Query gi|255764498|ref|YP_003065000.2| site-specific tyrosine recombinase XerD [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 300
No_of_seqs 163 out of 12975
Neff 9.6
Searched_HMMs 39220
Date Sun May 29 22:15:03 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 255764498.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02225 recomb_XerD tyrosine 100.0 0 0 544.3 16.2 288 1-292 6-305 (305)
2 TIGR02224 recomb_XerC tyrosine 100.0 0 0 526.1 16.4 289 1-294 6-313 (313)
3 COG4974 XerD Site-specific rec 100.0 0 0 465.6 16.4 283 1-292 15-300 (300)
4 PRK01287 xerC site-specific ty 100.0 0 0 444.5 18.5 287 2-298 34-330 (361)
5 PRK00283 xerD site-specific ty 100.0 0 0 442.0 18.5 283 2-292 13-296 (296)
6 PRK00236 xerC site-specific ty 100.0 0 0 432.2 18.3 278 2-292 17-295 (295)
7 cd00798 INT_XerDC XerD and Xer 100.0 0 0 404.1 18.7 276 1-285 7-284 (284)
8 COG4973 XerC Site-specific rec 100.0 0 0 392.4 16.9 283 1-295 16-299 (299)
9 PRK05084 xerS site-specific ty 100.0 0 0 389.9 17.5 281 5-288 30-356 (360)
10 cd01196 INT_VanD VanD integras 100.0 0 0 357.2 16.6 256 2-288 5-260 (263)
11 cd01185 INT_Tn4399 Tn4399 and 100.0 0 0 353.4 17.5 260 5-287 30-298 (299)
12 PRK02436 xerD site-specific ty 100.0 0 0 351.6 13.0 241 1-275 7-247 (247)
13 cd01190 INT_SG5 INT_SG5, DNA b 100.0 0 0 348.8 14.9 249 31-290 2-260 (260)
14 cd01187 INT_SG4 INT_SG4, DNA b 100.0 0 0 346.0 15.0 270 7-287 16-298 (299)
15 TIGR02249 integrase_gron integ 100.0 0 0 340.3 10.2 256 6-278 12-307 (320)
16 cd01193 INT_IntI IntI (E2) int 100.0 0 0 329.0 11.7 230 31-276 4-242 (242)
17 cd00799 INT_Cre Cre recombinas 100.0 0 0 301.7 14.1 258 10-279 1-278 (287)
18 PRK09870 tyrosine recombinase; 100.0 0 0 304.0 10.3 194 90-294 3-197 (200)
19 PRK09871 tyrosine recombinase; 100.0 0 0 299.1 9.1 192 96-297 3-195 (198)
20 cd00801 INT_P4 Bacteriophage P 100.0 1.4E-45 0 283.6 14.6 261 6-288 86-355 (357)
21 cd00796 INT_Rci Rci recombinas 100.0 1.4E-45 0 285.2 9.4 202 58-283 1-205 (206)
22 cd01188 INT_pAE1 pAE1 and rela 100.0 1.5E-44 0 278.4 9.3 181 96-286 1-184 (188)
23 cd01198 INT_ASSRA_C Archaeal s 100.0 5.7E-43 0 269.2 9.8 178 99-293 1-186 (186)
24 cd01197 INT_FimBE_C FimB and F 100.0 2.8E-42 0 265.2 8.2 178 97-285 2-180 (180)
25 cd01186 INT_SG3_C INT_SG3, DNA 100.0 7.4E-40 1.8E-44 251.1 9.7 172 100-289 7-179 (180)
26 cd01194 INT_Tn554A_C Tn544A an 100.0 4.8E-40 1.3E-44 252.2 8.4 172 100-287 1-186 (186)
27 cd01199 INT_Tn1545_C Tn1545-re 100.0 1.7E-38 4.2E-43 243.2 9.9 180 99-287 1-204 (205)
28 cd01183 INT_SG1_C INT_SG1, DNA 100.0 1.4E-38 3.7E-43 243.6 6.7 174 99-275 1-196 (196)
29 cd01192 INT_P22_C P22-like int 100.0 1.5E-37 3.7E-42 237.7 9.4 171 95-290 2-175 (177)
30 cd01195 INT_Tn544B_C Tn544B an 100.0 6.4E-37 1.6E-41 234.0 8.2 178 98-285 1-195 (195)
31 pfam00589 Phage_integrase Phag 100.0 9.9E-37 2.5E-41 232.9 7.2 169 98-280 1-170 (170)
32 cd01189 INT_phiLC3_C phiLC3 ph 100.0 4E-36 1E-40 229.4 8.2 171 98-280 1-190 (191)
33 cd00397 DNA_BRE_C DNA breaking 100.0 3.1E-34 7.8E-39 218.4 6.6 161 104-275 1-164 (164)
34 PRK09692 integrase; Provisiona 100.0 1.8E-31 4.5E-36 202.3 14.8 258 8-287 122-388 (413)
35 cd00797 HP1_INT_C Phage HP1 in 100.0 9.5E-33 2.4E-37 209.7 8.3 157 103-290 1-158 (158)
36 cd01184 INT_SG2_C INT_SG2, DNA 100.0 2.1E-33 5.5E-38 213.5 4.8 168 100-275 1-181 (181)
37 cd00800 INT_Lambda_C Lambda in 100.0 1.1E-32 2.9E-37 209.3 7.6 158 97-276 1-161 (162)
38 cd01191 INT_phiCTX_C phiCTX ph 100.0 2.9E-32 7.3E-37 206.9 7.5 167 97-276 1-195 (196)
39 cd01182 INT_REC_C DNA breaking 99.9 2.5E-27 6.3E-32 178.3 6.9 147 126-275 14-162 (162)
40 COG0582 XerC Integrase [DNA re 99.9 9.5E-21 2.4E-25 139.9 14.6 221 41-287 72-301 (309)
41 pfam02899 Phage_integr_N Phage 99.6 1.8E-15 4.5E-20 109.3 7.4 77 1-77 7-83 (83)
42 PHA00730 int integrase 98.4 2.2E-06 5.6E-11 56.4 9.5 199 20-276 98-303 (322)
43 pfam11917 DUF3435 Protein of u 98.4 6.1E-07 1.6E-11 59.6 5.0 64 209-274 170-235 (414)
44 COG4342 Uncharacterized protei 98.3 1.3E-05 3.3E-10 51.9 10.8 220 37-290 55-280 (291)
45 pfam01028 Topoisom_I Eukaryoti 97.4 0.00069 1.8E-08 41.9 7.4 134 131-276 58-225 (244)
46 cd00659 Topo_IB_C DNA topoisom 97.0 0.0026 6.6E-08 38.5 6.6 130 130-275 44-207 (218)
47 PRK00283 xerD site-specific ty 95.5 0.032 8.2E-07 32.2 5.2 40 38-77 2-42 (296)
48 PRK01287 xerC site-specific ty 95.5 0.016 4.1E-07 33.9 3.6 41 40-80 25-65 (361)
49 PRK05084 xerS site-specific ty 95.4 0.018 4.7E-07 33.6 3.6 48 35-82 14-61 (360)
50 PRK00236 xerC site-specific ty 94.6 0.082 2.1E-06 29.8 5.2 40 39-78 7-47 (295)
51 cd01193 INT_IntI IntI (E2) int 92.5 0.38 9.7E-06 25.9 5.6 48 2-49 22-83 (242)
52 cd00798 INT_XerDC XerD and Xer 92.4 0.092 2.3E-06 29.5 2.3 37 42-78 1-38 (284)
53 cd01190 INT_SG5 INT_SG5, DNA b 90.8 0.3 7.6E-06 26.6 3.5 48 2-49 20-87 (260)
54 cd01185 INT_Tn4399 Tn4399 and 90.5 0.26 6.6E-06 26.9 3.0 27 51-77 30-56 (299)
55 pfam02899 Phage_integr_N Phage 90.5 0.18 4.7E-06 27.8 2.2 35 42-76 1-36 (83)
56 COG4688 Uncharacterized protei 89.9 1.2 2.9E-05 23.1 6.0 52 235-286 448-499 (665)
57 pfam05202 Flp_C Recombinase Fl 87.5 1.1 2.9E-05 23.2 4.5 143 130-276 43-210 (244)
58 cd00217 INT_Flp Flp recombinas 81.7 2.9 7.4E-05 20.8 4.5 140 131-276 169-334 (339)
59 TIGR00973 leuA_bact 2-isopropy 73.2 5.9 0.00015 19.0 4.1 53 226-299 331-385 (514)
60 smart00435 TOPEUc DNA Topoisom 63.2 11 0.00028 17.5 4.0 82 132-225 119-216 (391)
61 PRK12541 RNA polymerase sigma 62.4 9.8 0.00025 17.7 3.4 30 252-282 128-157 (161)
62 pfam04852 DUF640 Protein of un 49.1 19 0.00048 16.1 4.3 38 17-54 25-64 (133)
63 PRK11511 DNA-binding transcrip 48.5 19 0.00049 16.0 5.9 79 211-293 36-124 (127)
64 pfam07900 DUF1670 Protein of u 48.1 20 0.0005 16.0 5.5 17 248-264 193-209 (220)
65 TIGR02759 TraD_Ftype type IV c 45.9 21 0.00054 15.8 3.1 81 199-287 414-514 (613)
66 PRK09393 ftrA transcriptional 44.4 22 0.00057 15.6 6.5 71 211-285 243-318 (320)
67 TIGR02057 PAPS_reductase phosp 42.9 13 0.00034 16.9 1.5 46 136-190 144-192 (239)
68 PRK05602 RNA polymerase sigma 35.1 32 0.00081 14.8 5.4 44 249-293 141-184 (186)
69 PRK10219 DNA-binding transcrip 34.9 32 0.00081 14.8 5.7 70 210-283 31-105 (107)
70 TIGR02394 rpoS_proteo RNA poly 33.5 18 0.00047 16.2 1.0 32 221-256 252-289 (292)
71 PRK09978 DNA-binding transcrip 33.0 34 0.00087 14.6 6.6 78 211-293 169-251 (274)
72 PRK13502 transcriptional activ 28.1 42 0.0011 14.1 6.0 73 211-287 203-280 (282)
73 PRK09647 RNA polymerase sigma 27.1 43 0.0011 14.0 5.6 52 239-292 161-212 (222)
74 PRK12511 RNA polymerase sigma 26.9 44 0.0011 14.0 4.3 18 130-147 117-134 (182)
75 pfam09968 DUF2202 Uncharacteri 25.0 48 0.0012 13.7 2.4 18 98-115 64-81 (162)
76 pfam07506 RepB RepB plasmid pa 23.6 51 0.0013 13.6 3.3 30 36-65 4-33 (185)
77 smart00342 HTH_ARAC helix_turn 23.1 52 0.0013 13.5 3.9 65 212-280 13-82 (84)
78 PRK09857 hypothetical protein; 22.5 53 0.0014 13.5 3.0 27 239-265 257-283 (292)
79 TIGR02639 ClpA ATP-dependent C 22.4 53 0.0014 13.4 2.3 47 200-255 529-577 (774)
80 pfam07638 Sigma70_ECF ECF sigm 21.5 56 0.0014 13.3 3.4 45 240-286 140-184 (185)
81 TIGR02194 GlrX_NrdH Glutaredox 21.5 31 0.00078 14.8 0.3 32 24-55 16-47 (72)
82 PRK09570 rpoH DNA-directed RNA 21.0 53 0.0013 13.5 1.4 50 98-154 16-65 (79)
No 1
>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=544.28 Aligned_cols=288 Identities=43% Similarity=0.650 Sum_probs=267.4
Q ss_pred CCHHHHHCCHHHHHHHHHHHHHHHHHHH--HCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 9646641389999999999999999975--44998688999999999999997799843532210112334321000122
Q gi|255764498|r 1 MMSSERASSINTLSAYKRDLKEMQNFLN--NKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGL 78 (300)
Q Consensus 1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~--~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~ 78 (300)
||..|||+|+||+.+|++||..|..|+. ..+ ++.+++..+|.+|+.++.+.|.+++|++|.+++||+||+||..+|+
T Consensus 6 ~L~~E~GLs~NT~~aYrrDL~~f~~~L~~~~~g-~~~~~~~~~i~~fl~~l~~~g~~~~S~AR~lsalR~Fy~fL~~e~~ 84 (305)
T TIGR02225 6 YLWVERGLSQNTLEAYRRDLEKFLEYLEESERG-DLAEVDRGDIEDFLAELKEAGLSARSIARALSALRSFYRFLLREGL 84 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 999986353888999999999999986222478-7641687899999999986687700288999999999999986887
Q ss_pred CCCCCCCC-CCCCCCCCCCCCCCCCHHHHHHHHHH-HHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf 22221222-21212221112233202469999864-32001256102776543110001221001343334320000011
Q gi|255764498|r 79 RKDNPSDT-LELPKKNHILPKTLHKDTIANLLEQA-KIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNL 156 (300)
Q Consensus 79 ~~~np~~~-i~~~k~~~~~~~~ls~~e~~~ll~~~-~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~ 156 (300)
++.||+.. |+.||..++.|++||.+||.+||++. +.+... ..... .+||+|||++||.||||+||+++|+..||++
T Consensus 85 ~~~dP~~~~~~~PK~~~~LP~vLt~~EV~~LL~~p~~~~~~~-g~kr~-~lRDrAmLElLYATGlRVSELv~L~~~d~~l 162 (305)
T TIGR02225 85 REDDPSALRIETPKVARKLPKVLTVEEVEALLAAPIDVDTPL-GGKRP-ALRDRAMLELLYATGLRVSELVGLRLEDVNL 162 (305)
T ss_pred CCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCC-CCCCH-HHHHHHHHHHHHHCCCCEEEEECCCHHHHHC
T ss_conf 455733664203422457888379899999985002467767-67640-1654799999986488355330561665200
Q ss_pred HHHC-CC-CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC---CCCCC---CCCCCCCCCCCCCCCCCCCHHHHHHHC
Q ss_conf 1100-01-1122211111000012478875323210012467---77520---012333222221111111012344201
Q gi|255764498|r 157 TERT-MI-IQGKGNKERLVILSPSALHALQMYKKTCSSMKMT---GNDLW---LFPSSTKTGHLSRQVFARDLKALAARA 228 (300)
Q Consensus 157 ~~~~-i~-v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~---~~~~~---lf~~~~~~~~~s~~~~~~~~~~~~~~~ 228 (300)
+.++ |. |.|||+|+|.|||.+.++++|.+|+++.++.... ...++ ||++...|++||++.||+.++++.++|
T Consensus 163 ~~g~~~~~v~GKG~KERlVP~G~~A~~~l~~Yl~~~R~~~~~~~~~~~d~~~~LFln~~~G~~lsRQ~~W~~~K~~A~~a 242 (305)
T TIGR02225 163 DEGVKVRKVRGKGSKERLVPLGEEAIEALERYLKEARPLLLKKKKKSSDAKSALFLNRREGGPLSRQGFWKILKEYAKRA 242 (305)
T ss_pred CCCEEEEEEEECCCCEEECCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf 27737999861688412022028999999999987406764177888755431124688888878899999999999981
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHH
Q ss_conf 4667642598858899999998588888999985589989989996459999999999828011
Q gi|255764498|r 229 GIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 (300)
Q Consensus 229 gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~ 292 (300)
||..+ +|||.|||+|||||+++|+|+.+||+||||+||+|||+||||+.+++++++.+|||||
T Consensus 243 GI~k~-isPHtLRHSFATHLLenGADLR~VQeLLGHadisTTQIYTHV~~~~L~~~~~~~HPRa 305 (305)
T TIGR02225 243 GIEKP-ISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 305 (305)
T ss_pred CCCCC-CCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 88989-9975104679999873688276887774322147889999987999999999628899
No 2
>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=526.07 Aligned_cols=289 Identities=41% Similarity=0.609 Sum_probs=266.0
Q ss_pred CCHHHHHCCHHHHHHHHHHHHHHHHHHHH----CCC----CHHHCCHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHH
Q ss_conf 96466413899999999999999999754----499----8688999999999999997--7998435322101123343
Q gi|255764498|r 1 MMSSERASSINTLSAYKRDLKEMQNFLNN----KEI----SLSAASTNHLISYLNHLSQ--RKLVTSSQRRKISVIRQFY 70 (300)
Q Consensus 1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~~----~~~----~~~~i~~~~i~~~~~~l~~--~~~s~~T~~~~~~~l~~~~ 70 (300)
+|+.||++|++|+.+|..||..|..|+.. .+. ++.+++..++..|+..+.+ +|++++|+++.+|+||+||
T Consensus 6 yL~~er~~S~hT~~aY~~DL~~f~~fl~~~~~~~~~~~~~~~~~~~~~d~R~~la~l~~~~~g~s~rS~~R~LSalRsFy 85 (313)
T TIGR02224 6 YLRVERNYSPHTLRAYRRDLEAFLEFLEEHKQEEGGPLLASLAEVTAADLRSFLAELHAKERGLSRRSLARKLSALRSFY 85 (313)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf 99988500089999999999999999999877520111015762488999999999984657876768999999999999
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHCCCHHHHHCCCCCCCCCC
Q ss_conf 210001222222122221212221112233202469999864320012561-0277654311000122100134333432
Q gi|255764498|r 71 NFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAP-GQWKRVRIFLLIELLYATGMRVSELVTL 149 (300)
Q Consensus 71 ~~~~~~~~~~~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~-~~~~~~R~~~il~ll~~tGlR~~Ei~~L 149 (300)
+|++++|+++.||+..|+.||.+++.|++|+.||+.+|++...... .. ..+..+||+|||.+||.||||+||+++|
T Consensus 86 ~~L~~~~~~~~nPa~~~~~PK~~~~LP~~L~~~~~~~ll~~~~~~~---~~~~~~~~~RDrA~lEllYssGlRvSEl~~L 162 (313)
T TIGR02224 86 RFLLRRGLIDANPAAGVRAPKKPKKLPKFLSEDEMEALLDAPEEDA---EDREDWLALRDRAILELLYSSGLRVSELVGL 162 (313)
T ss_pred HHHHHCCCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 9998728740223887226754467998889899999960123466---6677789998999999998746899998247
Q ss_pred CHH-HHHHHH--HCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC-----CCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 000-001111--00011122211111000012478875323210012467775-----2001233322222111111101
Q gi|255764498|r 150 SAH-TLNLTE--RTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGND-----LWLFPSSTKTGHLSRQVFARDL 221 (300)
Q Consensus 150 ~~~-di~~~~--~~i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~-----~~lf~~~~~~~~~s~~~~~~~~ 221 (300)
+++ |||++. ++++|+|||+|+|+|||.+.+.++|..|++.++......++ ++||.+ .+|++|++++|++.+
T Consensus 163 ~~~~D~d~~~~~~~vrV~GKG~KeR~VP~G~~A~~al~~YL~~~r~~~~~~~~~~~~~~~LF~~-~~G~rL~~R~v~~~l 241 (313)
T TIGR02224 163 DLSEDLDLDFSLGLVRVRGKGNKERIVPFGSYARDALQAYLEERREPLLAKEPPAQDHDALFLN-RRGGRLTPRGVRYRL 241 (313)
T ss_pred CCCCCCCCHHCCCEEEEEECCCCEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHH
T ss_conf 7133647322147677741488135303148999999999864472114566777752230017-888725777899999
Q ss_pred HHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHC
Q ss_conf 2344201466764259885889999999858888899998558998998999645999999999982801110
Q gi|255764498|r 222 KALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKK 294 (300)
Q Consensus 222 ~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~~ 294 (300)
.++..++|+.. ++|||.|||||||||+++|+|+..||+||||+|++|||+||||+.++++++++++||||||
T Consensus 242 ~~~~~~~~l~~-~~hPH~LRHSFATHLL~~gaDLRaVQELLGH~SLSTTQiYTHv~~~~L~~~Y~~AHPRA~k 313 (313)
T TIGR02224 242 QQLVAKAGLPK-HVHPHALRHSFATHLLENGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDKAHPRAKK 313 (313)
T ss_pred HHHHHHCCCCC-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99998568888-6787531131799997468835589897444643566798884099999999973777779
No 3
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=465.57 Aligned_cols=283 Identities=45% Similarity=0.695 Sum_probs=264.5
Q ss_pred CCHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC-CHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 96466413899999999999999999754499-86889999999999999977998435322101123343210001222
Q gi|255764498|r 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLR 79 (300)
Q Consensus 1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~-~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~ 79 (300)
||..|||+|.||+.+|+.|++.|..|+...++ ++.+++..++..|+.++.++|++++|+++.+++||+||.|+..+|++
T Consensus 15 ~l~~Er~ls~nTl~sYrrDL~~f~~~L~~~~~~~l~~~~~~di~~yl~~l~~~g~s~~S~aR~lsalR~fy~fl~~E~~~ 94 (300)
T COG4974 15 YLWIERGLSANTLSSYRRDLEDFREWLEERGITDLADATEADIREYLTELAEQGLSATSIARALSALRSFYQFLIREGLR 94 (300)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 99997543264499999999999999876279884546899999999999857867224889999999999999977985
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf 22212222121222111223320246999986432001256102776543110001221001343334320000011110
Q gi|255764498|r 80 KDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTER 159 (300)
Q Consensus 80 ~~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~ 159 (300)
..||+..+..||.+++.|++++.+||..+++..+ .....++||+||+.++|.||||+||+++|+..||++..+
T Consensus 95 ~~dP~~~l~~PK~~~~LPk~Ls~~eve~Ll~~~~-------~~~p~~LRdrAmlELLYATGlRVSElv~L~l~dv~~~~~ 167 (300)
T COG4974 95 EDDPTRLLDSPKLPKRLPKFLSEEEVEALLEAPD-------EDTPLGLRDRAMLELLYATGLRVSELVGLTLSDVDLRQG 167 (300)
T ss_pred CCCCHHHHCCCCCCCCCCCCCCHHHHHHHHHCCC-------CCCCHHHHHHHHHHHHHHCCCHHHHHHCCCHHHHCCCCC
T ss_conf 3382444247877776776259999999981888-------898075799999999998277599985675765132468
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCH
Q ss_conf 001112221111100001247887532321001246777--520012333222221111111012344201466764259
Q gi|255764498|r 160 TMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGN--DLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISP 237 (300)
Q Consensus 160 ~i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~--~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~ 237 (300)
.+.|.|||+|+|.||+++.+..+|..|+.+.++...... .++||++.. |+++|++++|+.++.+...+||. +.++|
T Consensus 168 ~v~V~GKG~KeR~VP~g~~A~~~l~~Yl~~~R~~l~~~~~~~~~LF~n~~-g~~ltrq~~w~~lk~~a~~Agi~-~~isP 245 (300)
T COG4974 168 VVRVRGKGNKERLVPFGEEAVEALEKYLEEARPKLLKGKSSTDALFPNQR-GGGLTRQGFWKRLKDYAERAGID-KKISP 245 (300)
T ss_pred EEEEECCCCCEEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCC-CCCCCHHHHHHHHHHHHHHHCCC-CCCCC
T ss_conf 68997158825552133999999999999865988425788985645489-99877999999999999981888-78681
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHH
Q ss_conf 8858899999998588888999985589989989996459999999999828011
Q gi|255764498|r 238 HIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 (300)
Q Consensus 238 H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~ 292 (300)
|.|||+|||+|+++|+|+.+||++|||+|++|||+|+||+.+++++.+.++|||+
T Consensus 246 H~LRHsFATHLL~~GADlRvVQeLLGHadisTTQIYTHV~~e~L~~~~~~~HPra 300 (300)
T COG4974 246 HTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVTKERLRDLYAQHHPRA 300 (300)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 3657889999986785399999984866501557879988999999999738999
No 4
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=100.00 E-value=0 Score=444.51 Aligned_cols=287 Identities=31% Similarity=0.435 Sum_probs=258.6
Q ss_pred CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC-CHHHCCHHHHHHHHHHHHH------CCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 6466413899999999999999999754499-8688999999999999997------79984353221011233432100
Q gi|255764498|r 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQ------RKLVTSSQRRKISVIRQFYNFLC 74 (300)
Q Consensus 2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~-~~~~i~~~~i~~~~~~l~~------~~~s~~T~~~~~~~l~~~~~~~~ 74 (300)
|. |||+|+||+++|+.+|+.|..||...++ ++.+++..++..|..++.. ++++.+|+++++++|++||+|+.
T Consensus 34 L~-er~~S~~Ti~aY~~dL~~F~~fl~~~g~~~~~~vt~~~l~~y~~~L~~~r~~~g~~ls~~T~~r~LsalrsFf~~l~ 112 (361)
T PRK01287 34 LQ-ERNWSERTLKVQTHHTYHFILWCEERGLYYAADVTRPVLERYQRYLYQYRKTNGEPLSQGTQRTQLTPLRVWFKWLT 112 (361)
T ss_pred HH-HCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 99-83998999999999999999999984899937589999999999999865406887799999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHH
Q ss_conf 012222221222212122211122-3320246999986432001256102776543110001221001343334320000
Q gi|255764498|r 75 YEGLRKDNPSDTLELPKKNHILPK-TLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHT 153 (300)
Q Consensus 75 ~~~~~~~np~~~i~~~k~~~~~~~-~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~d 153 (300)
+.|++..||+..+..||.+++.|+ +++.+|+.++++.+. ...+.++||++|+.|||.||||+||+++|+|+|
T Consensus 113 ~~~~i~~nP~~~i~~PK~~k~lP~~~Ls~~Ev~~LL~~~~-------~~~~~g~RDrAil~LLy~tGLRvsEl~~L~~~D 185 (361)
T PRK01287 113 KQNLILYNPAADIELPKLEKRLPRYILSIDETEAILAAPD-------PTTLQGLRDRALLELLWSTGIRRSELARLDLYD 185 (361)
T ss_pred HCCCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHCCC-------CCCCHHHHHHHHHHHHHHHCCHHHHHHHCCCCC
T ss_conf 8799353758763277765557776799999999984745-------588065999999999999377798887166646
Q ss_pred HHHHHHCCCC-CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf 0111100011-1222111110000124788753232100124-6777520012333222221111111012344201466
Q gi|255764498|r 154 LNLTERTMII-QGKGNKERLVILSPSALHALQMYKKTCSSMK-MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQ 231 (300)
Q Consensus 154 i~~~~~~i~v-~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~-~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~ 231 (300)
||++.+.+.| .|||+|+|+|||++.+..+|.+|+...++.. ...+..+||++. .|++++.+++++.++++++.+||+
T Consensus 186 Id~~~~~i~v~~GKG~KeR~VPl~~~~~~~L~~Yl~~~r~~~~~~~~~~~lFvs~-~G~~ls~~~v~~~vk~~~~~agi~ 264 (361)
T PRK01287 186 VDGSRKTVTVRQGKGNKDRVVPLGERALVWLQRYLQQVRPQLIVNPDSGALFVAM-DGDGLQRNGITNLVGRYIRAAGIE 264 (361)
T ss_pred CCCCCCEEEEECCCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEECC-CCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 6788883887348887400202769999999999998617641278877521288-999587899999999999980899
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHCCCCC
Q ss_conf 7642598858899999998588888999985589989989996459999999999828011100112
Q gi|255764498|r 232 KKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKH 298 (300)
Q Consensus 232 ~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~~~~~~ 298 (300)
. .++||+|||||||+|+++|+|+.+||++|||+|++||++|+||+.++++++++++||++++..|.
T Consensus 265 k-~~~pH~LRHTfAT~lL~~GadL~~VQelLGHasi~TTqiYtHv~~~~l~~v~~~~HP~~~~~~~~ 330 (361)
T PRK01287 265 K-KGACHLFRHAMATQMLENGADLRWIQAMLGHASLETTQIYTQVSIRHLQAVHASTHPAEQMADEK 330 (361)
T ss_pred C-CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC
T ss_conf 9-99821059999999998699999999986899778999998479999999999819988898633
No 5
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=100.00 E-value=0 Score=442.04 Aligned_cols=283 Identities=43% Similarity=0.670 Sum_probs=261.2
Q ss_pred CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 64664138999999999999999997544998688999999999999997799843532210112334321000122222
Q gi|255764498|r 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKD 81 (300)
Q Consensus 2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~ 81 (300)
|..|||+|++|+++|+++++.|..|++..++++.+++..++..|+.++.+++++++|+|+++++|++||+||+..|+++.
T Consensus 13 L~~erg~S~~Ti~~Y~~~l~~f~~~l~~~~~~~~~it~~~i~~y~~~L~~~~~s~~Tin~~l~~lr~~~~~a~~~~~i~~ 92 (296)
T PRK00283 13 LWVERGLAENTLSSYRRDLELFAEWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSALRRFFQFLLREGLRED 92 (296)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99987907999999999999999999875999477999999999999987799999999999999974799987074334
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCC
Q ss_conf 21222212122211122332024699998643200125610277654311000122100134333432000001111000
Q gi|255764498|r 82 NPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTM 161 (300)
Q Consensus 82 np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i 161 (300)
||+..+..|+.+++.+++++++|+.++++++.. ......||++|+.+++.||||+||+++|+|+||+++++.+
T Consensus 93 np~~~i~~~k~~~~~~~~lt~eei~~ll~~~~~-------~~~~~~Rd~ail~ll~~tGlR~~El~~L~~~di~~~~~~i 165 (296)
T PRK00283 93 DPTALLDSPKLPRRLPKTLSEAQVEALLDAPDI-------DTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQGVV 165 (296)
T ss_pred CHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCC-------CCHHHHHHHHHHHHHHHHCCCHHHHCCCCHHHCCCCCCCE
T ss_conf 878636677888889741437899998732377-------8657689999999999838761202178599923577955
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf 111222111110000124788753232100124-6777520012333222221111111012344201466764259885
Q gi|255764498|r 162 IIQGKGNKERLVILSPSALHALQMYKKTCSSMK-MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240 (300)
Q Consensus 162 ~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~-~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~l 240 (300)
.|.+||+|+|.||+++.+.+.|.+|+...++.. ...+.++||++. .|++++.+++++.++++++.+||..+++|||+|
T Consensus 166 ~v~~Kg~K~R~vpl~~~~~~~l~~yl~~~r~~~~~~~~~~~lF~~~-~g~~l~~~~~~~~~~~~~~~agi~~~~~tpH~l 244 (296)
T PRK00283 166 RVTGKGNKERLVPLGEEAVYAIERYLERGRPALLGGRSSDALFPSA-RGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHVL 244 (296)
T ss_pred EEECCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECC-CCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 7717898036997088999999999998657751489997475428-898467999999999999980899998899878
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHH
Q ss_conf 8899999998588888999985589989989996459999999999828011
Q gi|255764498|r 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 (300)
Q Consensus 241 Rht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~ 292 (300)
||||||+|+++|+|+..||++|||+|++||++|+|++.+++++++++|||||
T Consensus 245 RHt~at~ll~~G~~l~~i~~~LGHssi~TT~~Y~h~~~~~l~~~~~~~~p~~ 296 (296)
T PRK00283 245 RHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 296 (296)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf 7999999998798999999882899889999988689999999999868499
No 6
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=100.00 E-value=0 Score=432.19 Aligned_cols=278 Identities=40% Similarity=0.607 Sum_probs=254.6
Q ss_pred CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC-CHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 6466413899999999999999999754499-868899999999999999779984353221011233432100012222
Q gi|255764498|r 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRK 80 (300)
Q Consensus 2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~-~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~ 80 (300)
|..|||+||+|+++|+.+++.|..|+...+. ++.+++..++..|+.++.++|++++|+++++++|++||+||+..|++.
T Consensus 17 l~~~r~lS~~Ti~~Y~~~l~~f~~~~~~~~~~~l~~i~~~~i~~~~~~l~~~g~s~~Ti~~~l~~lr~~~~~a~~~~~i~ 96 (295)
T PRK00236 17 LRVERGLSPHTLRAYRRDLRAFLAFLEEVGLADLQQLDLADLRAFLARLRRQGLSARSLARRLSALRSFYRWLVRRGLLK 96 (295)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 99885907999999999999999999875999947699999999999998769999999999999999999887628614
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHC
Q ss_conf 22122221212221112233202469999864320012561027765431100012210013433343200000111100
Q gi|255764498|r 81 DNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERT 160 (300)
Q Consensus 81 ~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~ 160 (300)
.||+..++.|+..+..|++++.+|+.++++.... .....||++|+.+++.||||+||+++|+|+|||++++.
T Consensus 97 ~nP~~~i~~~k~~~~~~~~lt~~e~~~ll~~~~~--------~~~~~Rd~~i~~ll~~tGlR~~E~~~L~~~did~~~~~ 168 (295)
T PRK00236 97 ANPAAGLRAPKAPKRLPKPLDVDQAKRLLDADAD--------DPLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGT 168 (295)
T ss_pred CCHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCC--------CCHHHHHHHHHHHHHHHCCCHHHHCCCCHHHCCCCCCE
T ss_conf 5778751277766568850018999999971325--------80658999999999981978331205639772777898
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf 01112221111100001247887532321001246777520012333222221111111012344201466764259885
Q gi|255764498|r 161 MIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240 (300)
Q Consensus 161 i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~l 240 (300)
+.|.+||+|+|.||+++.+.++|.+|++.++. ..++.+||++. .|++++++++++.|+++++.+|++. +++||+|
T Consensus 169 i~i~~Kg~K~R~Vpl~~~~~~~L~~yl~~~~~---~~~~~~lF~~~-~g~~l~~~~i~~~~~~~~~~~gi~~-~~~~H~l 243 (295)
T PRK00236 169 VRVLGKGNKERTVPVGSAALEALEAYLARPLA---EEDDDALFLGA-RGGRLSPRVVQRRVKKLRKKAGLPE-HITPHKL 243 (295)
T ss_pred EEEECCCCEEEEEECCHHHHHHHHHHHHHCCC---CCCCCEEEECC-CCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCCC
T ss_conf 98817898168986599999999999996776---78998377568-9995878899999999999859999-9989978
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHH
Q ss_conf 8899999998588888999985589989989996459999999999828011
Q gi|255764498|r 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 (300)
Q Consensus 241 Rht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~ 292 (300)
||||||.|+++|+|+..||++|||+|++||++|+|++.++++++++++||||
T Consensus 244 RHt~At~l~~~G~~l~~vq~~LGHssi~tT~~Y~h~~~~~l~~~~~~~~p~~ 295 (295)
T PRK00236 244 RHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPRA 295 (295)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC
T ss_conf 8999999998799999999881899889999988689999999999878399
No 7
>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=404.05 Aligned_cols=276 Identities=41% Similarity=0.614 Sum_probs=250.5
Q ss_pred CCHHHHHCCHHHHHHHHHHHHHHHHHHHHCC-CCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9646641389999999999999999975449-986889999999999999977998435322101123343210001222
Q gi|255764498|r 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKE-ISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLR 79 (300)
Q Consensus 1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~-~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~ 79 (300)
+|..+||+|++|+++|..+++.|..||...+ ..+.+++..++.+|+.++.+++++++|+++++++|++||+||++.|++
T Consensus 7 ~l~~~r~lS~~T~~~Y~~~l~~f~~~~~~~~~~~~~~i~~~~i~~~~~~L~~~~~s~~Ti~~~~~~l~~~~~~~~~~~~i 86 (284)
T cd00798 7 YLAVERGLSENTLAAYRRDLERFLEFLEERGILFPADVTPDDIRRFLAELKDQGLSARSIARKLSALRSFFKFLLREGLI 86 (284)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 99998590799999999999999999998299994879999999999999876999999999999999999999865876
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf 22212222121222111223320246999986432001256102776543110001221001343334320000011110
Q gi|255764498|r 80 KDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTER 159 (300)
Q Consensus 80 ~~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~ 159 (300)
..||+..+..|+..+..+++++.+|+.++++++.. ......||++|+.++++||||++|+++|+|+|||++++
T Consensus 87 ~~np~~~i~~~k~~~~~~~~l~~~ei~~ll~~~~~-------~~~~~~Rd~~i~~ll~~tGlR~~E~~~L~~~did~~~~ 159 (284)
T cd00798 87 LANPAELIEPPKLKRSLPKVLTIEEVERLLAAPDG-------DTPLGLRDRALLELLYSTGLRVSELVGLKLSDVDLSRG 159 (284)
T ss_pred CCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCC-------CCHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCC
T ss_conf 56823202578868778886799998999986323-------77677999999999999679924461696999476677
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHH
Q ss_conf 00111222111110000124788753232100124-67775200123332222211111110123442014667642598
Q gi|255764498|r 160 TMIIQGKGNKERLVILSPSALHALQMYKKTCSSMK-MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPH 238 (300)
Q Consensus 160 ~i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~-~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H 238 (300)
++.|.+||+|+|.||+++.+.++|.+|++..++.. ...+..++|++. .|++++++++++.++++++.+|++. +++||
T Consensus 160 ~i~v~~K~~k~r~vpl~~~~~~~l~~~~~~~~~~~~~~~~~~~lF~~~-~g~~~~~~~~~~~~~~~~~~~g~~~-~~~~H 237 (284)
T cd00798 160 LIRVRGKGNKERIVPLGETAVEALQRYLEVRRPLLLKVGDSDALFLNQ-RGKRLSRRGVWKILKEYARRAGIEK-KISPH 237 (284)
T ss_pred EEEEECCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCEEECC-CCCCCCHHHHHHHHHHHHHHHCCCC-CCCCH
T ss_conf 799964799447886499999999999998334203678776332236-8982657999999999999909999-99914
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf 85889999999858888899998558998998999645999999999
Q gi|255764498|r 239 IIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLV 285 (300)
Q Consensus 239 ~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~ 285 (300)
+|||||||.|+++|+|+..||++|||+|++||++|+|++.++++|++
T Consensus 238 ~lRHt~at~l~~~g~~~~~i~~~lGH~s~~tT~~Y~h~~~~~l~e~~ 284 (284)
T cd00798 238 TLRHSFATHLLENGADLRAVQELLGHASLATTQIYTHVSFEHLKEVY 284 (284)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf 65999999999878999999988079879999987777999998519
No 8
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=392.45 Aligned_cols=283 Identities=34% Similarity=0.535 Sum_probs=260.4
Q ss_pred CCHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC-CHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 96466413899999999999999999754499-86889999999999999977998435322101123343210001222
Q gi|255764498|r 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLR 79 (300)
Q Consensus 1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~-~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~ 79 (300)
+|..||++|+.|+.+|++++.....+....++ ++..+++.++..|+.....+|++++++.+.+|++++||.|++++|.+
T Consensus 16 ~L~~Er~lS~hTl~~Y~rqL~~l~~~~~q~~~~~w~~ld~~~vr~~~a~~~~~Gl~a~SlA~rLSa~R~f~~wLv~~g~l 95 (299)
T COG4973 16 YLRVERQLSPHTLANYRRQLEALIALLAQMGLGSWQQLDPADVRAFVARSHRRGLSARSLARRLSALRSFYDWLVKQGEL 95 (299)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 99986146888899999999999999997276566656999999999998318855778999999999999999872764
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf 22212222121222111223320246999986432001256102776543110001221001343334320000011110
Q gi|255764498|r 80 KDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTER 159 (300)
Q Consensus 80 ~~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~ 159 (300)
..||+.+++.||.++..|+.++.||+.++++ .+ ......+||++|+++||.+|||.||+++|.+.|+|++.+
T Consensus 96 ~~nPa~GvsaPK~~r~LPk~ld~d~~~~ll~---~d-----~~dPlavRDrAllElmY~sGLRLSELvgLd~~~vdl~~g 167 (299)
T COG4973 96 KANPAKGVSAPKQPRHLPKNLDVDEANRLLD---ID-----GDDPLAVRDRALLELMYGSGLRLSELVGLDLKHVDLDEG 167 (299)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHC---CC-----CCCCHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCC
T ss_conf 6686456889887443777689999999966---78-----999334789999999984370089884788444545542
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHH
Q ss_conf 00111222111110000124788753232100124677752001233322222111111101234420146676425988
Q gi|255764498|r 160 TMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHI 239 (300)
Q Consensus 160 ~i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~ 239 (300)
.+.|.|||+|+|.||+.....++|..|+..+...... +.-+|++ ..|+++|.+.+++.++++..+.|+. .+++||.
T Consensus 168 eV~V~GKGnKeR~vP~g~~A~~al~~WL~lR~~~a~~--d~AlF~s-~~G~Ris~R~iQkR~~~wgikqg~~-~HvhPH~ 243 (299)
T COG4973 168 EVRVMGKGNKERRVPVGRKAVEALEHWLALRGLFASE--DDALFLS-RLGKRISARAIQKRLAQWGIKQGLN-SHVHPHK 243 (299)
T ss_pred EEEEECCCCCEEECCCHHHHHHHHHHHHHHHHCCCCC--CCEEEEC-CCCCCCCHHHHHHHHHHHHHHCCCC-CCCCHHH
T ss_conf 5899627873465352177999999998655103798--7605310-3688164889999999999860322-1387687
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHCC
Q ss_conf 58899999998588888999985589989989996459999999999828011100
Q gi|255764498|r 240 IRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKE 295 (300)
Q Consensus 240 lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~~~ 295 (300)
|||+|||+|+++..|+..||++|||+|++||++|+|++.+.+.+++|.+|||||++
T Consensus 244 LRHSFAtHmLesSgDLRaVQELLGHanlsTTQIYThLDFQHLA~vYD~AHPRAkrk 299 (299)
T COG4973 244 LRHSFATHMLESSGDLRAVQELLGHANLSTTQIYTHLDFQHLASVYDAAHPRAKRK 299 (299)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHHHCCCCCCC
T ss_conf 77788999987035489999985646512444323236899999986317411269
No 9
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=100.00 E-value=0 Score=389.87 Aligned_cols=281 Identities=25% Similarity=0.380 Sum_probs=234.7
Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHCCC------------CHHHCCHHHHHHHHHHHHH----------CCCCHHHHHHH
Q ss_conf 6413899999999999999999754499------------8688999999999999997----------79984353221
Q gi|255764498|r 5 ERASSINTLSAYKRDLKEMQNFLNNKEI------------SLSAASTNHLISYLNHLSQ----------RKLVTSSQRRK 62 (300)
Q Consensus 5 ~R~~S~~T~~~Y~~~l~~f~~~~~~~~~------------~~~~i~~~~i~~~~~~l~~----------~~~s~~T~~~~ 62 (300)
++++||+|+.+|.++++.|..|+...++ ++.+++..++..|+.+|.. ++++++|+|++
T Consensus 30 ~~~~Sp~Ti~~Y~~DL~~F~~fL~~~~~~~~~~~~~i~~~~l~~l~~~di~~y~~~L~~~~~~~~~~~~~~~s~~tinRk 109 (360)
T PRK05084 30 ATPYSPTTLYEYLTEYRRFFNWLIDEGLTVATKIKDIPLSTLENLTKKDVELFILYLRERPSLNGHLTGEGVSQTTINRT 109 (360)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHH
T ss_conf 05989899999999999999999864987555633277899975669999999999985222343212257678899999
Q ss_pred HHHHHHHHHHHCCCC-------CCCCCCCCCCCCCCCCCC--------CCCCCCCHHHHHHHHHHHHHCCCCCCHH----
Q ss_conf 011233432100012-------222221222212122211--------1223320246999986432001256102----
Q gi|255764498|r 63 ISVIRQFYNFLCYEG-------LRKDNPSDTLELPKKNHI--------LPKTLHKDTIANLLEQAKIEAENPAPGQ---- 123 (300)
Q Consensus 63 ~~~l~~~~~~~~~~~-------~~~~np~~~i~~~k~~~~--------~~~~ls~~e~~~ll~~~~~~~~~~~~~~---- 123 (300)
+++|++||+|+...+ ++..||+..+..++.... .++.++.+|+..+++.+...........
T Consensus 110 lsaLrsFfkyL~~~~~~~~~~~y~~~n~~~~i~~~k~~~~~~~r~~~~~~~~l~~~e~~~ll~~i~~~~~~~l~~~~~~~ 189 (360)
T PRK05084 110 LSALKSLFKYLTEETENEDGEPYFYRNVMKKISLKKKKETLAARAENLKQKLFLGDETVEFLDFIDNEYEQKLSNRALSS 189 (360)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHCCHHHHCCCCCCCCCCCCCCHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999985202232213311526525777653212231000012005567899999765244341202555443
Q ss_pred --HHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCC-CCCCCCC
Q ss_conf --7765431100012210013433343200000111100011122211111000012478875323210012-4677752
Q gi|255764498|r 124 --WKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSM-KMTGNDL 200 (300)
Q Consensus 124 --~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~-~~~~~~~ 200 (300)
....||+||+.|+|.||||+||+++|+|+|||++++.|.|.|||+|+|.||+++.+.+.|.+|++.+... ....++.
T Consensus 190 ~~~~~~RD~aIi~ll~~tGlRvsEl~~L~~~DId~~~~~i~V~~Kg~K~r~vpi~~~~~~~l~~yl~~r~~~~~~~~~~~ 269 (360)
T PRK05084 190 FKKNKERDLAIIALLLGSGIRVSELVNLDLKDLNLKQMTIDVTRKGGKRDSVPIAPFALPYLEEYLKIRAQRYKAEKNDT 269 (360)
T ss_pred HCCCCHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 01236799999999998587999997697998587899799984798446887789999999999997087435778888
Q ss_pred CCCCCCCC--CCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCH
Q ss_conf 00123332--2222111111101234420146676425988588999999985888889999855899899899964599
Q gi|255764498|r 201 WLFPSSTK--TGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLP 278 (300)
Q Consensus 201 ~lf~~~~~--~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~ 278 (300)
++|.+..+ +.+++.+++.+.+++++..+|+ ++|||.|||||||+|+++|+|+..||++|||+|++||++|+|++.
T Consensus 270 ~lF~~~~~~~~~rls~~~i~~~v~k~~~~~~~---~itpH~LRHtfAT~Ll~~G~dl~~vq~lLGH~si~TT~iYthv~~ 346 (360)
T PRK05084 270 ALFLTKYRGKPNRISASAIEKMVAKYSEAFGV---RVTPHKLRHTLATRLYDATKDQVLVADQLGHTSTQVTDLYTHIVN 346 (360)
T ss_pred CEEEECCCCCCCCCCHHHHHHHHHHHHHHCCC---CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCH
T ss_conf 15764689988822499999999999986799---978413299999999987999999999858998799999886899
Q ss_pred HHHHHHHHHH
Q ss_conf 9999999982
Q gi|255764498|r 279 DKLQKLVQDY 288 (300)
Q Consensus 279 ~~~~~~~~~~ 288 (300)
+.+++|+++.
T Consensus 347 ~~~r~a~~~l 356 (360)
T PRK05084 347 DEQKDALDKL 356 (360)
T ss_pred HHHHHHHHHH
T ss_conf 9999999863
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=357.21 Aligned_cols=256 Identities=23% Similarity=0.338 Sum_probs=216.9
Q ss_pred CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 64664138999999999999999997544998688999999999999997799843532210112334321000122222
Q gi|255764498|r 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKD 81 (300)
Q Consensus 2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~ 81 (300)
| .|+|+|++|+++|.+++..| |+. ..+++..++.+|..++.+ +++++|+|+.+++|++||+|+..+++
T Consensus 5 L-~e~g~S~~Ti~sY~~dl~~f--f~~-----~~~i~~~~i~~y~~~L~~-~~~~~Tin~~lsalr~F~~fl~~~~~--- 72 (263)
T cd01196 5 L-YKNNLSKNTVSSYLRTVVQY--FLN-----GKELTKPNLLEYKGYLQE-NFKAQTVNLRLQGINKYLEFIGWHDL--- 72 (263)
T ss_pred H-HHCCCCHHHHHHHHHHHHHH--HCC-----CCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCC---
T ss_conf 9-67697899999999999999--715-----588999999999999996-89899999999999999999655478---
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCC
Q ss_conf 21222212122211122332024699998643200125610277654311000122100134333432000001111000
Q gi|255764498|r 82 NPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTM 161 (300)
Q Consensus 82 np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i 161 (300)
+...++. +.....|..++++|+..+++.+... ...|+++|+.+||.||||+||+++|+++||+++ .+
T Consensus 73 -~~k~~k~-~~~~~l~~~l~~~e~~~l~~~~~~~---------~~~r~~~ii~lL~~tGlRvsEl~~L~~~di~~~--~~ 139 (263)
T cd01196 73 -KLKFVKV-QQKAFLENVISDADYKFLKTALKAD---------GNEEWYFVVWFLAATGARVSELIHIKVEHVQTG--YA 139 (263)
T ss_pred -CCCCCCC-CCCCCCCCCCCHHHHHHHHHHHCCC---------CCHHHHHHHHHHHHHCCHHHHHHCCCHHHHCCC--CE
T ss_conf -6556788-8889999989999999999763136---------677699999999984999999983689882668--64
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHH
Q ss_conf 11122211111000012478875323210012467775200123332222211111110123442014667642598858
Q gi|255764498|r 162 IIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIR 241 (300)
Q Consensus 162 ~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lR 241 (300)
.|.|||+|+|.|||++.+...+.+|++.+. .++.++|++. .|++++.+++++.++++++.+|++.+.++||+||
T Consensus 140 ~i~~KG~K~R~v~i~~~~~~~l~~y~~~~~-----~~~~~lF~~~-~g~~l~~~~i~~~~k~~~~~agi~~~~~~PH~lR 213 (263)
T cd01196 140 DIYSKGGKIRRLYIPKNLRVEALKWLKELN-----LDSGYIFLNR-FGKPITARGIAQQLKNYAAKYKMNPRVVYPHSFR 213 (263)
T ss_pred EEEECCCCEEEEEECHHHHHHHHHHHHHCC-----CCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHH
T ss_conf 999559937887307999999999999728-----8657716699-9498889999999999999859998778872269
Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf 89999999858888899998558998998999645999999999982
Q gi|255764498|r 242 HAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDY 288 (300)
Q Consensus 242 ht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~ 288 (300)
|||||+|+++|+|+..||++|||+|++||++|+|++.+.+++++|+-
T Consensus 214 HtfAt~ll~~g~dl~~vq~lLGH~si~TT~iY~~~~~~~~k~~~~k~ 260 (263)
T cd01196 214 HLFAKNFLAKYNDLALLADLMGHESIETTRIYLRKTATEQQRIVDKI 260 (263)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHH
T ss_conf 99999999869999999999589987899998807999999999987
No 11
>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=353.35 Aligned_cols=260 Identities=24% Similarity=0.345 Sum_probs=220.7
Q ss_pred HHHCCHHHHHHHHHHHHHHHHHHHH----CCCCHHHCCHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 6413899999999999999999754----499868899999999999999-77998435322101123343210001222
Q gi|255764498|r 5 ERASSINTLSAYKRDLKEMQNFLNN----KEISLSAASTNHLISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYEGLR 79 (300)
Q Consensus 5 ~R~~S~~T~~~Y~~~l~~f~~~~~~----~~~~~~~i~~~~i~~~~~~l~-~~~~s~~T~~~~~~~l~~~~~~~~~~~~~ 79 (300)
+|++|++|+++|..+++.|..|+.. .++++.+++..++.+|..+|. +++++++|+++++++|++||+||+++|++
T Consensus 30 ~k~~S~~Ti~~Y~~~l~~f~~Fl~~~~~~~di~~~~i~~~~i~~f~~~L~~~k~~s~~Ti~~~l~~lr~~~~~a~~~~~i 109 (299)
T cd01185 30 GKDKAQSTWKRYRTHLKNLREFIECTYKEIDIALLELTREFILEFKLFLRKEKKLSRNTAVHYLSWLKKLLKIAYRDKGL 109 (299)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 77567999999999999999999982887778878847999999999998757988889999999999999999988992
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf 22212222121222111223320246999986432001256102776543110001221001343334320000011110
Q gi|255764498|r 80 KDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTER 159 (300)
Q Consensus 80 ~~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~ 159 (300)
..||+..+..|+.++..+++|+.+|+.++++.... ......+|+.++| ++.||||+||+++|+|+||++++.
T Consensus 110 ~~nP~~~i~~~k~~~~~~~~Lt~eEi~~ll~~~~~------~~~~~~~r~~~l~--~~~TGlR~~El~~L~~~dI~~~~~ 181 (299)
T cd01185 110 RDNPFAKFKCKKEEETDREYLTPDELQKLAETPCK------DPRLELVRRAFLF--SCFTGLRYSDIKKLTWEEIVEDSD 181 (299)
T ss_pred CCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCC------CCCHHHHHHHHHH--HHHHCCCHHHHHHCCHHHHHHCCC
T ss_conf 11929656178889989999999999999827147------8746999999999--988098899998396998213369
Q ss_pred C---CCC-CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCC
Q ss_conf 0---011-122211111000012478875323210012467775200123332222211111110123442014667642
Q gi|255764498|r 160 T---MII-QGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNI 235 (300)
Q Consensus 160 ~---i~v-~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~ 235 (300)
. +.+ .+|+++.+.||+++.+.++|..|.. .++.++|+.. +...+++.++++++.+|++. ++
T Consensus 182 ~~~~i~~~~~Kt~~~~~ipl~~~~~~~l~~~~~--------~~~~~lF~~~------~~~~~~~~lk~~~~~agi~~-~i 246 (299)
T cd01185 182 GEKWIRKRRQKTKVEVYIPLLDEALQILGKYPD--------EKEGLVFPLL------KNSNMNKPLKEWAKLAGIKK-HI 246 (299)
T ss_pred CEEEEEECCCCCCEEEEEECHHHHHHHHHHHHC--------CCCCCCCCCC------CHHHHHHHHHHHHHHHCCCC-CC
T ss_conf 648998516744224320015999999998522--------6754406888------75689999999999828899-99
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHH
Q ss_conf 5988588999999985888889999855899899899964599999999998
Q gi|255764498|r 236 SPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQD 287 (300)
Q Consensus 236 t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~ 287 (300)
|||+|||||||+|+++|+|+..||++|||+|++||++|+|++++.+++++++
T Consensus 247 t~H~lRHTfAt~ll~~G~~l~~vq~~LGHssi~tT~~Y~hv~~e~~~e~~~k 298 (299)
T cd01185 247 TFHCARHTFATLQLLSGGPIETVSKMLGHTNIKTTQVYARVTDEKKSEDMNK 298 (299)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 8114099999999987989999998818998899999987798899999963
No 12
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed
Probab=100.00 E-value=0 Score=351.64 Aligned_cols=241 Identities=22% Similarity=0.304 Sum_probs=201.8
Q ss_pred CCHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 96466413899999999999999999754499868899999999999999779984353221011233432100012222
Q gi|255764498|r 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRK 80 (300)
Q Consensus 1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~ 80 (300)
+|.+|||+|+||+++|.+|++.|..|+++ .++..++..|..++. +++++|+++.+++|++||+|+.++|+++
T Consensus 7 ~l~~ek~lS~nTi~aY~~DL~~F~~fl~~------~i~~~~i~~y~~~L~--~~~~st~~Rklsslr~F~~fL~~~~~i~ 78 (247)
T PRK02436 7 PFLASKALSVNSQKSYRYDLQQFCQLVGE------RVNQTSLKLYQNSLA--NLKLSAQKRKLSAVNQFLYFLYQKKYLD 78 (247)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHH------HCCHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 99998691499999999999999999873------589999999999987--1679999999999999999999768766
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHC
Q ss_conf 22122221212221112233202469999864320012561027765431100012210013433343200000111100
Q gi|255764498|r 81 DNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERT 160 (300)
Q Consensus 81 ~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~ 160 (300)
..+ .....|+.++..+...+.+++..+++.. ...|+++++.++|.||||+||+++|+|+|||++.+.
T Consensus 79 ~~~-~~~~~~k~~~~~~~~~~~~~~~~~~~~~------------~~~~~r~i~~ll~~tGlRvSEl~~L~~~Did~~~~~ 145 (247)
T PRK02436 79 SFF-KLKETAKVMRSEKQQPEILDLSSFYQET------------PFPEGQLIALLILELGLTPSEIAGLKVADIDLDFQV 145 (247)
T ss_pred CCC-CHHCCCCCCCCCCCCCHHHHHHHHHCCC------------CCHHHHHHHHHHHHHCCHHHHHHCCCHHHHCCCCCE
T ss_conf 752-0420588988765413186799885646------------785689999999996947999978919991988787
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf 01112221111100001247887532321001246777520012333222221111111012344201466764259885
Q gi|255764498|r 161 MIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240 (300)
Q Consensus 161 i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~l 240 (300)
+.| +||+++|.|||++.+.++|+.|++. ++.|+|. .+|++++++++++.+++++..+|++ ++|||.|
T Consensus 146 i~v-~kg~k~R~Vpl~~~~~~~l~~y~~~--------~~~~l~~--~~g~~lsr~~~~~~lk~~~~~~g~~--~vtPH~L 212 (247)
T PRK02436 146 LTI-EKAGGKRVLPLPEALLPFLEQILNG--------KEVYLFE--HKGKPYSRQWFFNQLKSFVNSIGYP--GLTAQKL 212 (247)
T ss_pred EEE-ECCCEEEEEECCHHHHHHHHHHHHC--------CCCEEEC--CCCCCCCHHHHHHHHHHHHHHCCCC--CCCCHHH
T ss_conf 999-0799078754679999999998715--------8650116--8999667999999999999974999--9987100
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 88999999985888889999855899899899964
Q gi|255764498|r 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTH 275 (300)
Q Consensus 241 Rht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~ 275 (300)
||||||+|+++|+|+..||++|||+|++||++|+.
T Consensus 213 RHsFAthlL~~Gadlr~vQeLLGH~sisTTqiY~k 247 (247)
T PRK02436 213 REQFILKQKEAGKSIYELARLLGLKTPVTLEKYYK 247 (247)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCC
T ss_conf 99999999987999999998808998788553069
No 13
>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=348.76 Aligned_cols=249 Identities=26% Similarity=0.396 Sum_probs=213.1
Q ss_pred CCCHHHCCHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf 99868899999999999999-7799843532210112334321000122222---2122221212221112233202469
Q gi|255764498|r 31 EISLSAASTNHLISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYEGLRKD---NPSDTLELPKKNHILPKTLHKDTIA 106 (300)
Q Consensus 31 ~~~~~~i~~~~i~~~~~~l~-~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~---np~~~i~~~k~~~~~~~~ls~~e~~ 106 (300)
.+++.+++.++|.+|+.+|. ++|++++|+|+++++|++||+||..++.... +|+..++.++..+..+.+++.+|+.
T Consensus 2 ~l~l~dI~~~~i~~y~~~L~~~rg~s~~Tin~~l~~L~~f~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~l~~eei~ 81 (260)
T cd01190 2 RLEIEDIDAPLILAFLDHLENDRGNSIRTRNARLAALHSFFRYAAREVPEHLPTIQRVLAIPMKRFKRPLVTYLTREEVQ 81 (260)
T ss_pred CCCHHHCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf 88758799999999999999846999999999999999999999980840145537101488788899999889999999
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 99986432001256102776543110001221001343334320000011110-00111222111110000124788753
Q gi|255764498|r 107 NLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTER-TMIIQGKGNKERLVILSPSALHALQM 185 (300)
Q Consensus 107 ~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~-~i~v~~K~~k~R~ipi~~~~~~~l~~ 185 (300)
++++.... ..+.+.||++++.++++||||+||+++|+|+|||++++ .+.+.+||+++|.|||++.+.+.|.+
T Consensus 82 ~ll~~~~~-------~~~~~~rd~~i~~ll~~tGlR~sEl~~L~~~did~~~~~~~~~~~K~~k~r~vpi~~~~~~~L~~ 154 (260)
T cd01190 82 ALLAAPDR-------RTWSGRRDRAMLLFLYNTGARVSEATGLKVDDLQLDPPAQVRLIGKGRKERTVPLWRSTAAALRA 154 (260)
T ss_pred HHHHCCCC-------CCCCCHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEEECCHHHHHHHHH
T ss_conf 99818665-------67303689999999999575589786286976178998089996899804135468999999999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCC-----CCCCCCHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf 232100124677752001233322222111111101234420146-----676425988588999999985888889999
Q gi|255764498|r 186 YKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGI-----QKKNISPHIIRHAFASHLLEGGADLRTIQI 260 (300)
Q Consensus 186 y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi-----~~~~~t~H~lRht~at~l~~~G~~~~~v~~ 260 (300)
|++.+... ..+.++|++. .|.+++..++...++++...+|. ..++++||+|||||||+|+++|+|+..||+
T Consensus 155 ~~~~~~~~---~~~~~lF~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRHt~At~ll~~G~~l~~vq~ 230 (260)
T cd01190 155 WLRERGLH---AEDEPLFVNR-RGEPMTRFGVTYLLRKHAAKAAATAPTLATKRISPHVLRHTTAMHLLQSGVDIVVIAL 230 (260)
T ss_pred HHHHCCCC---CCCCEEEECC-CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf 99975446---8766151278-9994786889999999999972416432467767671389999999987999999999
Q ss_pred HHCCCCHHHHHHHHHCCHHHHHHHHHHHCC
Q ss_conf 855899899899964599999999998280
Q gi|255764498|r 261 LLGHTDISTTQIYTHLLPDKLQKLVQDYHP 290 (300)
Q Consensus 261 ~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p 290 (300)
+|||+|++||++|+|++.+.++++++++||
T Consensus 231 ~LGH~~i~tT~~Y~hv~~~~~r~a~~k~~p 260 (260)
T cd01190 231 WLGHASLETTNIYAEADLEMKRRALAKATP 260 (260)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf 868998899999984799999999998691
No 14
>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=345.96 Aligned_cols=270 Identities=23% Similarity=0.272 Sum_probs=223.7
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 13899999999999999999754499868899999999999999779984353221011233432100012222221222
Q gi|255764498|r 7 ASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDT 86 (300)
Q Consensus 7 ~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~~~ 86 (300)
|+|.+| |.++|+.|..||+.++. ..++.+.+..|+.. ..+.+++|+++.+++|++||+|+...|++..||...
T Consensus 16 G~~~~t---~~~~L~~F~~fl~~~~~--~~~~~~~~~~w~~~--~~~~s~~t~~~rls~lr~F~~~l~~~g~~~~~P~~~ 88 (299)
T cd01187 16 GYKYRT---PARLLRDFVRFLERHGA--GFITTDLALRWAAS--PPSAQPATWAGRLGVVRRFARHRRRADPRTEVPPAD 88 (299)
T ss_pred CCCHHH---HHHHHHHHHHHHHHCCC--CCCCHHHHHHHHHH--CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf 998156---89999999999986799--88899999999987--799988999999999999999999869956690765
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC-C
Q ss_conf 212122211122332024699998643200125610277654311000122100134333432000001111000111-2
Q gi|255764498|r 87 LELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ-G 165 (300)
Q Consensus 87 i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~-~ 165 (300)
+..++..+..|.+++++|+.++++++.... ........++++||.|+|.||||+||+++|+++|||++++.+.|. |
T Consensus 89 ~~~~k~~~~~P~~lt~~Ei~~Ll~a~~~~~---~~~~~~~~~~~~l~~Lly~tGlR~sEl~~L~~~Dvd~~~~~i~v~~g 165 (299)
T cd01187 89 LFPRRPRRPTPYIYTDEEIQRLLAAALQLP---PTSGLRPWTYRTLFGLLAVTGLRLGEALRLRLSDVDLDSGILTVRDS 165 (299)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCEEEEECC
T ss_conf 457899999999999999999984110169---96105768999999999995888999803343305676784765418
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCHHHHHHHCCCC-CCCCCHHHHH
Q ss_conf 2211111000012478875323210012467775200123332222211111---11012344201466-7642598858
Q gi|255764498|r 166 KGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVF---ARDLKALAARAGIQ-KKNISPHIIR 241 (300)
Q Consensus 166 K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~---~~~~~~~~~~~gi~-~~~~t~H~lR 241 (300)
||+|+|.|||++.+.++|.+|++.++......++.++|++.. |++++.... ...++.+...++.. ....+||+||
T Consensus 166 Kg~K~R~Vpl~~~~~~~L~~yl~~r~~~~~~~~~~~lF~~~~-g~~l~~~~~~~~~~~~r~~~~~~~~~~~~~~~pH~LR 244 (299)
T cd01187 166 KFGKSRLVPLHASTRAALRDYLARRDRLLPAPDSSAFFVSSR-GGRLSYGGHRVFYALSREIGLRGWAQRGRGPRLHDLR 244 (299)
T ss_pred CCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCEEEECCC-CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 899707985669999999999998476426898986745899-8978777899999999999986066668999976571
Q ss_pred HHHHHHHH----HCCCCHH----HHHHHHCCCCHHHHHHHHHCCHHHHHHHHHH
Q ss_conf 89999999----8588888----9999855899899899964599999999998
Q gi|255764498|r 242 HAFASHLL----EGGADLR----TIQILLGHTDISTTQIYTHLLPDKLQKLVQD 287 (300)
Q Consensus 242 ht~at~l~----~~G~~~~----~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~ 287 (300)
|||||+++ ++|+|+. .||++|||+|++||++|+|+++|.+++++++
T Consensus 245 HtfAt~~l~~~~~~G~di~~~L~~lq~~LGH~si~tT~~Y~h~~~e~l~~a~~r 298 (299)
T cd01187 245 HRFAVTRLTRWYRAGADVERKLPVLATYLGHANITDTYWYLHASPELMELAARR 298 (299)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHH
T ss_conf 389999999998679973433999999748998688898880399999999850
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=340.25 Aligned_cols=256 Identities=31% Similarity=0.479 Sum_probs=212.5
Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHC-CCCHHHCCHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 4138999999999999999997544-998688999999999999997-79984353221011233432100012222221
Q gi|255764498|r 6 RASSINTLSAYKRDLKEMQNFLNNK-EISLSAASTNHLISYLNHLSQ-RKLVTSSQRRKISVIRQFYNFLCYEGLRKDNP 83 (300)
Q Consensus 6 R~~S~~T~~~Y~~~l~~f~~~~~~~-~~~~~~i~~~~i~~~~~~l~~-~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np 83 (300)
|++|.+|+++|..=|++|..|-+++ ...+..+...+|+.|+.+|.- .+.|++|+|+-+++|--||+-..+..+--
T Consensus 12 ~hYs~~T~~aY~~Wi~rfI~frG~~C~~hp~~~g~~eVeaFLs~LAv~~~Vs~sTQ~QAL~ALlFLY~~iL~~~L~~--- 88 (320)
T TIGR02249 12 RHYSKRTEEAYLHWIKRFIRFRGHNCLRHPSTLGDTEVEAFLSDLAVDGKVSASTQNQALAALLFLYKEILKLELSL--- 88 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC---
T ss_conf 88789999999999999998850510138533075678888567764257476579999999999999984688874---
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-HHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf 222212122211122332024699998643-2001256102776543110001221001343334320000011110001
Q gi|255764498|r 84 SDTLELPKKNHILPKTLHKDTIANLLEQAK-IEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMI 162 (300)
Q Consensus 84 ~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~-~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~ 162 (300)
...+-.++.+++.|-++|.|||.++|+.++ .. ..+++.|||+||||+.|++.|++.||||+.+.|.
T Consensus 89 ~~~~~Ra~~~~kLPvVLT~eEV~~~l~~l~eg~-------------y~L~a~LLYGsGMRlmE~LRLRikDiDF~~~~I~ 155 (320)
T TIGR02249 89 MENFVRAKRPRKLPVVLTREEVARLLEHLEEGK-------------YRLIAKLLYGSGMRLMECLRLRIKDIDFDYGEIR 155 (320)
T ss_pred HHHCCCCCCCCCCCEECCHHHHHHHHHHCCCCC-------------HHHHHHHHCCCHHHHHHHHHCCCCEEEECCCEEE
T ss_conf 222206788873773359889999984257861-------------3112223125515898887510110343376689
Q ss_pred C-CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC--------------------------CCCCCCCCCCCCCC-------
Q ss_conf 1-1222111110000124788753232100124--------------------------67775200123332-------
Q gi|255764498|r 163 I-QGKGNKERLVILSPSALHALQMYKKTCSSMK--------------------------MTGNDLWLFPSSTK------- 208 (300)
Q Consensus 163 v-~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~--------------------------~~~~~~~lf~~~~~------- 208 (300)
| .|||+|+|.||+|.++..-|++.++..+... ..-...||||+.+.
T Consensus 156 vr~GKG~KdR~v~Lp~~L~~~L~~q~~~~~~~h~~Dl~~~G~g~V~LP~AL~rKYPnA~~~~~WqylFPs~~~S~DPrsG 235 (320)
T TIGR02249 156 VRDGKGGKDRVVTLPKSLAPPLREQLERARALHEKDLLAEGYGGVYLPHALARKYPNASKEWGWQYLFPSARLSRDPRSG 235 (320)
T ss_pred EEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCCCC
T ss_conf 97366898861268175579999999999999998640588530100455421578735667876653775015577778
Q ss_pred ---CCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCH
Q ss_conf ---2222111111101234420146676425988588999999985888889999855899899899964599
Q gi|255764498|r 209 ---TGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLP 278 (300)
Q Consensus 209 ---~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~ 278 (300)
...|...++++.++++..+|||++ .+|||.|||+|||+|+++|.||..||++|||+|++|||+||||-.
T Consensus 236 ~~~RHH~~e~~~QRav~~Av~~AGI~K-pvTcHTLRHSFATHLLe~G~DIRTVQelLGHsDVkTTqIYTHVL~ 307 (320)
T TIGR02249 236 RIRRHHIDEKTIQRAVRRAVERAGIEK-PVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLN 307 (320)
T ss_pred CCEEEECCCCHHHHHHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCEEEEEEC
T ss_conf 520010670043289999999578988-678874212244305651773678988617884224634530514
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=328.99 Aligned_cols=230 Identities=34% Similarity=0.575 Sum_probs=201.6
Q ss_pred CCCHHHCCHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 9986889999999999999977-998435322101123343210001222222122221212221112233202469999
Q gi|255764498|r 31 EISLSAASTNHLISYLNHLSQR-KLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLL 109 (300)
Q Consensus 31 ~~~~~~i~~~~i~~~~~~l~~~-~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~~~i~~~k~~~~~~~~ls~~e~~~ll 109 (300)
+..+.+++.+||++|+.++.++ +++++|+|+++++|++||+|+.+.++ +|+..+..++.+++.|++++++|+.+++
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 HHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 864320012561027765431100012210013433343200000111100011-1222111110000124788753232
Q gi|255764498|r 110 EQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVILSPSALHALQMYKK 188 (300)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v-~~K~~k~R~ipi~~~~~~~l~~y~~ 188 (300)
+++. ..|+++++.+++.||||+||+++|+|+|||++++++.| .+||+++|.||+++.+...|++|++
T Consensus 81 ~~~~------------~~r~~~~~~ll~~tGlR~~El~~L~~~did~~~~~i~i~~~K~~k~R~vpl~~~~~~~l~~~l~ 148 (242)
T cd01193 81 GALT------------GLKHRLILSLLYGCGLRLSECLRLRVKDIDFDRGQIRVRQGKGGKDRYVMLPEALLELLRAYWK 148 (242)
T ss_pred HCCC------------CCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 7387------------7679999999998289888898786631676751799861889960588759999999999999
Q ss_pred HHCCCCCCCCCCCCCCCCCC-------CCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 10012467775200123332-------22221111111012344201466764259885889999999858888899998
Q gi|255764498|r 189 TCSSMKMTGNDLWLFPSSTK-------TGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQIL 261 (300)
Q Consensus 189 ~~~~~~~~~~~~~lf~~~~~-------~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~ 261 (300)
..........+.|+|++..+ +.+++.+++++.++++++.+|++ ++++||+|||||||.|+++|+|+..||++
T Consensus 149 ~~~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~-~~~~~H~lRHT~at~ll~~G~~l~~v~~~ 227 (242)
T cd01193 149 RARALGRERPWQWLFPSTRRSRDPVERRHHLSERTLQRALKKAVEQAGID-KRVTPHTLRHSFATHLLEAGYDIRTIQEL 227 (242)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf 84653003652101356677757553677675999999999999984999-99886748999999999879999999988
Q ss_pred HCCCCHHHHHHHHHC
Q ss_conf 558998998999645
Q gi|255764498|r 262 LGHTDISTTQIYTHL 276 (300)
Q Consensus 262 lGH~s~~tT~~Y~~~ 276 (300)
|||+|++||++|+||
T Consensus 228 lGH~si~tT~~Y~Hv 242 (242)
T cd01193 228 LGHSDLKTTMIYTHV 242 (242)
T ss_pred CCCCCHHHHHHHHCC
T ss_conf 399888899870583
No 17
>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=301.66 Aligned_cols=258 Identities=21% Similarity=0.210 Sum_probs=203.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-C
Q ss_conf 999999999999999997544998688999999999999997799843532210112334321000122222212222-1
Q gi|255764498|r 10 INTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTL-E 88 (300)
Q Consensus 10 ~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~~~i-~ 88 (300)
+||+++|.++|+.|..||...++++.+++..++..|+.++.+ +++++|+++++++|++|+.|+...+....+|+..+ +
T Consensus 1 enT~~aY~~~l~~f~~wc~~~~~~~~~~t~~~v~~yl~~L~~-~~~~~Ti~~~lsalr~~~~~~~~~~~~~~~~~~~~~~ 79 (287)
T cd00799 1 DNTRKAYLSDWRRFAAWCQAHGRTPLPASPETVTLYLTDLAD-SLAPSTISRRLSALSQLHRRSGLPSPADSPLVRLVLR 79 (287)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
T ss_conf 905999999999999999974999788999999999999984-7787699999999999999970588654714888753
Q ss_pred C---C-CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH---CC
Q ss_conf 2---1-222111223320246999986432001256102776543110001221001343334320000011110---00
Q gi|255764498|r 89 L---P-KKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTER---TM 161 (300)
Q Consensus 89 ~---~-k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~---~i 161 (300)
. . ..+.+.+.+++.+++.++++.+.. .....++||.+|+.++|+||||.+|+++|+|+||+++++ .+
T Consensus 80 ~~~r~~~~~~~~~~~~~~~~l~~ll~~~~~------~~~~~~~Rd~ail~ll~~tGlR~~El~~L~~~di~~~~~~~~~i 153 (287)
T cd00799 80 GIRREEARPKRQALAILPEDLDKLRSLLDE------SDTLRDLRDLALLLLGFAGLLRRSELVRLRWEDLTFTDGGGLLV 153 (287)
T ss_pred HCCCCCCCCCCCCCCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCEEEE
T ss_conf 211236887657898999999999862555------78758799999999999862389999718398718578971799
Q ss_pred CC-CCCCCCC------CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCHHHHHHHCC
Q ss_conf 11-1222111------110000124788753232100124677752001233-----32222211111110123442014
Q gi|255764498|r 162 II-QGKGNKE------RLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSS-----TKTGHLSRQVFARDLKALAARAG 229 (300)
Q Consensus 162 ~v-~~K~~k~------R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~-----~~~~~~s~~~~~~~~~~~~~~~g 229 (300)
.+ .+|+++. +.+|........+..|+..... ...++|... ..+++++.++++..++++++.+|
T Consensus 154 ~~~~~K~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----~~~~lF~~~~~~~~~~~~~ls~~~v~~~~~~~~~~ag 228 (287)
T cd00799 154 TLRRSKTDQSGLGVLKLIPPLTTCPVRALERWLEAARI-----PKGPLFRRIDRWGVLGPGALSDNSLNRILKRLAEAAG 228 (287)
T ss_pred EECCCCEEECCCCCEEEECCCHHHHHHHHHHHHHHCCC-----CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 95587403548783675062158999999999987256-----7664302444467757887878999999999999859
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHH
Q ss_conf 66764259885889999999858888899998558998998999645999
Q gi|255764498|r 230 IQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPD 279 (300)
Q Consensus 230 i~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~ 279 (300)
++...++||+|||||||+|+++|+|+..||++|||+|++||++|+|..+.
T Consensus 229 ~~~~~~s~H~lRHt~At~ll~~G~~l~~Iq~~lGH~s~~tt~~Y~~~~d~ 278 (287)
T cd00799 229 LRSGSWSGHSLRRGFATEAARAGYSLLEIMRQGRWRSPKMVSRYIRDADR 278 (287)
T ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCH
T ss_conf 99999897513899999999879999999998589998899998537131
No 18
>PRK09870 tyrosine recombinase; Provisional
Probab=100.00 E-value=0 Score=304.01 Aligned_cols=194 Identities=26% Similarity=0.332 Sum_probs=172.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC-CCCC
Q ss_conf 122211122332024699998643200125610277654311000122100134333432000001111000111-2221
Q gi|255764498|r 90 PKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ-GKGN 168 (300)
Q Consensus 90 ~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~-~K~~ 168 (300)
+|.+++.+++||.+|+.++++++... ....||++|+.++|.||||+||+++|+|+|||++++.+.|. +|++
T Consensus 3 ~K~~~k~~~~LT~~Ev~~lL~~~~~~--------~~~~Rd~aii~ll~~tGlRvsEl~~L~~~DId~~~~~i~i~~~k~g 74 (200)
T PRK09870 3 NKADNKKRNFLTHSEIESLLKAANTG--------PHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRLKKG 74 (200)
T ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCC--------CHHHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCC
T ss_conf 87788889988999999998277999--------3758999999999996868999976959871877997999976789
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 11110000124788753232100124677752001233322222111111101234420146676425988588999999
Q gi|255764498|r 169 KERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHL 248 (300)
Q Consensus 169 k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l 248 (300)
+.+.+|+.+...+.|.+|++.+... ...++.+||++. .|.|++.+++++.++++++.+||+. +++||+|||||||+|
T Consensus 75 ~~~~~pl~~~~~~~l~~~l~~r~~~-~~~~~~~lF~s~-~G~~ls~~~i~~~~~~~~~~agi~~-~v~pH~LRHt~At~L 151 (200)
T PRK09870 75 FSTTHPLLNKEIQALKNWLSIRTSY-PHAESEWVFLSR-KGNPLSRQQFYHIISTSGGNAGLSL-EIHPHMLRHSCGFAL 151 (200)
T ss_pred CEEEEECHHHHHHHHHHHHHHHHHC-CCCCCCEECCCC-CCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCCCHHHHHHHH
T ss_conf 7578876799999999999987524-588887142579-9997779999999999999859997-768760289999999
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHC
Q ss_conf 9858888899998558998998999645999999999982801110
Q gi|255764498|r 249 LEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKK 294 (300)
Q Consensus 249 ~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~~ 294 (300)
+++|+|+..||++|||+|++||++|+|++.+++.++++++||+.|.
T Consensus 152 l~~G~di~~Iq~lLGHssi~TT~iYth~~~~~l~~i~~~~hpr~~~ 197 (200)
T PRK09870 152 ANMGIDTRLIQDYLGHRNIRHTVWYTASNAGRFYGIWDRARGRQRH 197 (200)
T ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCCHHC
T ss_conf 9869999999999489986689998817999999999984973100
No 19
>PRK09871 tyrosine recombinase; Provisional
Probab=100.00 E-value=0 Score=299.11 Aligned_cols=192 Identities=28% Similarity=0.339 Sum_probs=170.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCC-CCCCCCCCH
Q ss_conf 1223320246999986432001256102776543110001221001343334320000011110001112-221111100
Q gi|255764498|r 96 LPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQG-KGNKERLVI 174 (300)
Q Consensus 96 ~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~-K~~k~R~ip 174 (300)
..++||.+|+.+|++++.. ...+.||++|+.++|.||||+||+++|+|+|||++++.+.|.+ |+++.+++|
T Consensus 3 ~~ryLt~~Ev~~Ll~a~~~--------~~~~~Rd~aii~ll~~tGlR~sEl~~L~~~Did~~~~~i~i~~~k~g~~~~~p 74 (198)
T PRK09871 3 KRRYLTGKEVQAMMQAVCY--------GATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHP 74 (198)
T ss_pred CCCCCCHHHHHHHHHCCCC--------CCCCHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEEEECCCCEEEEEE
T ss_conf 6676999999999844143--------98544899999999997868999978888775877996999978997489874
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf 00124788753232100124677752001233322222111111101234420146676425988588999999985888
Q gi|255764498|r 175 LSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGAD 254 (300)
Q Consensus 175 i~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~ 254 (300)
+.+...+.|..|+..+..........++|++ ..|.+++.+++++.++++...+|+.. +++||+|||||||+|+++|+|
T Consensus 75 l~~~~~~~l~~~~~~r~~~~~~~~~~~lF~s-~~G~~ls~~~~~~~ik~~~~~aG~~~-~~~pH~LRHTfAt~Ll~~G~d 152 (198)
T PRK09871 75 LRFDEREAVERWTQERANWKGADRTDAIFIS-RRGSRLSRQQAYRIIRDAGIEAGTVT-QTHPHMLRHACGYELAERGAD 152 (198)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHCCCC
T ss_conf 8699999999999987775126778841435-88994799999999999999849998-889985579999999986999
Q ss_pred HHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHCCCC
Q ss_conf 8899998558998998999645999999999982801110011
Q gi|255764498|r 255 LRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKK 297 (300)
Q Consensus 255 ~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~~~~~ 297 (300)
+..||++|||+|++||++|+|++.+.++++++++||++.+.|+
T Consensus 153 l~~Iq~lLGHssi~TT~~Yth~~~~~l~~~~~~~~p~~~~~~~ 195 (198)
T PRK09871 153 TRLIQDYLGHRNIRHTVRYTASNAARFAGLWERNNLINEKLKR 195 (198)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf 9999999389977899998858999999999994961001000
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=1.4e-45 Score=283.64 Aligned_cols=261 Identities=21% Similarity=0.292 Sum_probs=207.7
Q ss_pred HHCCHHHHHHHHHHHHHH-HHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 413899999999999999-9997544998688999999999999997799843532210112334321000122222212
Q gi|255764498|r 6 RASSINTLSAYKRDLKEM-QNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPS 84 (300)
Q Consensus 6 R~~S~~T~~~Y~~~l~~f-~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~ 84 (300)
...+++|.+.|+..++.+ ..+++ +..+.+|+..+++.|+..+.+++ +++|+++.++.|+++|+||+..|++..||+
T Consensus 86 ~~~~~~t~~~~~~~l~~~i~p~~g--~~~l~~It~~~i~~~~~~l~~~~-~~~ta~~~~~~l~~~~~~A~~~~~i~~NP~ 162 (357)
T cd00801 86 PRWSEKHARQWRRTLEKHVLPVLG--KKPITEITARDLLDVLRRIEARG-ALETARRVRQRLKQVFRYAIARGLIEANPA 162 (357)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHC--CCCHHHCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf 024768999999999977589877--87489918899999999998569-899999999999999999998277443657
Q ss_pred CCCCCCCCC--CCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf 222121222--111223320246999986432001256102776543110001221001343334320000011110001
Q gi|255764498|r 85 DTLELPKKN--HILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMI 162 (300)
Q Consensus 85 ~~i~~~k~~--~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~ 162 (300)
..+..++.. ....++++.+|+..+++.+......+ ....++.+++.||||.||+++|+|+|||++++++.
T Consensus 163 ~~i~~~~~~~~~~r~r~lt~ee~~~l~~~l~~~~~~~--------~~~~~~~l~l~TG~R~gE~~~L~w~diD~~~~~~~ 234 (357)
T cd00801 163 ADLRGADGAPKKQHDRALSPDELPEFLQALDAASGSP--------VTRLALKLLLLTGVRPGELRGARWSEIDLENALWT 234 (357)
T ss_pred HHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCH--------HHHHHHHHHHHHCCCHHHHHCCCHHHEECCCCEEE
T ss_conf 6544410678877666789999999999998577883--------79999999999777888886387998777788489
Q ss_pred CC---CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHCCCCCCCCCHH
Q ss_conf 11---2221111100001247887532321001246777520012333-2222211111110123442014667642598
Q gi|255764498|r 163 IQ---GKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSST-KTGHLSRQVFARDLKALAARAGIQKKNISPH 238 (300)
Q Consensus 163 v~---~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~-~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H 238 (300)
|. .|+++.+.|||++.+.++|+++... .++..|||++.. .+.+++.+++++.+++ +|.. ++++||
T Consensus 235 Ip~~~tK~~~~~~vPL~~~~~~~L~~~~~~------~~~~~~vF~~~~~~~~~~~~~~~~~~~~~----~~~~-~~~t~H 303 (357)
T cd00801 235 IPAERMKTRRPHRVPLSDQALALLEELREL------SGHSEYVFPSRRDRGKPLSENTLNKALKR----MGYL-GEWTPH 303 (357)
T ss_pred EECCCCCCCCCEEEECCHHHHHHHHHHHHH------CCCCCEEECCCCCCCCCCCHHHHHHHHHH----HCCC-CCCEEE
T ss_conf 620236589936983989999999999886------49994582579999997748999999999----6599-995032
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHCC-HHHHHHHHHHH
Q ss_conf 858899999998588888999985589989989-996459-99999999982
Q gi|255764498|r 239 IIRHAFASHLLEGGADLRTIQILLGHTDISTTQ-IYTHLL-PDKLQKLVQDY 288 (300)
Q Consensus 239 ~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~-~Y~~~~-~~~~~~~~~~~ 288 (300)
+|||||||.|+++|+|+.+|+.+|||++..+|+ +|.|.+ .++.+++++..
T Consensus 304 dlRhT~aT~l~~~Gv~~~~i~~~LGH~~~~~t~~~Y~h~~y~~ekr~~l~~w 355 (357)
T cd00801 304 GLRRTARTWLNELGFPPDVIERQLAHVLGGKVRAAYNRADYLEERREAMQWW 355 (357)
T ss_pred CCHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 4889999999985989999999848999981899961744899999999986
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=285.16 Aligned_cols=202 Identities=26% Similarity=0.393 Sum_probs=172.9
Q ss_pred HHHHHHHHHHHHHHHHCCC-CC-CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCH
Q ss_conf 5322101123343210001-22-222212222121222111223320246999986432001256102776543110001
Q gi|255764498|r 58 SQRRKISVIRQFYNFLCYE-GL-RKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIEL 135 (300)
Q Consensus 58 T~~~~~~~l~~~~~~~~~~-~~-~~~np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~l 135 (300)
|+|++++.|+++|+||+++ |+ +..||+.+++.|+.++..+++++.+|+.++++++..... ..+..+++.+
T Consensus 1 Tinr~l~~L~~~f~~A~~~~~~~~~~NP~~~i~~pk~~~~r~r~lt~eE~~~ll~~~~~~~~--------~~~~~~~~~l 72 (206)
T cd00796 1 TVRRELALLSHLFTVARKEWGLDVLTNPVELVRKPPVGKGRDRRLTEEEEERLLRAFGEEEG--------SPRLPVIILL 72 (206)
T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC--------CHHHHHHHHH
T ss_conf 98899999999999999978887677927748588999999887999999999996764545--------7669999999
Q ss_pred HHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 2210013433343200000111100011-122211111000012478875323210012467775200123332222211
Q gi|255764498|r 136 LYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSR 214 (300)
Q Consensus 136 l~~tGlR~~Ei~~L~~~di~~~~~~i~v-~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~ 214 (300)
+++||||+||+++|+|+|||++++.+.| .+|+++.|.||+++.+.++|+.+... ..+.++|+ ++.
T Consensus 73 ~~~TG~R~~Ei~~L~~~did~~~~~i~i~~~K~~~~r~vpl~~~~~~~l~~~~~~-------~~~~~vf~-------~~~ 138 (206)
T cd00796 73 ALETAMRRGEILSLRWEQVDLKKRVAHLPDTKNGTSRDVPLSKRAVALLQMLPKV-------PDDGPVFP-------ITS 138 (206)
T ss_pred HHHHCCCHHHHHHCCCCCCCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHHHC-------CCCCCCCC-------CCH
T ss_conf 9990998899942857334533584898636789656852889999999999861-------47776678-------861
Q ss_pred CCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHH
Q ss_conf 111110123442014667642598858899999998588888999985589989989996459999999
Q gi|255764498|r 215 QVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQK 283 (300)
Q Consensus 215 ~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~ 283 (300)
.++...++++++.+|++ ++++|+|||||||.|+++|+|+..||++|||+|++||++|+|++++.++|
T Consensus 139 ~~~~~~~~~~~~~~gi~--~~~~H~lRHt~at~l~~~G~~~~~i~~~lGH~~~~~t~~Y~h~~~e~L~~ 205 (206)
T cd00796 139 DSVDAAFRRAKERAGLE--DLHFHDLRHEATSRLFEKGLSIMEVASISGHRDWRMLKRYTHLSAEDLAE 205 (206)
T ss_pred HHHHHHHHHHHHHHCCC--CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHC
T ss_conf 78999999999982777--87532048999999998698999999985899999998846739988704
No 22
>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=1.5e-44 Score=278.41 Aligned_cols=181 Identities=24% Similarity=0.362 Sum_probs=156.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCCCCCCH
Q ss_conf 12233202469999864320012561027765431100012210013433343200000111100011-12221111100
Q gi|255764498|r 96 LPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVI 174 (300)
Q Consensus 96 ~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v-~~K~~k~R~ip 174 (300)
.|++||+||+++|++++.. ....++||++||.++++||||+||+++|+|+|||++++.|.| .+||++.|.||
T Consensus 1 lpr~Ls~eEi~~Ll~a~~~-------~~~~~~Rd~ali~ll~~tGlR~~El~~L~~~Did~~~~~i~i~~~K~~k~r~vp 73 (188)
T cd01188 1 LPRALPWEDVERLLASCDR-------STPVGRRDYAILLLLARLGLRAGEVAALRLDDIDWRTGTIRVRQGKGGRVTRLP 73 (188)
T ss_pred CCCCCCHHHHHHHHHCCCC-------CCCHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCC
T ss_conf 9699999999999957576-------884517999999999998815999985698355656897788638998533446
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf 0012478875323210012467775200123--33222221111111012344201466764259885889999999858
Q gi|255764498|r 175 LSPSALHALQMYKKTCSSMKMTGNDLWLFPS--STKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGG 252 (300)
Q Consensus 175 i~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~--~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G 252 (300)
+++.+.+.|.+|++..+.. .+..++|.. ...+++.+..++++.++++++.+|++.++++||+|||||||+|+++|
T Consensus 74 l~~~~~~~l~~~l~~~~~~---~~~~~lf~~~~~~~~~~~~~~~i~~~~~~~~~~ag~~~~~~~~H~lRHt~at~l~~~G 150 (188)
T cd01188 74 LPAEVGAALADYLRDGRPA---TDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAG 150 (188)
T ss_pred CHHHHHHHHHHHHHHHCCC---CCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf 8499999999999980767---8876443505888888766999999999999984998898787614899999999969
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH
Q ss_conf 8888999985589989989996459999999999
Q gi|255764498|r 253 ADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286 (300)
Q Consensus 253 ~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~ 286 (300)
+|+..||++|||+|++||++|+|++.|.++++.-
T Consensus 151 ~~l~~vq~~lGH~si~tT~~Y~h~~~e~lr~~~~ 184 (188)
T cd01188 151 APLKEIGDVLGHRSPDSTAIYAKVDVDALRAIAL 184 (188)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 9999999983899889999988569999986647
No 23
>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=5.7e-43 Score=269.17 Aligned_cols=178 Identities=22% Similarity=0.301 Sum_probs=145.0
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCC-CCCCHHHH
Q ss_conf 33202469999864320012561027765431100012210013433343200000111100011122211-11100001
Q gi|255764498|r 99 TLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNK-ERLVILSP 177 (300)
Q Consensus 99 ~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k-~R~ipi~~ 177 (300)
.||.||+.+|++++. ..||+||+.+||+||||+||+++|+|+|||++++.+.|.++++| .+.+++++
T Consensus 1 iLt~eev~~li~~~~------------~~rdraii~lL~~TGlRvsEl~~L~~~DId~~~~~i~V~~~~~k~~~~~~~~~ 68 (186)
T cd01198 1 LISVEAMRELIADIT------------HPLERAVIVGLAKTGIRRGELINLDRRDVNLDKPTLYLKPASNKRSNRTLFPD 68 (186)
T ss_pred CCCHHHHHHHHHCCC------------CHHHHHHHHHHHHHCCHHHHHHCCCHHHCCCCCCEEEECCCCCCCCEEECCCH
T ss_conf 989999999998379------------87999999999995879999977928776865787885278898660555838
Q ss_pred HHH-HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCC------CCCCHHHHHHHHHHHHHH
Q ss_conf 247-8875323210012467775200123332222211111110123442014667------642598858899999998
Q gi|255764498|r 178 SAL-HALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQK------KNISPHIIRHAFASHLLE 250 (300)
Q Consensus 178 ~~~-~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~------~~~t~H~lRht~at~l~~ 250 (300)
... ..+..|+..+. ..+..++|++. .+++++...++..++++++++|+.. +++|||+|||||||+|++
T Consensus 69 ~~~~~~~~~~~~~r~----~~~~~~lF~~~-~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~vtPH~lRHtfAT~Ll~ 143 (186)
T cd01198 69 LETELFRWLAIRPRT----TSPADALFIGT-QDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRHFFTTWLRR 143 (186)
T ss_pred HHHHHHHHHHHHHHH----CCCCCCEEEEC-CCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 999999999987753----58998267617-9997768689999999999977643212114675851638999999998
Q ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHH
Q ss_conf 5888889999855899899899964599999999998280111
Q gi|255764498|r 251 GGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAK 293 (300)
Q Consensus 251 ~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~ 293 (300)
+|+|+..||++|||+|++||++|+|++.+.+++++++|||+.+
T Consensus 144 ~G~dl~~vq~lLGHssi~tT~~Y~h~~~~~l~e~y~k~~Pr~~ 186 (186)
T cd01198 144 RGGDRGVVQELRGDSRDEAIDTYTHIWGDELREAYLKHIPSLG 186 (186)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCC
T ss_conf 6999999999948998899999984799999999998588998
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=2.8e-42 Score=265.20 Aligned_cols=178 Identities=31% Similarity=0.427 Sum_probs=155.7
Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC-CCCCCCCCCHH
Q ss_conf 22332024699998643200125610277654311000122100134333432000001111000111-22211111000
Q gi|255764498|r 97 PKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ-GKGNKERLVIL 175 (300)
Q Consensus 97 ~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~-~K~~k~R~ipi 175 (300)
.++||+||+.++++++.. .....||++||.+++.||||+||+++|+|+|||++++.+.|. .|+++.+.+|+
T Consensus 2 r~~Lt~eEi~~ll~~~~~--------~~~~~Rd~~i~~ll~~tGlR~~El~~L~~~did~~~~~i~i~~~K~~~~~~~pl 73 (180)
T cd01197 2 RKYLTPSEVRSLLKAALD--------GRYSARDYCLMLLMFRHGLRVSEACGLKLSDIDLESRQIYIRRLKGGFSTTHPL 73 (180)
T ss_pred CCCCCHHHHHHHHHCCCC--------CCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEEEECCCCEEEECC
T ss_conf 989999999999965150--------764389999999999959529999518176561788848999704773036338
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCH
Q ss_conf 01247887532321001246777520012333222221111111012344201466764259885889999999858888
Q gi|255764498|r 176 SPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADL 255 (300)
Q Consensus 176 ~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~ 255 (300)
.+...+.+.+|++.+.... .++..++|++. .|+|++.+++++.++++++.+|++. +++||+|||||||+|+++|+|+
T Consensus 74 ~~~~~~~l~~~~~~~~~~~-~~~~~~lF~s~-~g~~l~~~~i~~~~~~~~~~agl~~-~~~~H~lRHt~At~l~~~G~~i 150 (180)
T cd01197 74 RDDELEALKNWLEIRAWKG-LPDSDWIFLSR-RGGPLSRQQVYKLIRRLGAQAGLSI-KVHPHMLRHACGYALANQGADT 150 (180)
T ss_pred CHHHHHHHHHHHHHHHHCC-CCCCCCEEECC-CCCCCCHHHHHHHHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHCCCCH
T ss_conf 2899999999999866204-77541122268-8884218889999999999828876-6789877899999999879999
Q ss_pred HHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf 899998558998998999645999999999
Q gi|255764498|r 256 RTIQILLGHTDISTTQIYTHLLPDKLQKLV 285 (300)
Q Consensus 256 ~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~ 285 (300)
..||++|||+|++||++|+|++.+++...+
T Consensus 151 ~~Iq~~LGH~~i~tT~~Yth~~~~~l~~~~ 180 (180)
T cd01197 151 RLIQDYLGHRNIRHTVIYTASNAARFLNLW 180 (180)
T ss_pred HHHHHHHCCCCHHHHHHHHHCCHHHHHHHC
T ss_conf 999998389987999999967999998629
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=7.4e-40 Score=251.08 Aligned_cols=172 Identities=26% Similarity=0.390 Sum_probs=150.4
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHH
Q ss_conf 32024699998643200125610277654311000122100134333432000001111000111222111110000124
Q gi|255764498|r 100 LHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSA 179 (300)
Q Consensus 100 ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k~R~ipi~~~~ 179 (300)
.++||+.++++++... ..||++||.+++.||||+||+++|+|+||+.++....+.+||++.|.||+++.+
T Consensus 7 ~~~eei~~i~~~l~~~----------~~Rd~~l~~l~~~TGlR~sEl~~Lk~~Di~~~~~i~i~~~K~~k~r~v~l~~~~ 76 (180)
T cd01186 7 RDKEQIKAIKDYLKNH----------SERNYLLFLIGINTGLRISDILALKVKDVRGDERISIKEKKTGKRKRIYLNPIL 76 (180)
T ss_pred CCHHHHHHHHHHHHCC----------CHHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCEEEEEECCCCCCCCCCCCHHH
T ss_conf 9999999999998756----------988999999999839239999637648727998299997878844651188999
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 78875323210012467775200123332-22221111111012344201466764259885889999999858888899
Q gi|255764498|r 180 LHALQMYKKTCSSMKMTGNDLWLFPSSTK-TGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTI 258 (300)
Q Consensus 180 ~~~l~~y~~~~~~~~~~~~~~~lf~~~~~-~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v 258 (300)
.++|.+|+... .++.|+|++..+ ..+++...+++.++++++.+|++ +++||+|||||||+++++|+|+..|
T Consensus 77 ~~~l~~y~~~~------~~~~~lF~s~~~~~~~is~~~~~~~~~~~~~~~gi~--~~~~H~lRHT~at~l~~~G~~l~~i 148 (180)
T cd01186 77 KEELLYYIKDL------EENEYLFQSRKGGNRPITRQQAYRILKKAAEQVGID--NIGTHTLRKTFGYHYYKQTKDIALL 148 (180)
T ss_pred HHHHHHHHHHC------CCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCC--CCCCCHHHHHHHHHHHHCCCCHHHH
T ss_conf 99999998843------877514323888998978999999999999980898--7667601789999999969999999
Q ss_pred HHHHCCCCHHHHHHHHHCCHHHHHHHHHHHC
Q ss_conf 9985589989989996459999999999828
Q gi|255764498|r 259 QILLGHTDISTTQIYTHLLPDKLQKLVQDYH 289 (300)
Q Consensus 259 ~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~ 289 (300)
|++|||+|++||++|+|++.+.+++++++|.
T Consensus 149 q~~LGH~si~tT~~Y~~~~~e~~~k~~~~~~ 179 (180)
T cd01186 149 MEIFNHSSPAITLRYIGINQDEIDKQLDNFK 179 (180)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 9993899989999985899999999997378
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=4.8e-40 Score=252.20 Aligned_cols=172 Identities=23% Similarity=0.403 Sum_probs=147.4
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC----------CCCCC
Q ss_conf 32024699998643200125610277654311000122100134333432000001111000111----------22211
Q gi|255764498|r 100 LHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ----------GKGNK 169 (300)
Q Consensus 100 ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~----------~K~~k 169 (300)
||++|+.+|++++. ..||++||.++++||||+||+++|+|+|||++++.+.|. .|+++
T Consensus 1 LT~~Ev~~ll~a~~------------~~Rd~~i~~ll~~TGlR~gE~~~L~~~Did~~~~~i~i~~~~~~~~~~~~K~~~ 68 (186)
T cd01194 1 LTPSEVQRLINACG------------NLRDKFLFALLYETGLRIGEALGLRIEDIDLAENQIWLVPREDNANGARAKSGR 68 (186)
T ss_pred CCHHHHHHHHHHCC------------HHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEEECCCCCCCCCCCCCC
T ss_conf 99899999998154------------038999999999969898889708898725769989998544555552036884
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf 111000012478875323210012467775200123332---22221111111012344201466764259885889999
Q gi|255764498|r 170 ERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTK---TGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFAS 246 (300)
Q Consensus 170 ~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~---~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at 246 (300)
+|.||+++.+.+.+.+|+....... ..+..++|++..+ +.+++...+...++++.+.+|+ +++||+|||||||
T Consensus 69 ~r~vpi~~~l~~~~~~~~~~~~~~~-~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~---~~~~H~lRHT~at 144 (186)
T cd01194 69 ERRIPVSQYLIDLYVDYVTEIYYLE-ELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGI---DFTPHMFRHTHAT 144 (186)
T ss_pred EEEEECCHHHHHHHHHHHHHHHHHH-CCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCC---CCCCCCCHHHHHH
T ss_conf 2588777999999999999976332-15777445633577568877799999999999998499---8774575999999
Q ss_pred HHHHCCCCHHHHHHHHCCCCHHHH-HHHHHCCHHHHHHHHHH
Q ss_conf 999858888899998558998998-99964599999999998
Q gi|255764498|r 247 HLLEGGADLRTIQILLGHTDISTT-QIYTHLLPDKLQKLVQD 287 (300)
Q Consensus 247 ~l~~~G~~~~~v~~~lGH~s~~tT-~~Y~~~~~~~~~~~~~~ 287 (300)
+|+++|+|+..||++|||+|++|| ++|+|+++++++++++|
T Consensus 145 ~l~~~G~~~~~v~~~lGH~~~~tT~~~Y~h~~~e~~~~~~~k 186 (186)
T cd01194 145 ELIRAGWSIEVVADRLGHAHVQTTLNTYGHLSEEDIRREFNK 186 (186)
T ss_pred HHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHCC
T ss_conf 999879999999998289987999998456899999998658
No 27
>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=1.7e-38 Score=243.24 Aligned_cols=180 Identities=27% Similarity=0.393 Sum_probs=143.2
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCC-------------
Q ss_conf 3320246999986432001256102776543110001221001343334320000011110001112-------------
Q gi|255764498|r 99 TLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQG------------- 165 (300)
Q Consensus 99 ~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~------------- 165 (300)
+||.||+.++++++..... ..++++++.++++||||+||+++|+|+|||++++++.|.+
T Consensus 1 yLt~eEi~~ll~~~~~~~~--------~~~~~~ii~ll~~TGlR~~Ei~~L~~~did~~~~~i~i~~~~~~~~~~~~~~~ 72 (205)
T cd01199 1 YLEKNELKALLDVLNSYKN--------NQLYADILEFLFLTGMRIGELLALQEKDIDFENKLINIDGTLDSHTGKEENGY 72 (205)
T ss_pred CCCHHHHHHHHHHHHHCCC--------CHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCCEEEEEEEEEEECCCCCCCE
T ss_conf 9398999999970514778--------76999999999997734888975909880655898999778864125666624
Q ss_pred ----CCC-CCCCCHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCCCCCCCCCCCC-CCCCCCHHHHHHHCCCC-CCCC
Q ss_conf ----221-1111000012478875323210012---467775200123332222211-11111012344201466-7642
Q gi|255764498|r 166 ----KGN-KERLVILSPSALHALQMYKKTCSSM---KMTGNDLWLFPSSTKTGHLSR-QVFARDLKALAARAGIQ-KKNI 235 (300)
Q Consensus 166 ----K~~-k~R~ipi~~~~~~~l~~y~~~~~~~---~~~~~~~~lf~~~~~~~~~s~-~~~~~~~~~~~~~~gi~-~~~~ 235 (300)
|+. ..|.|||++.+.++|++|++..... ....++.|+|++..+ .++.. ......++.+.+.+|+. .+++
T Consensus 73 ~~~~Kt~~~~R~vpl~~~~~~~l~~~~~~~~~~~~~~~~~~~~~lf~~~~g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (205)
T cd01199 73 KDTPKTKSSIRTISLSERAVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKG-NPLDLGPINSKILSKFLKDLGSQSKKHV 151 (205)
T ss_pred ECCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCC-CCCCCHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 345778886368617999999999999971441035456877637761689-8476408999999999998575546775
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHCCHHHHHHHHHH
Q ss_conf 598858899999998588888999985589989989-9964599999999998
Q gi|255764498|r 236 SPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQ-IYTHLLPDKLQKLVQD 287 (300)
Q Consensus 236 t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~-~Y~~~~~~~~~~~~~~ 287 (300)
+||+|||||||.|+++|+|+..||++|||+|++||+ +|+|++++..++++++
T Consensus 152 ~~H~lRHT~at~l~~~G~~~~~v~~~lGHss~~tT~~iY~h~~~~~~~e~~~k 204 (205)
T cd01199 152 TTHIFRHTHISFLAEEGVPLKAIMDRVGHSDGKTTLRIYSHVTEKMKDEIVKK 204 (205)
T ss_pred CCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHC
T ss_conf 76455999999999869999999998679988999888661698999999960
No 28
>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=1.4e-38 Score=243.59 Aligned_cols=174 Identities=32% Similarity=0.417 Sum_probs=138.8
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHH----CCCC-CCCCCCCCCC
Q ss_conf 3320246999986432001256102776543110001221001343334320000011110----0011-1222111110
Q gi|255764498|r 99 TLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTER----TMII-QGKGNKERLV 173 (300)
Q Consensus 99 ~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~----~i~v-~~K~~k~R~i 173 (300)
+||.||+.++++++.... ......+.||++|+.++|.||||+||+++|+|+||+++.+ ++.| .|||+|+|.|
T Consensus 1 ~lt~~~~~~~~~~~~~~p---~~~~~~~~Rd~ail~ll~~tGlR~sEl~~L~~~Di~~~~~~~~~~l~i~~gKg~k~R~v 77 (196)
T cd01183 1 ALTEDQWAFVIDTVASLP---AQDPEHAARLLFLLALLYSTGLRISELAAATGPDLEAFVQGGGWWLYVPVGKGGKERRV 77 (196)
T ss_pred CCCHHHHHHHHHHHHHCC---CCCCCHHHHHHHHHHHHHHHCCHHHHHHCCCHHHHCHHCCCCCEEEEEEECCCCCEEEE
T ss_conf 979999999999998577---78970769999999999996662999983988870231167860599885889850030
Q ss_pred HHHHHHHHHHHHHHHHHCC--CCCCCCCCCCCCC---CCCCCCCCCCCCCCCHHHHHHHCCC------------CCCCCC
Q ss_conf 0001247887532321001--2467775200123---3322222111111101234420146------------676425
Q gi|255764498|r 174 ILSPSALHALQMYKKTCSS--MKMTGNDLWLFPS---STKTGHLSRQVFARDLKALAARAGI------------QKKNIS 236 (300)
Q Consensus 174 pi~~~~~~~l~~y~~~~~~--~~~~~~~~~lf~~---~~~~~~~s~~~~~~~~~~~~~~~gi------------~~~~~t 236 (300)
|+++.+.+.|++|++.+.. .........+|+. ...+++++.++++..++++...++. ..+++|
T Consensus 78 pl~~~~~~~L~~yl~~r~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~~~v~~~~~~a~~~~~~~~~~~~~~~~~~~s 157 (196)
T cd01183 78 PVSDELLAALARYRQARGLPPEPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAAADRLQADGFEEDAAQLRAAS 157 (196)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCC
T ss_conf 18899999999999984776555546676401036777667875199999999999999999976412176751037678
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 988588999999985888889999855899899899964
Q gi|255764498|r 237 PHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTH 275 (300)
Q Consensus 237 ~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~ 275 (300)
||+|||||||+|+++|+|+..||++|||+|++||++|+|
T Consensus 158 pH~LRHt~At~ll~~G~~l~~Vq~~LGH~si~TT~~Y~H 196 (196)
T cd01183 158 THWLRHTHASHDLAAGVPLEHVQDNLGHASIDTTSRYLH 196 (196)
T ss_pred CCCCHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHCCC
T ss_conf 832589999999987999999998808998678734339
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=1.5e-37 Score=237.72 Aligned_cols=171 Identities=25% Similarity=0.374 Sum_probs=142.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC---CCCCCCC
Q ss_conf 1122332024699998643200125610277654311000122100134333432000001111000111---2221111
Q gi|255764498|r 95 ILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ---GKGNKER 171 (300)
Q Consensus 95 ~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~---~K~~k~R 171 (300)
+..++||++|+.+|++++.. +.+.++.+++.||||+||+++|+|+|||++++.+.|. +|+++.|
T Consensus 2 kr~r~Lt~eE~~~ll~~~~~-------------~~r~~i~l~~~TG~R~~El~~L~~~did~~~~~i~i~~~~~K~~~~r 68 (177)
T cd01192 2 KRVRWLTPEEAERLIAELPP-------------HLKPAVLFALNTGLRRSEILGLEWSQVDLDNRVAWVRPATSKGGRAI 68 (177)
T ss_pred CCCCCCCHHHHHHHHHHCCH-------------HHHHHHHHHHHHCCCHHHHHHCCCHHHHHHCCHHCCCCCCCCCCCEE
T ss_conf 87789999999999982898-------------79999999999783499998387866663011101144568888544
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 10000124788753232100124677752001233322222111111101234420146676425988588999999985
Q gi|255764498|r 172 LVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEG 251 (300)
Q Consensus 172 ~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~ 251 (300)
.||+++.+.++|.+|... .+..|+|++.. +.+.. ...+.++++++.+|++ ++++|+|||||||.|+++
T Consensus 69 ~vpl~~~~~~~l~~~~~~-------~~~~~vf~~~~-~~~~~--~~~~~~~~~~~~agi~--~~~~H~lRHt~at~l~~~ 136 (177)
T cd01192 69 RVPLNDEALQVLKRQKAG-------AHKPWVFAGAG-GDPRI--DSKTAWRQALQRAGIS--DFRWHDLRHTWASWLVQS 136 (177)
T ss_pred ECCCHHHHHHHHHHHHHC-------CCCCCEECCCC-CCCCC--HHHHHHHHHHHHCCCC--CCCCCCCCHHHHHHHHHC
T ss_conf 261309999999998723-------57751411589-98510--1789999999973799--998688968899999996
Q ss_pred CCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCC
Q ss_conf 888889999855899899899964599999999998280
Q gi|255764498|r 252 GADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHP 290 (300)
Q Consensus 252 G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p 290 (300)
|+|+..||++|||+|++||++|+|++++.+++++++...
T Consensus 137 G~~~~~i~~~lGH~~~~~T~~Y~h~~~~~~r~a~~~l~~ 175 (177)
T cd01192 137 GVPLYVLQELLGHSSLQMVRRYAHLSPEHLRAAARALDA 175 (177)
T ss_pred CCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 989999999958998999999886699999999999873
No 30
>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=6.4e-37 Score=233.98 Aligned_cols=178 Identities=22% Similarity=0.344 Sum_probs=139.0
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHC------CCC-CCCCCCC
Q ss_conf 233202469999864320012561027765431100012210013433343200000111100------011-1222111
Q gi|255764498|r 98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERT------MII-QGKGNKE 170 (300)
Q Consensus 98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~------i~v-~~K~~k~ 170 (300)
+++++++++++.+.+....+ ..+.|+.+++.||||+||+++|+|+||+.+... +.. ..++.++
T Consensus 1 ~~i~~~~~~~l~~~l~~l~~----------~~~~~~~ll~~TGlRisE~l~L~~~~i~~~~~~~~~~~~~~~~~k~~~k~ 70 (195)
T cd01195 1 RFIPEFVLEQLNSHIDKLPE----------YIIPMTMIVQETGMRISDLLTLKKNCLLEDKDGDFFYKYYQCIWKTKIKE 70 (195)
T ss_pred CCCCHHHHHHHHHHHHHCCH----------HHHHHHHHHHHCCCHHHHHHCCCHHHHHHHCCCCCEEEEEEEECCCCCEE
T ss_conf 98998999999999986899----------89999999998087399996386114555036555267999967988743
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCC---CCCCCCCCCCCCCCHHHHHHHCCCCCC-----CCCHHHH
Q ss_conf 11000012478875323210012--4677752001233---322222111111101234420146676-----4259885
Q gi|255764498|r 171 RLVILSPSALHALQMYKKTCSSM--KMTGNDLWLFPSS---TKTGHLSRQVFARDLKALAARAGIQKK-----NISPHII 240 (300)
Q Consensus 171 R~ipi~~~~~~~l~~y~~~~~~~--~~~~~~~~lf~~~---~~~~~~s~~~~~~~~~~~~~~~gi~~~-----~~t~H~l 240 (300)
|.||+++++.++|+.|+...... ...+++.|||++. ..+.+++.+.+...++++++..|+.++ +++||+|
T Consensus 71 r~ipi~~~~~~~l~~~~~~~~~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~~~~~~H~l 150 (195)
T cd01195 71 HIIPISKKVALLIKVREDKTKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYHFHAHAF 150 (195)
T ss_pred EEEECCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 68867899999999999998987302069885487678898088876199999999999998186533477256688877
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf 889999999858888899998558998998999645999999999
Q gi|255764498|r 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLV 285 (300)
Q Consensus 241 Rht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~ 285 (300)
||||||+|+++|+|+..||++|||+|++||++|+|++++.+++++
T Consensus 151 RHT~aT~L~~~Gv~i~~Iq~~LGH~s~~tT~~Yahv~~e~l~~~~ 195 (195)
T cd01195 151 RHTVATRMINNGMPIHIIQKFLGHESPEMTSRYAHIFDETLKNEF 195 (195)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf 489999999869999999999489998999998857989998629
No 31
>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=9.9e-37 Score=232.90 Aligned_cols=169 Identities=38% Similarity=0.556 Sum_probs=147.9
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC-CCCCCCCCCHHH
Q ss_conf 2332024699998643200125610277654311000122100134333432000001111000111-222111110000
Q gi|255764498|r 98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ-GKGNKERLVILS 176 (300)
Q Consensus 98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~-~K~~k~R~ipi~ 176 (300)
++||+||+.+|++++.. ...+||++||.++++||||++|+++|+|+||+++++.+.|. +|+++.|.+|++
T Consensus 1 ~~lt~~e~~~ll~~~~~---------~~~lR~~~l~~l~~~tG~R~~El~~L~~~di~~~~~~i~i~~~K~~~~r~i~i~ 71 (170)
T pfam00589 1 RRLTEDEVERLLAALEE---------PLNIRDRALVELLLLTGLRISELLSLRWSDIDLDNGTIRIPQTKTRKSRTVPLS 71 (170)
T ss_pred CCCCHHHHHHHHHHHCC---------CCCHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCCCEEEEECCCCCCCCEECCCC
T ss_conf 98999999999986463---------459779999999999686988897421300467651787304411331001467
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHH
Q ss_conf 12478875323210012467775200123332222211111110123442014667642598858899999998588888
Q gi|255764498|r 177 PSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLR 256 (300)
Q Consensus 177 ~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~ 256 (300)
+.+...+.+|+...... ....++|++ .++++++.+.+.+.+++++..+|++. ++++|+|||||||.|+++|+|+.
T Consensus 72 ~~~~~~l~~~~~~~~~~---~~~~~lf~~-~~~~~~~~~~~~~~~~~~~~~~g~~~-~~s~Hs~Rht~at~l~~~g~~~~ 146 (170)
T pfam00589 72 DAALEALKEWLGDRKEA---EESEFLFVS-RRGKPLSRSTVNRAFRRAGKRAGIEK-DLTPHDLRHTFATHLAENGVPLR 146 (170)
T ss_pred HHHHHHHHHHHHHHCCC---CCCCEEEEE-CCCCCCCCHHHHHHHHHHHHHCCCCC-CCCCCCCHHHHHHHHHHCCCCHH
T ss_conf 77999999999973146---777614320-16885531346788888888607787-67878884899999999699999
Q ss_pred HHHHHHCCCCHHHHHHHHHCCHHH
Q ss_conf 999985589989989996459999
Q gi|255764498|r 257 TIQILLGHTDISTTQIYTHLLPDK 280 (300)
Q Consensus 257 ~v~~~lGH~s~~tT~~Y~~~~~~~ 280 (300)
.||+++||+|++||++|+|+++++
T Consensus 147 ~v~~~lGH~~~~tT~~Y~~~~~~~ 170 (170)
T pfam00589 147 VIQKLLGHSSISMTMRYTHVAAER 170 (170)
T ss_pred HHHHHHCCCCHHHHHHHCCCCCCC
T ss_conf 999996899989999820838559
No 32
>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=4e-36 Score=229.39 Aligned_cols=171 Identities=33% Similarity=0.481 Sum_probs=140.8
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC-------------
Q ss_conf 2332024699998643200125610277654311000122100134333432000001111000111-------------
Q gi|255764498|r 98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ------------- 164 (300)
Q Consensus 98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~------------- 164 (300)
++||++|+.+|++++.... ..|+++++.++++||||++|+++|+|+|||++++.+.|.
T Consensus 1 ~yLt~~Ei~~ll~~~~~~~---------~~~~~~~~~l~~~tGlR~~Ei~~L~~~did~~~~~i~v~~~~~~~~~~~~~~ 71 (191)
T cd01189 1 KFLTKEELKKLLEYLKKHE---------NSFSKLLILLLAYTGLRIGEALALTWSDIDFENNTITINKTWDYKTGGYIFK 71 (191)
T ss_pred CCCCHHHHHHHHHHHHHCC---------CHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEEEEECCEEECCCCEEEC
T ss_conf 9899999999999875668---------9789999999999781499997289999465558589841012113530335
Q ss_pred -CCCCC-CCCCHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHH
Q ss_conf -22211-111000012478875323210012---4677752001233322222111111101234420146676425988
Q gi|255764498|r 165 -GKGNK-ERLVILSPSALHALQMYKKTCSSM---KMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHI 239 (300)
Q Consensus 165 -~K~~k-~R~ipi~~~~~~~l~~y~~~~~~~---~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~ 239 (300)
.|++. .|.|||++++..+|.+|+...... .......++|.+ ..+.+++.++++..++++++.+|++ +++||+
T Consensus 72 ~~Kt~~~~R~v~i~~~~~~~L~~~~~~~~~~~~~~~~~~~~~if~~-~~~~~~~~~~~~~~~~~~~~~~gi~--~~~~H~ 148 (191)
T cd01189 72 PPKTKSSIRTIPLDKKTIAILKEYKKEQKKYLLGEINNDDELVFTN-KGGKISTPSTINKRLKRICKKAGIP--KITFHG 148 (191)
T ss_pred CCCCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEC-CCCCCCCHHHHHHHHHHHHHHCCCC--CCCHHH
T ss_conf 7778887248847999999999999997776403578987437646-9999178889999999999980898--056343
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHH-HHHHHCCHHH
Q ss_conf 5889999999858888899998558998998-9996459999
Q gi|255764498|r 240 IRHAFASHLLEGGADLRTIQILLGHTDISTT-QIYTHLLPDK 280 (300)
Q Consensus 240 lRht~at~l~~~G~~~~~v~~~lGH~s~~tT-~~Y~~~~~~~ 280 (300)
|||||||.|+++|+|+..||++|||+|++|| ++|+|+++++
T Consensus 149 lRHT~aT~l~~~G~~~~~i~~~lGH~s~~~T~~~Y~h~~~~~ 190 (191)
T cd01189 149 LRHTHASLLLEAGVSIKYVSERLGHADISTTLDTYSHLLPEK 190 (191)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCCCC
T ss_conf 599999999996999999999858998899997711669465
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=100.00 E-value=3.1e-34 Score=218.41 Aligned_cols=161 Identities=42% Similarity=0.630 Sum_probs=134.5
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHH
Q ss_conf 4699998643200125610277654311000122100134333432000001111000111-222111110000124788
Q gi|255764498|r 104 TIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ-GKGNKERLVILSPSALHA 182 (300)
Q Consensus 104 e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~-~K~~k~R~ipi~~~~~~~ 182 (300)
|+++++++++.. ...|++++|.+++.||||++|+++|+|+||+++++++.|. .|+++.|.||+++.+...
T Consensus 1 e~~~~~~~~~~~---------~~~r~r~~~~l~~~tGlR~~Ei~~L~~~di~~~~~~i~i~~~K~~~~r~vpi~~~~~~~ 71 (164)
T cd00397 1 EIERLLAAAEAS---------TPERLYLALLLLLATGLRISELCALRWSDIDLDKRVIHITGTKTKKERTVPLSEEALKL 71 (164)
T ss_pred CHHHHHHHHHHC---------CCHHHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCHHHHH
T ss_conf 989999765146---------79889999999999781999996384620567764799835646653336676012346
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf 75323210012467775200123332--2222111111101234420146676425988588999999985888889999
Q gi|255764498|r 183 LQMYKKTCSSMKMTGNDLWLFPSSTK--TGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQI 260 (300)
Q Consensus 183 l~~y~~~~~~~~~~~~~~~lf~~~~~--~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~ 260 (300)
|.+|........ .+..++|+...+ ....+...+...+++++..+|+..++++||+||||+||.++++|+|+..||+
T Consensus 72 l~~~~~~~~~~~--~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~~g~~~~~I~~ 149 (164)
T cd00397 72 LKEYLKKRRPAN--GDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLRHTFASALLNAGLDLEAVQD 149 (164)
T ss_pred HHHHHHHHCCCC--CCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf 888898850146--875412113689866520467899997899998336765677566589999999996999999999
Q ss_pred HHCCCCHHHHHHHHH
Q ss_conf 855899899899964
Q gi|255764498|r 261 LLGHTDISTTQIYTH 275 (300)
Q Consensus 261 ~lGH~s~~tT~~Y~~ 275 (300)
+|||+|++||++|+|
T Consensus 150 ~lGHs~~~tT~~Y~h 164 (164)
T cd00397 150 LLGHSSIAMTMRYAH 164 (164)
T ss_pred HHCCCCHHHHHHCCC
T ss_conf 968999889711839
No 34
>PRK09692 integrase; Provisional
Probab=99.98 E-value=1.8e-31 Score=202.34 Aligned_cols=258 Identities=20% Similarity=0.233 Sum_probs=187.1
Q ss_pred CCHHHHHHHHHHHHHH-HHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 3899999999999999-999754499868899999999999999779984353221011233432100012222221222
Q gi|255764498|r 8 SSINTLSAYKRDLKEM-QNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDT 86 (300)
Q Consensus 8 ~S~~T~~~Y~~~l~~f-~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~~~ 86 (300)
.+..+.+.+.+.++.. +..+ .+.++.+|+..++.+.+..+..++ +..+.++.++.++.+|+||+..|+++.||+..
T Consensus 122 ~~~~~~~~~~r~le~~v~p~i--G~~~i~~I~~~di~~~l~~i~~rg-~~~~a~r~~~~l~~i~~~A~~~gli~~nP~~~ 198 (413)
T PRK09692 122 VTEDYAEDIWRSLERDVFPAI--GDVSVTDIKAHTLVQAVQPVQARG-ALETVRRLCQRINEVMIYAQNTGLIDAVPSVN 198 (413)
T ss_pred CCHHHHHHHHHHHHHHHHHHH--CCCCCCCCCHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 257799999999998887985--888410078999999987999739-89999999999999999999658644585434
Q ss_pred CCCC--CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf 2121--22211122332024699998643200125610277654311000122100134333432000001111000111
Q gi|255764498|r 87 LELP--KKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ 164 (300)
Q Consensus 87 i~~~--k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~ 164 (300)
+... +........++++|+..++..+...... ... .+++.+++.||+|++|++.++|++||++++.+.|.
T Consensus 199 ~~~~~~~p~~~~~~~l~~~el~~l~~~l~~~~~~------~~~--~~~l~l~lLt~~R~~Ev~~arW~eiD~~~~~W~IP 270 (413)
T PRK09692 199 IGKAFEKPQKKNMPSIRPDQLPQLMQTMRTASIS------LST--RCLFMWQLLTITRPAEAAEARWEEVDIEAQEWKIP 270 (413)
T ss_pred HHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC------HHH--HHHHHHHHHHCCCHHHHHCCCHHHEECCCCEEEEC
T ss_conf 3452568754577768989999999999857997------357--89999999972326877367799955788879975
Q ss_pred ---CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf ---222111110000124788753232100124677752001233-3222221111111012344201466764259885
Q gi|255764498|r 165 ---GKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSS-TKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240 (300)
Q Consensus 165 ---~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~-~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~l 240 (300)
.|+++...||+++.++++|++.. ...++.+||||+. ..+.|++..+++..++ .+|... .+++|+|
T Consensus 271 aer~K~~~~h~VPLs~qA~~iL~~l~------~~~~~~~~vFps~~~~~~~~s~~t~~~al~----~~~~~~-~~t~Hd~ 339 (413)
T PRK09692 271 AARMKMNRDHTVPLSDEAIAILEMMK------PLSGNREFIFPSRIKPNQPMNSQTVNASLK----RAGFGG-VLVSHGL 339 (413)
T ss_pred HHHCCCCCCCEECCCHHHHHHHHHHH------HHCCCCEEECCCCCCCCCCCCHHHHHHHHH----HCCCCC-CEECCCC
T ss_conf 68848988715278699999999999------861997698036999999788899999999----669999-7658484
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCHH-HHHHHHHCCH-HHHHHHHHH
Q ss_conf 8899999998588888999985589989-9899964599-999999998
Q gi|255764498|r 241 RHAFASHLLEGGADLRTIQILLGHTDIS-TTQIYTHLLP-DKLQKLVQD 287 (300)
Q Consensus 241 Rht~at~l~~~G~~~~~v~~~lGH~s~~-tT~~Y~~~~~-~~~~~~~~~ 287 (300)
|+||+|.|-+.|++.++|-.+|||.... +...|-+.+. ++.+++++.
T Consensus 340 RrT~~T~l~e~g~~~~viE~~L~H~~~~~v~~~Ynr~~yl~eRr~~mq~ 388 (413)
T PRK09692 340 RSIASTALNEQGFPPDVIEAALAHVDKNEVRRAYNRSDYLEQRRPMMQW 388 (413)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHCHHHHHHHHHHHHHH
T ss_conf 5779998997699999999986899998289995677599999999999
No 35
>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=99.98 E-value=9.5e-33 Score=209.73 Aligned_cols=157 Identities=30% Similarity=0.400 Sum_probs=120.0
Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCCCCCCHHHHHHHH
Q ss_conf 2469999864320012561027765431100012210013433343200000111100011-122211111000012478
Q gi|255764498|r 103 DTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVILSPSALH 181 (300)
Q Consensus 103 ~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v-~~K~~k~R~ipi~~~~~~ 181 (300)
||+.+|+++++... ...+|+.+ .++++||||.||+++|+|+||+ ++.+.+ .+|+++.|.|||++.+.+
T Consensus 1 eE~~rLl~~~~~~~-------~~~~r~~~--~l~~~TGlR~sEi~~L~~~di~--~~~i~~~~~K~~~~r~ipl~~~~~~ 69 (158)
T cd00797 1 DEEERLLAALDALG-------SGDLKDVA--ILCLDTGARWGEALGLKAEDIQ--EGRVTFWKTKSGKSRTVPISERVAA 69 (158)
T ss_pred CHHHHHHHHHHHCC-------CHHHHHHH--HHHHHHCCCHHHHHHHHHHHCC--CCEEEEEECCCCCEEEECCCHHHHH
T ss_conf 98999998730557-------86399999--9999948888886262797726--8858988757997547334199999
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 87532321001246777520012333222221111111012344201466764259885889999999858888899998
Q gi|255764498|r 182 ALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQIL 261 (300)
Q Consensus 182 ~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~ 261 (300)
+|.++.. ..++|+... ...+...++++... ++ ++++||+|||||||+++++|+|+..||++
T Consensus 70 ~l~~~~~----------~~~~f~~~~------~~~~~~~~~~~~~~--~~-~~~~~H~lRHt~At~l~~~G~~i~~v~~~ 130 (158)
T cd00797 70 MLKRRRM----------RGGLFPDLY------YESFRHIWKRAKIE--LP-KGQATHILRHTFASHFMMNGGNIATLQHI 130 (158)
T ss_pred HHHHHHH----------CCCCCCCCC------HHHHHHHHHHHHHC--CC-CCCCCCHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 9996154----------178888854------78999999999824--79-88662278899999999849989999998
Q ss_pred HCCCCHHHHHHHHHCCHHHHHHHHHHHCC
Q ss_conf 55899899899964599999999998280
Q gi|255764498|r 262 LGHTDISTTQIYTHLLPDKLQKLVQDYHP 290 (300)
Q Consensus 262 lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p 290 (300)
|||+|++||++|+|+++|.+++|++. ||
T Consensus 131 lGH~s~~~T~~Y~hl~~~~l~~av~~-~p 158 (158)
T cd00797 131 LGHATIEMTMRYAHLAPDHLDDAVSL-NP 158 (158)
T ss_pred HCCCCHHHHHHCCCCCHHHHHHHHHH-CC
T ss_conf 48999999977748699999999985-82
No 36
>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=99.98 E-value=2.1e-33 Score=213.50 Aligned_cols=168 Identities=18% Similarity=0.263 Sum_probs=126.6
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCC--C-------CCCCC-
Q ss_conf 3202469999864320012561027765431100012210013433343200000111100011--1-------22211-
Q gi|255764498|r 100 LHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII--Q-------GKGNK- 169 (300)
Q Consensus 100 ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v--~-------~K~~k- 169 (300)
+|.+|++.||.+.............. ++++.|+++||||+||+++|+|+||+++++.+.| . .|+..
T Consensus 1 f~~~e~~~ll~~~~~~~~~~~~~~~~----y~~~ll~~~TGlR~~Ei~~L~~~Di~~~~g~~~i~i~~~~~~~~~Kt~~s 76 (181)
T cd01184 1 FTTEELKAIFASPAYTGWASQKDPHR----YWLPLLGLYTGARVNEIAQLQVDDIREEDGVPCIDITNDDEDQSLKNAAS 76 (181)
T ss_pred CCHHHHHHHHCCCCCCCCCCCCCCHH----HHHHHHHHHHCCCHHHHHCCCHHHEEEECCEEEEEEECCCCCCCCCCCCC
T ss_conf 99899999967800034546798059----99999999969079999719798971359989999963787765678775
Q ss_pred CCCCHHHHHHHHH-HHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHH
Q ss_conf 1110000124788-7532321001246777520012333-2222211111110123442014667642598858899999
Q gi|255764498|r 170 ERLVILSPSALHA-LQMYKKTCSSMKMTGNDLWLFPSST-KTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASH 247 (300)
Q Consensus 170 ~R~ipi~~~~~~~-l~~y~~~~~~~~~~~~~~~lf~~~~-~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~ 247 (300)
.|.|||++.+.++ +.+|++..+. ..+.++|+... .+.+.....+.+.++++++++|+..++++||+|||||||.
T Consensus 77 ~R~vPl~~~l~~~~~~~~~~~~~~----~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~gi~~~~~~~H~lRHT~aT~ 152 (181)
T cd01184 77 RRTIPVHPELIELGFLDYVEARRA----AGHKRLFPDLPAGKTGGYGSAVSKWFSRYLKKLGLKDKGKSFHSFRHTFITE 152 (181)
T ss_pred EEEECCCHHHHHHHHHHHHHHHHH----CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHH
T ss_conf 364168899999999999999871----5996124444478888610579999999999849997889786468999999
Q ss_pred HHHCCCCHHHHHHHHCCCCHHHHH-HHHH
Q ss_conf 998588888999985589989989-9964
Q gi|255764498|r 248 LLEGGADLRTIQILLGHTDISTTQ-IYTH 275 (300)
Q Consensus 248 l~~~G~~~~~v~~~lGH~s~~tT~-~Y~~ 275 (300)
|+++|+|+.+||++|||+|++||+ +|.+
T Consensus 153 l~~~gv~~~~v~~~lGHss~~tT~~~Ygk 181 (181)
T cd01184 153 LRNAGVSRELIAAIMGHEEGTTTFGRYGK 181 (181)
T ss_pred HHHCCCCHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 99869899999998289998864253081
No 37
>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=99.98 E-value=1.1e-32 Score=209.33 Aligned_cols=158 Identities=23% Similarity=0.308 Sum_probs=131.6
Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCC-CCCCCCCCCCHH
Q ss_conf 2233202469999864320012561027765431100012210013433343200000111100011-122211111000
Q gi|255764498|r 97 PKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMII-QGKGNKERLVIL 175 (300)
Q Consensus 97 ~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v-~~K~~k~R~ipi 175 (300)
.++||+||+.++++++... +.++++.|++.||||.||+++|+|+||+ ++.+.| .+|+++.+.||+
T Consensus 1 ~R~Lt~eE~~~l~~~~~~~------------~~~~~~~l~~~TGlR~~Ei~~L~w~di~--~~~i~i~~~Ktg~~~~ipl 66 (162)
T cd00800 1 RRYLTDEEYRAIYEAADAP------------WLRCAMDLALLTGQRVGDVLRMKWSDID--DDGLHIEQSKTGAKLAIPL 66 (162)
T ss_pred CCCCCHHHHHHHHHHCCCH------------HHHHHHHHHHHHCCCHHHHHCCCHHHCC--CCEEEEEECCCCCEEEEEC
T ss_conf 9989999999999857886------------6899999999978899999719197645--6879998478870467657
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCC--CCCCHHHHHHHHHHHHHHCCC
Q ss_conf 012478875323210012467775200123332222211111110123442014667--642598858899999998588
Q gi|255764498|r 176 SPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQK--KNISPHIIRHAFASHLLEGGA 253 (300)
Q Consensus 176 ~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~--~~~t~H~lRht~at~l~~~G~ 253 (300)
++.+.++|+++.+.. .....++|++..++.+++..++.+.|+++++.+|+.. .++++|+|||||||.+.++|.
T Consensus 67 ~~~l~~~l~~~~~~~-----~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~agi~~~~~~~t~H~lRht~at~~~~~g~ 141 (162)
T cd00800 67 SPSLREVIERCRDLS-----RVSSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTFHDIRAKAASDYEEQGK 141 (162)
T ss_pred CHHHHHHHHHHHHHC-----CCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCH
T ss_conf 899999999999843-----677860763179999778679999999999984997687766018889999999873748
Q ss_pred CHHHHHHHHCCCCHHHHHHHHHC
Q ss_conf 88899998558998998999645
Q gi|255764498|r 254 DLRTIQILLGHTDISTTQIYTHL 276 (300)
Q Consensus 254 ~~~~v~~~lGH~s~~tT~~Y~~~ 276 (300)
.+|.+|||+|++||++|++.
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 38
>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=2.9e-32 Score=206.94 Aligned_cols=167 Identities=27% Similarity=0.323 Sum_probs=126.1
Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCC----------C
Q ss_conf 223320246999986432001256102776543110001221001343334320000011110001112----------2
Q gi|255764498|r 97 PKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQG----------K 166 (300)
Q Consensus 97 ~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~----------K 166 (300)
|++||.||+.++++++... .+++.++.++++||||.||+++|+|+|||++.+.|.|.. |
T Consensus 1 p~plT~eE~~~ll~a~~~~-----------~~~~~~~~l~~~TGlR~gE~~~L~w~dId~~~~~i~v~~~~~~~~~~~~K 69 (196)
T cd01191 1 PDPFTRDEFAALIEAARVC-----------QQEQNLWEFAVFTGLRPSELIALAWEDVDLERGTVYVRRALVRGIFKVPK 69 (196)
T ss_pred CCCCCHHHHHHHHHHCCCC-----------HHHHHHHHHHHHHCCHHHHHHHCCHHHCCCCCCEEEEEEEEEECCCCCCC
T ss_conf 9898999999999806606-----------41899999999979169999707799847568989999616845656887
Q ss_pred C-CCCCCCHHHHHHHHHHHHHHHHHCCC--------------CCCCCCCCCCCCCCCCCCC--CCCCCCCCHHHHHHHCC
Q ss_conf 2-11111000012478875323210012--------------4677752001233322222--11111110123442014
Q gi|255764498|r 167 G-NKERLVILSPSALHALQMYKKTCSSM--------------KMTGNDLWLFPSSTKTGHL--SRQVFARDLKALAARAG 229 (300)
Q Consensus 167 ~-~k~R~ipi~~~~~~~l~~y~~~~~~~--------------~~~~~~~~lf~~~~~~~~~--s~~~~~~~~~~~~~~~g 229 (300)
+ +..|.||+++.+.+.|+++....+.. .......++|.....+.+. ......+.+...++++|
T Consensus 70 t~~~~R~v~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vf~~~~~~~~~~~~~~~~~~~~~~~~~~~g 149 (196)
T cd01191 70 TKAGTRDVDLNPPALAALKEQAKLTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAG 149 (196)
T ss_pred CCCCCCEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf 78853122189999999999999850101024566653114445667745843787788865068999999999999829
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH-HHHHC
Q ss_conf 667642598858899999998588888999985589989989-99645
Q gi|255764498|r 230 IQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQ-IYTHL 276 (300)
Q Consensus 230 i~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~-~Y~~~ 276 (300)
+. ..+||+|||||||.|+++|+|+..||++|||+|++||+ +|+|.
T Consensus 150 i~--~~~~H~lRHT~aT~ll~~G~~~~~v~~~lGHss~~~T~~~Ya~~ 195 (196)
T cd01191 150 IR--YRNPYQMRHTFASWMLTAGANPAFIADQMGHKSAEMVFKHYGKW 195 (196)
T ss_pred CC--CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 99--67777884799999998798999999996899799999998833
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=2.5e-27 Score=178.26 Aligned_cols=147 Identities=42% Similarity=0.577 Sum_probs=121.2
Q ss_pred HHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 654311000122100134333432000001111000111-2221111100001247887532321001246777520012
Q gi|255764498|r 126 RVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ-GKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFP 204 (300)
Q Consensus 126 ~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~-~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~~~~~~lf~ 204 (300)
..|+.+++.+++.||||++|++.|+|+||++++..+.|. .|+++.|.||+++.+...|.+|...... ......+||+
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-CCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 33322-222111111101234420146676425988588999999985888889999855899899899964
Q gi|255764498|r 205 SSTKT-GHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTH 275 (300)
Q Consensus 205 ~~~~~-~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~ 275 (300)
...++ .+.+...++..++++....|.. .++++|+|||||||.++++|+++..|+.++||+++.||++|++
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~h~lRh~~~t~~~~~g~~~~~i~~~~GH~~~~~t~~Y~~ 162 (162)
T cd01182 92 SRRGGPKRLTRRAVRRLLKKAGKRAGIP-ERLTPHDLRHTFATRLLEAGVPLEVIQELLGHSSISTTERYLH 162 (162)
T ss_pred ECCCCCCCCHHHHHHHHHHHHHHHCCCC-CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHCCCCCC
T ss_conf 2689976510356777666555413787-8997016199999999996999999999928999898152819
No 40
>COG0582 XerC Integrase [DNA replication, recombination, and repair]
Probab=99.86 E-value=9.5e-21 Score=139.95 Aligned_cols=221 Identities=36% Similarity=0.498 Sum_probs=149.2
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf 999999999977998435322101123343210001222222122221-2122211122332024699998643200125
Q gi|255764498|r 41 HLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLE-LPKKNHILPKTLHKDTIANLLEQAKIEAENP 119 (300)
Q Consensus 41 ~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~~~i~-~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~ 119 (300)
.+..+....... +..+.+.....++.++.|+...+ +|...+. .++.....++.++.+++..++..+...
T Consensus 72 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~---- 141 (309)
T COG0582 72 ELRGKLETALRE--STLTRVFRLAALRGFFAYLDNPG----APLKALREKPKRRKKLPKALTAEEVEALLEALDRY---- 141 (309)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHCCCC----CHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH----
T ss_conf 888999999764--47779999999988888621631----04666531134454454548999999999998750----
Q ss_pred CCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCC---CCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 6102776543110001221001343334320000011110001112---2211111000012478875323210012467
Q gi|255764498|r 120 APGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQG---KGNKERLVILSPSALHALQMYKKTCSSMKMT 196 (300)
Q Consensus 120 ~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~---K~~k~R~ipi~~~~~~~l~~y~~~~~~~~~~ 196 (300)
....++.+++. .||||.+|+++|+|+|+++....+.+.. |+++.|.+|+++.+...+..|........
T Consensus 142 ----~~~~~~~~~~~---~tG~R~~E~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-- 212 (309)
T COG0582 142 ----RDALRLALLIL---LTGLRVSELLGLRWSDIDLENGTIWIRGTKTKGRKERRVPLSEQALEALKKYLLIRRPRE-- 212 (309)
T ss_pred ----HHHHHHHHHHH---HHCCCHHHHHHCCHHHCCCCCCEEEEEECCCCCCCCEEEEECHHHHHHHHHHHHHCCCCC--
T ss_conf ----57899999998---718779999827666505456727996135556651589605999999999998544433--
Q ss_pred CCCCCCCCCCCCCCCC----CCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHH
Q ss_conf 7752001233322222----111111101234420146676425988588999999985888889999855899899899
Q gi|255764498|r 197 GNDLWLFPSSTKTGHL----SRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQI 272 (300)
Q Consensus 197 ~~~~~lf~~~~~~~~~----s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~ 272 (300)
++|+........ +...+...+...+...|+. .++||+||||+++.+++.| +...|++++||++..+|+.
T Consensus 213 ----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~h~lRht~~~~~~~~~-~~~~~~~~~gH~~~~~~~~ 285 (309)
T COG0582 213 ----YLFLSLRGPRLSRSALTINRLLRARAKAAKEAGIR--KITPHGLRHTFATLLLAGG-DERVIQKLLGHASLNTTQT 285 (309)
T ss_pred ----CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC--CCCCCCCHHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHH
T ss_conf ----00653235653310367999999999973222788--8787740789999998568-7658999837870878999
Q ss_pred HH-HCCHHHHHHHHHH
Q ss_conf 96-4599999999998
Q gi|255764498|r 273 YT-HLLPDKLQKLVQD 287 (300)
Q Consensus 273 Y~-~~~~~~~~~~~~~ 287 (300)
|. +...+...+....
T Consensus 286 ~~~~~~~~~~~~~~~~ 301 (309)
T COG0582 286 VYYHASDERLKEAALK 301 (309)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9998710667899986
No 41
>pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain.
Probab=99.61 E-value=1.8e-15 Score=109.32 Aligned_cols=77 Identities=38% Similarity=0.599 Sum_probs=73.2
Q ss_pred CCHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 96466413899999999999999999754499868899999999999999779984353221011233432100012
Q gi|255764498|r 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEG 77 (300)
Q Consensus 1 ~l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~ 77 (300)
+|..|||+|++|+.+|..+|+.|..|+.....++.+++..++.+|+.++.++|++++|+++.+++|++||+|+..+|
T Consensus 7 ~L~~er~~S~~Ti~aY~~dL~~f~~~l~~~~~~~~~i~~~~i~~yl~~l~~~~~s~~Ti~r~lsalr~F~~~l~~eG 83 (83)
T pfam02899 7 YLSLERGLSPNTVRAYRRDLKAFLKFLAEGGLSLDQLTTDDVRAFLAELLREGLSAASLARRLSALRSFFQFLKREG 83 (83)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99988584999999999999999999987499988868998999999987089889999999999999999999719
No 42
>PHA00730 int integrase
Probab=98.44 E-value=2.2e-06 Score=56.38 Aligned_cols=199 Identities=23% Similarity=0.334 Sum_probs=107.8
Q ss_pred HHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 99999997544998688999999999999997799843532210112334321000122222212222121222111223
Q gi|255764498|r 20 LKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKT 99 (300)
Q Consensus 20 l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~~~i~~~k~~~~~~~~ 99 (300)
+..|.+|+-.+ ..++.+.+.+|+..+.. +... -|+.+.+.+.|++|....+ |...++..| ....-+.
T Consensus 98 ~~effe~~l~~----k~ise~T~K~Yv~~l~k-p~~~--sn~~~kA~r~f~~~~~~r~-----~~~~lK~kK-~~pDl~V 164 (322)
T PHA00730 98 NSEFFELTLRQ----RKISEKTIKDYINCIKQ-PRKE--SNNCIKAYRLFYRFLLNRD-----PPKELKVKK-TKPDLRI 164 (322)
T ss_pred HHHHHHHHHHH----CCCCHHHHHHHHHHHHH-HHHH--HHHHHHHHHHHHHHHHCCC-----CHHHHHHCC-CCCCCCC
T ss_conf 89999999875----26768899999999875-6554--0214999999999972246-----377652203-6886247
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCH-----HHHHHHHHCCCCCCCCCCCCCCH
Q ss_conf 3202469999864320012561027765431100012210013433343200-----00011110001112221111100
Q gi|255764498|r 100 LHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSA-----HTLNLTERTMIIQGKGNKERLVI 174 (300)
Q Consensus 100 ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~-----~di~~~~~~i~v~~K~~k~R~ip 174 (300)
.|.||+.+.|+.+... . +-+++..|++.+|.|.+|++.+-- .||+ +++.... |
T Consensus 165 PT~eeVk~tL~~~key-~----------~vy~vYrllLESG~RlsEaLkvLn~y~p~~dv~-e~~~~~y----------~ 222 (322)
T PHA00730 165 PTLEEIKRTLQLVKEY-E----------NLYLLYRLLLESGSRLSEALKVLNNYNPQNDIR-EDGFSIY----------I 222 (322)
T ss_pred CCHHHHHHHHHHHCCC-C----------CHHHHHHHHHHHCHHHHHHHHHHHCCCHHHHCC-CCCEEEE----------E
T ss_conf 8889999999875047-6----------414689999871302899999974148054303-5876999----------8
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 001247887532321001246777520012333-2222211111110123442014667642598858899999998588
Q gi|255764498|r 175 LSPSALHALQMYKKTCSSMKMTGNDLWLFPSST-KTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGA 253 (300)
Q Consensus 175 i~~~~~~~l~~y~~~~~~~~~~~~~~~lf~~~~-~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~ 253 (300)
+ .|.+ ......++|.-.. +.-.++...+.+.+++. + -+-|--+|..+||.|++-|+
T Consensus 223 L-----~w~R----------g~K~~fy~fhit~Lk~~~It~~~i~~~~~~~----~----~v~~KYiRKfvatKm~elgi 279 (322)
T PHA00730 223 L-----NWTR----------GQKKSFYLFHITPLKQIKITKAYIDKYVRRL----N----LVPPKYIRKFVATKMLELGI 279 (322)
T ss_pred E-----HHHC----------CCCCEEEEEEECCCEEEEECHHHHHHHHHCC----C----CCCHHHHHHHHHHHHHHHCC
T ss_conf 3-----2221----------6775699999425424566188886665404----6----68789999999999999689
Q ss_pred CHHHHHHHHCCCCHHH-HHHHHHC
Q ss_conf 8889999855899899-8999645
Q gi|255764498|r 254 DLRTIQILLGHTDIST-TQIYTHL 276 (300)
Q Consensus 254 ~~~~v~~~lGH~s~~t-T~~Y~~~ 276 (300)
|.++|-=+-|-..-+. |++|+.+
T Consensus 280 p~dvvdFiqGR~p~~ilt~HY~dL 303 (322)
T PHA00730 280 PSEVVDFIQGRTPSRILTKHYLDL 303 (322)
T ss_pred CHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 688999964788550468999999
No 43
>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=98.36 E-value=6.1e-07 Score=59.64 Aligned_cols=64 Identities=25% Similarity=0.340 Sum_probs=53.2
Q ss_pred CCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHCCCCHHHHHH-HH
Q ss_conf 22221111111012344201466764259885889999999858-88889999855899899899-96
Q gi|255764498|r 209 TGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGG-ADLRTIQILLGHTDISTTQI-YT 274 (300)
Q Consensus 209 ~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G-~~~~~v~~~lGH~s~~tT~~-Y~ 274 (300)
..+++.++++..+++.++.+|+.. .+++|+||.+.|..+ ++| ++...=..+|||++..|-.. |.
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 DQALTASTLNSWLKRLGEIAGFED-PLTPYCLRYGAAKAL-NSGEVSEAERNLILGHASSRTFLKHYL 235 (414)
T ss_pred CCCCCHHHHHHHHHHHHHHHCCCC-CCCCHHHHHHHHHHC-CCCCCCHHHHHHHHCCCCCCHHHHHCC
T ss_conf 778898999999999988841111-454002357899852-665699899978744787405776256
No 44
>COG4342 Uncharacterized protein conserved in archaea [Function unknown]
Probab=98.31 E-value=1.3e-05 Score=51.93 Aligned_cols=220 Identities=19% Similarity=0.245 Sum_probs=113.2
Q ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC-CCCCCC--CCCC-CCHHHHHHHHHH
Q ss_conf 999999999999997799843532210112334321000122222212222121-222111--2233-202469999864
Q gi|255764498|r 37 ASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELP-KKNHIL--PKTL-HKDTIANLLEQA 112 (300)
Q Consensus 37 i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~np~~~i~~~-k~~~~~--~~~l-s~~e~~~ll~~~ 112 (300)
+......+|+..+..-=-+.+...++..+.+.|.+||...|++..+.+..+..+ |..+.. .-++ +++++.+-++..
T Consensus 55 ~~~k~ardyls~l~r~ig~~~~kdKy~kA~R~f~~fl~~rgiise~~Ae~lrk~lk~k~~~g~dlyIp~de~ir~~~~l~ 134 (291)
T COG4342 55 LCGKTARDYLSALNRPIGSVREKDKYQKAYRLFIKFLTSRGIISEEFAEKLRKPLKVKKSNGVDLYIPSDEEIRATEELA 134 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCEECCCHHHHHHHHHHH
T ss_conf 65789999999988764431100579999999999998704133999999999864576788633249879998899999
Q ss_pred HHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 32001256102776543110001221001343334320000011110001112221111100001247887532321001
Q gi|255764498|r 113 KIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSS 192 (300)
Q Consensus 113 ~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~ 192 (300)
.... -|...++.++..+|+|.+|++.+-.+ .|-+.-...+.|++ -..-|++ +.+-
T Consensus 135 r~~~----------e~~y~v~~ll~~SGaRLse~v~~L~~-~D~s~~~~~~ng~~--icyy~l~-----w~rg------- 189 (291)
T COG4342 135 REYS----------ERAYLVYLLLLFSGARLSEAVAVLRN-LDHSRLYCVVNGKV--ICYYPLS-----WSRG------- 189 (291)
T ss_pred HHHC----------CHHHHHHHHHHHCCCHHHHHHHHHHC-CCHHHHEEECCCEE--EEEECCC-----HHHC-------
T ss_conf 8854----------01899999998634309999999967-14312023128737--8850110-----3204-------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC-CCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCH-HHH
Q ss_conf 2467775200123332222211111-11012344201466764259885889999999858888899998558998-998
Q gi|255764498|r 193 MKMTGNDLWLFPSSTKTGHLSRQVF-ARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDI-STT 270 (300)
Q Consensus 193 ~~~~~~~~~lf~~~~~~~~~s~~~~-~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~-~tT 270 (300)
....-|+|.....+.++..-.+ +..+....... ++..--+|.-.+|.|++.|+|..+|-=+-||+-- -.|
T Consensus 190 ---~K~afyif~P~~~~~~l~kidisy~~vq~~~~~~-----~Vk~kyiRkwv~nkmlelgvP~~VvdFIqGrk~~~V~~ 261 (291)
T COG4342 190 ---HKRAFYIFHPKDFAESLRKIDISYHRVQRFENRR-----GVKAKYIRKWVYNKMLELGVPEDVVDFIQGRKQSRVGT 261 (291)
T ss_pred ---CCCEEEEECCHHHHHHCHHCCCHHHHHHHHHHCC-----CCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHH
T ss_conf ---5411568663665200110111299999998605-----82099999999999998099588999987467221578
Q ss_pred HHHHHCCHHHHHHHHHHHCC
Q ss_conf 99964599999999998280
Q gi|255764498|r 271 QIYTHLLPDKLQKLVQDYHP 290 (300)
Q Consensus 271 ~~Y~~~~~~~~~~~~~~~~p 290 (300)
++|+.+.. ..++-+.++-|
T Consensus 262 rHY~nL~~-~Ake~Y~kyl~ 280 (291)
T COG4342 262 RHYANLLG-QAKEWYSKYLE 280 (291)
T ss_pred HHHHHHHH-HHHHHHHHHHH
T ss_conf 99999999-99999999999
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=97.45 E-value=0.00069 Score=41.86 Aligned_cols=134 Identities=24% Similarity=0.332 Sum_probs=81.5
Q ss_pred HCCCHHHHHCCCCCC-----------CCCCCHHHHHHHHHCCCC--CCCCCCCCCCHHH-HHHHHHHHHHHHHHCCCCCC
Q ss_conf 100012210013433-----------343200000111100011--1222111110000-12478875323210012467
Q gi|255764498|r 131 LLIELLYATGMRVSE-----------LVTLSAHTLNLTERTMII--QGKGNKERLVILS-PSALHALQMYKKTCSSMKMT 196 (300)
Q Consensus 131 ~il~ll~~tGlR~~E-----------i~~L~~~di~~~~~~i~v--~~K~~k~R~ipi~-~~~~~~l~~y~~~~~~~~~~ 196 (300)
+++.|+-.|.+|+|- ++.|+..+|.++++.+.+ .||.|+.+.+-|. +.+...|+.... ..+
T Consensus 58 ~~~~Lld~~~iRvGne~Y~~~n~S~GltTLr~~Hv~i~~~~i~~~F~GK~gv~~~~~v~d~~l~~~l~~l~~-----~~p 132 (244)
T pfam01028 58 VAVYLLDKTALRVGNEKYARENATVGLTTLRNRHVTLEGDVIRFDFLGKDGIRHENTVRDKRLAKNLKRLKQ-----KLP 132 (244)
T ss_pred HHHHHHHHHCCCCCCHHHHHHCCCCCEEECCCCCEEEECCEEEEEEECCCCCEEEEEECCHHHHHHHHHHHH-----CCC
T ss_conf 999999984413687434553398650100104478989989999877987478988688899999999985-----299
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHH-----HHHCCCC--------------HHH
Q ss_conf 775200123332222211111110123442014667642598858899999-----9985888--------------889
Q gi|255764498|r 197 GNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASH-----LLEGGAD--------------LRT 257 (300)
Q Consensus 197 ~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~-----l~~~G~~--------------~~~ 257 (300)
+++.|-+..+....+++...++..++++.. .++|+.+||=-.||- |.+.+.+ +..
T Consensus 133 g~~LF~y~~~g~~~~v~s~dvN~yLk~~~g------~~~TaKdFRTw~at~~a~~~L~~~~~~~~~~~~~k~~i~~a~~~ 206 (244)
T pfam01028 133 GDELFQYLDDGERDRVSSSDLNAYLRELMG------EGFTAKDFRTWNASVTALEALAELGKSLESVAEKKKAINAANKE 206 (244)
T ss_pred CCHHEEEECCCCEEECCHHHHHHHHHHHHC------CCCCHHHHHHHCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf 732168716996342788999999999835------88752122221207999999996589988999999999999999
Q ss_pred HHHHHCCCCHHHH-HHHHHC
Q ss_conf 9998558998998-999645
Q gi|255764498|r 258 IQILLGHTDISTT-QIYTHL 276 (300)
Q Consensus 258 v~~~lGH~s~~tT-~~Y~~~ 276 (300)
|+..|||+- ++. .-|+|.
T Consensus 207 vA~~LgnTp-aV~R~sYi~p 225 (244)
T pfam01028 207 VAILLGNTP-AVSRKSYIHP 225 (244)
T ss_pred HHHHHCCCC-CCHHHHCCCH
T ss_conf 999858984-1137744587
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=97.02 E-value=0.0026 Score=38.54 Aligned_cols=130 Identities=22% Similarity=0.307 Sum_probs=77.5
Q ss_pred HHCCCHHHHHCCCCCC-----------CCCCCHHHHHHHHHCCCC--CCCCCCCCCCHHH--HHHHHHHHHHHHHHCCCC
Q ss_conf 1100012210013433-----------343200000111100011--1222111110000--124788753232100124
Q gi|255764498|r 130 FLLIELLYATGMRVSE-----------LVTLSAHTLNLTERTMII--QGKGNKERLVILS--PSALHALQMYKKTCSSMK 194 (300)
Q Consensus 130 ~~il~ll~~tGlR~~E-----------i~~L~~~di~~~~~~i~v--~~K~~k~R~ipi~--~~~~~~l~~y~~~~~~~~ 194 (300)
.+++.|+-.|++|+|- ++.|+..+|.++++.+.+ .||.|+.+.+-|. +.+...+..... .
T Consensus 44 A~~v~LlD~~~~RvGne~Ya~en~SyGltTLr~~Hv~~~~~~i~~~F~GK~gv~~~~~i~d~~~l~~~~~~~~~-----~ 118 (218)
T cd00659 44 ATAVYLIDKFALRVGNEKYERENDTVGLCTLRKEHVTLKPNVVRFDFLGKDSIRYENEVEVEPRLFKNLRKFLD-----K 118 (218)
T ss_pred HHHHHHHHHHCEECCCCCCCCCCCCEEEEEECHHHEEEECCEEEEEEECCCCCEEEEEEECCHHHHHHHHHHHH-----C
T ss_conf 99999999856416882333137976255401311657699899998568882899997065999999999973-----6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHH-----HCCCC-------------HH
Q ss_conf 6777520012333222221111111012344201466764259885889999999-----85888-------------88
Q gi|255764498|r 195 MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLL-----EGGAD-------------LR 256 (300)
Q Consensus 195 ~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~-----~~G~~-------------~~ 256 (300)
.++++ ||.... ..+++...++..++++. .++|+-+||=-.||.++ +...+ +.
T Consensus 119 ~pg~~--LF~y~~-~~~v~s~~vN~yLk~~~-------~~~TaKdFRTw~at~~~~~~L~~~~~~~s~~~~k~~i~~a~~ 188 (218)
T cd00659 119 LPGDD--LFQYLQ-VDRLNSSKLNAYLREFM-------EGLTAKVFRTYNASLTALEQLARLPASLSLAEKKKAYNDANR 188 (218)
T ss_pred CCCHH--HEECCC-CCCCCHHHHHHHHHHHC-------CCCCHHCEEEHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 99066--403467-88669899999999975-------999700233137899999999866887788999999999999
Q ss_pred HHHHHHCCCCHHHHH-HHHH
Q ss_conf 999985589989989-9964
Q gi|255764498|r 257 TIQILLGHTDISTTQ-IYTH 275 (300)
Q Consensus 257 ~v~~~lGH~s~~tT~-~Y~~ 275 (300)
.|+..|||+- ++.. -|+|
T Consensus 189 ~vA~~LgnTp-aV~r~sYi~ 207 (218)
T cd00659 189 EVAILLNHTP-AISKINYID 207 (218)
T ss_pred HHHHHHCCCC-CCCHHHCCC
T ss_conf 9999968986-562230588
No 47
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=95.52 E-value=0.032 Score=32.18 Aligned_cols=40 Identities=18% Similarity=0.267 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999999999-779984353221011233432100012
Q gi|255764498|r 38 STNHLISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYEG 77 (300)
Q Consensus 38 ~~~~i~~~~~~l~-~~~~s~~T~~~~~~~l~~~~~~~~~~~ 77 (300)
+.+.|.+|+++|. ++|+|++|+..|.+.|+.|+.|+...+
T Consensus 2 ~~~~i~~fl~~L~~erg~S~~Ti~~Y~~~l~~f~~~l~~~~ 42 (296)
T PRK00283 2 DRALIEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARG 42 (296)
T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 18999999999999879079999999999999999998759
No 48
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=95.48 E-value=0.016 Score=33.90 Aligned_cols=41 Identities=15% Similarity=0.211 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 99999999999779984353221011233432100012222
Q gi|255764498|r 40 NHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRK 80 (300)
Q Consensus 40 ~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~ 80 (300)
.-+.+|+++|.++++|++|+..|...|+.|+.||...|...
T Consensus 25 ~ll~~Fl~yL~er~~S~~Ti~aY~~dL~~F~~fl~~~g~~~ 65 (361)
T PRK01287 25 ALLLRFVEWLQERNWSERTLKVQTHHTYHFILWCEERGLYY 65 (361)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 99999999999839989999999999999999999848999
No 49
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=95.37 E-value=0.018 Score=33.59 Aligned_cols=48 Identities=19% Similarity=0.281 Sum_probs=40.3
Q ss_pred HHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 889999999999999977998435322101123343210001222222
Q gi|255764498|r 35 SAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDN 82 (300)
Q Consensus 35 ~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~n 82 (300)
..--+..+.+|+.++...++|++|+..|...|+.||+|+..++....+
T Consensus 14 ~~~~P~~i~ey~~~~~~~~~Sp~Ti~~Y~~DL~~F~~fL~~~~~~~~~ 61 (360)
T PRK05084 14 KAEMPWYVLEYYQSKLATPYSPTTLYEYLTEYRRFFNWLIDEGLTVAT 61 (360)
T ss_pred HHHCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 886709999999988605989899999999999999999864987555
No 50
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=94.59 E-value=0.082 Score=29.80 Aligned_cols=40 Identities=30% Similarity=0.355 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 9999999999997-799843532210112334321000122
Q gi|255764498|r 39 TNHLISYLNHLSQ-RKLVTSSQRRKISVIRQFYNFLCYEGL 78 (300)
Q Consensus 39 ~~~i~~~~~~l~~-~~~s~~T~~~~~~~l~~~~~~~~~~~~ 78 (300)
.+-|.+|+.++.. +|+|++|+..+...|+.|+.|+...+.
T Consensus 7 ~~~i~~fl~~l~~~r~lS~~Ti~~Y~~~l~~f~~~~~~~~~ 47 (295)
T PRK00236 7 PAALEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEVGL 47 (295)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 99999999999988590799999999999999999987599
No 51
>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=92.49 E-value=0.38 Score=25.93 Aligned_cols=48 Identities=15% Similarity=0.100 Sum_probs=34.8
Q ss_pred CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCH--------------HHCCHHHHHHHHHHH
Q ss_conf 646641389999999999999999975449986--------------889999999999999
Q gi|255764498|r 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEISL--------------SAASTNHLISYLNHL 49 (300)
Q Consensus 2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~--------------~~i~~~~i~~~~~~l 49 (300)
|..++++|++|++.|...++.|..|+...+... .-++.+++..+++.+
T Consensus 22 L~~~~~~s~~Tin~~l~~l~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~lt~eEi~~ll~~~ 83 (242)
T cd01193 22 LAVEGNVSASTQNQALSALLFFYRHTLKRDLPWLQRIRRPRKPRKLPVVLSPEEVRRLLGAL 83 (242)
T ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCCCHHHHHHHHHCC
T ss_conf 99848989999999999999999999876896566565578999899889999999999738
No 52
>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=92.37 E-value=0.092 Score=29.53 Aligned_cols=37 Identities=22% Similarity=0.380 Sum_probs=31.1
Q ss_pred HHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 999999999-7799843532210112334321000122
Q gi|255764498|r 42 LISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYEGL 78 (300)
Q Consensus 42 i~~~~~~l~-~~~~s~~T~~~~~~~l~~~~~~~~~~~~ 78 (300)
+++|+.++. ++|+|++|+..+.+.|+.|+.|+...|.
T Consensus 1 i~~fl~~l~~~r~lS~~T~~~Y~~~l~~f~~~~~~~~~ 38 (284)
T cd00798 1 IERFLDYLAVERGLSENTLAAYRRDLERFLEFLEERGI 38 (284)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 97899999998590799999999999999999998299
No 53
>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=90.79 E-value=0.3 Score=26.57 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=34.2
Q ss_pred CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC------------C--------HHHCCHHHHHHHHHHH
Q ss_conf 6466413899999999999999999754499------------8--------6889999999999999
Q gi|255764498|r 2 MSSERASSINTLSAYKRDLKEMQNFLNNKEI------------S--------LSAASTNHLISYLNHL 49 (300)
Q Consensus 2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~------------~--------~~~i~~~~i~~~~~~l 49 (300)
|..+||+|++|+..|...|+.|+.|+...+. + +.-++.+++..+++..
T Consensus 20 L~~~rg~s~~Tin~~l~~L~~f~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~l~~eei~~ll~~~ 87 (260)
T cd01190 20 LENDRGNSIRTRNARLAALHSFFRYAAREVPEHLPTIQRVLAIPMKRFKRPLVTYLTREEVQALLAAP 87 (260)
T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCC
T ss_conf 99846999999999999999999999980840145537101488788899999889999999998186
No 54
>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=90.51 E-value=0.26 Score=26.91 Aligned_cols=27 Identities=11% Similarity=0.164 Sum_probs=22.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 779984353221011233432100012
Q gi|255764498|r 51 QRKLVTSSQRRKISVIRQFYNFLCYEG 77 (300)
Q Consensus 51 ~~~~s~~T~~~~~~~l~~~~~~~~~~~ 77 (300)
+++.|++|++.+...++.|..|+...+
T Consensus 30 ~k~~S~~Ti~~Y~~~l~~f~~Fl~~~~ 56 (299)
T cd01185 30 GKDKAQSTWKRYRTHLKNLREFIECTY 56 (299)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 775679999999999999999999828
No 55
>pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain.
Probab=90.50 E-value=0.18 Score=27.79 Aligned_cols=35 Identities=26% Similarity=0.383 Sum_probs=29.9
Q ss_pred HHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999999999-77998435322101123343210001
Q gi|255764498|r 42 LISYLNHLS-QRKLVTSSQRRKISVIRQFYNFLCYE 76 (300)
Q Consensus 42 i~~~~~~l~-~~~~s~~T~~~~~~~l~~~~~~~~~~ 76 (300)
|++|+.++. ++++|++|+..+...|+.|+.|+...
T Consensus 1 i~~fl~~L~~er~~S~~Ti~aY~~dL~~f~~~l~~~ 36 (83)
T pfam02899 1 IDQFLEYLSLERGLSPNTVRAYRRDLKAFLKFLAEG 36 (83)
T ss_pred CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 988899999885849999999999999999999874
No 56
>COG4688 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.95 E-value=1.2 Score=23.13 Aligned_cols=52 Identities=17% Similarity=0.339 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH
Q ss_conf 2598858899999998588888999985589989989996459999999999
Q gi|255764498|r 235 ISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286 (300)
Q Consensus 235 ~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~ 286 (300)
+-.|.+||-.-|.+...|+|.-.|+.+.|-++++----|-|-+..+.-+++.
T Consensus 448 L~SH~lRHllnT~a~r~Gmde~~ia~w~gR~~Vaqn~~YDHRs~~e~s~~Ir 499 (665)
T COG4688 448 LESHMLRHLLNTEAFRLGMDETIIAKWFGRRSVAQNYEYDHRSLAEQSDQIR 499 (665)
T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf 4357888988788887470478888763303554212423141888865422
No 57
>pfam05202 Flp_C Recombinase Flp protein.
Probab=87.48 E-value=1.1 Score=23.21 Aligned_cols=143 Identities=21% Similarity=0.229 Sum_probs=71.2
Q ss_pred HHCCCHHHHHCCCCCCCCCCCHHHHHHHHH-----CCC--C-CCCCCCCCCC---HHHHH--HHHHHHHHHHHHCCCCCC
Q ss_conf 110001221001343334320000011110-----001--1-1222111110---00012--478875323210012467
Q gi|255764498|r 130 FLLIELLYATGMRVSELVTLSAHTLNLTER-----TMI--I-QGKGNKERLV---ILSPS--ALHALQMYKKTCSSMKMT 196 (300)
Q Consensus 130 ~~il~ll~~tGlR~~Ei~~L~~~di~~~~~-----~i~--v-~~K~~k~R~i---pi~~~--~~~~l~~y~~~~~~~~~~ 196 (300)
..|+.+-+.-+||.+++.++.++-+.+-.. .++ | .+|++++|.| |+... ..-.|.+|+....+.+..
T Consensus 43 ~flll~tf~NCcR~sDLkN~DP~TFeiv~nk~lG~ilra~V~eTKTr~~R~IyFfPv~gr~DpllaL~d~l~~~~Pv~Ks 122 (244)
T pfam05202 43 RFLLLATFFNCCRHSDLKNADPKTFEIVKNKFLGRILRALVTETKTRKSRFIYFFPVNGRCDPLLALHDYLRETEPVPKS 122 (244)
T ss_pred HHHHHHHHHHHHCCHHCCCCCCCCEEEECCCHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCC
T ss_conf 99999999845210001458943157624520545776420225566510499974489876468799998742887644
Q ss_pred CCCCCCCCCCCCCCCCCC----CCCCCCHHHHHHH--CCCCCCCCCHHHHHHHHHHHHHHCCCCHHH--HHHHHCCCC-H
Q ss_conf 775200123332222211----1111101234420--146676425988588999999985888889--999855899-8
Q gi|255764498|r 197 GNDLWLFPSSTKTGHLSR----QVFARDLKALAAR--AGIQKKNISPHIIRHAFASHLLEGGADLRT--IQILLGHTD-I 267 (300)
Q Consensus 197 ~~~~~lf~~~~~~~~~s~----~~~~~~~~~~~~~--~gi~~~~~t~H~lRht~at~l~~~G~~~~~--v~~~lGH~s-~ 267 (300)
-...- .+ ....++=+ .+..+.+.+.... .+|.. +--.|--||-.++.|-.++.+..+ ...|.+-.+ +
T Consensus 123 rts~~--~s-~q~~Qllrdslv~~YdrFl~k~~~e~iF~I~n-GPKSHlGRHLM~SyLs~~~l~~~vs~~GNWsa~~~~~ 198 (244)
T pfam05202 123 RTSNR--ES-NQEYQLLRDSLVRSYDRFLAKHAPEPIFAIKN-GPKSHLGRHLMASYLSNNELGEWVSPYGNWSAGDDEI 198 (244)
T ss_pred CCCCC--CH-HHHHHHHHHHHHHHHHHHHHHCCCCCEEECCC-CCHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCHH
T ss_conf 34564--11-56788889888888999997379876451478-9667887899998853056775111466624344414
Q ss_pred HH-H--HHHHHC
Q ss_conf 99-8--999645
Q gi|255764498|r 268 ST-T--QIYTHL 276 (300)
Q Consensus 268 ~t-T--~~Y~~~ 276 (300)
++ + ..|+|.
T Consensus 199 ~S~vARs~Y~H~ 210 (244)
T pfam05202 199 ESAVARSKYTHG 210 (244)
T ss_pred HHHHHHHCCCCC
T ss_conf 656654203456
No 58
>cd00217 INT_Flp Flp recombinase, C-terminal catalytic domain. Yeast Flp-like recombinases mediate the amplification of the 2 micron circular plasmid copy number by catalyzing the intra-molecular recombination between two inverted repeats during replication. They belong to the DNA breaking-rejoining enzyme superfamily, which also includes prokaryotic tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism. Flp-like recombinases are almost exclusively found in yeast and are highly diverged in sequence from the prokaryotic tyrosine recombinases. They cleave their target DNA in trans with a composite active site in which the catalytic tyrosine is provided by a promoter bound to a site other than the one being cleaved. Thus each active site within Flp complexes is assembled by domain swapping and contains catalytic residues from two different monomers. T
Probab=81.66 E-value=2.9 Score=20.81 Aligned_cols=140 Identities=20% Similarity=0.250 Sum_probs=69.8
Q ss_pred HCCCHHHHHCCCCCCCCCCCHHHHHHHHH-----CCCC---CCCCCCCCCC---HHHH--HHHHHHHHHHHHHCCCCCCC
Q ss_conf 10001221001343334320000011110-----0011---1222111110---0001--24788753232100124677
Q gi|255764498|r 131 LLIELLYATGMRVSELVTLSAHTLNLTER-----TMII---QGKGNKERLV---ILSP--SALHALQMYKKTCSSMKMTG 197 (300)
Q Consensus 131 ~il~ll~~tGlR~~Ei~~L~~~di~~~~~-----~i~v---~~K~~k~R~i---pi~~--~~~~~l~~y~~~~~~~~~~~ 197 (300)
.++.+-+.-++|.+++.++...-+..-.. .++. .+|++++|.| |+.. +..-.|.+|+....+....-
T Consensus 169 ~ll~~tffNCcR~sDlkN~Dp~tFeiv~n~~lG~ilra~V~eTKtr~~R~iyFfp~~g~~DplvaL~d~l~~~~P~~Ks~ 248 (339)
T cd00217 169 FLLLATFFNCCRYSDLKNLDPKTFEIVPNKFLGVILRALVTETKTRKTRFIYFFPVRGRCDPLVALHDLLRHTTPTKKSR 248 (339)
T ss_pred HHHHHHHHCCCCHHHHHCCCHHHHHCCCCHHHHHHHEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCC
T ss_conf 99998770642077675238576510563055446002321355675105999754898763787999987438876443
Q ss_pred ------CCCCCCCCCCCCCCCCCCCCCCCHHHHHHH--CCCCCCCCCHHHHHHHHHHHHHHCCCCHHH--HHHHHCCCCH
Q ss_conf ------752001233322222111111101234420--146676425988588999999985888889--9998558998
Q gi|255764498|r 198 ------NDLWLFPSSTKTGHLSRQVFARDLKALAAR--AGIQKKNISPHIIRHAFASHLLEGGADLRT--IQILLGHTDI 267 (300)
Q Consensus 198 ------~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~--~gi~~~~~t~H~lRht~at~l~~~G~~~~~--v~~~lGH~s~ 267 (300)
+.+|-+.-.. ...++.+.+.+.... .+|.. +--.|--||-+++-|..+|.+..+ +..|.+-...
T Consensus 249 ~s~~~s~q~~Qllrds-----l~~~ydrFi~K~~~~~iF~I~~-GPKSHlGRHLmtsfLs~~~l~~~~~~~GNWs~~~~~ 322 (339)
T cd00217 249 TSNRNSDQEWQLLRES-----LVNSYDRFLNKHADESIFAIKN-GPKSHLGRHLMTSFLSDNELGELVSSLGNWSASREI 322 (339)
T ss_pred CCCCCCHHHHHHHHHH-----HHHHHHHHHHHCCCCCEEECCC-CCHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCHHH
T ss_conf 4575305678888988-----8887999997279875440578-966777788999884415676401046664233006
Q ss_pred -HHH--HHHHHC
Q ss_conf -998--999645
Q gi|255764498|r 268 -STT--QIYTHL 276 (300)
Q Consensus 268 -~tT--~~Y~~~ 276 (300)
+.+ ..|+|.
T Consensus 323 ~s~vAr~~Y~H~ 334 (339)
T cd00217 323 ISAVARSDYTHG 334 (339)
T ss_pred HHHHHHHCCCCC
T ss_conf 777764034432
No 59
>TIGR00973 leuA_bact 2-isopropylmalate synthase; InterPro: IPR005671 The branched-chain amino acids are synthesised by a common pathway that leads from pyruvate and alpha-ketobutyrate to valine and isoleucine, and a branch that leads from the immediate precursor of valine, alpha-ketoisovalerate, to leucine . This pathway operates in archaea, bacteria, fungi and plants, but not mammals, making the enzymes suitable targets for the development of novel antibiotics and herbicides. Isopropylmalate synthase is the enzyme responsible for the the first committed step in the leucine branch of this biosynthetic pathway, the conversion of alpha-ketoisovalerate to alpha-isopropylmalate. It is either dimeric or tetrameric, depending on the organism, with a monomer molecular mass of 60-70 kDa, a dependence on divalent metal ions for activity, and an alkaline pH optimum , , , . Like many other biosynthetic enzymes it is subject to feedback inhibition by the end product of the pathway, leucine. This entry represents the isopropylmalate synthase most commonly found in bacteria. A related form of this enzyme is found mainly in eukaryotes and some other bacteria (IPR005668 from INTERPRO). A homologous family in archaea may represent isozymes and/or related enzymes (IPR005675 from INTERPRO). ; GO: 0003852 2-isopropylmalate synthase activity, 0009098 leucine biosynthetic process.
Probab=73.24 E-value=5.9 Score=19.03 Aligned_cols=53 Identities=34% Similarity=0.509 Sum_probs=40.8
Q ss_pred HHCCCCCCC--CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHHCCCCCC
Q ss_conf 201466764--25988588999999985888889999855899899899964599999999998280111001127
Q gi|255764498|r 226 ARAGIQKKN--ISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHY 299 (300)
Q Consensus 226 ~~~gi~~~~--~t~H~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~~~~~~~ 299 (300)
+..|++... ++-||-||.+-.+|-+-|.+ .+.+.+.+.+++|--||-|+||=|
T Consensus 331 E~iG~~~~~lvLg~~SGR~A~k~rL~~lGf~---------------------~~~~~l~k~F~~F~eLADkKkev~ 385 (514)
T TIGR00973 331 EDIGLTKEQLVLGKHSGRHALKKRLEELGFK---------------------LDEEELDKLFEKFKELADKKKEVY 385 (514)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC---------------------CCHHHHHHHHHHHHHHHHCCCCEE
T ss_conf 0048652121122444689998899982878---------------------575579899998887530378510
No 60
>smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
Probab=63.15 E-value=11 Score=17.46 Aligned_cols=82 Identities=23% Similarity=0.348 Sum_probs=49.2
Q ss_pred CCCHHHHHCCCCC-C----------CCCCCHHHHHHHH-HCCC--CCCCCCC--CCCCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 0001221001343-3----------3432000001111-0001--1122211--11100001247887532321001246
Q gi|255764498|r 132 LIELLYATGMRVS-E----------LVTLSAHTLNLTE-RTMI--IQGKGNK--ERLVILSPSALHALQMYKKTCSSMKM 195 (300)
Q Consensus 132 il~ll~~tGlR~~-E----------i~~L~~~di~~~~-~~i~--v~~K~~k--~R~ipi~~~~~~~l~~y~~~~~~~~~ 195 (300)
.+.|....+||+| | +|+|++.+|.+.. ..+. ..||-+- .-.||+.+.+..-|..+.+ ...
T Consensus 119 A~YlIDklALRaGnEKdedeADTVGcCSLRvEHI~l~~~n~v~fDFLGKDSIRy~n~V~V~~~VfkNL~~F~k----~Kk 194 (391)
T smart00435 119 ALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLKPPNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMK----PKK 194 (391)
T ss_pred HEEEHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCCEEEECCEECCHHHHHHHHHHHC----CCC
T ss_conf 0000578887406766766576311010157655864898068875167642554104448999999999942----899
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 777520012333222221111111012344
Q gi|255764498|r 196 TGNDLWLFPSSTKTGHLSRQVFARDLKALA 225 (300)
Q Consensus 196 ~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~ 225 (300)
+++ -|| ..++++.++..+..+.
T Consensus 195 ~~D--dlF------Drl~ts~LN~hL~~~M 216 (391)
T smart00435 195 PGD--DLF------DRLNTSKLNKHLKELM 216 (391)
T ss_pred CCC--HHH------HCCCHHHHHHHHHHHC
T ss_conf 843--101------0368899988799755
No 61
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=62.43 E-value=9.8 Score=17.72 Aligned_cols=30 Identities=17% Similarity=0.236 Sum_probs=11.1
Q ss_pred CCCHHHHHHHHCCCCHHHHHHHHHCCHHHHH
Q ss_conf 8888899998558998998999645999999
Q gi|255764498|r 252 GADLRTIQILLGHTDISTTQIYTHLLPDKLQ 282 (300)
Q Consensus 252 G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~ 282 (300)
|.+...|+++||- |++|.....|-....++
T Consensus 128 g~s~~EIA~~lgi-s~~tVk~~l~RArk~Lr 157 (161)
T PRK12541 128 GFSYKEIAEMTGL-SLAKVKIELHRGRKETK 157 (161)
T ss_pred CCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
T ss_conf 9999999999893-99999999999999998
No 62
>pfam04852 DUF640 Protein of unknown function (DUF640). This family represents a conserved region found in plant proteins including Resistance protein-like protein.
Probab=49.06 E-value=19 Score=16.07 Aligned_cols=38 Identities=32% Similarity=0.541 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHC--CCCHHHCCHHHHHHHHHHHHHCCC
Q ss_conf 99999999997544--998688999999999999997799
Q gi|255764498|r 17 KRDLKEMQNFLNNK--EISLSAASTNHLISYLNHLSQRKL 54 (300)
Q Consensus 17 ~~~l~~f~~~~~~~--~~~~~~i~~~~i~~~~~~l~~~~~ 54 (300)
+++|+.|.+|+.++ .+++...+..++.+|+.++.+-|.
T Consensus 25 rrdw~tf~qyL~n~rPPl~l~~csg~hvl~FL~~~d~fGk 64 (133)
T pfam04852 25 RRDWNTFGQYLRNQRPPLNLSKCSGNHVLDFLRYLDQFGK 64 (133)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHCCC
T ss_conf 5308999999871699986120683899999998761276
No 63
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=48.51 E-value=19 Score=16.02 Aligned_cols=79 Identities=18% Similarity=0.139 Sum_probs=52.5
Q ss_pred CCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHH-HCCCCHHHHHHHHCCCCHHHH----HHHHHCCHHHHHHHH
Q ss_conf 221111111012344201466764259885889999999-858888899998558998998----999645999999999
Q gi|255764498|r 211 HLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLL-EGGADLRTIQILLGHTDISTT----QIYTHLLPDKLQKLV 285 (300)
Q Consensus 211 ~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~-~~G~~~~~v~~~lGH~s~~tT----~~Y~~~~~~~~~~~~ 285 (300)
.+|...+.+.|++. .|.....+ ...+|-.-|..++ +.+.++..|+..+|-+|.+.. ..|..+++..-|+..
T Consensus 36 ~~S~~~l~r~Fk~~---~G~s~~~Y-i~~~Rl~~A~~lL~~t~~~I~~IA~~~Gf~~~~~F~r~Fkk~~G~tP~~yR~~n 111 (127)
T PRK11511 36 GYSKWHLQRMFKKE---TGHSLGQY-IRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTN 111 (127)
T ss_pred CCCHHHHHHHHHHH---HCCCHHHH-HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHC
T ss_conf 95999999999999---89199999-999999999999998599899999996899889999999998890999999772
Q ss_pred H-----HHCCHHH
Q ss_conf 9-----8280111
Q gi|255764498|r 286 Q-----DYHPLAK 293 (300)
Q Consensus 286 ~-----~~~p~~~ 293 (300)
- -.||++-
T Consensus 112 ~~~~~~~~~p~~~ 124 (127)
T PRK11511 112 MQGESRFLHPLNH 124 (127)
T ss_pred CCCCCCCCCCCCC
T ss_conf 7787665786024
No 64
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=48.05 E-value=20 Score=15.98 Aligned_cols=17 Identities=29% Similarity=0.390 Sum_probs=8.7
Q ss_pred HHHCCCCHHHHHHHHCC
Q ss_conf 99858888899998558
Q gi|255764498|r 248 LLEGGADLRTIQILLGH 264 (300)
Q Consensus 248 l~~~G~~~~~v~~~lGH 264 (300)
+.+.|++...++-.+|+
T Consensus 193 l~~kg~~~~ei~~~tG~ 209 (220)
T pfam07900 193 LTEKGMSEEEIRYITGI 209 (220)
T ss_pred HHHCCCCHHHHHHHHCC
T ss_conf 99867879999999776
No 65
>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD; InterPro: IPR014128 The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM) , .; GO: 0000746 conjugation.
Probab=45.89 E-value=21 Score=15.78 Aligned_cols=81 Identities=20% Similarity=0.256 Sum_probs=47.3
Q ss_pred CCCCCCCCCCCC-----CCCCCCCCCCHHHHHHHCCCCCCC--------CCHHHHHHHHHHHHHHCCCCHHHHHH-----
Q ss_conf 520012333222-----221111111012344201466764--------25988588999999985888889999-----
Q gi|255764498|r 199 DLWLFPSSTKTG-----HLSRQVFARDLKALAARAGIQKKN--------ISPHIIRHAFASHLLEGGADLRTIQI----- 260 (300)
Q Consensus 199 ~~~lf~~~~~~~-----~~s~~~~~~~~~~~~~~~gi~~~~--------~t~H~lRht~at~l~~~G~~~~~v~~----- 260 (300)
+.|||.++.... |+=..++.-+++.+....-=++++ -|.|-|+--..| +.+|.+
T Consensus 414 ~gwLFiSS~~~~H~sL~PLiS~WL~~A~~~lL~L~pn~~RRiW~i~DELPsLHkLp~L~~~--------~AE~RKFGGC~ 485 (613)
T TIGR02759 414 NGWLFISSNAQQHASLKPLISMWLSIASRSLLSLAPNDDRRIWFIMDELPSLHKLPDLAET--------IAEVRKFGGCY 485 (613)
T ss_pred CCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCHHHHHH--------HHHHHHHHHHH
T ss_conf 6631572164668413527899999999887346889997278887323354455104535--------20000324689
Q ss_pred HHCCCCH-HHHHHHHHCC-HHHHHHHHHH
Q ss_conf 8558998-9989996459-9999999998
Q gi|255764498|r 261 LLGHTDI-STTQIYTHLL-PDKLQKLVQD 287 (300)
Q Consensus 261 ~lGH~s~-~tT~~Y~~~~-~~~~~~~~~~ 287 (300)
++||.|. +...+|..-. ...+-+.++.
T Consensus 486 vlG~QS~aQL~~IYG~~~GA~~l~dllnT 514 (613)
T TIGR02759 486 VLGIQSFAQLEKIYGQNAGAATLFDLLNT 514 (613)
T ss_pred HHHHCCHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 88712367765423771458999977765
No 66
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=44.43 E-value=22 Score=15.64 Aligned_cols=71 Identities=21% Similarity=0.203 Sum_probs=45.6
Q ss_pred CCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHCCCCHHHHH----HHHHCCHHHHHHHH
Q ss_conf 22111111101234420146676425988588999999985-88888999985589989989----99645999999999
Q gi|255764498|r 211 HLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEG-GADLRTIQILLGHTDISTTQ----IYTHLLPDKLQKLV 285 (300)
Q Consensus 211 ~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~-G~~~~~v~~~lGH~s~~tT~----~Y~~~~~~~~~~~~ 285 (300)
.+|.+++.+.|++. .|.....+ ...+|-..|-.|++. ..++..|+..+|-+|.+... .+..+++.+.|+.+
T Consensus 243 ~~S~R~l~R~Fk~~---~G~tp~~y-~~~~Rl~~Ar~lL~~t~~si~~IA~~~Gf~~~s~F~r~Fk~~~G~tP~~yR~rF 318 (320)
T PRK09393 243 AMSPRTFLRRFEAA---TGMTPAEW-LLRERLARARDLLESSALSIAQIAARAGFGSEESLRHHFRRRAATSPAAYRKRF 318 (320)
T ss_pred CCCHHHHHHHHHHH---HCCCHHHH-HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 87987999899788---69699999-999999999999876899999999995899999999999998890989999872
No 67
>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=42.86 E-value=13 Score=16.93 Aligned_cols=46 Identities=17% Similarity=0.176 Sum_probs=35.5
Q ss_pred HHHHCCCCCCC---CCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 22100134333---43200000111100011122211111000012478875323210
Q gi|255764498|r 136 LYATGMRVSEL---VTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTC 190 (300)
Q Consensus 136 l~~tGlR~~Ei---~~L~~~di~~~~~~i~v~~K~~k~R~ipi~~~~~~~l~~y~~~~ 190 (300)
.+-||+|.+-. .+|++-+||..+|.++| .||-+...+.+.+|+...
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 68
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=35.06 E-value=32 Score=14.77 Aligned_cols=44 Identities=9% Similarity=0.089 Sum_probs=34.7
Q ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHHH
Q ss_conf 985888889999855899899899964599999999998280111
Q gi|255764498|r 249 LEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAK 293 (300)
Q Consensus 249 ~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~~ 293 (300)
.-.|.+...|++.||= |+.|.....+-....+++.+++.+|-..
T Consensus 141 ~~~g~s~~EIA~~l~i-s~~tVk~~l~RAr~~Lr~~L~e~~~~~~ 184 (186)
T PRK05602 141 YYQGLSNIEAARVMGL-SVDALESLLARARRALRAQLAELPPSED 184 (186)
T ss_pred HHCCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 8638999999999893-9999999999999999999766797624
No 69
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=34.90 E-value=32 Score=14.76 Aligned_cols=70 Identities=14% Similarity=0.071 Sum_probs=47.2
Q ss_pred CCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHCCCCHHHH----HHHHHCCHHHHHH
Q ss_conf 222111111101234420146676425988588999999985-8888899998558998998----9996459999999
Q gi|255764498|r 210 GHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEG-GADLRTIQILLGHTDISTT----QIYTHLLPDKLQK 283 (300)
Q Consensus 210 ~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~-G~~~~~v~~~lGH~s~~tT----~~Y~~~~~~~~~~ 283 (300)
-.+|...+.+.|++.. |..... .....|=..|..++.. ..++..|+..+|-+|.+.. ..+..+++..-|+
T Consensus 31 ~~~S~~~l~r~Fk~~~---g~t~~~-yi~~~Rl~~A~~lL~~t~~~I~eIA~~~Gf~~~~~Fsr~Fkk~~G~tP~~yR~ 105 (107)
T PRK10219 31 SGYSKWYLQRMFRTVT---HQTLGD-YIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRH 105 (107)
T ss_pred HCCCHHHHHHHHHHHH---CCCHHH-HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHH
T ss_conf 8939999999999998---909999-99999999999998869998999999928998899999999988909999986
No 70
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=33.54 E-value=18 Score=16.15 Aligned_cols=32 Identities=19% Similarity=0.416 Sum_probs=17.2
Q ss_pred HHHHHHHCCCCCCCC------CHHHHHHHHHHHHHHCCCCHH
Q ss_conf 123442014667642------598858899999998588888
Q gi|255764498|r 221 LKALAARAGIQKKNI------SPHIIRHAFASHLLEGGADLR 256 (300)
Q Consensus 221 ~~~~~~~~gi~~~~~------t~H~lRht~at~l~~~G~~~~ 256 (300)
+..+.+..|+..+++ ..-.||+.+.+ .|++..
T Consensus 252 LE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~----~G~~~e 289 (292)
T TIGR02394 252 LEEVAKELGLTRERVRQIQVEALKKLRRILER----KGVDRE 289 (292)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH----CCCCHH
T ss_conf 99999872881047899889999999999986----488455
No 71
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=33.02 E-value=34 Score=14.57 Aligned_cols=78 Identities=14% Similarity=0.179 Sum_probs=55.2
Q ss_pred CCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHCCCCH----HHHHHHHHCCHHHHHHHH
Q ss_conf 22111111101234420146676425988588999999985-8888899998558998----998999645999999999
Q gi|255764498|r 211 HLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEG-GADLRTIQILLGHTDI----STTQIYTHLLPDKLQKLV 285 (300)
Q Consensus 211 ~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~-G~~~~~v~~~lGH~s~----~tT~~Y~~~~~~~~~~~~ 285 (300)
.||+..+.+.++ .-|.....+ .-.+|--.|..|+.. ..++..|+..+|=.++ .....|..+++.+-|+.+
T Consensus 169 ~MSpS~LkKkLK----eEGtSFS~y-Lte~RMqkAkqLL~~t~~sI~EIA~~cGY~stSYFIkvFKK~~G~TP~EYRkr~ 243 (274)
T PRK09978 169 LMSPSLLKKKLR----EEETSYSQL-LTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQERS 243 (274)
T ss_pred CCCHHHHHHHHH----HCCCCHHHH-HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHH
T ss_conf 279999999999----849999999-999999999999755898899999983899864899999987098939999999
Q ss_pred HHHCCHHH
Q ss_conf 98280111
Q gi|255764498|r 286 QDYHPLAK 293 (300)
Q Consensus 286 ~~~~p~~~ 293 (300)
.+.||.+-
T Consensus 244 ~~~~~~~~ 251 (274)
T PRK09978 244 AQGLPNRD 251 (274)
T ss_pred HCCCCCCC
T ss_conf 73788741
No 72
>PRK13502 transcriptional activator RhaR; Provisional
Probab=28.06 E-value=42 Score=14.07 Aligned_cols=73 Identities=19% Similarity=0.255 Sum_probs=50.0
Q ss_pred CCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHCCCCHHHH----HHHHHCCHHHHHHHH
Q ss_conf 22111111101234420146676425988588999999985-8888899998558998998----999645999999999
Q gi|255764498|r 211 HLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEG-GADLRTIQILLGHTDISTT----QIYTHLLPDKLQKLV 285 (300)
Q Consensus 211 ~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~-G~~~~~v~~~lGH~s~~tT----~~Y~~~~~~~~~~~~ 285 (300)
.+|+..+.+.|++.. |.....+ ....|=..|..|+.. ..++..|+..+|-+|.+.- ..++.+++.+-|+..
T Consensus 203 ~~S~~~lsr~FK~~t---G~t~~~Y-l~~~Ri~~A~~LL~~t~~sI~eIA~~~GF~d~syF~r~FKk~~G~TP~eYRkl~ 278 (282)
T PRK13502 203 QCSERVLRQQFRAQT---GMTINQY-LRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWRHLS 278 (282)
T ss_pred CCCHHHHHHHHHHHH---CCCHHHH-HHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 979999999999998---9299999-999999999999865999899999980999879999999988890989997131
Q ss_pred HH
Q ss_conf 98
Q gi|255764498|r 286 QD 287 (300)
Q Consensus 286 ~~ 287 (300)
++
T Consensus 279 ~~ 280 (282)
T PRK13502 279 NQ 280 (282)
T ss_pred CC
T ss_conf 04
No 73
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=27.10 E-value=43 Score=13.97 Aligned_cols=52 Identities=19% Similarity=0.145 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCCHH
Q ss_conf 858899999998588888999985589989989996459999999999828011
Q gi|255764498|r 239 IIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA 292 (300)
Q Consensus 239 ~lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~~~~p~~ 292 (300)
..|-.+.- ..-.|.+...|++.||- ++.|.....+-..+.+++.++.+.|..
T Consensus 161 ~qR~vl~L-r~~eglS~~EIAe~Lgi-s~gTVKsrl~RAr~~LR~~Lea~~~~~ 212 (222)
T PRK09647 161 EFRAAVVL-CDIEGLSYEEIAATLGV-KLGTVRSRIHRGRQALRAYLAAHAPHG 212 (222)
T ss_pred HHHHHHHH-HHHCCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 99889987-99639999999999893-999999999999999999987109972
No 74
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=26.94 E-value=44 Score=13.95 Aligned_cols=18 Identities=17% Similarity=0.207 Sum_probs=9.9
Q ss_pred HHCCCHHHHHCCCCCCCC
Q ss_conf 110001221001343334
Q gi|255764498|r 130 FLLIELLYATGMRVSELV 147 (300)
Q Consensus 130 ~~il~ll~~tGlR~~Ei~ 147 (300)
+.+|.|.+.-|+-..|+.
T Consensus 117 R~vl~L~~~egls~~EIA 134 (182)
T PRK12511 117 RAALHLVAIEGLSYQEAA 134 (182)
T ss_pred HHHEEEEEECCCCHHHHH
T ss_conf 501124100799999999
No 75
>pfam09968 DUF2202 Uncharacterized protein domain (DUF2202). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=24.96 E-value=48 Score=13.74 Aligned_cols=18 Identities=11% Similarity=0.139 Sum_probs=11.6
Q ss_pred CCCCCHHHHHHHHHHHHH
Q ss_conf 233202469999864320
Q gi|255764498|r 98 KTLHKDTIANLLEQAKIE 115 (300)
Q Consensus 98 ~~ls~~e~~~ll~~~~~~ 115 (300)
-.++..+++.+.+.+...
T Consensus 64 G~F~npelQ~LYn~L~~~ 81 (162)
T pfam09968 64 GVFTNPDLQELYNQLVEK 81 (162)
T ss_pred CCCCCHHHHHHHHHHHHH
T ss_conf 852887799999999997
No 76
>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=23.61 E-value=51 Score=13.58 Aligned_cols=30 Identities=10% Similarity=0.079 Sum_probs=18.4
Q ss_pred HCCHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 899999999999999779984353221011
Q gi|255764498|r 36 AASTNHLISYLNHLSQRKLVTSSQRRKISV 65 (300)
Q Consensus 36 ~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~ 65 (300)
+++.-+-..|+..+.++|++...|...+++
T Consensus 4 ~Ls~Ie~~~~a~rl~~~G~~~~~I~~aL~v 33 (185)
T pfam07506 4 DLSFIERARFAARLLERGVPRAEIAAALGL 33 (185)
T ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 422999999999999869999999999867
No 77
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=23.15 E-value=52 Score=13.53 Aligned_cols=65 Identities=20% Similarity=0.189 Sum_probs=39.8
Q ss_pred CCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHCCCCHHHH----HHHHHCCHHH
Q ss_conf 21111111012344201466764259885889999999858-888899998558998998----9996459999
Q gi|255764498|r 212 LSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGG-ADLRTIQILLGHTDISTT----QIYTHLLPDK 280 (300)
Q Consensus 212 ~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G-~~~~~v~~~lGH~s~~tT----~~Y~~~~~~~ 280 (300)
+|.+++.+.|++.. |.....+ .+.+|=..|..++..+ .++..|+..+|=+|.+.. ..|...++.+
T Consensus 13 ~S~~~l~~~f~~~~---g~s~~~~-i~~~Rl~~a~~~L~~~~~~i~~ia~~~Gy~~~s~f~r~Fk~~~g~tP~~ 82 (84)
T smart00342 13 MSPRHLQRLFKKET---GTTPKQY-LRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82 (84)
T ss_pred CCHHHHHHHHHHHH---CCCHHHH-HHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHH
T ss_conf 09999999999988---9399999-9999999999999857634999988819999999999999989909999
No 78
>PRK09857 hypothetical protein; Provisional
Probab=22.47 E-value=53 Score=13.45 Aligned_cols=27 Identities=26% Similarity=0.271 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCC
Q ss_conf 858899999998588888999985589
Q gi|255764498|r 239 IIRHAFASHLLEGGADLRTIQILLGHT 265 (300)
Q Consensus 239 ~lRht~at~l~~~G~~~~~v~~~lGH~ 265 (300)
.-.-..|-.|+.+|+|+..|++++|=|
T Consensus 257 ~~~~~iAr~mL~~G~~~~~I~k~TGLS 283 (292)
T PRK09857 257 SKALHIAKIMLESGVPLADIMRFTGLS 283 (292)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCC
T ss_conf 999999999998699989999996979
No 79
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461 Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=22.41 E-value=53 Score=13.44 Aligned_cols=47 Identities=26% Similarity=0.411 Sum_probs=27.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCC--CCCHHHHHHHHHHHHHHCCCCH
Q ss_conf 2001233322222111111101234420146676--4259885889999999858888
Q gi|255764498|r 200 LWLFPSSTKTGHLSRQVFARDLKALAARAGIQKK--NISPHIIRHAFASHLLEGGADL 255 (300)
Q Consensus 200 ~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~--~~t~H~lRht~at~l~~~G~~~ 255 (300)
.|||.+.++-|. ...-|++.+.+||+-. ++|=|+=+||.+ +|+ |.|+
T Consensus 529 SFLF~GPTGVGK------TElak~LA~~LGv~l~RFDMSEYmEKHTVs-RLI--GsPP 577 (774)
T TIGR02639 529 SFLFVGPTGVGK------TELAKQLAEELGVHLLRFDMSEYMEKHTVS-RLI--GSPP 577 (774)
T ss_pred EEEEECCCCCCH------HHHHHHHHHHHCCHHCCCCCHHHHHHHHHH-HHH--CCCC
T ss_conf 888647989625------788999999708200104650446899998-741--6888
No 80
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=21.53 E-value=56 Score=13.34 Aligned_cols=45 Identities=16% Similarity=0.030 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH
Q ss_conf 58899999998588888999985589989989996459999999999
Q gi|255764498|r 240 IRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286 (300)
Q Consensus 240 lRht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~~ 286 (300)
-|-.+. .-.-.|.+...|++.|| -|+.|...+.+.....+++.+.
T Consensus 140 ~r~v~~-L~~~eglS~~EIAe~Lg-is~~TVk~rl~~Ar~~Lr~~l~ 184 (185)
T pfam07638 140 QARLVE-LRFFAGLSNDEIAERLG-VSERTVERNWALARAWLHRELR 184 (185)
T ss_pred HHHHHH-HHHHCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHC
T ss_conf 888988-89975999999999979-6998999999999999998824
No 81
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH; InterPro: IPR011909 Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system . Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterised by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=21.48 E-value=31 Score=14.85 Aligned_cols=32 Identities=6% Similarity=0.096 Sum_probs=19.7
Q ss_pred HHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCC
Q ss_conf 99975449986889999999999999977998
Q gi|255764498|r 24 QNFLNNKEISLSAASTNHLISYLNHLSQRKLV 55 (300)
Q Consensus 24 ~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s 55 (300)
.+|+..+++++..++.+.--++++++.+.|..
T Consensus 16 Kk~L~~~~i~Fe~inid~~pea~d~vk~lGF~ 47 (72)
T TIGR02194 16 KKALEEHGIAFEEINIDEQPEAVDYVKALGFR 47 (72)
T ss_pred HHHHHHCCCCEEEEECCCCHHHHHHHHHCCCE
T ss_conf 76676379961576358884378999874863
No 82
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=20.95 E-value=53 Score=13.48 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=29.1
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHH
Q ss_conf 233202469999864320012561027765431100012210013433343200000
Q gi|255764498|r 98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTL 154 (300)
Q Consensus 98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di 154 (300)
..++++|..++++........ .+.- +++-.+ .-+.|+|+|+++.+....-
T Consensus 16 ~il~~ee~~~~l~~y~i~~~q-LP~I---~~~DPv---a~~lg~~~GdvvkI~R~S~ 65 (79)
T PRK09570 16 EILSEEEAKKLLKEYGIKPEQ-LPKI---KASDPV---VKAIGAKPGDVVKIVRKSP 65 (79)
T ss_pred EECCHHHHHHHHHHHCCCHHH-CCCC---CCCCHH---HHHHCCCCCCEEEEEECCC
T ss_conf 887999999999994959889-9921---351988---8984999996899997577
Done!