880541799
Q gi|254780882|r  193 KGDK-IRIVPLLPSVRKAILEYYDLCPFD---LNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHS  268 (328)
Q Consensus       193 Kg~K-~R~Vpi~~~~~~~l~~yl~~~~~~---~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHt  268 (328)
                      |++. .|.|||++++.+.|..|+......   .......++|.+..|.+++.++++..++++++++|++ +++||+||||
T Consensus        74 Kt~~~~R~v~i~~~~~~~L~~~~~~~~~~~~~~~~~~~~~if~~~~~~~~~~~~~~~~~~~~~~~~gi~-~~~~H~lRHT  152 (191)
T cd01189          74 KTKSSIRTIPLDKKTIAILKEYKKEQKKYLLGEINNDDELVFTNKGGKISTPSTINKRLKRICKKAGIP-KITFHGLRHT  152 (191)
T ss_pred             CCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCC-CCCHHHHHHH
T ss_conf             788872488479999999999999977764035789874376469999178889999999999980898-0563435999


Q ss_pred             HHHHHHHCCCCHHHHHHHHCCCCHHHH-HHHHHHCHHH
Q ss_conf             999999848998899998378887897-9999619899
Q gi|254780882|r  269 FATHLLSNGGDLRSIQSILGHFRLSTT-QIYTNVNSKN  305 (328)
Q Consensus       269 fAt~ll~~G~~~~~v~~~lGH~s~~tT-~~Y~h~~~~~  305 (328)
                      |||.|+++|+|+..||++|||+|++|| ++|+|+++|+
T Consensus       153 ~aT~l~~~G~~~~~i~~~lGH~s~~~T~~~Y~h~~~~~  190 (191)
T cd01189         153 HASLLLEAGVSIKYVSERLGHADISTTLDTYSHLLPEK  190 (191)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCCCC
T ss_conf             99999996999999999858998899997711669465


No 32 
>cd01195 INT_Tn544B_C Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes various bacterial transposases similar to TnpB from transposon Tn554.
Probab=100.00  E-value=1.6e-36  Score=247.39  Aligned_cols=175  Identities=23%  Similarity=0.235  Sum_probs=136.3

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC------CEEE-CCCCCCCCC
Q ss_conf             111110156787765310135677577532012221001123322222112222233232------2033-237853100
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS------TLRI-QGKGDKIRI  199 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~------~i~v-~gKg~K~R~  199 (328)
                      ++++.+++.++.+++....+.        .+.|+.+++.||||+||+++|+|+||+.+..      .+.. .++|.|+|.
T Consensus         1 ~~i~~~~~~~l~~~l~~l~~~--------~~~~~~ll~~TGlRisE~l~L~~~~i~~~~~~~~~~~~~~~~~k~~~k~r~   72 (195)
T cd01195           1 RFIPEFVLEQLNSHIDKLPEY--------IIPMTMIVQETGMRISDLLTLKKNCLLEDKDGDFFYKYYQCIWKTKIKEHI   72 (195)
T ss_pred             CCCCHHHHHHHHHHHHHCCHH--------HHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCCCCEEEEEEEECCCCCEEEE
T ss_conf             989989999999999868998--------999999999808739999638611455503655526799996798874368


Q ss_pred             CCCCCCCHHHHHHHHHHHCCCC--CCCCCCCCCCCCCCC----CCCCCCHHHHHHHHHHHCCCC------CCCCCCCCHH
Q ss_conf             0112210023432211100123--446655432111122----111000123567899976869------9988054179
Q gi|254780882|r  200 VPLLPSVRKAILEYYDLCPFDL--NLNIQLPLFRGIRGK----PLNPGVFQRYIRQLRRYLGLP------LSTTAHTLRH  267 (328)
Q Consensus       200 Vpi~~~~~~~l~~yl~~~~~~~--~~~~~~~lF~~~~g~----~ls~~~i~~~~~~~~~~~gi~------~~~spH~lRH  267 (328)
                      |||++++.+.|..|++..+...  ..+.+++||++..|+    +++...++..+++++++.|+.      .+++||+|||
T Consensus        73 ipi~~~~~~~l~~~~~~~~~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~~~~~~H~lRH  152 (195)
T cd01195          73 IPISKKVALLIKVREDKTKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYHFHAHAFRH  152 (195)
T ss_pred             EECCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH
T ss_conf             86789999999999999898730206988548767889808887619999999999999818653347725668887748


Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHH
Q ss_conf             999999984899889999837888789799996198999999
Q gi|254780882|r  268 SFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDW  309 (328)
Q Consensus       268 tfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~  309 (328)
                      ||||+|+++|+|+.+||++|||+|++||++|+|++++..+++
T Consensus       153 T~aT~L~~~Gv~i~~Iq~~LGH~s~~tT~~Yahv~~e~l~~~  194 (195)
T cd01195         153 TVATRMINNGMPIHIIQKFLGHESPEMTSRYAHIFDETLKNE  194 (195)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999999986999999999948999899999885798999862


No 33 
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl gener
Probab=99.98  E-value=4.8e-33  Score=225.74  Aligned_cols=159  Identities=33%  Similarity=0.401  Sum_probs=135.7

Q ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCCCHHHHH
Q ss_conf             15678776531013567757753201222100112332222211222223323220332-37853100011221002343
Q gi|254780882|r  133 QALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPSVRKAIL  211 (328)
Q Consensus       133 e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~~~~~l~  211 (328)
                      |+.++++++....+       .|++++|.+++.||||++|+++|+|+||+++++++.|. +|+++.|.||+++.+...|.
T Consensus         1 e~~~~~~~~~~~~~-------~r~r~~~~l~~~tGlR~~Ei~~L~~~di~~~~~~i~i~~~K~~~~r~vpi~~~~~~~l~   73 (164)
T cd00397           1 EIERLLAAAEASTP-------ERLYLALLLLLATGLRISELCALRWSDIDLDKRVIHITGTKTKKERTVPLSEEALKLLK   73 (164)
T ss_pred             CHHHHHHHHHHCCC-------HHHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHH
T ss_conf             98999976514679-------88999999999978199999638462056776479983564665333667601234688


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCC---CCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             22111001234466554321111221---11000123567899976869-998805417999999998489988999983
Q gi|254780882|r  212 EYYDLCPFDLNLNIQLPLFRGIRGKP---LNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFATHLLSNGGDLRSIQSIL  287 (328)
Q Consensus       212 ~yl~~~~~~~~~~~~~~lF~~~~g~~---ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt~ll~~G~~~~~v~~~l  287 (328)
                      +|.......  ....+++|++..+.+   .+...+...+++++..+|+. .+++||+|||||||+|+++|+|+..||++|
T Consensus        74 ~~~~~~~~~--~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~~g~~~~~I~~~l  151 (164)
T cd00397          74 EYLKKRRPA--NGDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLRHTFASALLNAGLDLEAVQDLL  151 (164)
T ss_pred             HHHHHHCCC--CCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             889885014--687541211368986652046789999789999833676567756658999999999699999999996


Q ss_pred             CCCCHHHHHHHHH
Q ss_conf             7888789799996
Q gi|254780882|r  288 GHFRLSTTQIYTN  300 (328)
Q Consensus       288 GH~s~~tT~~Y~h  300 (328)
                      ||+|++||++|+|
T Consensus       152 GHs~~~tT~~Y~h  164 (164)
T cd00397         152 GHSSIAMTMRYAH  164 (164)
T ss_pred             CCCCHHHHHHCCC
T ss_conf             8999889711839


No 34 
>cd01191 INT_phiCTX_C phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various phage and bacterial integrases, including those similar to phage integrases: Bordetella and Pseudomonas phiCTX;  E. coli  Rac, Qin, and Shiga toxin 2 933W; and Salmonella typhimurium LT2 Gifsy-2 and Fels-1; and a putative pore-forming cytotoxin integrase from Vibrio parahaemolyticus O3:K6.
Probab=99.97  E-value=2.1e-32  Score=221.78  Aligned_cols=166  Identities=19%  Similarity=0.254  Sum_probs=127.5

Q ss_pred             CCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC----------CC-
Q ss_conf             1111110156787765310135677577532012221001123322222112222233232203323----------78-
Q gi|254780882|r  126 PRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG----------KG-  194 (328)
Q Consensus       126 p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~g----------Kg-  194 (328)
                      |+|||.||+.++++++...         .+++.++.|+++||||.||+++|+|+|||++.++|.|..          |+ 
T Consensus         1 p~plT~eE~~~ll~a~~~~---------~~~~~~~~l~~~TGlR~gE~~~L~w~dId~~~~~i~v~~~~~~~~~~~~Kt~   71 (196)
T cd01191           1 PDPFTRDEFAALIEAARVC---------QQEQNLWEFAVFTGLRPSELIALAWEDVDLERGTVYVRRALVRGIFKVPKTK   71 (196)
T ss_pred             CCCCCHHHHHHHHHHCCCC---------HHHHHHHHHHHHHCCHHHHHHHCCHHHCCCCCCEEEEEEEEEECCCCCCCCC
T ss_conf             9898999999999806606---------4189999999997916999970779984756898999961684565688778


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHCC--------------CCCCCCCCCCCCCCC-CCCC--CCCCHHHHHHHHHHHCCCC
Q ss_conf             5310001122100234322111001--------------234466554321111-2211--1000123567899976869
Q gi|254780882|r  195 DKIRIVPLLPSVRKAILEYYDLCPF--------------DLNLNIQLPLFRGIR-GKPL--NPGVFQRYIRQLRRYLGLP  257 (328)
Q Consensus       195 ~K~R~Vpi~~~~~~~l~~yl~~~~~--------------~~~~~~~~~lF~~~~-g~~l--s~~~i~~~~~~~~~~~gi~  257 (328)
                      +..|.||+++.+.++|.++....+.              ........++|.+.. |.+.  +.....+.+.++++++|++
T Consensus        72 ~~~R~v~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vf~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~  151 (196)
T cd01191          72 AGTRDVDLNPPALAALKEQAKLTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGIR  151 (196)
T ss_pred             CCCCEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             85312218999999999999985010102456665311444566774584378778886506899999999999982999


Q ss_pred             CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHH
Q ss_conf             998805417999999998489988999983788878979-99961
Q gi|254780882|r  258 LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQ-IYTNV  301 (328)
Q Consensus       258 ~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~-~Y~h~  301 (328)
                       .++||+|||||||.|+++|+|+.+||++|||+|++||+ +|+|.
T Consensus       152 -~~~~H~lRHT~aT~ll~~G~~~~~v~~~lGHss~~~T~~~Ya~~  195 (196)
T cd01191         152 -YRNPYQMRHTFASWMLTAGANPAFIADQMGHKSAEMVFKHYGKW  195 (196)
T ss_pred             -CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             -67777884799999998798999999996899799999998833


No 35 
>PRK09692 integrase; Provisional
Probab=99.97  E-value=3.3e-30  Score=208.01  Aligned_cols=280  Identities=13%  Similarity=0.105  Sum_probs=196.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999999986254889999999999999999985121478878968989999999999998612101332112
Q gi|254780882|r   12 FELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRS   91 (328)
Q Consensus        12 ~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~   91 (328)
                      .++....++|+...+.  +.+..+.+.+...++   .++    .+.++..++.+|+..++...+.....++ +..|.++.
T Consensus       105 ~tf~~va~~w~~~~~~--~~~~~~~~~~~r~le---~~v----~p~iG~~~i~~I~~~di~~~l~~i~~rg-~~~~a~r~  174 (413)
T PRK09692        105 NTFQLVAERWWNVKKA--SVTEDYAEDIWRSLE---RDV----FPAIGDVSVTDIKAHTLVQAVQPVQARG-ALETVRRL  174 (413)
T ss_pred             HHHHHHHHHHHHHHHH--HCCHHHHHHHHHHHH---HHH----HHHHCCCCCCCCCHHHHHHHHHHHHHCC-HHHHHHHH
T ss_conf             1999999999998754--325779999999999---888----7985888410078999999987999739-89999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC
Q ss_conf             3444222233321012322222222222--22212111111101567877653101356775775320122210011233
Q gi|254780882|r   92 LSGIKSFLKYLKKRKITTESNILNMRNL--KKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLR  169 (328)
Q Consensus        92 ls~lr~f~~~~~~~~~i~~np~~~i~~~--k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR  169 (328)
                      +..++.+|+||+..++++.||+..+...  +..++--..++.+|+..++..+......    ...|  +++.|++.||+|
T Consensus       175 ~~~l~~i~~~A~~~gli~~nP~~~~~~~~~~p~~~~~~~l~~~el~~l~~~l~~~~~~----~~~~--~~l~l~lLt~~R  248 (413)
T PRK09692        175 CQRINEVMIYAQNTGLIDAVPSVNIGKAFEKPQKKNMPSIRPDQLPQLMQTMRTASIS----LSTR--CLFMWQLLTITR  248 (413)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC----HHHH--HHHHHHHHHCCC
T ss_conf             9999999999996586445854343452568754577768989999999999857997----3578--999999997232


Q ss_pred             CCCCCCCCCCCCCCCCCCEEE---CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCCCCCCHH
Q ss_conf             222221122222332322033---2378531000112210023432211100123446655432111--12211100012
Q gi|254780882|r  170 ISEALSLTPQNIMDDQSTLRI---QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI--RGKPLNPGVFQ  244 (328)
Q Consensus       170 ~~El~~L~~~did~~~~~i~v---~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~--~g~~ls~~~i~  244 (328)
                      .+|+++++|++||++.+.++|   +.|+++...|||++.++++|+.-...      ....+|||++.  .++|++..+++
T Consensus       249 ~~Ev~~arW~eiD~~~~~W~IPaer~K~~~~h~VPLs~qA~~iL~~l~~~------~~~~~~vFps~~~~~~~~s~~t~~  322 (413)
T PRK09692        249 PAEAAEARWEEVDIEAQEWKIPAARMKMNRDHTVPLSDEAIAILEMMKPL------SGNREFIFPSRIKPNQPMNSQTVN  322 (413)
T ss_pred             HHHHHCCCHHHEECCCCEEEECHHHCCCCCCCEECCCHHHHHHHHHHHHH------CCCCEEECCCCCCCCCCCCHHHHH
T ss_conf             68773677999557888799756884898871527869999999999986------199769803699999978889999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHH-HHHHHHHHCHHHHHHHHHHHHHHH
Q ss_conf             3567899976869998805417999999998489988999983788878-979999619899999999999981
Q gi|254780882|r  245 RYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLS-TTQIYTNVNSKNGGDWMMEIYDQT  317 (328)
Q Consensus       245 ~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~-tT~~Y~h~~~~~~~~~l~~~~~~~  317 (328)
                      ..+    +.+|.....+||+||+||+|.|-+.|++..+|-.+|||..-. +..+|-+-+--..+-.+.+.+..|
T Consensus       323 ~al----~~~~~~~~~t~Hd~RrT~~T~l~e~g~~~~viE~~L~H~~~~~v~~~Ynr~~yl~eRr~~mq~Wady  392 (413)
T PRK09692        323 ASL----KRAGFGGVLVSHGLRSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQWWADF  392 (413)
T ss_pred             HHH----HHCCCCCCEECCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_conf             999----9669999765848457799989976999999999868999982899956775999999999999999


No 36 
>cd00797 HP1_INT_C Phage HP1 integrase, C-terminal catalytic domain.  Bacteriophage HP1 and related integrases are found in eubacteria, plasmids and temperate bacteriophages of the P2 family.  They belong to the DNA breaking-rejoining enzyme superfamily, which includes tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their C-terminal catalytic domain containing six conserved active site residues and the overall reaction mechanism. The HP1 recombinase controls phage replication by site-specific recombination between the HP1 genome and the chromosomal DNA. It is a heterobifunctional DNA-binding protein, which recognizes two different DNA sequence motifs (type I and type II binding sites). The C-terminal catalytic domain of the HP1 integrase binds to the type I site, while the less conserved N-terminal domain is largely responsible for binding to the type II site.
Probab=99.97  E-value=4.1e-32  Score=219.94  Aligned_cols=154  Identities=27%  Similarity=0.398  Sum_probs=120.4

Q ss_pred             CHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCCCHHHH
Q ss_conf             01567877653101356775775320122210011233222221122222332322033-23785310001122100234
Q gi|254780882|r  132 KQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAI  210 (328)
Q Consensus       132 ~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~~~~~l  210 (328)
                      ||+.++++++....     ..++||.++  |+++||||+||+++|+|+||+  .+.+.+ .+|+++.|.|||++.+.++|
T Consensus         1 eE~~rLl~~~~~~~-----~~~~r~~~~--l~~~TGlR~sEi~~L~~~di~--~~~i~~~~~K~~~~r~ipl~~~~~~~l   71 (158)
T cd00797           1 DEEERLLAALDALG-----SGDLKDVAI--LCLDTGARWGEALGLKAEDIQ--EGRVTFWKTKSGKSRTVPISERVAAML   71 (158)
T ss_pred             CHHHHHHHHHHHCC-----CHHHHHHHH--HHHHHCCCHHHHHHHHHHHCC--CCEEEEEECCCCCEEEECCCHHHHHHH
T ss_conf             98999998730557-----863999999--999948888886262797726--885898875799754733419999999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCC
Q ss_conf             32211100123446655432111122111000123567899976869998805417999999998489988999983788
Q gi|254780882|r  211 LEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHF  290 (328)
Q Consensus       211 ~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~  290 (328)
                      ..+.          ...++|++..     ...+.+.++++...  ++.+++||+|||||||+|+++|+|+.+||++|||+
T Consensus        72 ~~~~----------~~~~~f~~~~-----~~~~~~~~~~~~~~--~~~~~~~H~lRHt~At~l~~~G~~i~~v~~~lGH~  134 (158)
T cd00797          72 KRRR----------MRGGLFPDLY-----YESFRHIWKRAKIE--LPKGQATHILRHTFASHFMMNGGNIATLQHILGHA  134 (158)
T ss_pred             HHHH----------HCCCCCCCCC-----HHHHHHHHHHHHHC--CCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCC
T ss_conf             9615----------4178888854-----78999999999824--79886622788999999998499899999984899


Q ss_pred             CHHHHHHHHHHCHHHHHHHHH
Q ss_conf             878979999619899999999
Q gi|254780882|r  291 RLSTTQIYTNVNSKNGGDWMM  311 (328)
Q Consensus       291 s~~tT~~Y~h~~~~~~~~~l~  311 (328)
                      |++||++|+|++++..++++.
T Consensus       135 s~~~T~~Y~hl~~~~l~~av~  155 (158)
T cd00797         135 TIEMTMRYAHLAPDHLDDAVS  155 (158)
T ss_pred             CHHHHHHCCCCCHHHHHHHHH
T ss_conf             999997774869999999998


No 37 
>cd01184 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinases and phage-related integrases. Some have N-terminal domains, which show little sequence similarity to each other. Members of this subgroup are predominantly found in proteobacteria.
Probab=99.97  E-value=1.7e-32  Score=222.38  Aligned_cols=163  Identities=21%  Similarity=0.301  Sum_probs=126.6

Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCHHHHHH---HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE--C-------CCCCC
Q ss_conf             1110156787765310135677577532---0122210011233222221122222332322033--2-------37853
Q gi|254780882|r  129 LNEKQALTLVDNVLLHTSHETKWIDARN---SAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI--Q-------GKGDK  196 (328)
Q Consensus       129 lt~~e~~~ll~~~~~~~~~~~~~~~~Rd---~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v--~-------gKg~K  196 (328)
                      +|++|+..++.+...     ..|.+.||   +.++.|+++||||+||+++|+|+|||++++.+.|  .       .|++.
T Consensus         1 f~~~e~~~ll~~~~~-----~~~~~~~~~~~y~~~ll~~~TGlR~~Ei~~L~~~Di~~~~g~~~i~i~~~~~~~~~Kt~~   75 (181)
T cd01184           1 FTTEELKAIFASPAY-----TGWASQKDPHRYWLPLLGLYTGARVNEIAQLQVDDIREEDGVPCIDITNDDEDQSLKNAA   75 (181)
T ss_pred             CCHHHHHHHHCCCCC-----CCCCCCCCCHHHHHHHHHHHHCCCHHHHHCCCHHHEEEECCEEEEEEECCCCCCCCCCCC
T ss_conf             998999999678000-----345467980599999999996907999971979897135998999996378776567877


Q ss_pred             -CCCCCCCCCCHHH-HHHHHHHHCCCCCCCCCCCCCCCCC--CCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHH
Q ss_conf             -1000112210023-4322111001234466554321111--22111000123567899976869-99880541799999
Q gi|254780882|r  197 -IRIVPLLPSVRKA-ILEYYDLCPFDLNLNIQLPLFRGIR--GKPLNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFAT  271 (328)
Q Consensus       197 -~R~Vpi~~~~~~~-l~~yl~~~~~~~~~~~~~~lF~~~~--g~~ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt  271 (328)
                       .|.|||++.+.++ +.+|++..+    ....+++|++..  +.+.+...+.+.++++++++|++ .+++||+|||||||
T Consensus        76 s~R~vPl~~~l~~~~~~~~~~~~~----~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~~H~lRHT~aT  151 (181)
T cd01184          76 SRRTIPVHPELIELGFLDYVEARR----AAGHKRLFPDLPAGKTGGYGSAVSKWFSRYLKKLGLKDKGKSFHSFRHTFIT  151 (181)
T ss_pred             CEEEECCCHHHHHHHHHHHHHHHH----HCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHH
T ss_conf             536416889999999999999987----1599612444447888861057999999999984999788978646899999


Q ss_pred             HHHHCCCCHHHHHHHHCCCCHHHHH-HHHH
Q ss_conf             9998489988999983788878979-9996
Q gi|254780882|r  272 HLLSNGGDLRSIQSILGHFRLSTTQ-IYTN  300 (328)
Q Consensus       272 ~ll~~G~~~~~v~~~lGH~s~~tT~-~Y~h  300 (328)
                      +|+++|+|+.+||++|||+|++||+ +|.+
T Consensus       152 ~l~~~gv~~~~v~~~lGHss~~tT~~~Ygk  181 (181)
T cd01184         152 ELRNAGVSRELIAAIMGHEEGTTTFGRYGK  181 (181)
T ss_pred             HHHHCCCCHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             999869899999998289998864253081


No 38 
>cd00800 INT_Lambda_C Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome.  They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites.  The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.
Probab=99.97  E-value=6.6e-31  Score=212.38  Aligned_cols=155  Identities=25%  Similarity=0.336  Sum_probs=128.4

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-CCCCCCCCCCCCCCC
Q ss_conf             1111101567877653101356775775320122210011233222221122222332322033-237853100011221
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPS  205 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v-~gKg~K~R~Vpi~~~  205 (328)
                      ++||.+|+.++++++..      .+    .++++.|++.||||+||+++|+|+||+  .+.+.| .+|+++.+.|||+++
T Consensus         2 R~Lt~eE~~~l~~~~~~------~~----~~~~~~l~~~TGlR~~Ei~~L~w~di~--~~~i~i~~~Ktg~~~~ipl~~~   69 (162)
T cd00800           2 RYLTDEEYRAIYEAADA------PW----LRCAMDLALLTGQRVGDVLRMKWSDID--DDGLHIEQSKTGAKLAIPLSPS   69 (162)
T ss_pred             CCCCHHHHHHHHHHCCC------HH----HHHHHHHHHHHCCCHHHHHCCCHHHCC--CCEEEEEECCCCCEEEEECCHH
T ss_conf             98999999999985788------66----899999999978899999719197645--6879998478870467657899


Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHCCCCC---CCCCCCCHHHHHHHHHHCCCCHH
Q ss_conf             00234322111001234466554321111-221110001235678999768699---98805417999999998489988
Q gi|254780882|r  206 VRKAILEYYDLCPFDLNLNIQLPLFRGIR-GKPLNPGVFQRYIRQLRRYLGLPL---STTAHTLRHSFATHLLSNGGDLR  281 (328)
Q Consensus       206 ~~~~l~~yl~~~~~~~~~~~~~~lF~~~~-g~~ls~~~i~~~~~~~~~~~gi~~---~~spH~lRHtfAt~ll~~G~~~~  281 (328)
                      +.++|+.+.+..     ...++++|++.. |.|++..++++.|+++++++|++.   ++++|+|||||||.+.++|.   
T Consensus        70 l~~~l~~~~~~~-----~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~agi~~~~~~~t~H~lRht~at~~~~~g~---  141 (162)
T cd00800          70 LREVIERCRDLS-----RVSSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTFHDIRAKAASDYEEQGK---  141 (162)
T ss_pred             HHHHHHHHHHHC-----CCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCH---
T ss_conf             999999999843-----677860763179999778679999999999984997687766018889999999873748---


Q ss_pred             HHHHHHCCCCHHHHHHHHHH
Q ss_conf             99998378887897999961
Q gi|254780882|r  282 SIQSILGHFRLSTTQIYTNV  301 (328)
Q Consensus       282 ~v~~~lGH~s~~tT~~Y~h~  301 (328)
                      .+|++|||+|++||++|.+.
T Consensus       142 ~~q~llGH~s~~~T~~Y~r~  161 (162)
T cd00800         142 DAQALLGHKDEKMTKIYRRK  161 (162)
T ss_pred             HHHHHCCCCCHHHHHHHCCC
T ss_conf             89998099998997066068


No 39 
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=99.94  E-value=3.9e-27  Score=188.84  Aligned_cols=146  Identities=36%  Similarity=0.514  Sum_probs=126.2

Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             753201222100112332222211222223323220332-3785310001122100234322111001234466554321
Q gi|254780882|r  153 DARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQ-GKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFR  231 (328)
Q Consensus       153 ~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~-gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~  231 (328)
                      ..|+++++.+++.||||++|+++|+|+||+++.+.+.|. .||++.|.||+++.+...|..|......  .....++||+
T Consensus        14 ~~~~~~~~~l~~~tG~R~~El~~l~~~di~~~~~~i~i~~~K~~~~~~i~i~~~~~~~l~~~~~~~~~--~~~~~~~lF~   91 (162)
T cd01182          14 APRDRALILLLLYTGLRVSELLALRWSDIDLDKGTITVRRTKTGKERTVPLSPELAELLREYLELRRP--APKPDDYLFP   91 (162)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHCCHHEEECCCCEEEECCCCCCCEEEEECCHHHHHHHHHHHHHHCC--CCCCCCEEEE
T ss_conf             99999999999997849888984431108067986873378776203762563776799999998422--3688771554


Q ss_pred             CCCCC--CCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             11122--1110001235678999768699988054179999999984899889999837888789799996
Q gi|254780882|r  232 GIRGK--PLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTN  300 (328)
Q Consensus       232 ~~~g~--~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h  300 (328)
                      +..+.  +.+...++..++++....|.+.+++||+|||||||.|+++|+++..|+++|||+++.||++|.+
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRh~~~t~~~~~g~~~~~i~~~~GH~~~~~t~~Y~~  162 (162)
T cd01182          92 SRRGGPKRLTRRAVRRLLKKAGKRAGIPERLTPHDLRHTFATRLLEAGVPLEVIQELLGHSSISTTERYLH  162 (162)
T ss_pred             ECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCC
T ss_conf             26899765103567776665554137878997016199999999996999999999928999898152819


No 40 
>COG0582 XerC Integrase [DNA replication, recombination, and repair]
Probab=99.90  E-value=4.1e-22  Score=157.42  Aligned_cols=208  Identities=29%  Similarity=0.387  Sum_probs=150.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCC
Q ss_conf             0133211234442222333210123222222222-222221211111110156787765310135677577532012221
Q gi|254780882|r   84 GDRSLKRSLSGIKSFLKYLKKRKITTESNILNMR-NLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYL  162 (328)
Q Consensus        84 s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~-~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~l  162 (328)
                      +..+.+.....++.++.|+....    +|...+. .++.....++.++.+++..+++++...      ....++.+++. 
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~------~~~~~~~~~~~-  152 (309)
T COG0582          84 STLTRVFRLAALRGFFAYLDNPG----APLKALREKPKRRKKLPKALTAEEVEALLEALDRY------RDALRLALLIL-  152 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCC----CHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH------HHHHHHHHHHH-
T ss_conf             47779999999988888621631----04666531134454454548999999999998750------57899999998-


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCEEECC---CCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-
Q ss_conf             001123322222112222233232203323---7853100011221002343221110012344665543211112211-
Q gi|254780882|r  163 LYGCGLRISEALSLTPQNIMDDQSTLRIQG---KGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPL-  238 (328)
Q Consensus       163 l~~TGlR~~El~~L~~~did~~~~~i~v~g---Kg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~l-  238 (328)
                        .||||.+|+++|+|+||++....+.+.+   |+++.|.||+++.+...+..|....+...      ++|+...|... 
T Consensus       153 --~tG~R~~E~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~------~~~~~~~~~~~~  224 (309)
T COG0582         153 --LTGLRVSELLGLRWSDIDLENGTIWIRGTKTKGRKERRVPLSEQALEALKKYLLIRRPRE------YLFLSLRGPRLS  224 (309)
T ss_pred             --HHCCCHHHHHHCCHHHCCCCCCEEEEEECCCCCCCCEEEEECHHHHHHHHHHHHHCCCCC------CCCCCCCCCCCC
T ss_conf             --718779999827666505456727996135556651589605999999999998544433------006532356533


Q ss_pred             ----CCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH-HHCHHHHHHHHHH
Q ss_conf             ----1000123567899976869998805417999999998489988999983788878979999-6198999999999
Q gi|254780882|r  239 ----NPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYT-NVNSKNGGDWMME  312 (328)
Q Consensus       239 ----s~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~-h~~~~~~~~~l~~  312 (328)
                          +...+...+...+...|++ .++||.|||||++.+++.| +...|++++||++..+|+.|. +...+........
T Consensus       225 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~h~lRht~~~~~~~~~-~~~~~~~~~gH~~~~~~~~~~~~~~~~~~~~~~~~  301 (309)
T COG0582         225 RSALTINRLLRARAKAAKEAGIR-KITPHGLRHTFATLLLAGG-DERVIQKLLGHASLNTTQTVYYHASDERLKEAALK  301 (309)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCC-CCCCCCCHHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             10367999999999973222788-8787740789999998568-76589998378708789999998710667899986


No 41 
>pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain.
Probab=99.65  E-value=7.6e-16  Score=118.28  Aligned_cols=83  Identities=35%  Similarity=0.570  Sum_probs=77.1

Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999986254889999999999999999985121478878968989999999999998612101332112344422
Q gi|254780882|r   18 RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKS   97 (328)
Q Consensus        18 ~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~   97 (328)
                      +|+|++||+.|||+|++|+.+|+.||+.|..|+...      ..++.+++..+|..|+.++..+|++++|+++++++||+
T Consensus         1 i~~fl~~L~~er~~S~~Ti~aY~~dL~~f~~~l~~~------~~~~~~i~~~~i~~yl~~l~~~~~s~~Ti~r~lsalr~   74 (83)
T pfam02899         1 IDQFLEYLSLERGLSPNTVRAYRRDLKAFLKFLAEG------GLSLDQLTTDDVRAFLAELLREGLSAASLARRLSALRS   74 (83)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC------CCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             988899999885849999999999999999999874------99988868998999999987089889999999999999


Q ss_pred             HHHHHHHHC
Q ss_conf             223332101
Q gi|254780882|r   98 FLKYLKKRK  106 (328)
Q Consensus        98 f~~~~~~~~  106 (328)
                      ||+|+.++|
T Consensus        75 F~~~l~~eG   83 (83)
T pfam02899        75 FFQFLKREG   83 (83)
T ss_pred             HHHHHHHHC
T ss_conf             999999719


No 42 
>PHA00730 int integrase
Probab=98.62  E-value=1e-06  Score=61.26  Aligned_cols=198  Identities=18%  Similarity=0.246  Sum_probs=111.0

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             99999999851214788789689899999999999986121013321123444222233321012322222222222222
Q gi|254780882|r   43 TRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKS  122 (328)
Q Consensus        43 l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~k~~  122 (328)
                      +..|++||-...          .++...+..|+.++... +..+  |.-+.++|.|++|....+.++     .++..|..
T Consensus        98 ~~effe~~l~~k----------~ise~T~K~Yv~~l~kp-~~~s--n~~~kA~r~f~~~~~~r~~~~-----~lK~kK~~  159 (322)
T PHA00730         98 NSEFFELTLRQR----------KISEKTIKDYINCIKQP-RKES--NNCIKAYRLFYRFLLNRDPPK-----ELKVKKTK  159 (322)
T ss_pred             HHHHHHHHHHHC----------CCCHHHHHHHHHHHHHH-HHHH--HHHHHHHHHHHHHHHCCCCHH-----HHHHCCCC
T ss_conf             899999998752----------67688999999998756-5540--214999999999972246377-----65220368


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCEEECCCCCCC
Q ss_conf             12111111101567877653101356775775320122210011233222221122-----2223323220332378531
Q gi|254780882|r  123 NSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTP-----QNIMDDQSTLRIQGKGDKI  197 (328)
Q Consensus       123 ~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~-----~did~~~~~i~v~gKg~K~  197 (328)
                      ..+ ++-|.+|+.+.++.+....+-         +++..|+..+|+|.+|++.+--     .||+.++-.+.        
T Consensus       160 pDl-~VPT~eeVk~tL~~~key~~v---------y~vYrllLESG~RlsEaLkvLn~y~p~~dv~e~~~~~y--------  221 (322)
T PHA00730        160 PDL-RIPTLEEIKRTLQLVKEYENL---------YLLYRLLLESGSRLSEALKVLNNYNPQNDIREDGFSIY--------  221 (322)
T ss_pred             CCC-CCCCHHHHHHHHHHHCCCCCH---------HHHHHHHHHHCHHHHHHHHHHHCCCHHHHCCCCCEEEE--------
T ss_conf             862-478889999999875047641---------46899998713028999999741480543035876999--------


Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             000112210023432211100123446655432111--122111000123567899976869998805417999999998
Q gi|254780882|r  198 RIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI--RGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLS  275 (328)
Q Consensus       198 R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~--~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~  275 (328)
                         |+         +|..      +....-++|.-.  +--.++..++...+    .+.+   -+.|--+|.-+||-|++
T Consensus       222 ---~L---------~w~R------g~K~~fy~fhit~Lk~~~It~~~i~~~~----~~~~---~v~~KYiRKfvatKm~e  276 (322)
T PHA00730        222 ---IL---------NWTR------GQKKSFYLFHITPLKQIKITKAYIDKYV----RRLN---LVPPKYIRKFVATKMLE  276 (322)
T ss_pred             ---EE---------HHHC------CCCCEEEEEEECCCEEEEECHHHHHHHH----HCCC---CCCHHHHHHHHHHHHHH
T ss_conf             ---83---------2221------6775699999425424566188886665----4046---68789999999999999


Q ss_pred             CCCCHHHHHHHHCCCCHHH-HHHHHHH
Q ss_conf             4899889999837888789-7999961
Q gi|254780882|r  276 NGGDLRSIQSILGHFRLST-TQIYTNV  301 (328)
Q Consensus       276 ~G~~~~~v~~~lGH~s~~t-T~~Y~h~  301 (328)
                      -|.|..+|--+=|-..-+. |++|+.+
T Consensus       277 lgip~dvvdFiqGR~p~~ilt~HY~dL  303 (322)
T PHA00730        277 LGIPSEVVDFIQGRTPSRILTKHYLDL  303 (322)
T ss_pred             HCCCHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             689688999964788550468999999


No 43 
>COG4342 Uncharacterized protein conserved in archaea [Function unknown]
Probab=98.45  E-value=9.6e-07  Score=61.44  Aligned_cols=205  Identities=18%  Similarity=0.182  Sum_probs=113.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-CCCCCCC--CCC-CCCHHHHHHHHHHH
Q ss_conf             9999999999986121013321123444222233321012322222222222-2221211--111-11015678776531
Q gi|254780882|r   68 YTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNL-KKSNSLP--RAL-NEKQALTLVDNVLL  143 (328)
Q Consensus        68 ~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i~~np~~~i~~~-k~~~~~p--~~l-t~~e~~~ll~~~~~  143 (328)
                      .....+|+..+...=-+...-..+-.+.|.|.+||...|+|..+-+..+..+ |..+..+  -++ +.+++.+-++....
T Consensus        57 ~k~ardyls~l~r~ig~~~~kdKy~kA~R~f~~fl~~rgiise~~Ae~lrk~lk~k~~~g~dlyIp~de~ir~~~~l~r~  136 (291)
T COG4342          57 GKTARDYLSALNRPIGSVREKDKYQKAYRLFIKFLTSRGIISEEFAEKLRKPLKVKKSNGVDLYIPSDEEIRATEELARE  136 (291)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCEECCCHHHHHHHHHHHHH
T ss_conf             78999999998876443110057999999999999870413399999999986457678863324987999889999988


Q ss_pred             CCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             01356775775320122210011233222221122222332322033237853100011221002343221110012344
Q gi|254780882|r  144 HTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNL  223 (328)
Q Consensus       144 ~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~  223 (328)
                      ..        .|-++++.++..+|+|++|++.+-.+ +|-+.-.-.+.||+  -+.-|+         .|..      +.
T Consensus       137 ~~--------e~~y~v~~ll~~SGaRLse~v~~L~~-~D~s~~~~~~ng~~--icyy~l---------~w~r------g~  190 (291)
T COG4342         137 YS--------ERAYLVYLLLLFSGARLSEAVAVLRN-LDHSRLYCVVNGKV--ICYYPL---------SWSR------GH  190 (291)
T ss_pred             HC--------CHHHHHHHHHHHCCCHHHHHHHHHHC-CCHHHHEEECCCEE--EEEECC---------CHHH------CC
T ss_conf             54--------01899999998634309999999967-14312023128737--885011---------0320------45


Q ss_pred             CCCCCCC-CCCCCCCCCCCCH-HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHH-HHHHHH
Q ss_conf             6655432-1111221110001-235678999768699988054179999999984899889999837888789-799996
Q gi|254780882|r  224 NIQLPLF-RGIRGKPLNPGVF-QRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLST-TQIYTN  300 (328)
Q Consensus       224 ~~~~~lF-~~~~g~~ls~~~i-~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~t-T~~Y~h  300 (328)
                      ...-++| |...+.++-.-.+ +..++......|    +..--+|.-.++-|++.|+|..+|--+-||+.-.. |++|+.
T Consensus       191 K~afyif~P~~~~~~l~kidisy~~vq~~~~~~~----Vk~kyiRkwv~nkmlelgvP~~VvdFIqGrk~~~V~~rHY~n  266 (291)
T COG4342         191 KRAFYIFHPKDFAESLRKIDISYHRVQRFENRRG----VKAKYIRKWVYNKMLELGVPEDVVDFIQGRKQSRVGTRHYAN  266 (291)
T ss_pred             CCEEEEECCHHHHHHCHHCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             4115686636652001101112999999986058----209999999999999809958899998746722157899999


Q ss_pred             HC
Q ss_conf             19
Q gi|254780882|r  301 VN  302 (328)
Q Consensus       301 ~~  302 (328)
                      +.
T Consensus       267 L~  268 (291)
T COG4342         267 LL  268 (291)
T ss_pred             HH
T ss_conf             99


No 44 
>pfam11917 DUF3435 Protein of unknown function (DUF3435). This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to pfam00589 suggesting it may be an integrase enzyme.
Probab=97.78  E-value=3.8e-05  Score=51.45  Aligned_cols=64  Identities=23%  Similarity=0.279  Sum_probs=51.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCC-CCHHHHHHHHCCCCHHHHHH-HH
Q ss_conf             2211100012356789997686999880541799999999848-99889999837888789799-99
Q gi|254780882|r  235 GKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNG-GDLRSIQSILGHFRLSTTQI-YT  299 (328)
Q Consensus       235 g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G-~~~~~v~~~lGH~s~~tT~~-Y~  299 (328)
                      ..||+..+++.+++++++.+|+...+++|.||.+.|..+ ++| ++-..=..+|||++..|=.. |.
T Consensus       170 ~~~lt~st~~~~lk~lgei~Gf~~~~~~y~~R~g~a~~~-n~~~vs~a~rn~im~Ha~~~tF~k~Y~  235 (414)
T pfam11917       170 DQALTASTLNSWLKRLGEIAGFEDPLTPYCLRYGAAKAL-NSGEVSEAERNLILGHASSRTFLKHYL  235 (414)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHC-CCCCCCHHHHHHHHCCCCCCHHHHHCC
T ss_conf             778898999999999988841111454002357899852-665699899978744787405776256


No 45 
>pfam01028 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic core. Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.
Probab=96.88  E-value=0.0023  Score=40.35  Aligned_cols=115  Identities=18%  Similarity=0.236  Sum_probs=68.9

Q ss_pred             CCCCCCCCCCCCCCCEEE--CCCCCCCCCCCCCCC-CHHHHHHHHHHHCCCCCCCCCCCCCCCC-CC--CCCCCCCHHHH
Q ss_conf             221122222332322033--237853100011221-0023432211100123446655432111-12--21110001235
Q gi|254780882|r  173 ALSLTPQNIMDDQSTLRI--QGKGDKIRIVPLLPS-VRKAILEYYDLCPFDLNLNIQLPLFRGI-RG--KPLNPGVFQRY  246 (328)
Q Consensus       173 l~~L~~~did~~~~~i~v--~gKg~K~R~Vpi~~~-~~~~l~~yl~~~~~~~~~~~~~~lF~~~-~g--~~ls~~~i~~~  246 (328)
                      ++.|+.+||.+..+.|.+  .||+|+.+.+-|.+. +...|....       ...++..||.-. .|  .+++...++.+
T Consensus        84 ltTLr~~Hv~i~~~~i~~~F~GK~gv~~~~~v~d~~l~~~l~~l~-------~~~pg~~LF~y~~~g~~~~v~s~dvN~y  156 (244)
T pfam01028        84 LTTLRNRHVTLEGDVIRFDFLGKDGIRHENTVRDKRLAKNLKRLK-------QKLPGDELFQYLDDGERDRVSSSDLNAY  156 (244)
T ss_pred             EEECCCCCEEEECCEEEEEEECCCCCEEEEEECCHHHHHHHHHHH-------HCCCCCHHEEEECCCCEEECCHHHHHHH
T ss_conf             010010447898998999987798747898868889999999998-------5299732168716996342788999999


Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHH-----HHHCCCC--------------HHHHHHHHCCCCHHHH-HHHHH
Q ss_conf             67899976869998805417999999-----9984899--------------8899998378887897-99996
Q gi|254780882|r  247 IRQLRRYLGLPLSTTAHTLRHSFATH-----LLSNGGD--------------LRSIQSILGHFRLSTT-QIYTN  300 (328)
Q Consensus       247 ~~~~~~~~gi~~~~spH~lRHtfAt~-----ll~~G~~--------------~~~v~~~lGH~s~~tT-~~Y~h  300 (328)
                      ++.+.   |  ..+|+.+||--.||.     |.+.+.+              +..|++.|||.- ++. .-|.|
T Consensus       157 Lk~~~---g--~~~TaKdFRTw~at~~a~~~L~~~~~~~~~~~~~k~~i~~a~~~vA~~LgnTp-aV~R~sYi~  224 (244)
T pfam01028       157 LRELM---G--EGFTAKDFRTWNASVTALEALAELGKSLESVAEKKKAINAANKEVAILLGNTP-AVSRKSYIH  224 (244)
T ss_pred             HHHHH---C--CCCCHHHHHHHCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHCCC
T ss_conf             99983---5--88752122221207999999996589988999999999999999999858984-113774458


No 46 
>cd00659 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic domain.  Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination.  Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses and bacterial versions of Topo IB.  They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases.  The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.
Probab=96.85  E-value=0.00074  Score=43.40  Aligned_cols=114  Identities=17%  Similarity=0.159  Sum_probs=68.4

Q ss_pred             CCCCCCCCCCCCCCCEEE--CCCCCCCCCCCCCC--CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             221122222332322033--23785310001122--10023432211100123446655432111122111000123567
Q gi|254780882|r  173 ALSLTPQNIMDDQSTLRI--QGKGDKIRIVPLLP--SVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIR  248 (328)
Q Consensus       173 l~~L~~~did~~~~~i~v--~gKg~K~R~Vpi~~--~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~  248 (328)
                      ++.|+.+||.+..+.|.+  .||+|+.+..-|.+  .+...+....       ...++..||.-..+.+++...++.+++
T Consensus        71 ltTLr~~Hv~~~~~~i~~~F~GK~gv~~~~~i~d~~~l~~~~~~~~-------~~~pg~~LF~y~~~~~v~s~~vN~yLk  143 (218)
T cd00659          71 LCTLRKEHVTLKPNVVRFDFLGKDSIRYENEVEVEPRLFKNLRKFL-------DKLPGDDLFQYLQVDRLNSSKLNAYLR  143 (218)
T ss_pred             EEEECHHHEEEECCEEEEEEECCCCCEEEEEEECCHHHHHHHHHHH-------HCCCCHHHEECCCCCCCCHHHHHHHHH
T ss_conf             5540131165769989999856888289999706599999999997-------369906640346788669899999999


Q ss_pred             HHHHHCCCCCCCCCCCCHHHHHHHHHH-----CCCC-------------HHHHHHHHCCCCHHHH-HHHHH
Q ss_conf             899976869998805417999999998-----4899-------------8899998378887897-99996
Q gi|254780882|r  249 QLRRYLGLPLSTTAHTLRHSFATHLLS-----NGGD-------------LRSIQSILGHFRLSTT-QIYTN  300 (328)
Q Consensus       249 ~~~~~~gi~~~~spH~lRHtfAt~ll~-----~G~~-------------~~~v~~~lGH~s~~tT-~~Y~h  300 (328)
                      .+    +  .++|+-+||--.||.++.     ...+             +..|++.|||.- .+. .-|.|
T Consensus       144 ~~----~--~~~TaKdFRTw~at~~~~~~L~~~~~~~s~~~~k~~i~~a~~~vA~~LgnTp-aV~r~sYi~  207 (218)
T cd00659         144 EF----M--EGLTAKVFRTYNASLTALEQLARLPASLSLAEKKKAYNDANREVAILLNHTP-AISKINYID  207 (218)
T ss_pred             HH----C--CCCCHHCEEEHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHCCC
T ss_conf             97----5--9997002331378999999998668877889999999999999999968986-562230588


No 47 
>cd01190 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases.
Probab=96.18  E-value=0.018  Score=34.67  Aligned_cols=62  Identities=21%  Similarity=0.236  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--------------CCCCHHHCCHHHHHHHHHH
Q ss_conf             9999999999986254889999999999999999985121478--------------8789689899999999999
Q gi|254780882|r   16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKI--------------TIQTIRQLSYTEIRAFISK   77 (328)
Q Consensus        16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~--------------~~~~~~~i~~~~i~~~l~~   77 (328)
                      +.+++|+.||..++|+|++|+..|...|+.|+.|+........              ......-++.+++..+++.
T Consensus        11 ~~i~~y~~~L~~~rg~s~~Tin~~l~~L~~f~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~l~~eei~~ll~~   86 (260)
T cd01190          11 PLILAFLDHLENDRGNSIRTRNARLAALHSFFRYAAREVPEHLPTIQRVLAIPMKRFKRPLVTYLTREEVQALLAA   86 (260)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHC
T ss_conf             9999999999984699999999999999999999998084014553710148878889999988999999999818


No 48 
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=95.61  E-value=0.034  Score=32.98  Aligned_cols=71  Identities=15%  Similarity=0.073  Sum_probs=47.2

Q ss_pred             CCHHHCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--------CCCCHHHCCHHHHHHHHH
Q ss_conf             304314989999999999999986254889999999999999999985121478--------878968989999999999
Q gi|254780882|r    5 NLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKI--------TIQTIRQLSYTEIRAFIS   76 (328)
Q Consensus         5 ~~~~~~~~~l~~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~--------~~~~~~~i~~~~i~~~l~   76 (328)
                      +-|+.+..   +.+++|+.||..++++|++|+..|...|+.|+.|+........        ......-++.+++...++
T Consensus         5 k~~~~it~---~dI~~y~~~L~~~~~~s~~Tin~~l~~l~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~lt~eEi~~ll~   81 (242)
T cd01193           5 RSPDELGE---EDVRAFLTLLAVEGNVSASTQNQALSALLFFYRHTLKRDLPWLQRIRRPRKPRKLPVVLSPEEVRRLLG   81 (242)
T ss_pred             CCHHHCCH---HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             89588999---999999999998489899999999999999999998768965665655789998998899999999997


Q ss_pred             HH
Q ss_conf             99
Q gi|254780882|r   77 KR   78 (328)
Q Consensus        77 ~l   78 (328)
                      .+
T Consensus        82 ~~   83 (242)
T cd01193          82 AL   83 (242)
T ss_pred             CC
T ss_conf             38


No 49 
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=95.02  E-value=0.067  Score=31.16  Aligned_cols=39  Identities=18%  Similarity=0.023  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999998625488999999999999999998512
Q gi|254780882|r   16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYT   54 (328)
Q Consensus        16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~   54 (328)
                      +.+++|+.||..++|+|++|+..|...++.|+.|+....
T Consensus        69 ~~i~~f~~~L~~~k~~s~~Ti~~~l~~lr~~~~~a~~~~  107 (299)
T cd01185          69 EFILEFKLFLRKEKKLSRNTAVHYLSWLKKLLKIAYRDK  107 (299)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999999987579888899999999999999999889


No 50 
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=94.92  E-value=0.028  Score=33.50  Aligned_cols=39  Identities=15%  Similarity=0.278  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999986121013321123444222233321012
Q gi|254780882|r   69 TEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKI  107 (328)
Q Consensus        69 ~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~  107 (328)
                      ..+..|+.||.++++|+.|+..|...|+.|+.||.+.|.
T Consensus        25 ~ll~~Fl~yL~er~~S~~Ti~aY~~dL~~F~~fl~~~g~   63 (361)
T PRK01287         25 ALLLRFVEWLQERNWSERTLKVQTHHTYHFILWCEERGL   63 (361)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999998399899999999999999999998489


No 51 
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=94.63  E-value=0.037  Score=32.78  Aligned_cols=41  Identities=12%  Similarity=0.204  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99999999999861210133211234442222333210123
Q gi|254780882|r   68 YTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKIT  108 (328)
Q Consensus        68 ~~~i~~~l~~l~~~~~s~~T~~~~ls~lr~f~~~~~~~~~i  108 (328)
                      +.-|.+|+.++...++|++|+..|..-|+.||+|+..++..
T Consensus        18 P~~i~ey~~~~~~~~~Sp~Ti~~Y~~DL~~F~~fL~~~~~~   58 (360)
T PRK05084         18 PWYVLEYYQSKLATPYSPTTLYEYLTEYRRFFNWLIDEGLT   58 (360)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             09999999988605989899999999999999999864987


No 52 
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=93.78  E-value=0.073  Score=30.93  Aligned_cols=38  Identities=21%  Similarity=0.230  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999998625488999999999999999998512
Q gi|254780882|r   16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYT   54 (328)
Q Consensus        16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~   54 (328)
                      +.+++|+.++.. +|+|++|+..|...++.|+.|+....
T Consensus        51 ~~i~~y~~~L~~-~~~s~~Tin~~l~~lr~~~~~a~~~~   88 (296)
T PRK00283         51 DDLQAFLAELAE-GGYKATSSARRLSALRRFFQFLLREG   88 (296)
T ss_pred             HHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999999987-79999999999999997479998707


No 53 
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=92.89  E-value=0.12  Score=29.55  Aligned_cols=37  Identities=24%  Similarity=0.307  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999862548899999999999999999851
Q gi|254780882|r   16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFY   53 (328)
Q Consensus        16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~   53 (328)
                      +.++.|+.++.. +|+|++|+..|...++.|+.|+...
T Consensus        56 ~~i~~~~~~l~~-~g~s~~Ti~~~l~~lr~~~~~a~~~   92 (295)
T PRK00236         56 ADLRAFLARLRR-QGLSARSLARRLSALRSFYRWLVRR   92 (295)
T ss_pred             HHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999999987-6999999999999999999988762


No 54 
>COG4688 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.10  E-value=0.22  Score=27.93  Aligned_cols=66  Identities=18%  Similarity=0.191  Sum_probs=49.5

Q ss_pred             HHHHHHHHCC--CCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHH
Q ss_conf             5678999768--69998805417999999998489988999983788878979999619899999999
Q gi|254780882|r  246 YIRQLRRYLG--LPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMM  311 (328)
Q Consensus       246 ~~~~~~~~~g--i~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~l~  311 (328)
                      .|++++..+.  -.-++-.|.+||-.-|.+-..|+|-..|+.+.|-+++.----|-|=+.+++-+.++
T Consensus       432 lferhg~~~edG~~~rL~SH~lRHllnT~a~r~Gmde~~ia~w~gR~~Vaqn~~YDHRs~~e~s~~Ir  499 (665)
T COG4688         432 LFERHGQSAEDGKQLRLESHMLRHLLNTEAFRLGMDETIIAKWFGRRSVAQNYEYDHRSLAEQSDQIR  499 (665)
T ss_pred             HHHHHCCCCCCCCEEECHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf             89874755568865544357888988788887470478888763303554212423141888865422


No 55 
>pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain.
Probab=91.28  E-value=0.59  Score=25.28  Aligned_cols=34  Identities=21%  Similarity=0.437  Sum_probs=28.9

Q ss_pred             HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999998-6121013321123444222233321
Q gi|254780882|r   71 IRAFISKRR-TQKIGDRSLKRSLSGIKSFLKYLKK  104 (328)
Q Consensus        71 i~~~l~~l~-~~~~s~~T~~~~ls~lr~f~~~~~~  104 (328)
                      |+.|+.++. ++++|+.|+..|..-|+.|++|+..
T Consensus         1 i~~fl~~L~~er~~S~~Ti~aY~~dL~~f~~~l~~   35 (83)
T pfam02899         1 IDQFLEYLSLERGLSPNTVRAYRRDLKAFLKFLAE   35 (83)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             98889999988584999999999999999999987


No 56 
>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776    This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.; GO: 0008948 oxaloacetate decarboxylase activity, 0006814 sodium ion transport.
Probab=73.50  E-value=3.2  Score=20.72  Aligned_cols=91  Identities=20%  Similarity=0.284  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCC-CCCCCCCCCCHHHHHHH----HHHCCCCH-
Q ss_conf             0234322111001234466554321111221110001235678999768-69998805417999999----99848998-
Q gi|254780882|r  207 RKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLG-LPLSTTAHTLRHSFATH----LLSNGGDL-  280 (328)
Q Consensus       207 ~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~g-i~~~~spH~lRHtfAt~----ll~~G~~~-  280 (328)
                      +.-|+.|++..+...... -|-+.+-.-.+=|||..-+..++.+.++.| ++-++|.|+- -.+|..    .+|+|+|. 
T Consensus       146 vHTl~~yl~la~~L~~~G-~DSI~IKDMaGlLTP~~AYELV~alK~~~~n~pvhLH~H~T-tGmA~~AllkA~EAG~d~i  223 (616)
T TIGR01108       146 VHTLEKYLELAKELLEMG-VDSICIKDMAGLLTPKVAYELVSALKKEFGNLPVHLHSHAT-TGMAEMALLKAIEAGADMI  223 (616)
T ss_pred             HHHHHHHHHHHHHHHHHC-CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCC-HHHHHHHHHHHHHCCCCCC
T ss_conf             367888999999999818-86055202004644158999999997423974688632472-3379999998887078800


Q ss_pred             -HHHHHHHCCCCHHH--HHHHH
Q ss_conf             -89999837888789--79999
Q gi|254780882|r  281 -RSIQSILGHFRLST--TQIYT  299 (328)
Q Consensus       281 -~~v~~~lGH~s~~t--T~~Y~  299 (328)
                       ..|+-+-|-.|--.  ||+|+
T Consensus       224 DTAisS~S~gtSHPptE~lv~~  245 (616)
T TIGR01108       224 DTAISSMSGGTSHPPTETLVAA  245 (616)
T ss_pred             HHCCCCCCCCCCCCHHHHHHHH
T ss_conf             2005523478888747999999


No 57 
>smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
Probab=59.50  E-value=5.2  Score=19.37  Aligned_cols=92  Identities=21%  Similarity=0.175  Sum_probs=52.0

Q ss_pred             CCCCCCCC-C----------CCCCCCCCCCCCC-CCEE--ECCCCC--CCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             01123322-2----------2211222223323-2203--323785--31000112210023432211100123446655
Q gi|254780882|r  164 YGCGLRIS-E----------ALSLTPQNIMDDQ-STLR--IQGKGD--KIRIVPLLPSVRKAILEYYDLCPFDLNLNIQL  227 (328)
Q Consensus       164 ~~TGlR~~-E----------l~~L~~~did~~~-~~i~--v~gKg~--K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~  227 (328)
                      .-.+||.| |          +|+|+++||.+.. ..|.  ..||-+  -.-.||+.+.+...|..+..      +..+++
T Consensus       124 DklALRaGnEKdedeADTVGcCSLRvEHI~l~~~n~v~fDFLGKDSIRy~n~V~V~~~VfkNL~~F~k------~Kk~~D  197 (391)
T smart00435      124 DKLALRAGNEKGEDEADTVGCCSLRVEHVTLKPPNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMK------PKKPGD  197 (391)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCEEEECCEECCHHHHHHHHHHHC------CCCCCC
T ss_conf             78887406766766576311010157655864898068875167642554104448999999999942------899843


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             432111122111000123567899976869998805417999999
Q gi|254780882|r  228 PLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATH  272 (328)
Q Consensus       228 ~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~  272 (328)
                      .||-     +|++..++..++.+-      ..+|+-.||-.-||.
T Consensus       198 dlFD-----rl~ts~LN~hL~~~M------~GLTAKVFRTYNAS~  231 (391)
T smart00435      198 DLFD-----RLNTSKLNKHLKELM------PGLTAKVFRTYNASI  231 (391)
T ss_pred             HHHH-----CCCHHHHHHHHHHHC------CCCCEEEEEEECCCH
T ss_conf             1010-----368899988799755------675213465204777


No 58 
>TIGR01983 UbiG ubiquinone biosynthesis O-methyltransferase; InterPro: IPR010233   This entry represents an O-methyltransferase, which is believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and mitochondria (COQ3) , . A separate methylase (MenG/UbiE) catalyses the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase.; GO: 0008425 2-polyprenyl-6-methoxy-14-benzoquinone methyltransferase activity, 0006744 ubiquinone biosynthetic process.
Probab=49.39  E-value=15  Score=16.53  Aligned_cols=11  Identities=18%  Similarity=0.006  Sum_probs=5.0

Q ss_pred             CCHHHHHHHHC
Q ss_conf             99889999837
Q gi|254780882|r  278 GDLRSIQSILG  288 (328)
Q Consensus       278 ~~~~~v~~~lG  288 (328)
                      +.+..+..+|.
T Consensus       229 i~P~EL~~~l~  239 (275)
T TIGR01983       229 IKPSELTSWLE  239 (275)
T ss_pred             CCHHHHHHHHH
T ss_conf             38799999985


No 59 
>PRK11582 flagella biosynthesis protein FliZ; Provisional
Probab=48.39  E-value=19  Score=15.88  Aligned_cols=68  Identities=13%  Similarity=0.123  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             8999999999999999998512147887896898999999999999861-21013321123444222233321012
Q gi|254780882|r   33 KLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQ-KIGDRSLKRSLSGIKSFLKYLKKRKI  107 (328)
Q Consensus        33 ~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~-~~s~~T~~~~ls~lr~f~~~~~~~~~  107 (328)
                      +.+...+...|..+++||+...-..       +-+.=||..|-.++.++ .+|.+|++-|..-||.+=..+...++
T Consensus        58 d~~W~~~Q~~l~aLCRFCs~i~c~~-------~~~yFDI~gFkQyL~eQTeMshsTvrEYVVRLRRLd~~L~~~n~  126 (179)
T PRK11582         58 DNGWQKEQKEWAALCRFCGDLHCKT-------QSDYFDIIGFKQYLFEQTEMSHSTVREYVVRLRRLGNHLHEQNI  126 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCC-------CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf             8889999999999999988875178-------87601089999999985015221299999999999888763358


No 60 
>pfam08849 DUF1819 Putative inner membrane protein (DUF1819). These proteins are functionally uncharacterized. Several are annotated as putative inner membrane proteins.
Probab=47.41  E-value=19  Score=15.78  Aligned_cols=20  Identities=5%  Similarity=-0.032  Sum_probs=9.8

Q ss_pred             CCCCCHHHHHHHHHHHCCCC
Q ss_conf             11110156787765310135
Q gi|254780882|r  128 ALNEKQALTLVDNVLLHTSH  147 (328)
Q Consensus       128 ~lt~~e~~~ll~~~~~~~~~  147 (328)
                      .|+.+++..+++......+.
T Consensus       116 ~L~~~d~~~F~~~k~~~~~~  135 (191)
T pfam08849       116 DLPKEDWDAFFEAKAEWDPE  135 (191)
T ss_pred             CCCHHHHHHHHHHHHHCCCC
T ss_conf             88999999999987665910


No 61 
>TIGR00802 nico transition metal uptake transporter, Ni2+-Co2+ transporter (NiCoT) family; InterPro: IPR004688 This family is found in both Gram-negative and Gram-positive bacteria. The functionally characterised members of the family catalyze uptake of either Ni2+ or Co2+ in a proton motive force-dependent process. Topological analyses with the HoxN Ni2+ transporter of Ralstonia eutropha suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm.; GO: 0015099 nickel ion transmembrane transporter activity, 0015675 nickel ion transport, 0016021 integral to membrane.
Probab=43.33  E-value=15  Score=16.47  Aligned_cols=26  Identities=15%  Similarity=0.042  Sum_probs=12.0

Q ss_pred             CCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             356775775320122210011233222221122
Q gi|254780882|r  146 SHETKWIDARNSAILYLLYGCGLRISEALSLTP  178 (328)
Q Consensus       146 ~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~  178 (328)
                      ++-..++|.    +|-|.++|.   +|+.=|-.
T Consensus       151 SWHMYPvGf----LFGLGFDTA---tEvaLL~l  176 (290)
T TIGR00802       151 SWHMYPVGF----LFGLGFDTA---TEVALLGL  176 (290)
T ss_pred             CHHHHHHHH----HHHCCCHHH---HHHHHHHH
T ss_conf             524313588----762121189---99999999


No 62 
>TIGR00016 ackA acetate kinase; InterPro: IPR004372 Acetate kinase is involved in the activation of acetate to acetyl CoA and in the secretion of acetate. It catalyzes the reaction ATP + acetate = ADP + acetyl phosphate.; GO: 0016301 kinase activity, 0016774 phosphotransferase activity carboxyl group as acceptor, 0006082 organic acid metabolic process.
Probab=39.82  E-value=12  Score=17.05  Aligned_cols=14  Identities=14%  Similarity=0.223  Sum_probs=7.3

Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             32222211222223
Q gi|254780882|r  169 RISEALSLTPQNIM  182 (328)
Q Consensus       169 R~~El~~L~~~did  182 (328)
                      |..|+++...+|+.
T Consensus       204 ~~~~~Lnkp~~~l~  217 (416)
T TIGR00016       204 RAAKLLNKPLDDLN  217 (416)
T ss_pred             HHHHHHCCCHHHCC
T ss_conf             99997178101368


No 63 
>COG0282 ackA Acetate kinase [Energy production and conversion]
Probab=39.41  E-value=16  Score=16.26  Aligned_cols=13  Identities=23%  Similarity=0.376  Sum_probs=5.2

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             3222221122222
Q gi|254780882|r  169 RISEALSLTPQNI  181 (328)
Q Consensus       169 R~~El~~L~~~di  181 (328)
                      |..|+++-..+|+
T Consensus       188 ~aa~~L~k~~~~l  200 (396)
T COG0282         188 RAAEILGKPLEDL  200 (396)
T ss_pred             HHHHHHCCCCCCC
T ss_conf             9999868975334


No 64 
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=36.20  E-value=29  Score=14.70  Aligned_cols=32  Identities=28%  Similarity=0.389  Sum_probs=23.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCC
Q ss_conf             9998805417999999998489988999983788
Q gi|254780882|r  257 PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHF  290 (328)
Q Consensus       257 ~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~  290 (328)
                      +..+|+...+.  |..|+++|.+...|+..+|=+
T Consensus         3 ~~~lt~~q~~~--ar~l~~~G~~~~~iA~~~GVs   34 (42)
T cd00569           3 PPKLTPEQIEE--ARRLLAAGESVAEIARRLGVS   34 (42)
T ss_pred             CCCCCHHHHHH--HHHHHHCCCCHHHHHHHHCCC
T ss_conf             98699999999--999999789899999997979


No 65 
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=35.94  E-value=29  Score=14.67  Aligned_cols=20  Identities=25%  Similarity=0.325  Sum_probs=8.4

Q ss_pred             CHHHHHHHHCCCCHHHHHHHH
Q ss_conf             988999983788878979999
Q gi|254780882|r  279 DLRSIQSILGHFRLSTTQIYT  299 (328)
Q Consensus       279 ~~~~v~~~lGH~s~~tT~~Y~  299 (328)
                      ....+++.+|=|- .|-.+|.
T Consensus       175 Taeela~~~giSR-vTaRRYL  194 (224)
T COG4565         175 TAEELAQALGISR-VTARRYL  194 (224)
T ss_pred             CHHHHHHHHCCCH-HHHHHHH
T ss_conf             7999998837219-9999999


No 66 
>TIGR01304 IMP_DH_rel_2 IMP dehydrogenase family protein; InterPro: IPR005992    This family of proteins, often annotated as a putative IMP dehydrogenase, are related to IMP dehydrogenase and GMP reductase. Most species with a member of this family belong to the high GC Gram-positive bacteria..
Probab=34.39  E-value=17  Score=16.21  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=9.1

Q ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf             8805417999999998489988999
Q gi|254780882|r  260 TTAHTLRHSFATHLLSNGGDLRSIQ  284 (328)
Q Consensus       260 ~spH~lRHtfAt~ll~~G~~~~~v~  284 (328)
                      +||-..+. ||.-++++|+|+.+||
T Consensus       140 lsPq~~~~-~a~~vv~AG~DLLvIq  163 (376)
T TIGR01304       140 LSPQNASK-LAPVVVEAGADLLVIQ  163 (376)
T ss_pred             ECCHHHHH-HHHHHHHHCCCEEEEH
T ss_conf             66531678-8899997173004200


No 67 
>pfam05202 Flp_C Recombinase Flp protein.
Probab=34.05  E-value=31  Score=14.48  Aligned_cols=132  Identities=17%  Similarity=0.112  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCC-----CEE--E-CCCCCCCCCCCC---CCCC--HHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             23322222112222233232-----203--3-237853100011---2210--023432211100123446655432111
Q gi|254780882|r  167 GLRISEALSLTPQNIMDDQS-----TLR--I-QGKGDKIRIVPL---LPSV--RKAILEYYDLCPFDLNLNIQLPLFRGI  233 (328)
Q Consensus       167 GlR~~El~~L~~~did~~~~-----~i~--v-~gKg~K~R~Vpi---~~~~--~~~l~~yl~~~~~~~~~~~~~~lF~~~  233 (328)
                      -||-+++-+++.+-+..-..     .|+  | ..|++|+|.|..   ...+  .-+|.+|+.......+...++-  .+.
T Consensus        53 CcR~sDLkN~DP~TFeiv~nk~lG~ilra~V~eTKTr~~R~IyFfPv~gr~DpllaL~d~l~~~~Pv~Ksrts~~--~s~  130 (244)
T pfam05202        53 CCRHSDLKNADPKTFEIVKNKFLGRILRALVTETKTRKSRFIYFFPVNGRCDPLLALHDYLRETEPVPKSRTSNR--ESN  130 (244)
T ss_pred             HHCCHHCCCCCCCCEEEECCCHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCC--CHH
T ss_conf             521000145894315762452054577642022556651049997448987646879999874288764434564--115


Q ss_pred             CCCCCCCCCHHHHHHHHH-HHC-----CCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCC-----HH-H-H-HHHH
Q ss_conf             122111000123567899-976-----8699988054179999999984899889999837888-----78-9-7-9999
Q gi|254780882|r  234 RGKPLNPGVFQRYIRQLR-RYL-----GLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFR-----LS-T-T-QIYT  299 (328)
Q Consensus       234 ~g~~ls~~~i~~~~~~~~-~~~-----gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s-----~~-t-T-~~Y~  299 (328)
                      +--+|-+.++-.-..+.. +.+     +|+-.--.|-=||-.||.|-.++.+-.  ...+|..|     ++ - - ..|+
T Consensus       131 q~~Qllrdslv~~YdrFl~k~~~e~iF~I~nGPKSHlGRHLM~SyLs~~~l~~~--vs~~GNWsa~~~~~~S~vARs~Y~  208 (244)
T pfam05202       131 QEYQLLRDSLVRSYDRFLAKHAPEPIFAIKNGPKSHLGRHLMASYLSNNELGEW--VSPYGNWSAGDDEIESAVARSKYT  208 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCCE--ECCCCCCCCCCCHHHHHHHHHCCC
T ss_conf             678888988888899999737987645147896678878999988530567751--114666243444146566542034


Q ss_pred             HHC
Q ss_conf             619
Q gi|254780882|r  300 NVN  302 (328)
Q Consensus       300 h~~  302 (328)
                      |..
T Consensus       209 H~~  211 (244)
T pfam05202       209 HGQ  211 (244)
T ss_pred             CCC
T ss_conf             566


No 68 
>KOG0440 consensus
Probab=31.12  E-value=26  Score=15.03  Aligned_cols=81  Identities=22%  Similarity=0.333  Sum_probs=41.8

Q ss_pred             CCCCCCCCCCCCCCCCCCC-CCCC--CCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1001123322222112222-2332--322033237853100011221002343221110012344665543211112211
Q gi|254780882|r  162 LLYGCGLRISEALSLTPQN-IMDD--QSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPL  238 (328)
Q Consensus       162 ll~~TGlR~~El~~L~~~d-id~~--~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~~~~~~~~~lF~~~~g~~l  238 (328)
                      ++|+|   ++|.|.-.-.- ...+  ..++|.-.+|.+. .|| .+..++.+..|.+..      -.+.-|||++.|.+.
T Consensus        99 ~lYGt---itEfCT~~sCp~Msag~~yeY~W~D~~~kp~-~~s-ApqYId~lmtw~q~~------~dde~iFPtK~g~~F  167 (243)
T KOG0440          99 LLYGT---ITEFCTQQSCPHMSAGPNYEYLWADEKGKPV-RVS-APQYIDYLMTWCQNQ------LDDENIFPTKYGNPF  167 (243)
T ss_pred             HHHHH---HHHHHCCCCCCCCCCCCCCEEEEECCCCCCC-CCC-CHHHHHHHHHHHHHH------CCCCCCCCCCCCCCC
T ss_conf             98878---8877074458654678861156100258852-147-158999999999873------453002764357879


Q ss_pred             CCCCHHHHHHHHHHHC
Q ss_conf             1000123567899976
Q gi|254780882|r  239 NPGVFQRYIRQLRRYL  254 (328)
Q Consensus       239 s~~~i~~~~~~~~~~~  254 (328)
                      - ..+...++++.+++
T Consensus       168 P-~nF~~~vk~Ilr~l  182 (243)
T KOG0440         168 P-GNFESVVKKILRRL  182 (243)
T ss_pred             C-CHHHHHHHHHHHHH
T ss_conf             8-00899999999999


No 69 
>TIGR01822 2am3keto_CoA 2-amino-3-ketobutyrate coenzyme A ligase; InterPro: IPR011282   This entry represents a narrowly defined clade of animal and bacterial (almost exclusively proteobacterial) 2-amino-3-ketobutyrate--CoA ligase. This enzyme can act in threonine catabolism. The closest homologue from Bacillus subtilis, and sequences like it, may be functionally equivalent but were not included in the model because of difficulty in finding reports of function.; GO: 0008890 glycine C-acetyltransferase activity.
Probab=29.65  E-value=37  Score=14.03  Aligned_cols=34  Identities=26%  Similarity=0.426  Sum_probs=20.6

Q ss_pred             HHHHHHHHHCCCCCC-----CCC---CCCH--HHHHHHHHHCCC
Q ss_conf             356789997686999-----880---5417--999999998489
Q gi|254780882|r  245 RYIRQLRRYLGLPLS-----TTA---HTLR--HSFATHLLSNGG  278 (328)
Q Consensus       245 ~~~~~~~~~~gi~~~-----~sp---H~lR--HtfAt~ll~~G~  278 (328)
                      ++|+.-...+|++-+     |.|   ++.+  -.||..|++.|+
T Consensus       305 ~~FR~~m~AaGFd~~p~~hpI~pvMlyDA~~Aq~~A~~Ll~~Gi  348 (395)
T TIGR01822       305 RYFRERMEAAGFDVKPAEHPIIPVMLYDAKLAQRFAERLLEEGI  348 (395)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCEEEECCCHHHHHHHHHHHHHCCE
T ss_conf             98787534247401789885102321147899999999987792


No 70 
>pfam07506 RepB RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.
Probab=29.08  E-value=38  Score=13.97  Aligned_cols=19  Identities=11%  Similarity=0.240  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999986121013321123
Q gi|254780882|r   74 FISKRRTQKIGDRSLKRSL   92 (328)
Q Consensus        74 ~l~~l~~~~~s~~T~~~~l   92 (328)
                      |+..+.+.|++..+|...+
T Consensus        13 ~a~rl~~~G~~~~~I~~aL   31 (185)
T pfam07506        13 FAARLLERGVPRAEIAAAL   31 (185)
T ss_pred             HHHHHHHCCCCHHHHHHHH
T ss_conf             9999998699999999998


No 71 
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=29.00  E-value=38  Score=13.96  Aligned_cols=44  Identities=18%  Similarity=0.188  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHCC--CCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             86999880541799999999848--99889999837888789799996
Q gi|254780882|r  255 GLPLSTTAHTLRHSFATHLLSNG--GDLRSIQSILGHFRLSTTQIYTN  300 (328)
Q Consensus       255 gi~~~~spH~lRHtfAt~ll~~G--~~~~~v~~~lGH~s~~tT~~Y~h  300 (328)
                      .+|+.+++.+|..-. ..+-++|  .....|++.+|= |-.|..+|.-
T Consensus       154 ~lpKGl~~~Tl~~v~-~~l~~~~~~~ta~eva~~~gi-SrvTaRRYLe  199 (225)
T PRK10046        154 ELPTGIDPLTLNAVR-KLFKEPGVQHTAETVAQALTI-SRTTARRYLE  199 (225)
T ss_pred             CCCCCCCHHHHHHHH-HHHHCCCCCCCHHHHHHHHCC-CHHHHHHHHH
T ss_conf             589999989999999-999717998689999998585-1999999999


No 72 
>pfam04852 DUF640 Protein of unknown function (DUF640). This family represents a conserved region found in plant proteins including Resistance protein-like protein.
Probab=27.57  E-value=40  Score=13.80  Aligned_cols=39  Identities=13%  Similarity=0.031  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHH
Q ss_conf             9999999999985121478878968989999999999998612
Q gi|254780882|r   40 ECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQK   82 (328)
Q Consensus        40 ~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~   82 (328)
                      ++|+..|..|+..+.+    ...+...+..||.+|+.++..-|
T Consensus        25 rrdw~tf~qyL~n~rP----Pl~l~~csg~hvl~FL~~~d~fG   63 (133)
T pfam04852        25 RRDWNTFGQYLRNQRP----PLNLSKCSGNHVLDFLRYLDQFG   63 (133)
T ss_pred             HHHHHHHHHHHHCCCC----CCCHHHCCHHHHHHHHHHHHHCC
T ss_conf             5308999999871699----98612068389999999876127


No 73 
>TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit; InterPro: IPR012062   Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases , . However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity . It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ  and other members of this family turned out to be erroneous , .; GO: 0009024 tagatose-6-phosphate kinase activity, 0019402 galactitol metabolic process.
Probab=27.20  E-value=39  Score=13.88  Aligned_cols=35  Identities=14%  Similarity=0.088  Sum_probs=20.7

Q ss_pred             CCCCHHHHHHHHCCCCHHHHHHHHHHCH--------HHHHHHHHHHHHHH
Q ss_conf             4899889999837888789799996198--------99999999999981
Q gi|254780882|r  276 NGGDLRSIQSILGHFRLSTTQIYTNVNS--------KNGGDWMMEIYDQT  317 (328)
Q Consensus       276 ~G~~~~~v~~~lGH~s~~tT~~Y~h~~~--------~~~~~~l~~~~~~~  317 (328)
                      .-+|+..|++.|+       .-|..|..        +=..+.++++...|
T Consensus       383 ~~iPl~LlSQYLP-------~qy~av~~G~l~p~P~~l~~~~i~~VL~~Y  425 (430)
T TIGR02810       383 QPIPLTLLSQYLP-------EQYAAVRAGELAPKPRELILDKIRDVLADY  425 (430)
T ss_pred             CCCCHHHHHHHHH-------HHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             8896477999858-------999999718888764899999999999999


No 74 
>PRK02615 thiamine-phosphate pyrophosphorylase; Provisional
Probab=26.38  E-value=42  Score=13.67  Aligned_cols=67  Identities=15%  Similarity=0.248  Sum_probs=41.9

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC----CCCCCCCCHHHHHHHHHHCCCC-HHHHHHHHCCCCHHHHHH
Q ss_conf             655432111122111000123567899976869----9988054179999999984899-889999837888789799
Q gi|254780882|r  225 IQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP----LSTTAHTLRHSFATHLLSNGGD-LRSIQSILGHFRLSTTQI  297 (328)
Q Consensus       225 ~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~----~~~spH~lRHtfAt~ll~~G~~-~~~v~~~lGH~s~~tT~~  297 (328)
                      .-+|+|++..-.-..+.++ ..++.+++.+.+|    ..|+++.+     ..++++|++ +-+|+.+|+..++..+-.
T Consensus       263 g~Gpvf~T~TK~~~~p~Gl-~~l~~~~~~~~iPvvAIGGI~~~N~-----~~v~~aGa~gvAVisAI~~A~DP~~aa~  334 (345)
T PRK02615        263 GVGPVFPTPTKPGKAPAGL-EYLKYARKEANIPWFAIGGIDKSNI-----SEVLQAGADRVAVVRAIMNAEDPKQATQ  334 (345)
T ss_pred             EECCEEECCCCCCCCCCCH-HHHHHHHHHCCCCEEEECCCCHHHH-----HHHHHCCCCEEEEEHHHHCCCCHHHHHH
T ss_conf             9887742588888887899-9999999837999999999699999-----9999859999998228557999999999


No 75 
>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed
Probab=25.75  E-value=44  Score=13.60  Aligned_cols=65  Identities=20%  Similarity=0.290  Sum_probs=37.9

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC----CCCCCCCCHHHHHHHHHHCCCC-HHHHHHHHCCCCHHHH
Q ss_conf             55432111122111000123567899976869----9988054179999999984899-8899998378887897
Q gi|254780882|r  226 QLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP----LSTTAHTLRHSFATHLLSNGGD-LRSIQSILGHFRLSTT  295 (328)
Q Consensus       226 ~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~----~~~spH~lRHtfAt~ll~~G~~-~~~v~~~lGH~s~~tT  295 (328)
                      -+++|++.......+..=...++.+++...+|    ..+++..+     ..+++.|++ +-+++.++++.+++.+
T Consensus       129 ~Gpvf~T~tK~~~~~~~g~~~l~~~~~~~~iPvvAIGGI~~~ni-----~~~~~~Ga~giAvis~I~~a~dp~~a  198 (210)
T PRK00043        129 VGPIFPTPTKKDAKPAVGLELLREAREAIDIPIVAIGGITPENA-----AEVLEAGADGVAVVSAITAAEDPAAA  198 (210)
T ss_pred             ECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCHHHH-----HHHHHCCCCEEEEEHHHHCCCCHHHH
T ss_conf             74521479888887778999999999847999899808899999-----99998099999970897769999999


No 76 
>TIGR02057 PAPS_reductase phosphoadenosine phosphosulfate reductase; InterPro: IPR011800    Requiring thioredoxin as an electron donor, phosphoadenosine phosphosulphate reductase catalyzes the reduction of 3'-phosphoadenylylsulphate (PAPS) to sulphite and phospho-adenosine-phosphate (PAP). Found in enterobacteria, cyanobacteria, and yeast, PAPS reductase is related to a group of plant (IPR004508 from INTERPRO) and bacterial (IPR011798 from INTERPRO) enzymes preferring 5'-adenylylsulphate (APS) over PAPS as a substrate for reduction to sulphite.; GO: 0004604 phosphoadenylyl-sulfate reductase (thioredoxin) activity, 0019344 cysteine biosynthetic process.
Probab=25.27  E-value=34  Score=14.24  Aligned_cols=46  Identities=22%  Similarity=0.303  Sum_probs=35.3

Q ss_pred             CCCCCCCCCCCC---CCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             001123322222---1122222332322033237853100011221002343221110
Q gi|254780882|r  163 LYGCGLRISEAL---SLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLC  217 (328)
Q Consensus       163 l~~TGlR~~El~---~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~  217 (328)
                      .+-||+|.+-..   +|.+=+||..+|.++|         .||-+.-.+.+.+|+...
T Consensus       144 Aw~tG~Rr~Q~~~R~nL~v~~~D~~~G~lKv---------~Pl~~W~~~~~~~Y~~~h  192 (239)
T TIGR02057       144 AWFTGRRRDQASARANLPVLELDLQNGILKV---------NPLIDWTRKQVYQYLAAH  192 (239)
T ss_pred             HHHHCCCHHHHCCCCCCCCEEEECCCCCCEE---------CCCCCCCHHHHHHHHHHC
T ss_conf             9874255434202236861000014781032---------021026502279999867


No 77 
>TIGR01262 maiA maleylacetoacetate isomerase; InterPro: IPR005955    Maleylacetoacetate isomerase is an enzyme of tyrosine and phenylalanine catabolism. It requires glutathione and belongs by homology to the zeta family of glutathione S-transferases. The enzyme (5.2.1.2 from EC) is described as active also on maleylpyruvate.; GO: 0003824 catalytic activity, 0009072 aromatic amino acid family metabolic process, 0005737 cytoplasm.
Probab=24.47  E-value=46  Score=13.45  Aligned_cols=37  Identities=27%  Similarity=0.462  Sum_probs=21.8

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             35678999768699988054179999999984899889999837
Q gi|254780882|r  245 RYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILG  288 (328)
Q Consensus       245 ~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lG  288 (328)
                      ++++.+.++.|++.     ..|+.++-+++.+|-.  .+=++|+
T Consensus       115 ~Vl~~L~~~~g~~~-----~~~~~W~~~wI~~Gl~--A~E~lL~  151 (218)
T TIGR01262       115 RVLQYLREKLGVDE-----EERRRWYQHWISKGLA--ALEALLQ  151 (218)
T ss_pred             HHHHHHHHHCCCCH-----HHHHHHHHHHHHHHHH--HHHHHHH
T ss_conf             99988865328998-----8888899999998899--9999860


No 78 
>pfam09968 DUF2202 Uncharacterized protein domain (DUF2202). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=23.89  E-value=47  Score=13.38  Aligned_cols=16  Identities=6%  Similarity=0.158  Sum_probs=8.1

Q ss_pred             CCCCCHHHHHHHHHHH
Q ss_conf             1111015678776531
Q gi|254780882|r  128 ALNEKQALTLVDNVLL  143 (328)
Q Consensus       128 ~lt~~e~~~ll~~~~~  143 (328)
                      .++..++..+.+.+..
T Consensus        65 ~F~npelQ~LYn~L~~   80 (162)
T pfam09968        65 VFTNPDLQELYNQLVE   80 (162)
T ss_pred             CCCCHHHHHHHHHHHH
T ss_conf             5288779999999999


No 79 
>PRK02249 DNA primase large subunit; Validated
Probab=22.71  E-value=50  Score=13.23  Aligned_cols=51  Identities=20%  Similarity=0.282  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCC---CHHHHH
Q ss_conf             00123567899976869998805417999999998489988999983788---878979
Q gi|254780882|r  241 GVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHF---RLSTTQ  296 (328)
Q Consensus       241 ~~i~~~~~~~~~~~gi~~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~---s~~tT~  296 (328)
                      --+...+..+.  .|  .++ ||.-|=+.||-|+.-|++...|-++...+   +.++|.
T Consensus       223 PCmk~~i~~l~--~G--~Nl-~H~~Rf~Lasfl~~iG~~~d~i~~lf~~aPDf~e~~t~  276 (333)
T PRK02249        223 PCMKALLSALQ--AG--ENL-PHTARFAITSFLHNIGMDVDEIVELFRNAPDFDEEITR  276 (333)
T ss_pred             HHHHHHHHHHH--CC--CCC-CHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHH
T ss_conf             07999999986--69--987-71789999999997699889999998419986602467


Done!