Query 002904
Match_columns 868
No_of_seqs 268 out of 579
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 13:08:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0981 DNA topoisomerase I [R 100.0 2E-188 3E-193 1537.9 42.0 649 196-859 1-675 (759)
2 smart00435 TOPEUc DNA Topoisom 100.0 1E-104 2E-109 860.3 30.8 303 542-846 1-304 (391)
3 cd03489 Topoisomer_IB_N_Ldtopo 100.0 1.7E-95 4E-100 731.5 21.0 211 402-614 1-212 (212)
4 cd03490 Topoisomer_IB_N_1 Topo 100.0 1.3E-94 2.7E-99 727.3 21.1 212 402-614 1-217 (217)
5 cd00660 Topoisomer_IB_N Topois 100.0 3.5E-94 7.7E-99 723.2 21.0 211 402-614 1-215 (215)
6 cd03488 Topoisomer_IB_N_htopoI 100.0 3.9E-94 8.4E-99 723.0 21.0 211 402-614 1-215 (215)
7 PF02919 Topoisom_I_N: Eukaryo 100.0 4.8E-93 1E-97 717.3 13.1 211 401-613 1-215 (215)
8 PHA03101 DNA topoisomerase typ 100.0 3E-65 6.6E-70 541.4 21.2 265 546-824 2-284 (314)
9 PF01028 Topoisom_I: Eukaryoti 100.0 7.4E-63 1.6E-67 508.4 12.4 230 615-844 1-234 (234)
10 cd00659 Topo_IB_C DNA topoisom 100.0 1.1E-55 2.4E-60 451.2 18.8 197 618-816 1-203 (218)
11 COG3569 Topoisomerase IB [DNA 100.0 1.9E-51 4E-56 434.5 -8.3 335 383-776 13-354 (354)
12 COG3569 Topoisomerase IB [DNA 100.0 1.4E-45 3.1E-50 389.9 12.1 273 518-824 13-307 (354)
13 cd00397 DNA_BRE_C DNA breaking 96.4 0.01 2.2E-07 54.9 7.5 123 656-812 14-156 (164)
14 PF00589 Phage_integrase: Phag 95.3 0.17 3.6E-06 47.6 10.4 106 656-775 20-141 (173)
15 cd01193 INT_IntI IntI (E2) int 94.8 0.12 2.7E-06 51.3 8.3 100 660-774 89-213 (242)
16 PRK02436 xerD site-specific ty 94.7 0.066 1.4E-06 54.5 6.5 110 662-810 117-235 (245)
17 TIGR02224 recomb_XerC tyrosine 94.7 0.17 3.6E-06 51.5 9.3 117 660-810 132-266 (295)
18 cd01187 INT_SG4 INT_SG4, DNA b 94.5 0.46 1E-05 49.5 12.0 129 658-811 127-277 (299)
19 cd01188 INT_pAE1 pAE1 and rela 94.4 0.41 8.8E-06 46.7 10.9 117 662-811 30-164 (188)
20 cd00801 INT_P4 Bacteriophage P 94.4 0.14 3.1E-06 53.8 8.2 122 659-812 201-332 (357)
21 cd01182 INT_REC_C DNA breaking 93.5 0.37 8E-06 43.7 8.1 123 658-813 16-155 (162)
22 cd01192 INT_P22_C P22-like int 93.5 0.35 7.5E-06 46.6 8.4 119 660-811 24-151 (177)
23 cd01186 INT_SG3_C INT_SG3, DNA 92.9 0.39 8.5E-06 47.1 7.9 116 661-810 28-155 (180)
24 cd01194 INT_Tn554A_C Tn544A an 92.9 0.63 1.4E-05 44.8 9.2 120 660-811 19-164 (186)
25 PRK00283 xerD site-specific ty 92.9 0.75 1.6E-05 47.2 10.2 99 660-774 137-254 (299)
26 PRK01287 xerC site-specific ty 92.8 0.42 9.1E-06 52.1 8.7 118 661-811 161-296 (358)
27 cd01190 INT_SG5 INT_SG5, DNA b 92.6 0.87 1.9E-05 46.1 10.0 125 659-811 97-236 (260)
28 cd01189 INT_phiLC3_C phiLC3 ph 91.9 2 4.4E-05 41.1 11.2 103 660-775 24-157 (191)
29 PRK09692 integrase; Provisiona 91.7 1 2.2E-05 50.1 10.2 153 661-849 237-400 (413)
30 TIGR02225 recomb_XerD tyrosine 91.6 1.1 2.3E-05 45.4 9.4 118 659-810 127-264 (291)
31 cd00799 INT_Cre Cre recombinas 90.9 1.8 3.9E-05 44.9 10.3 123 660-811 119-265 (287)
32 PRK00236 xerC site-specific ty 90.8 1.1 2.4E-05 45.5 8.6 93 660-768 139-246 (297)
33 cd01185 INT_Tn4399 Tn4399 and 90.8 0.54 1.2E-05 48.9 6.5 94 668-776 160-260 (299)
34 cd00800 INT_Lambda_C Lambda in 90.4 0.49 1.1E-05 45.3 5.3 99 658-773 20-134 (162)
35 cd00796 INT_Rci Rci recombinas 90.1 0.45 9.8E-06 47.2 5.0 100 659-775 66-170 (206)
36 cd01199 INT_Tn1545_C Tn1545-re 90.1 2.3 5E-05 41.5 9.7 123 659-811 23-182 (205)
37 cd01197 INT_FimBE_C FimB and F 89.9 0.58 1.2E-05 45.5 5.5 99 662-775 29-143 (180)
38 cd01183 INT_SG1_C INT_SG1, DNA 89.4 1.5 3.2E-05 43.2 7.9 105 659-776 28-170 (196)
39 PRK05084 xerS site-specific ty 89.3 1.4 3E-05 47.6 8.3 117 660-810 198-333 (357)
40 PRK09870 tyrosine recombinase; 89.3 0.93 2E-05 45.6 6.5 101 662-777 37-153 (200)
41 cd00798 INT_XerDC XerD and Xer 88.7 3 6.5E-05 41.9 9.6 97 661-773 131-245 (284)
42 cd01184 INT_SG2_C INT_SG2, DNA 86.1 4.1 8.9E-05 39.4 8.7 103 661-776 28-154 (181)
43 PHA03397 vlf-1 very late expre 85.8 2.1 4.5E-05 48.7 7.3 145 611-775 147-311 (363)
44 PRK09871 tyrosine recombinase; 84.8 2 4.3E-05 42.9 5.9 101 661-776 30-147 (198)
45 TIGR02249 integrase_gron integ 84.5 2.9 6.2E-05 44.2 7.3 101 661-776 120-273 (315)
46 cd01195 INT_Tn544B_C Tn544B an 81.4 16 0.00034 36.2 10.7 123 659-811 22-176 (195)
47 cd01191 INT_phiCTX_C phiCTX ph 80.0 7.1 0.00015 38.8 7.7 119 661-811 24-184 (196)
48 cd01196 INT_VanD VanD integras 78.0 6.9 0.00015 40.5 7.3 99 660-776 110-221 (263)
49 cd00797 HP1_INT_C Phage HP1 in 77.0 8 0.00017 36.9 6.9 96 659-775 18-117 (158)
50 PRK15417 integrase/recombinase 76.3 15 0.00032 40.2 9.4 56 661-731 135-190 (337)
51 cd01198 INT_ASSRA_C Archaeal s 71.7 24 0.00053 34.4 8.9 103 659-776 19-142 (186)
52 KOG0981 DNA topoisomerase I [R 55.9 28 0.00061 42.1 6.9 117 723-843 565-700 (759)
53 PF09266 VirDNA-topo-I_N: Vira 42.6 6.1 0.00013 34.5 -0.8 28 555-588 14-41 (58)
54 COG0582 XerC Integrase [DNA re 42.5 39 0.00084 32.2 4.5 88 668-770 153-258 (309)
55 PHA02601 int integrase; Provis 41.9 60 0.0013 34.9 6.3 111 658-810 192-306 (333)
56 KOG2289 Rhomboid family protei 38.1 12 0.00027 42.0 0.5 41 12-53 215-256 (316)
57 PF05276 SH3BP5: SH3 domain-bi 26.5 1.4E+02 0.0031 32.6 6.0 54 790-843 145-208 (239)
58 PF07106 TBPIP: Tat binding pr 24.4 4.9E+02 0.011 26.2 9.1 45 806-850 94-140 (169)
59 PF07106 TBPIP: Tat binding pr 22.0 1E+02 0.0022 31.1 3.7 22 746-767 30-53 (169)
60 PRK10856 cytoskeletal protein 22.0 54 0.0012 37.0 2.0 23 414-436 290-317 (331)
61 PF12835 Integrase_1: Integras 20.7 2.3E+02 0.005 29.4 6.1 129 658-810 32-175 (187)
No 1
>KOG0981 consensus DNA topoisomerase I [Replication, recombination and repair]
Probab=100.00 E-value=1.6e-188 Score=1537.93 Aligned_cols=649 Identities=53% Similarity=0.813 Sum_probs=557.1
Q ss_pred CCCCcccccccccccccCcccccCCCcchhhhhcc----ccCCCCCCCCCCcccccccc-CCCCCCCCCCCCCCCCCCcc
Q 002904 196 DSEDDKPLSARLKGNSKNVNQGIGASKADAAISEV----NVKTDPEDSDDEVPLSSRFP-KSNAGTSGAKPIDSDEKKPL 270 (868)
Q Consensus 196 DSDDDkPLSsRlk~nSn~~nk~~~~~~~~~~~~~~----~~~~k~dDSDDekPLSSrf~-k~gsg~S~~~~~~~~~~~~~ 270 (868)
||+|+.|||..+..++.++..+. .....-.-..+ .-.....+||++.|+|+.+. +.-+ +|.......++.+|+
T Consensus 1 ~sed~~~~s~~~~~~~~~~~~~~-~~~~~~~~~~k~~~~se~~~~~~s~~~~p~s~~~~kk~~s-~s~~~~~~~ek~k~~ 78 (759)
T KOG0981|consen 1 DSEDSNPLSNFNGNSTSSGVNSS-DQREKKVKDEKPESDSEVPKKSDSDDDKPESKTKKKKKES-GSDEDDLSIEKRKPS 78 (759)
T ss_pred CcccccchhccccCCcccccccc-cchhhhhcccccchhcccccccccccccchHHHhhhcccc-cCCcccCchhhcccc
Confidence 68899999988733332222200 00000000000 01123488999999999999 4444 666777778888888
Q ss_pred ccccccCCCCccccccCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCcccchhceeeeeccccCC----------CCCCCc
Q 002904 271 ASKVQQNGSTSRETQQKSSSVPVKRPLQKASSSGASSAKKPKVSDTSKEVKVKQVTVKVEKKAD----------DDDHIP 340 (868)
Q Consensus 271 ~~~~~~~~~~~~~~~~~~~~~~~kr~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~k~~----------~d~~~p 340 (868)
+..++|.....+ ...+..+.+|++.+.+.+.+++.+....+++..+++.++.+.-.-.+.+ +|+|
T Consensus 79 --~~~~~~~~~~s~-~~~~~~~~~r~~kk~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~d~~~~~~~~vk~e~sd-- 153 (759)
T KOG0981|consen 79 --NDSDKGKDVKSD-KEDDKVPGKRKLKKNSKSKQSSSKEDDDSESEPSVKEKDVKPVKPKKDEKGKALKKVKEEDSD-- 153 (759)
T ss_pred --cccccccccccc-ccccccccccccccccccCcccccCCcccccCCCCchhhccccccccchhhhhhhhhhhcccc--
Confidence 777777766443 3567899999999999999999999999999999999988733322211 1111
Q ss_pred hhhhcccCCCCCCCcccccccccccccCcchhh-hhhhhhhhcccCcccccccCCCCCCcccccceeeeccccCCCCCC-
Q 002904 341 ISQRMKNSAPSVKKSVTNTAKATKSVSSSSNKI-NKKTKKVIKNSQYSKSTKMLPGSGDGQKKWTTLVHNGVIFPPPYL- 418 (868)
Q Consensus 341 ~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~-~~~~k~~~~~~~~~kww~~~~~~~~g~~kW~tLeHnGv~Fpp~Y~- 418 (868)
.+.++. .+..+..+.+..+.+..+++..-. +++.+..++++..|+||+.+. .++|+ ||+||+||||+|||||+
T Consensus 154 --k~~k~~-~~~~~~~s~k~~~sk~~~~~~~~~~~~~~~~k~e~e~~~kww~~e~-~d~~~-KW~tLeH~G~iFaPPYep 228 (759)
T KOG0981|consen 154 --KDKKSD-LSNVKTKSAKPSASKLPAGARTEPKKKKKKAKDEEEDKWKWWEEEK-GDDGV-KWTTLEHNGPIFAPPYEP 228 (759)
T ss_pred --hhhhcc-ccccCccccCcccccCcccCcCCccccccccchhhhhhhhhccccc-CCCcc-ceeeeeecCcccCCCCcC
Confidence 111111 111111111111111111111111 233344455667799999644 56777 99999999999999999
Q ss_pred -CCcceEEEcCEeccCChhhHHHHHHHHHhcCCCCCchhhHHhhhHHHHHHHhC--cCCCcccCCCCCchHHHHHHHHHH
Q 002904 419 -PHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHQEQK 495 (868)
Q Consensus 419 -P~~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~d~~~~l~--~~~~I~~~~kcDF~~i~~~~~~~k 495 (868)
|+||+|||||+||+|||+|||||||||+||+|+|+++++||+|||+|||++|+ +.++|++|++||||+||+||++++
T Consensus 229 lP~~Vk~~YdGkpv~L~~eaEEvAtfyA~mle~ey~tk~vF~~NFf~Dwrk~m~~~~~~~Ik~l~kCDFt~i~~yf~~~~ 308 (759)
T KOG0981|consen 229 LPSGVKFYYDGKPVDLTPEAEEVATFYAAMLEHEYATKEVFRKNFFNDWRKVMTVEEREVIKDLSKCDFTPIFEYFKEQK 308 (759)
T ss_pred CCCCceEEeCCccccCCHHHHHHHHHHHHHHhcchhccHHHHHHHHHHHHHHhhhhhhhhhccccccCCHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999 568999999999999999999999
Q ss_pred HHHHcCCHHHHHHHHHHHHHHhhhcCeEEEcCceeeecccccCCCccccCCCCCCCCCccccccCCChhHHhccCCCCCC
Q 002904 496 EKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIP 575 (868)
Q Consensus 496 e~kk~~s~eEKk~~K~e~~~~~~~yg~~~vDg~~ekvgNfrvEpPGLfRGRGfhpk~GklK~RI~PdditInrik~l~IP 575 (868)
|+||+||+|||+++|+|+++++++||||+||||+|+||||||||||||||||.||+||+||+||+|+||||||+++++||
T Consensus 309 E~rK~mskEEK~~iKeEkek~ee~y~~cilDG~kEkigNFriEPPgLFRGRG~HPKmG~lKrRI~Pedi~iN~gkda~iP 388 (759)
T KOG0981|consen 309 EKRKQMSKEEKLKIKEEKEKLEEKYGWCILDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRIMPEDITINCGKDAPIP 388 (759)
T ss_pred HHHhhcCHHHHHHHHHHHHHHHHHcCeEEecCcHhhhcccccCCCccccCCCCCCcccchhcccchhheEEecCCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCcceeecCCCCcEEEEeecCCCCceeeeeeccCCchhhcCccHHHHHHHHHHHHHHHHHHHHHHHhccCCCCC
Q 002904 576 ECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGT 655 (868)
Q Consensus 576 P~P~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl~ahs~wk~~rD~~Kyerar~Lk~~Lp~IR~~y~kDLksk~~~ 655 (868)
+ |||||.|++|+|||+|||||+|+|+|++. ++||||+|+|+++|++|++|||+||+|+.+|+.||++|++||++++|+
T Consensus 389 ~-pppGhkWkEVrHDNTVTWLa~W~e~i~~~-~KYi~L~~~SslKGesD~~KyE~ARrLk~~Id~IR~~Y~~d~ksk~m~ 466 (759)
T KOG0981|consen 389 E-PPPGHKWKEVRHDNTVTWLASWTENINGS-FKYIMLNPSSSLKGESDKEKYETARRLKKYIDKIRATYTKDFKSKEMK 466 (759)
T ss_pred C-CCCCCcccccccCCeeeeeeecccccCCc-eeEEEecCcccccCchhHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHH
Confidence 9 89999999999999999999999999995 999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCe-----EEEEeeCCCCeEEEEEEeeChHHHHHHH
Q 002904 656 RRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNK-----LKFDFLGKDSIQYVNTVEVELPVYKAIG 730 (868)
Q Consensus 656 ~RqlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~-----V~FdFlGKdgir~~~tV~VD~~V~knLk 730 (868)
.||+||||||||+||||+|||+++++||||||||||++||+|+|++. |.|||||||||||+|+|+|+++||+||.
T Consensus 467 ~RQravAlY~IDklALRAGnEKdedeADTVGCCsLrvehV~l~p~~~~~e~vv~FDFLGKDSIrYyN~VeVek~VyKnl~ 546 (759)
T KOG0981|consen 467 VRQRAVALYFIDKLALRAGNEKDEDEADTVGCCSLRVEHVTLHPPNKGKEFVVEFDFLGKDSIRYYNEVEVEKRVYKNLK 546 (759)
T ss_pred HHHHHHHHHHHHHHHHhccCcccccccccccceeeeeeeeEeeCccccccceEEeeccCccceeeeeeccccHHHHHHHH
Confidence 99999999999999999999999999999999999999999998754 5999999999999999999999999999
Q ss_pred hhhcCCCCCCcccccCChhHHHHHHHhhCCCCcceeeccccchHHHHHHHhcCCC-CCCHHHHHHHHHHHHHHHHHHcCC
Q 002904 731 QFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNH 809 (868)
Q Consensus 731 ~f~k~K~PGd~LFd~L~ss~LN~yLkelM~glTAKdFRTynASvta~~~L~~~~~-~~s~~eK~~~yn~Anr~VAilCNH 809 (868)
.|++++.|||+|||+|+|+.||+||++||+|||||||||||||+|||++|..++. .+++++|++.||+|||+|||||||
T Consensus 547 ~F~~~K~~~ddLFDrLdt~~LN~hL~~lM~GLTAKVFRTYNASiTlqeqL~~lt~p~~~v~~KIl~YnrANr~VAIlCNH 626 (759)
T KOG0981|consen 547 IFMEGKKPGDDLFDRLDTSSLNKHLQELMDGLTAKVFRTYNASITLQEQLDKLTNPDGNVAAKILSYNRANRTVAILCNH 626 (759)
T ss_pred HHhcCCCccchhhhhhchHHHHHHHHHHhccchhhhhhhcchhhHHHHHHHhccCCCccHHHHHHHHhhccceeeeeecc
Confidence 9999999999999999999999999999999999999999999999999999998 569999999999999999999999
Q ss_pred CcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCcc
Q 002904 810 QRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGK 859 (868)
Q Consensus 810 qR~V~K~~~~sm~kl~~ki~~lk~q~~~~~~~l~~~k~~~~~~~~~~~~~ 859 (868)
||+|+|+|+.||++|+++|+++++||.+++.+|..++++.++. .+++++
T Consensus 627 QR~v~K~h~~smekl~~kI~~~keql~e~~~~l~~ak~~~~~~-~~~~~~ 675 (759)
T KOG0981|consen 627 QRAVSKTHEKSMEKLAEKIKAKKEQLKEAEAELKSAKADEKKQ-EGSKEK 675 (759)
T ss_pred cccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc-cccccc
Confidence 9999999999999999999999999999999999999999888 555554
No 2
>smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
Probab=100.00 E-value=1e-104 Score=860.30 Aligned_cols=303 Identities=68% Similarity=1.010 Sum_probs=297.3
Q ss_pred cccCCCCCCCCCccccccCCChhHHhccCCCCCCCCCCCCCCcceeecCCCCcEEEEeecCCCCceeeeeeccCCchhhc
Q 002904 542 LFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKG 621 (868)
Q Consensus 542 LfRGRGfhpk~GklK~RI~PdditInrik~l~IPP~P~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl~ahs~wk~ 621 (868)
||||||+||+||+||+||+|+||||||+++++||+ |||||.|++|+||++|||||+|+|+|+++ ++||||+|+|+|++
T Consensus 1 lFrGRG~hpk~G~lK~Rv~pedv~iN~~k~a~vP~-pp~gh~Wk~v~hd~~vtWLa~w~e~i~~~-~KYv~l~a~S~wk~ 78 (391)
T smart00435 1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPE-PPPGHKWKEVRHDNTVTWLASWKENINGS-IKYVFLAASSSLKG 78 (391)
T ss_pred CCCCCCCCCCccccccccChhheEEecCCCCCCCc-cCCCCCcceeecCCCceEEEEeeccCCCc-eeEEEECCCchhhh
Confidence 79999999999999999999999999999999999 77999999999999999999999999986 99999999999999
Q ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCC
Q 002904 622 QSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPN 701 (868)
Q Consensus 622 ~rD~~Kyerar~Lk~~Lp~IR~~y~kDLksk~~~~RqlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~ 701 (868)
++|+.|||+|++|+.+||+||++|++||+++++++||+||||||||.+|||||||+|+++|+||||||||++||++++++
T Consensus 79 ~rD~~Kfera~~f~~~Lp~IR~~~~~dL~s~~~r~rqlAvav~LID~~alRvGnEkYa~en~T~Gl~TLR~eHV~l~~~~ 158 (391)
T smart00435 79 QSDRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLKPPN 158 (391)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhHHHHHHHHHHHhcccCCChhhhhcCCCEeecccchhheEecCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998789
Q ss_pred eEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCCcccccCChhHHHHHHHhhCCCCcceeeccccchHHHHHHHh
Q 002904 702 KLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASITLDGMLN 781 (868)
Q Consensus 702 ~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd~LFd~L~ss~LN~yLkelM~glTAKdFRTynASvta~~~L~ 781 (868)
+|+|+|+|||||+|+++|.||++||++|+.|++++.||++||++|++++||+||+++|+|||||||||||||+||+++|.
T Consensus 159 ~v~fdF~GKdgir~~~~v~vd~~l~k~L~~~~~~k~pg~~LF~~l~s~~lN~yLke~mgglTAKdFRTwnASvta~~~L~ 238 (391)
T smart00435 159 KVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQEQLK 238 (391)
T ss_pred EEEEEEeCCCCcEEEEEEecCHHHHHHHHHHhcCCCChHHHHhhCCHHHHHHHHHHHcCCCeeeeeecChHHHHHHHHHH
Confidence 99999999999999999999999999999999888999999999999999999999999999999999999999999999
Q ss_pred cCCC-CCCHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002904 782 KGTG-DGDVAVKIDVYQRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAK 846 (868)
Q Consensus 782 ~~~~-~~s~~eK~~~yn~Anr~VAilCNHqR~V~K~~~~sm~kl~~ki~~lk~q~~~~~~~l~~~k 846 (868)
+++. .+++++++.+||+||++|||+|||||+|||+|+.||++|+++|+++++|+.+++.+|..++
T Consensus 239 ~~~~~~~s~~ek~~~yn~Anr~VAi~cnntraV~k~~~~~m~k~~~ki~~~~~~~~~~~~~~~~~~ 304 (391)
T smart00435 239 ELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKRLKKMILLFE 304 (391)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9887 5799999999999999999999999999999999999999999999999999999998776
No 3
>cd03489 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human
Probab=100.00 E-value=1.7e-95 Score=731.53 Aligned_cols=211 Identities=70% Similarity=1.245 Sum_probs=207.7
Q ss_pred ccceeeeccccCCCCCCCCcceEEEcCEeccCChhhHHHHHHHHHhcCCCCCchhhHHhhhHHHHHHHhCcCC-CcccCC
Q 002904 402 KWTTLVHNGVIFPPPYLPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGKNH-VIQNLE 480 (868)
Q Consensus 402 kW~tLeHnGv~Fpp~Y~P~~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~d~~~~l~~~~-~I~~~~ 480 (868)
||+|||||||+|||+|+||||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|++++ .|++|+
T Consensus 1 KW~tLeHnGv~FpP~YeP~~Vk~~YdG~pv~L~pe~EEvAtf~a~ml~t~y~~~~~F~kNFf~df~~~l~~~~~~I~~f~ 80 (212)
T cd03489 1 RWTTLVHNGVLFPPPYKPHGIPILYNGQPFDMTPEEEEVATMFAVMKEHDYYRKEVFRRNFFESWREILDKRHHPIRKLE 80 (212)
T ss_pred CceeeeeCCccCCCCccCCCccEeECCeECcCCHHHHHHHHHHHHHcCCccccchHHHHHHHHHHHHHhcccCccccchh
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999887 999999
Q ss_pred CCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcCeEEEcCceeeecccccCCCccccCCCCCCCCCccccccC
Q 002904 481 GCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQ 560 (868)
Q Consensus 481 kcDF~~i~~~~~~~ke~kk~~s~eEKk~~K~e~~~~~~~yg~~~vDg~~ekvgNfrvEpPGLfRGRGfhpk~GklK~RI~ 560 (868)
+|||++||+||++++|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||+||+||+||+||+
T Consensus 81 kcDF~~i~~~~~~~~e~kK~~tkeEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNFrvEPPgLFrGRG~HPK~G~lK~Rv~ 160 (212)
T cd03489 81 LCDFTPIYEWHLREKEKKKSRTKEEKKALKEEKDKEAEPYMWCVWDGVKEQVANFRVEPPGLFRGRGEHPKMGKLKKRIQ 160 (212)
T ss_pred hCCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhccCCEEEECCEEEeeCCcccCCCcccccCCCCCCCcccccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChhHHhccCCCCCCCCCCCCCCcceeecCCCCcEEEEeecCCCCceeeeeecc
Q 002904 561 PSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (868)
Q Consensus 561 PdditInrik~l~IPP~P~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl~ 614 (868)
|+||||||+++++||+ |||||+|++|+||++|||||+|+|+|++. ++||||+
T Consensus 161 PedVtINigkda~vP~-pp~Gh~WkeV~HDntVtWLA~W~enIn~~-~KYV~La 212 (212)
T cd03489 161 PEDITINIGKGAPIPE-CPAGHKWKEVKHDNTVTWLAMWRDPIAGN-FKYVMLA 212 (212)
T ss_pred hhheEEecCCCCCCCc-cCCCCCcceeecCCCceEEEEeEeccCCc-eeEEEeC
Confidence 9999999999999999 56999999999999999999999999975 9999986
No 4
>cd03490 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanoso
Probab=100.00 E-value=1.3e-94 Score=727.31 Aligned_cols=212 Identities=49% Similarity=0.916 Sum_probs=207.6
Q ss_pred ccceeeeccccCCCCCCCCcceEEEcCEeccCChhhHHHHHHHHHhcCCCCCchhhHHhhhHHHHHHHhCcCC---Cccc
Q 002904 402 KWTTLVHNGVIFPPPYLPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGKNH---VIQN 478 (868)
Q Consensus 402 kW~tLeHnGv~Fpp~Y~P~~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~d~~~~l~~~~---~I~~ 478 (868)
+|+|||||||+|||+|+||||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|++.+ .|++
T Consensus 1 kW~tLeHnGv~FpP~Y~P~~Vk~~YdG~pv~L~peaEEvAtf~a~ml~t~y~~~~~F~kNFf~df~~~l~~~~~~~~i~~ 80 (217)
T cd03490 1 QWKYLEHNGMIFTPPYVPHNVPIMYKGETIHLPPNLEEIATYWAQSMGTNYETKEKFCKNFWKVFVNSFEKDHKFIRRCK 80 (217)
T ss_pred CceeeeeCCccCCCCccCCCccEeECCeECcCCHHHHHHHHHHHHHhCCccccchHHHHHHHHHHHHHhccccCcccccc
Confidence 7999999999999999999999999999999999999999999999999999999999999999999998665 8999
Q ss_pred CCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcCeEEEcCceeeecccccCCCccccCCCCCCCCCccccc
Q 002904 479 LEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKR 558 (868)
Q Consensus 479 ~~kcDF~~i~~~~~~~ke~kk~~s~eEKk~~K~e~~~~~~~yg~~~vDg~~ekvgNfrvEpPGLfRGRGfhpk~GklK~R 558 (868)
|++|||++||+||++++|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||.||+||+||+|
T Consensus 81 f~kcDF~~i~~~~~~~ke~kK~~tkeEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNfriEPPgLFrGRG~HPK~G~lK~R 160 (217)
T cd03490 81 LSDADFSLIKNHLEEEKEKKKNLNKEEKEAKKKERAKREYPFNYALVDWIREKVSSNKLEPPGLFKGRGEHPKQGLLKSR 160 (217)
T ss_pred hhhCCCHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhccCCEEEECCEEEeeCCcccCCCcccccCCCCCCCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCChhHHhccCCCCCCCCC--CCCCCcceeecCCCCcEEEEeecCCCCceeeeeecc
Q 002904 559 IQPSDITINIGKDVPIPECP--IPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (868)
Q Consensus 559 I~PdditInrik~l~IPP~P--~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl~ 614 (868)
|+|+||||||+++++||+|| +|||+|++|+||++|||||+|+|+|++. +|||||+
T Consensus 161 V~PedVtINigkda~vP~~p~~~~GH~WkeV~HDntVtWLA~W~enIn~~-~KYV~Ls 217 (217)
T cd03490 161 IFPEDVILNISKDAPVPKVTNFMEGHSWKDIYHDNSVTWLAYYKDSINDQ-FKYMFLS 217 (217)
T ss_pred cChhheEEecCCCCCCCcCCCCCCCCccceeecCCCceEEEEeecCCCCc-eeEEEeC
Confidence 99999999999999999986 5999999999999999999999999974 9999985
No 5
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=100.00 E-value=3.5e-94 Score=723.24 Aligned_cols=211 Identities=70% Similarity=1.195 Sum_probs=206.0
Q ss_pred ccceeeeccccCCCCCCCC--cceEEEcCEeccCChhhHHHHHHHHHhcCCCCCchhhHHhhhHHHHHHHhCc--CCCcc
Q 002904 402 KWTTLVHNGVIFPPPYLPH--GVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGK--NHVIQ 477 (868)
Q Consensus 402 kW~tLeHnGv~Fpp~Y~P~--~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~d~~~~l~~--~~~I~ 477 (868)
||+|||||||+|||+|+|| ||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|++ ++.|+
T Consensus 1 kW~tLeHnGv~FpP~YeplP~~Vk~~YdG~pv~L~peaEEvAtf~a~ml~t~y~~~~~F~kNFf~Df~~~l~~~~~~~i~ 80 (215)
T cd00660 1 KWTTLEHNGVIFPPPYEPLPKNVKFYYDGKPVKLPPEAEEVATFFAVMLETDYATKEVFRKNFFKDFRKILTKEEKHIIK 80 (215)
T ss_pred CceeeeeCCccCCCCcccCcCCCCEEECCEECcCCHHHHHHHHHHHHHcCCccccChHHHHHHHHHHHHHhccccCcccc
Confidence 7999999999999999965 9999999999999999999999999999999999999999999999999965 58999
Q ss_pred cCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcCeEEEcCceeeecccccCCCccccCCCCCCCCCcccc
Q 002904 478 NLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKK 557 (868)
Q Consensus 478 ~~~kcDF~~i~~~~~~~ke~kk~~s~eEKk~~K~e~~~~~~~yg~~~vDg~~ekvgNfrvEpPGLfRGRGfhpk~GklK~ 557 (868)
+|++|||++||+||++|+|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||.||+||+||+
T Consensus 81 ~f~kcDF~~i~~~~~~~~e~kK~~s~eEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNfrvEPPgLFrGRG~HPK~G~lK~ 160 (215)
T cd00660 81 KLSKCDFTPIYQYFEEEKEKKKAMSKEEKKAIKEEKEKLEEPYGYCLVDGHKEKVGNFRIEPPGLFRGRGEHPKMGKLKR 160 (215)
T ss_pred chhhCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccCCEEEECCEEEeeCCcccCCCcccccCCCCCCCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCChhHHhccCCCCCCCCCCCCCCcceeecCCCCcEEEEeecCCCCceeeeeecc
Q 002904 558 RIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (868)
Q Consensus 558 RI~PdditInrik~l~IPP~P~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl~ 614 (868)
||+|+||||||+++++||+ ||+||+|++|+||++|||||+|+|+|++. ++||||+
T Consensus 161 Rv~PedVtINigkda~vP~-pp~Gh~WkeV~HDntVtWLA~W~enIn~~-~KYV~La 215 (215)
T cd00660 161 RIMPEDITINIGKDAPVPE-PPAGHKWKEVRHDNTVTWLASWKENINGQ-FKYVMLA 215 (215)
T ss_pred ccChhhEEEecCCCCCCCc-cCCCCCcceeecCCCceEEEEeEeccCCc-eeEEEeC
Confidence 9999999999999999999 55899999999999999999999999975 9999986
No 6
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=100.00 E-value=3.9e-94 Score=722.95 Aligned_cols=211 Identities=60% Similarity=1.070 Sum_probs=206.0
Q ss_pred ccceeeeccccCCCCCC--CCcceEEEcCEeccCChhhHHHHHHHHHhcCCCCCchhhHHhhhHHHHHHHhCc--CCCcc
Q 002904 402 KWTTLVHNGVIFPPPYL--PHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGK--NHVIQ 477 (868)
Q Consensus 402 kW~tLeHnGv~Fpp~Y~--P~~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~d~~~~l~~--~~~I~ 477 (868)
||+|||||||+|||+|+ ||||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|++ ++.|+
T Consensus 1 KW~tLeHnGv~FpP~YeplP~~Vk~~YdG~pv~L~peaEEvAtf~a~ml~t~y~~~~~F~kNFf~Df~~~l~~~~~~~I~ 80 (215)
T cd03488 1 KWTTLEHNGPVFAPPYEPLPKNVKFYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80 (215)
T ss_pred CceeeeeCCccCCCCCccCCCCCCEEECCEECcCCHHHHHHHHHHHHHcCCccccChHHHHHHHHHHHHHhccccCcccc
Confidence 79999999999999999 569999999999999999999999999999999999999999999999999965 58999
Q ss_pred cCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcCeEEEcCceeeecccccCCCccccCCCCCCCCCcccc
Q 002904 478 NLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKK 557 (868)
Q Consensus 478 ~~~kcDF~~i~~~~~~~ke~kk~~s~eEKk~~K~e~~~~~~~yg~~~vDg~~ekvgNfrvEpPGLfRGRGfhpk~GklK~ 557 (868)
+|++|||++||+||++|+|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||+||+||+||+
T Consensus 81 ~f~kcDF~~i~~~~~~~~e~kK~~tkeEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNfrvEPPgLFrGRG~HPK~G~lK~ 160 (215)
T cd03488 81 DFSKCDFTQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKR 160 (215)
T ss_pred chhhCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccCCEEEECCEEEeeCCcccCCCccccCCCCCCCCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCChhHHhccCCCCCCCCCCCCCCcceeecCCCCcEEEEeecCCCCceeeeeecc
Q 002904 558 RIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (868)
Q Consensus 558 RI~PdditInrik~l~IPP~P~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl~ 614 (868)
||+|+||||||+++++||+ ||+||+|++|+||++|||||+|+|+|++. ++||||+
T Consensus 161 Rv~PedVtINigkda~vP~-pp~Gh~WkeV~HDntVtWLA~W~enIn~~-~KYV~La 215 (215)
T cd03488 161 RIMPEDIIINIGKDAKVPE-PPPGHKWKEVRHDNTVTWLASWTENINGS-IKYVMLN 215 (215)
T ss_pred ccChhhEEEecCCCCCCCc-cCCCCCcceeecCCCceEEEEeEeccCCc-eeEEEeC
Confidence 9999999999999999999 56999999999999999999999999985 9999986
No 7
>PF02919 Topoisom_I_N: Eukaryotic DNA topoisomerase I, DNA binding fragment; InterPro: IPR008336 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the N-terminal DNA-binding domain found in eukaryotic topoisomerase I, which is a type IB enzymes. To cleave the DNA backbone, these enzymes must make a transient phosphotyrosine bond. The N-terminal domain of human topoisomerase I is thought to coordinate the restriction of free strand rotation during the topoisomerisation step of catalysis. A conserved tryptophan residue may be important for the DNA-interaction ability of the N-terminal domain []. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=100.00 E-value=4.8e-93 Score=717.35 Aligned_cols=211 Identities=68% Similarity=1.191 Sum_probs=162.9
Q ss_pred cccceeeeccccCCCCCC--CCcceEEEcCEeccCChhhHHHHHHHHHhcCCCCCchhhHHhhhHHHHHHHhCcCC--Cc
Q 002904 401 KKWTTLVHNGVIFPPPYL--PHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGKNH--VI 476 (868)
Q Consensus 401 ~kW~tLeHnGv~Fpp~Y~--P~~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~d~~~~l~~~~--~I 476 (868)
+||+|||||||+|||+|+ ||||+|+|||+||+|+|+|||||||||+||+|+|+++++||+|||+||+++|++.+ .|
T Consensus 1 ~kW~tLeHnG~~FpP~Y~pLP~~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~Df~~~l~~~~~~~i 80 (215)
T PF02919_consen 1 VKWKTLEHNGVLFPPPYEPLPHGVKFYYDGKPVKLSPEAEEVATFYAKMLDTDYATKPVFNKNFFKDFRKVLTKEERKKI 80 (215)
T ss_dssp -S-S-EEE---B---------TTS-EEETTEEE---HHHHHHHHHHHTTTTSGGGGSHHHHHHHHHHHHHHHCHCCHHH-
T ss_pred CCceeeeeCCcccCCCcccCCCCccEEECCEEeecCHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHhhhccCccc
Confidence 399999999999999999 89999999999999999999999999999999999999999999999999999886 89
Q ss_pred ccCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcCeEEEcCceeeecccccCCCccccCCCCCCCCCccc
Q 002904 477 QNLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLK 556 (868)
Q Consensus 477 ~~~~kcDF~~i~~~~~~~ke~kk~~s~eEKk~~K~e~~~~~~~yg~~~vDg~~ekvgNfrvEpPGLfRGRGfhpk~GklK 556 (868)
++|++|||++||+||++++|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||.||+||+||
T Consensus 81 ~~~~kcDF~~i~~~~~~~~e~kk~~skeEK~~~K~~k~~~~~~y~~~~vDG~~ekVGNfrvEPPGLFrGRG~HPK~G~lK 160 (215)
T PF02919_consen 81 KDFDKCDFSPIYEYFEKEKEKKKNMSKEEKKALKEEKEELEEKYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKMGMLK 160 (215)
T ss_dssp S-GGGEETHHHHHHHHHHHHHHCTS-CCHHHHHHHHHHHHHHHHSEEEETTEEEEBSS-B---SEE---SSS-TTTT-EE
T ss_pred CchhhCCCHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCcEEEECCcccccCceecCCCeeeecCCCCCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCChhHHhccCCCCCCCCCCCCCCcceeecCCCCcEEEEeecCCCCceeeeeec
Q 002904 557 KRIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFL 613 (868)
Q Consensus 557 ~RI~PdditInrik~l~IPP~P~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl 613 (868)
+||+|+||||||+++++||+ |||||+|++|+||++|||||+|+|+|+++ +|||||
T Consensus 161 ~Ri~PedVtIN~~k~a~vP~-pp~Gh~Wk~V~HDntvtWLA~W~enI~~~-~KYV~L 215 (215)
T PF02919_consen 161 KRIYPEDVTINIGKDAPVPE-PPPGHKWKEVVHDNTVTWLASWTENINGQ-FKYVML 215 (215)
T ss_dssp ----GGGEEEE--TTS------STT---SEEE--TTSS-SEEEEETTTTE-EEEEEB
T ss_pred cccChhhEEEeCCCCCCCCc-ccCCCCcceeEeCCCceEEEEeEeccCCc-eeEEeC
Confidence 99999999999999999999 55999999999999999999999999998 999997
No 8
>PHA03101 DNA topoisomerase type I; Provisional
Probab=100.00 E-value=3e-65 Score=541.39 Aligned_cols=265 Identities=21% Similarity=0.252 Sum_probs=242.4
Q ss_pred CCCCCCCCc------cccccCCChhHHhccCCCCCCCCCCCCCCcceee--c----CCCCcEEEEeecCCCCceeeeeec
Q 002904 546 RGEHPKMGK------LKKRIQPSDITINIGKDVPIPECPIPGESWKEVK--H----DNTVTWLAFWNDPINPKEFKYVFL 613 (868)
Q Consensus 546 RGfhpk~Gk------lK~RI~PdditInrik~l~IPP~P~~GhaWkeV~--h----D~~vhwlAtw~D~igrkQyKYvyl 613 (868)
|-+||++|+ .+++|.-++.++.||+.|+||| ||++|| + ++++|+||||+|++||+||+|
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~RI~~LaIPP------Aw~dVwI~p~~~e~~~~hlQAtG~Da~GRKQYrY--- 72 (314)
T PHA03101 2 RALFYKDGKLFEDKEFTNPVSDDNPTYEILKKVKIPP------HLTDVVVYEQTYEEALTGLIFVGSDSKGRKQYFY--- 72 (314)
T ss_pred cceecccCeeeechhhCCCCCCccHHHHHHHHcCCCC------CcceEEEeeccccCCCCceEEEeecCCCCeeeee---
Confidence 456777777 5789988889999999999999 999999 5 489999999999999999999
Q ss_pred cCCchhhcCccHHHHHHHHHHHHHHHHHHHHHHHhccCCCC-CchHHHHHHHHHHhc-ccccCCCCCccCCCceeeccCC
Q 002904 614 AASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDG-TRRQIAVATYLIDKL-ALRAGNEKDDDEADTVGCCTLK 691 (868)
Q Consensus 614 ~ahs~wk~~rD~~Kyerar~Lk~~Lp~IR~~y~kDLksk~~-~~RqlAvAlyLIDkl-ALRvGNEKy~deadTvG~cTLR 691 (868)
||.|+..|+..||+++.+|+++||+||++|.+||+.+++ +++++|++++|||.+ +||||||+|+++|+||||||||
T Consensus 73 --H~~W~~~R~~~Kf~r~~~f~~~LP~iR~~v~~dL~~~~~~~~kvlAavv~LLd~~~~iRvGne~Ya~~N~SyGltTLr 150 (314)
T PHA03101 73 --GKLHVKNRNANRDKIFVRVHNVIKKINCFIDKNIKIKKKNDVNFQLAVFLLMETSFFIRTGKMKYLKENETVGLLTLK 150 (314)
T ss_pred --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhccceecCCHhHHHhcCCccccccc
Confidence 999999999999999999999999999999999998888 899999999999999 7999999999999999999999
Q ss_pred CCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCCcccccCChhHHHHHHHhhCCCCcceeecccc
Q 002904 692 VGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYN 771 (868)
Q Consensus 692 ~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd~LFd~L~ss~LN~yLkelM~glTAKdFRTyn 771 (868)
++||++. |+.|+|+|+||+|++|..+|..|++|+++|+.|++.+.||++||+|+++++||+||++. ||||||||||+
T Consensus 151 ~rHv~v~-g~~i~f~F~GKsG~~~~~~i~dD~rL~~~v~~l~~~~~Pg~~LF~y~d~~~VN~Ylre~--~fTAKDFRTW~ 227 (314)
T PHA03101 151 NKHITIS-NDKILIKFVGKDKVSHEFVVHKSNRLYKPLLKLIDKTNPDDFLFNKLSERKVYKFMKQF--GIRLKDLRTYG 227 (314)
T ss_pred hhceEEE-CCEEEEEEECCCCcEEEEEecccHHHHHHHHHHHcCCCChHHHhhcCCHHHHHHHHHhC--CCcceeecCch
Confidence 9999999 78999999999999999999866999999999998778999999999999999999996 99999999999
Q ss_pred chHHHHHHHhc-CCCCCCHHHHHHHHHHHHHHHHHHcCCCcccccc---hHHHHHHH
Q 002904 772 ASITLDGMLNK-GTGDGDVAVKIDVYQRANKEVAIICNHQRTVSKT---HSAQMSRL 824 (868)
Q Consensus 772 ASvta~~~L~~-~~~~~s~~eK~~~yn~Anr~VAilCNHqR~V~K~---~~~sm~kl 824 (868)
||++|+..|.. .....+..+..+.+..|+++||..|+|+++||++ |-.-++-.
T Consensus 228 gTv~a~~~l~~~~~~~~~~~~~kk~i~~~i~~vA~~LGNTPaV~R~sYIhP~V~~~~ 284 (314)
T PHA03101 228 VNYTFLYNFWTNVKSLDPLPSIKKLISLSIKQTAEIVGHTPSISKSAYMATTVLELL 284 (314)
T ss_pred HHHHHHHHHHhhccccCChhHHHHHHHHHHHHHHHHhCCCHhhHHhcccCHHHHHHH
Confidence 99999999844 2333455667788999999999999999999996 44544443
No 9
>PF01028 Topoisom_I: Eukaryotic DNA topoisomerase I, catalytic core; InterPro: IPR013500 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the catalytic core of eukaryotic and viral topoisomerase I (type IB) enzymes, which occurs near the C-terminal region of the protein. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity []. The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. The crystal structure of an amino-terminal fragment of vaccinia virus DNA topoisomerase I shows that the fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2F4Q_A 3M4A_A 3IGC_A 2H7G_X 2H7F_X 1A41_A 1VCC_A 1TL8_A 1K4T_A 1A36_A ....
Probab=100.00 E-value=7.4e-63 Score=508.43 Aligned_cols=230 Identities=33% Similarity=0.433 Sum_probs=209.8
Q ss_pred CCchhhcCccHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcccccCCCCCccCCC-ceeeccCCCC
Q 002904 615 ASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEAD-TVGCCTLKVG 693 (868)
Q Consensus 615 ahs~wk~~rD~~Kyerar~Lk~~Lp~IR~~y~kDLksk~~~~RqlAvAlyLIDklALRvGNEKy~dead-TvG~cTLR~e 693 (868)
|.+.||+++|+.||+++++|+.+||+||++|.+||.+..+++||+|+||||||.++||||||+|+++|+ ||||||||++
T Consensus 1 ~Ds~gRkQrd~~Kf~r~~~f~~~Lp~iR~~v~~dL~~~~~~~r~lA~a~~LlD~~~lRvGne~Y~~~n~ds~GltTLr~~ 80 (234)
T PF01028_consen 1 ADSKGRKQRDEEKFDRARRFARALPKIRRRVRKDLRSGLPRERVLAVAVRLLDRTALRVGNEKYAEENGDSYGLTTLRVK 80 (234)
T ss_dssp -TTCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTCHHHHHHHHHHHHHHH------HHHHCCHHSHHHCCT-BGG
T ss_pred CCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcchhHHHHHHHHHHhhheecCCcccccccCCCeeeCcCcHH
Confidence 356788889999999999999999999999999997777799999999999999999999999998887 9999999999
Q ss_pred ceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCCcccccCChhHHHHHHHhhCCCCcceeeccccch
Q 002904 694 NVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNAS 773 (868)
Q Consensus 694 HV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd~LFd~L~ss~LN~yLkelM~glTAKdFRTynAS 773 (868)
||++.+++.|+|+|+||||++|+++|.||++||++|+.|++++.||++||+.|++++||+||+++|+||||||||||+||
T Consensus 81 Hv~~~~~~~i~f~F~GK~g~~~~~~v~~d~~l~~~l~~~~~~~~pg~~LF~~v~s~~vN~yL~~~~~~~TaKdFRTw~at 160 (234)
T PF01028_consen 81 HVKLSGDNVIRFDFPGKSGVRQEITVRVDPRLAKNLKRLLRRKLPGDRLFHPVTSTDVNAYLREIMEDFTAKDFRTWNAT 160 (234)
T ss_dssp GEEEETTCEEEEEEEEGGGEEEEEEEETTHHHHHHHHHHHTTTSTTSBTTTT--HHHHHHHHHHCTTTS-HHHHHHHHHH
T ss_pred HeeecCCcEEEEEeeCCCCeEEEEEEecCHHHHHHHHHHHhCCCChhhccCCCCHHHHHHHHHHhcCCCceeeeeeccHH
Confidence 99999666999999999999999999999999999999998899999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCC---CCCCHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002904 774 ITLDGMLNKGT---GDGDVAVKIDVYQRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDR 844 (868)
Q Consensus 774 vta~~~L~~~~---~~~s~~eK~~~yn~Anr~VAilCNHqR~V~K~~~~sm~kl~~ki~~lk~q~~~~~~~l~~ 844 (868)
++|+++|.+.+ ...+..+++.+||.||++||++|||||+||+++.-.+..+...+++.+.++.+++++|++
T Consensus 161 ~~a~~~L~~~~~~~~~~~~~~~~~~~~~a~~~VA~~LgnTpaV~r~sYi~p~v~~~~~~~~~~~~~~~~~~~~~ 234 (234)
T PF01028_consen 161 VLAAEALAKAPRVPPPESEKERKKAYNAAVKEVAELLGNTPAVCRKSYIHPRVLDLYIKELKEQIKELKKQLKE 234 (234)
T ss_dssp HHHHHHHHHHH--HHSSSHHHHHHHHHHHHHHHHHHHTSEHHHHHHHTSHHHHHHHTTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHhCCCccccchhhhCHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999986 677999999999999999999999999999999999999999999999999999999874
No 10
>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=100.00 E-value=1.1e-55 Score=451.25 Aligned_cols=197 Identities=48% Similarity=0.685 Sum_probs=189.9
Q ss_pred hhhcCccHHHHHHHHHHHHHHHHHHHHHHHhccCCCC-CchHHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceE
Q 002904 618 SLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDG-TRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVE 696 (868)
Q Consensus 618 ~wk~~rD~~Kyerar~Lk~~Lp~IR~~y~kDLksk~~-~~RqlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~ 696 (868)
+|+..++..||+++.+|+.+||+||++|.+||+++++ +++|+|+||||||.++||+|||+|+++|+||||||||++||+
T Consensus 1 ~w~~~r~~~K~~~~~~f~~~Lp~iR~~v~~dl~~~~~~~~~vlA~~~~Lld~~~iRvGne~Ya~~n~s~GltTLr~~Hv~ 80 (218)
T cd00659 1 DWKKYRKARKLKRLLAFGRALPKIRRRYTKDLKSKGMPRERQLATAVYLIDKFALRVGNEKYERENDTVGLCTLRKEHVT 80 (218)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchHhHHHHHHHHHHHhcccCCChhhhhcCCCEeecccchhhee
Confidence 4899999999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred EcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCCccc-----ccCChhHHHHHHHhhCCCCcceeecccc
Q 002904 697 CIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLF-----DKLDTAKLNAHLKELMPGLTAKVFRTYN 771 (868)
Q Consensus 697 l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd~LF-----d~L~ss~LN~yLkelM~glTAKdFRTyn 771 (868)
+. ++.|+|+|+||||++|+++|..+++|+++|+.|++ +.||++|| +.|++++||+||+++|+||||||||||+
T Consensus 81 ~~-~~~i~f~F~GK~g~~~~~~v~d~~~l~~~l~~~~~-k~pg~~LF~y~~~~~v~s~~vN~yl~e~~~~~TaKdFRTw~ 158 (218)
T cd00659 81 LK-PNVVRFDFLGKDSIRYENEVEVEPRLFKNLRKFLD-KLPGDDLFQYLQVDRLNSSKLNAYLREFMEGLTAKVFRTYN 158 (218)
T ss_pred Ee-CCEEEEEEECCCCcEEEEEECChHHHHHHHHHHHH-cCCcHHhhccCCCCcCCHHHHHHHHHHHhCCCChhhcccch
Confidence 99 79999999999999999999933999999999995 59999999 6699999999999999999999999999
Q ss_pred chHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCcccccc
Q 002904 772 ASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQRTVSKT 816 (868)
Q Consensus 772 ASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCNHqR~V~K~ 816 (868)
||++|+..|.+.+...+..+++..|+.|+++||++||||++||+.
T Consensus 159 at~~a~~~L~~~~~~~~~~~~~~~i~~a~~~vA~~LgnTpav~r~ 203 (218)
T cd00659 159 ASLTALEQLARLPASLSLAEKKKAYNDANREVAILLNHTPAISKI 203 (218)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCCCcchhHH
Confidence 999999999988888899999999999999999999999999985
No 11
>COG3569 Topoisomerase IB [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.9e-51 Score=434.47 Aligned_cols=335 Identities=24% Similarity=0.246 Sum_probs=314.6
Q ss_pred ccCcccccccCCCCCCcccccceeeeccccCCCCCCC--CcceEEEcCEeccCChhhHHHHHHHHHhcCCCCCchhhHHh
Q 002904 383 NSQYSKSTKMLPGSGDGQKKWTTLVHNGVIFPPPYLP--HGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRE 460 (868)
Q Consensus 383 ~~~~~kww~~~~~~~~g~~kW~tLeHnGv~Fpp~Y~P--~~V~~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~ 460 (868)
+++.++||+.+ ++|+.+|+|+. |++|+|||.| .+++++|+|++|.|+|+.||| |+.|++++|.|++.| .
T Consensus 13 e~~~l~yv~d~---epgirr~~~gk--gf~y~~Pdg~l~sd~~~~~ri~~l~lPPay~dV---wi~ld~~gHlqatg~-D 83 (354)
T COG3569 13 EEAGLKYVSDE---EPGIRREKTGK--GFIYRPPDGPLVSDAKLLRRIAALALPPAYEDV---WICLDENGHLQATGR-D 83 (354)
T ss_pred hhhcceeeccc---CcchhhhccCC--ceEecCCCCCCCccHHHHhcccccCCCcchhhh---eeecCccccccccch-h
Confidence 45679999864 46767999999 9999999996 999999999999999999999 999999999999999 9
Q ss_pred hhHHHHHHHhCcC----CCcccCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcCeEEEcCceeeecccc
Q 002904 461 NFWNDWRKLLGKN----HVIQNLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFR 536 (868)
Q Consensus 461 NFf~d~~~~l~~~----~~I~~~~kcDF~~i~~~~~~~ke~kk~~s~eEKk~~K~e~~~~~~~yg~~~vDg~~ekvgNfr 536 (868)
|||++|-.+.++- .-|+.|.+|||+.++-+|....+++++++.++++++.+. .+|++||.+++||||
T Consensus 84 argRkqyryhpew~~~r~~~K~~~l~~F~kalp~lrr~~~~~~~~~~~~~~~v~a~--------~~~lLD~~~~rVGN~- 154 (354)
T COG3569 84 ARGRKQYRYHPEWAALRDGIKYFSLVRFGKALPSLRRTIDADLRLPGLPKEKVVAA--------KVCLLDGARIRVGNF- 154 (354)
T ss_pred hhhhhhheeCchhhhcccchhHHHHHHHHHHhHHHHHHHHHhhcCCCccHHHHHHH--------HHHHhhhhHhhcccH-
Confidence 9999999888753 349999999999999999999999999999999988876 799999999999999
Q ss_pred cCCCccccCCCCCCCCCccccccCCChhHHhccCCCCCCCCCCCCCCcceeecCCCCcEEEEeecCCCCceeeeeeccCC
Q 002904 537 VEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAAS 616 (868)
Q Consensus 537 vEpPGLfRGRGfhpk~GklK~RI~PdditInrik~l~IPP~P~~GhaWkeV~hD~~vhwlAtw~D~igrkQyKYvyl~ah 616 (868)
+||||+|-|+++|.++++|.|++++|+.....+. ||.|+++ .+|+.|++
T Consensus 155 ----~y~r~ngsyg~TtllkRhV~~~~~ti~~~f~gk~------G~~~~~~--------------------l~~~rLaa- 203 (354)
T COG3569 155 ----AYARDNGSYGLTTLLKRHVDVEGSTIRFRFKGKS------GKEWKER--------------------LKDPRLAA- 203 (354)
T ss_pred ----HHhhccCCcCcccceeeeeccCCCEEEEEecCCc------chhhhhh--------------------hhhHHHHH-
Confidence 8999999999999999999999999999988764 9999998 79999999
Q ss_pred chhhcCccHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceE
Q 002904 617 SSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVE 696 (868)
Q Consensus 617 s~wk~~rD~~Kyerar~Lk~~Lp~IR~~y~kDLksk~~~~RqlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~ 696 (868)
.++++.|.- .+.|..+|+.|+..++.|+++..+..||.+.+.|++|.+++|.|++.-+++++|+|||+++.+||+
T Consensus 204 -~L~~~~DLp----gr~Lf~y~D~~~~~~r~~s~~ln~ylr~~~g~~~sak~Frtw~Gt~~a~~~a~t~g~~s~~~~~v~ 278 (354)
T COG3569 204 -ILRGQLDLP----GRKLFQYLDEDGRERRIDSKSLNAYLRQVTGAPFSAKDFRTWGGTLLAEEEADTVGCCSEAPELVS 278 (354)
T ss_pred -HHHHhhcCc----hHHHHHhhcccCCcccCCchhHHHHHHHhcccceehhHHHhccCchHHHHHHhhhcchhcchhhhh
Confidence 889999985 999999999999999999999888999999999999999999999999999999999999999999
Q ss_pred EcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhh-cCCCCCCcccccCChhHHHHHHHhhCCCCcceeeccccchHH
Q 002904 697 CIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQ-TGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASIT 775 (868)
Q Consensus 697 l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~-k~K~PGd~LFd~L~ss~LN~yLkelM~glTAKdFRTynASvt 775 (868)
+.+.....|+|+++.++++| |+|+||++...++ ..+.+|..||++.... ||+|++.+|.+|++|+|||||||.|
T Consensus 279 ~~~~~A~~Lgnt~aisRr~Y----IhPqVf~~~~~~K~~~~~~g~~lr~r~~~~-L~~ee~~Ll~~L~~~~~~~~~~~~t 353 (354)
T COG3569 279 LVAAVAAVLGNTPAISRRCY----IHPQVFDNYLIGKRLPKKSGRQLRDRARLE-LNKEEQRLLRFLEAKVRRRYRASKT 353 (354)
T ss_pred hccchhhhccCCccccccce----ecHHHHhhhhhcccCcccchhHHHhhcccc-ccHHHHHHHhhhchhhhhhhhhhcc
Confidence 99889999999999999998 6999999999998 5689999999999988 9999999999999999999999976
Q ss_pred H
Q 002904 776 L 776 (868)
Q Consensus 776 a 776 (868)
+
T Consensus 354 ~ 354 (354)
T COG3569 354 M 354 (354)
T ss_pred C
Confidence 3
No 12
>COG3569 Topoisomerase IB [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.4e-45 Score=389.92 Aligned_cols=273 Identities=19% Similarity=0.264 Sum_probs=248.8
Q ss_pred hhcCeEEEcCceeeecccccCCCcccc---CCCCCC--CCCc-cccccCCChhHHhccCCCCCCCCCCCCCCcceee--c
Q 002904 518 EKYMWAIVDGVKEKVGNFRVEPPGLFR---GRGEHP--KMGK-LKKRIQPSDITINIGKDVPIPECPIPGESWKEVK--H 589 (868)
Q Consensus 518 ~~yg~~~vDg~~ekvgNfrvEpPGLfR---GRGfhp--k~Gk-lK~RI~PdditInrik~l~IPP~P~~GhaWkeV~--h 589 (868)
|+.||+||++ +.|||.| |+||.| .+|. ++ |...|.+|+.+.||| +|.||| .
T Consensus 13 e~~~l~yv~d----------~epgirr~~~gkgf~y~~Pdg~l~s-----d~~~~~ri~~l~lPP------ay~dVwi~l 71 (354)
T COG3569 13 EEAGLKYVSD----------EEPGIRREKTGKGFIYRPPDGPLVS-----DAKLLRRIAALALPP------AYEDVWICL 71 (354)
T ss_pred hhhcceeecc----------cCcchhhhccCCceEecCCCCCCCc-----cHHHHhcccccCCCc------chhhheeec
Confidence 6789999999 6999999 889999 5776 55 888899999999999 999999 9
Q ss_pred CCCCcEEEEeecCCCCceeeeeeccCCchhhcCccHHHHHHHHHHHHHHHHHHHHHHHhccCCCC-CchHHHHHHHHHHh
Q 002904 590 DNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDG-TRRQIAVATYLIDK 668 (868)
Q Consensus 590 D~~vhwlAtw~D~igrkQyKYvyl~ahs~wk~~rD~~Kyerar~Lk~~Lp~IR~~y~kDLksk~~-~~RqlAvAlyLIDk 668 (868)
|+++|+||||+|+.||+|||| ||+|.+.++..||..+.+|++.||.||+.++.||+..++ .++++|.++.|||-
T Consensus 72 d~~gHlqatg~DargRkqyry-----hpew~~~r~~~K~~~l~~F~kalp~lrr~~~~~~~~~~~~~~~v~a~~~~lLD~ 146 (354)
T COG3569 72 DENGHLQATGRDARGRKQYRY-----HPEWAALRDGIKYFSLVRFGKALPSLRRTIDADLRLPGLPKEKVVAAKVCLLDG 146 (354)
T ss_pred Cccccccccchhhhhhhhhee-----CchhhhcccchhHHHHHHHHHHhHHHHHHHHHhhcCCCccHHHHHHHHHHHhhh
Confidence 999999999999999999999 999999999999999999999999999999999999888 79999999999999
Q ss_pred cccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCCcccccC--
Q 002904 669 LALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKL-- 746 (868)
Q Consensus 669 lALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd~LFd~L-- 746 (868)
..+||||-.|++.|+|||+|||+.+||.+. +++|+|.|.||.|++|...+. +++|+.+|+.+. ++||..||+||
T Consensus 147 ~~~rVGN~~y~r~ngsyg~TtllkRhV~~~-~~ti~~~f~gk~G~~~~~~l~-~~rLaa~L~~~~--DLpgr~Lf~y~D~ 222 (354)
T COG3569 147 ARIRVGNFAYARDNGSYGLTTLLKRHVDVE-GSTIRFRFKGKSGKEWKERLK-DPRLAAILRGQL--DLPGRKLFQYLDE 222 (354)
T ss_pred hHhhcccHHHhhccCCcCcccceeeeeccC-CCEEEEEecCCcchhhhhhhh-hHHHHHHHHHhh--cCchHHHHHhhcc
Confidence 999999999999999999999999999999 899999999999999999997 999999999999 89999999885
Q ss_pred -------ChhHHHHHHHhhC-CCCcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCcccccc--
Q 002904 747 -------DTAKLNAHLKELM-PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQRTVSKT-- 816 (868)
Q Consensus 747 -------~ss~LN~yLkelM-~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCNHqR~V~K~-- 816 (868)
++.++|.||++.. .+|||||||||+||..+.+.+......+.. ...+....+||..+.++++||..
T Consensus 223 ~~~~~r~~s~~ln~ylr~~~g~~~sak~Frtw~Gt~~a~~~a~t~g~~s~~----~~~v~~~~~~A~~Lgnt~aisRr~Y 298 (354)
T COG3569 223 DGRERRIDSKSLNAYLRQVTGAPFSAKDFRTWGGTLLAEEEADTVGCCSEA----PELVSLVAAVAAVLGNTPAISRRCY 298 (354)
T ss_pred cCCcccCCchhHHHHHHHhcccceehhHHHhccCchHHHHHHhhhcchhcc----hhhhhhccchhhhccCCccccccce
Confidence 4899999999999 599999999999999999999876555421 22356778888888888888885
Q ss_pred -hHHHHHHH
Q 002904 817 -HSAQMSRL 824 (868)
Q Consensus 817 -~~~sm~kl 824 (868)
|-+.+.++
T Consensus 299 IhPqVf~~~ 307 (354)
T COG3569 299 IHPQVFDNY 307 (354)
T ss_pred ecHHHHhhh
Confidence 44555553
No 13
>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=96.44 E-value=0.01 Score=54.90 Aligned_cols=123 Identities=21% Similarity=0.279 Sum_probs=86.3
Q ss_pred chHHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeC-CCCeEEEEEEeeChHHHHHHHhhhc
Q 002904 656 RRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLG-KDSIQYVNTVEVELPVYKAIGQFQT 734 (868)
Q Consensus 656 ~RqlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlG-Kdgir~~~tV~VD~~V~knLk~f~k 734 (868)
....++++.|+-.+.+|.|. +|.|+.+||... ... |.|.+ |.+..+ .+.+.+.+...|..+..
T Consensus 14 ~~~~~~~~~l~~~tG~R~~E-----------i~~l~~~~~~~~-~~~--~~i~~~K~~~~~--~i~i~~~~~~~l~~~~~ 77 (164)
T cd00397 14 PERLYLALLLLLATGLRISE-----------LCALRWSDIDLD-KRV--IHITGTKTKKER--TVPLSEEALKLLKEYLK 77 (164)
T ss_pred ccHHHHHHHHHHHhCCCHHH-----------HhCCchhhhccc-cCE--EEEecCCCCCee--EEecCHHHHHHHHHHHH
Confidence 34677788888889999985 789999999876 334 55555 887544 56667777777776653
Q ss_pred C----CCCCCccccc--------CChhHHHHHHHhhC--CC-----CcceeeccccchHHHHHHHhcCCCCCCHHHHHHH
Q 002904 735 G----KKQNDDLFDK--------LDTAKLNAHLKELM--PG-----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDV 795 (868)
Q Consensus 735 ~----K~PGd~LFd~--------L~ss~LN~yLkelM--~g-----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~ 795 (868)
. ..+++.||.. ++...++.+++.++ .+ ++..+||...||.++.... +
T Consensus 78 ~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~R~t~~t~~~~~g~-----~--------- 143 (164)
T cd00397 78 KRRPANGDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLRHTFASALLNAGL-----D--------- 143 (164)
T ss_pred HhccccCCCCceeecCCCCCccCCcHHHHHHHHHHHHHHcCCCCCCCCchHhHHHHHHHHHHcCC-----C---------
Confidence 2 2467788854 44567999999887 23 7888888877776443221 1
Q ss_pred HHHHHHHHHHHcCCCcc
Q 002904 796 YQRANKEVAIICNHQRT 812 (868)
Q Consensus 796 yn~Anr~VAilCNHqR~ 812 (868)
..++|.+|+|...
T Consensus 144 ----~~~i~~~~gH~~~ 156 (164)
T cd00397 144 ----LEAVQDLLGHSSI 156 (164)
T ss_pred ----HHHHHHHhCCCcH
Confidence 4578888998643
No 14
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins 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 (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1A0P_A 1Z1G_B 1Z19_A 1AE9_A 1Z1B_A 1P7D_B 2A3V_C 1Q3V_E 1Q3U_A 1OUQ_F ....
Probab=95.32 E-value=0.17 Score=47.59 Aligned_cols=106 Identities=15% Similarity=0.187 Sum_probs=74.0
Q ss_pred chHHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEE-eeCCCCeEEEEEEeeChHHHHHHHhhhc
Q 002904 656 RRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFD-FLGKDSIQYVNTVEVELPVYKAIGQFQT 734 (868)
Q Consensus 656 ~RqlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~Fd-FlGKdgir~~~tV~VD~~V~knLk~f~k 734 (868)
.-..++++.|+=.+.+|+|- +++|+.+||.+. ++.+.+. -.+|-+.. ..|.+.+.++..|+.+..
T Consensus 20 ~~~~~~~~~l~~~tG~R~~E-----------l~~l~~~~v~~~-~~~~~i~~~~~K~~~~--~~~~i~~~~~~~l~~~~~ 85 (173)
T PF00589_consen 20 PLRNRLIILLLLYTGLRPSE-----------LLRLRWDDVDLE-NGEIYIPIRRTKTGKS--RTVPISPELAELLREYIK 85 (173)
T ss_dssp HHHHHHHHHHHHHHT--HHH-----------HHT-BGGGEETT-TTEEEEEEEECSSSEE--EEEECTHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHccchhh-----------hhhhhhhhhhcc-cccccccccccccccc--cccccccccccccccccc
Confidence 34556677788889999976 899999999888 5677664 46666666 567778999999988764
Q ss_pred C----CCCCCccc-----ccCChhHHHHHHHhhC-----C-CCcceeeccccchHH
Q 002904 735 G----KKQNDDLF-----DKLDTAKLNAHLKELM-----P-GLTAKVFRTYNASIT 775 (868)
Q Consensus 735 ~----K~PGd~LF-----d~L~ss~LN~yLkelM-----~-glTAKdFRTynASvt 775 (868)
. ..+.+.|| ..++...++..++.++ + ++|..+||--.++.+
T Consensus 86 ~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lR~t~~t~l 141 (173)
T PF00589_consen 86 RRKRQNDDDDYLFPSSDGKPLSRQTINKIFRRIIKKAGIEKKFTPHSLRHTFATNL 141 (173)
T ss_dssp HHCHCHCCSSBSSBETTSSB--HHHHHHHHHHHHHHTT-SSCTCHHHHHHHHHHHH
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 2 35677888 3478999999999987 2 466777774444433
No 15
>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=94.77 E-value=0.12 Score=51.28 Aligned_cols=100 Identities=18% Similarity=0.252 Sum_probs=71.1
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCC---
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK--- 736 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K--- 736 (868)
.+++.|+-.+++|+|. ++.|+.+||.+. ++.+.+. .+|.+..+ .|.+.+.+...|+.+....
T Consensus 89 ~~~~~l~~~tG~R~~E-----------~~~L~~~di~~~-~~~~~i~-~~K~~~~~--~ipl~~~~~~~l~~~~~~~~~~ 153 (242)
T cd01193 89 RLILSLLYGCGLRLSE-----------CLRLRVKDIDFD-RGQIRVR-QGKGGKDR--YVMLPEALLELLRAYWKRARAL 153 (242)
T ss_pred HHHHHHHHHcCCcHHH-----------HhcCCHHHcCCC-CCeEEEE-eCCCCCce--EEeccHHHHHHHHHHHHHHHhc
Confidence 4555566668899987 788999999988 6777774 36776555 5666788888888776432
Q ss_pred ---CCCCccc-------------ccCChhHHHHHHHhhC--C----CCcceeeccccchH
Q 002904 737 ---KQNDDLF-------------DKLDTAKLNAHLKELM--P----GLTAKVFRTYNASI 774 (868)
Q Consensus 737 ---~PGd~LF-------------d~L~ss~LN~yLkelM--~----glTAKdFRTynASv 774 (868)
.+++.|| ..++...+|.+++.++ . .+|..+||-.-||.
T Consensus 154 ~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~s~h~lRht~at~ 213 (242)
T cd01193 154 GRERPWQWLFPSTRRSRDPVERRHHLSERTLQRALKKAVEQAGIDKRVTPHTLRHSFATH 213 (242)
T ss_pred ccCCCCceecccCCCCcccccccCCCCHHHHHHHHHHHHHHcCCCCCCCcCcchHHHHHH
Confidence 4566777 2367889999999986 2 36777777444443
No 16
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed
Probab=94.75 E-value=0.066 Score=54.48 Aligned_cols=110 Identities=18% Similarity=0.193 Sum_probs=77.9
Q ss_pred HHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCCc
Q 002904 662 ATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDD 741 (868)
Q Consensus 662 AlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd~ 741 (868)
+++|+-.+.||+|- +|.|+.+||.+. .+.|.+ +|.+..+ +|.+.+.++..|+... ++..
T Consensus 117 ~~~ll~~tGlR~~E-----------l~~L~~~dId~~-~~~i~i---~k~~~~R--~vpl~~~l~~~L~~~~----~~~~ 175 (245)
T PRK02436 117 IALLILELGLTPSE-----------IAGLKVADIDLD-FQVLTI---EKAGGKR--VLTLPEALLPFLEAIL----NQTY 175 (245)
T ss_pred HHHHHHHcCCCHHH-----------HhcCcHHHcCcc-CCEEEE---cCCCcee--EEECCHHHHHHHHHHh----CCCe
Confidence 45666689999987 999999999988 567765 4555443 6888999999999886 4567
Q ss_pred ccc----cCChhHHHHHHHhhC-----CCCcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002904 742 LFD----KLDTAKLNAHLKELM-----PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (868)
Q Consensus 742 LFd----~L~ss~LN~yLkelM-----~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCNHq 810 (868)
||. .++...++..++.++ +.+|+.+||=--||.++ +.+. + ..+|+.+++|.
T Consensus 176 lF~~~g~~~~~~~~~~~~~~~~~~~gi~~~t~H~lRHtfat~~~-----~~g~--~-----------~~~l~~~lGH~ 235 (245)
T PRK02436 176 LFEHKGKPYSRQWFFNQLKSFVKSIGYPGLSAQKLREQFILKQK-----EAGK--S-----------IYELARLLGLK 235 (245)
T ss_pred eecCCCCcccHHHHHHHHHHHHHHcCCCCCCcchhHHHHHHHHH-----HcCC--C-----------HHHHHHHhCCC
Confidence 884 356656666666654 46788888865566544 2211 2 34688899995
No 17
>TIGR02224 recomb_XerC tyrosine recombinase XerC. 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 model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK.
Probab=94.74 E-value=0.17 Score=51.47 Aligned_cols=117 Identities=17% Similarity=0.223 Sum_probs=79.9
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC----
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG---- 735 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~---- 735 (868)
++++.|+-.+.+|+|. +|.|+.+||.+. ++.+.+. ||.+..+ .|.+.+.++..|..+++.
T Consensus 132 ~~~~~l~~~tG~R~~E-----------l~~l~~~di~~~-~~~~~i~--~k~~~~r--~vpl~~~~~~~l~~~~~~~~~~ 195 (295)
T TIGR02224 132 RAILELLYSSGLRVSE-----------LVGLDLDDLDLD-SGLVRVR--GKGNKER--IVPFGSYAKDALQAYLEARREK 195 (295)
T ss_pred HHHHHHHHHhcchHHH-----------HhCCCchhcccC-cceEEEe--cCCCcee--EEECCHHHHHHHHHHHHHhhhc
Confidence 3556666779999986 889999999998 4666654 7776554 577789999999988751
Q ss_pred ---CCCCCcccc-----cCChhHHHHHHHhhC------CCCcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q 002904 736 ---KKQNDDLFD-----KLDTAKLNAHLKELM------PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANK 801 (868)
Q Consensus 736 ---K~PGd~LFd-----~L~ss~LN~yLkelM------~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr 801 (868)
..+++.||. .++...++..|+.++ .++|+.+||--.||..+ +.+. + ..
T Consensus 196 ~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~~t~~~-----~~g~--~-----------~~ 257 (295)
T TIGR02224 196 LLASEGQDALFLNRRGGRLTPRGVQYRLQQLVAKAGLPKHVHPHALRHSFATHLL-----ENGA--D-----------LR 257 (295)
T ss_pred cchhcCCCeeEEeCCCCCCCHHHHHHHHHHHHHHcCCCCCcChHHHHHHHHHHHH-----HcCC--C-----------HH
Confidence 223336884 477888898888885 24677777744444433 2211 1 34
Q ss_pred HHHHHcCCC
Q 002904 802 EVAIICNHQ 810 (868)
Q Consensus 802 ~VAilCNHq 810 (868)
.|+.+++|.
T Consensus 258 ~i~~~lGH~ 266 (295)
T TIGR02224 258 AVQELLGHA 266 (295)
T ss_pred HHHHHhcCC
Confidence 678888995
No 18
>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=94.46 E-value=0.46 Score=49.51 Aligned_cols=129 Identities=18% Similarity=0.149 Sum_probs=89.7
Q ss_pred HHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhc---
Q 002904 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQT--- 734 (868)
Q Consensus 658 qlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k--- 734 (868)
...++++|+-.+.+|+|- +|.|+.+||.+. ++.|.|. -+|.+..+ .|.+.+.+...|..+..
T Consensus 127 ~~~~~i~ll~~tGlR~~E-----------~~~L~~~did~~-~~~i~i~-~~K~~~~r--~vpl~~~l~~~l~~~~~~~~ 191 (299)
T cd01187 127 TYRTLFGLLAVTGLRLGE-----------ALRLRLSDVDLD-SGILTVR-DSKFGKSR--LVPLHASTRAALRDYLARRD 191 (299)
T ss_pred HHHHHHHHHHHhCCcHHH-----------HHhCcHHhcCCC-CCeEEEE-ecCCCCcc--EEeCCHHHHHHHHHHHHHHH
Confidence 345678888999999987 899999999988 4566553 37877654 57888999999987642
Q ss_pred ---CCCCCCccccc-----CChh---HHHHHHHhhCC--------CCcceeeccccchHHHHHHHhcCCCCCCHHHHHHH
Q 002904 735 ---GKKQNDDLFDK-----LDTA---KLNAHLKELMP--------GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDV 795 (868)
Q Consensus 735 ---~K~PGd~LFd~-----L~ss---~LN~yLkelM~--------glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~ 795 (868)
...+++.||.. ++.+ .+..+++.+.. .+|..+||-.-||.++...+ +.+. ++.
T Consensus 192 ~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRHt~at~~l~~~~-~~g~--~~~----- 263 (299)
T cd01187 192 RLLPAPDSSAFFVSSRGGRLSYGGHRVFYALSREIGLRGWAQRGRGPRLHDLRHRFAVTRLTRWY-RAGA--DVE----- 263 (299)
T ss_pred hhccCCCCcceeeCCCCCCCCcccchHHHHHHHHhCcccCCCCCCCCCcccccHHHHHHHHHHHH-HcCC--Chh-----
Confidence 12356778843 5555 78888888852 36888898777786654333 2221 221
Q ss_pred HHHHHHHHHHHcCCCc
Q 002904 796 YQRANKEVAIICNHQR 811 (868)
Q Consensus 796 yn~Anr~VAilCNHqR 811 (868)
.....|+.+.+|..
T Consensus 264 --~~~~~v~~~lGH~~ 277 (299)
T cd01187 264 --RKLPVLATYLGHAN 277 (299)
T ss_pred --hhhHHHHHHcCCCC
Confidence 12367899999973
No 19
>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=94.43 E-value=0.41 Score=46.72 Aligned_cols=117 Identities=17% Similarity=0.275 Sum_probs=77.7
Q ss_pred HHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC---CCC
Q 002904 662 ATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG---KKQ 738 (868)
Q Consensus 662 AlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~---K~P 738 (868)
+++|+-.+.+|.|. ||.|+..||.+. .+.+.+. .+|.+..+ .|.+.+.+...|..+... ..+
T Consensus 30 ~~~l~~~tGlR~~E-----------l~~l~~~di~~~-~~~i~i~-~~K~~~~r--~vpl~~~~~~~l~~~~~~~~~~~~ 94 (188)
T cd01188 30 ILLLLARLGLRAGE-----------VAALRLDDIDWR-TGTIRVR-QGKGGRVT--RLPLPAEVGAALADYLRDGRPATD 94 (188)
T ss_pred HHHHHHHHCCCHHH-----------HHhCcccccCCC-CCeEEEE-eCCCCcce--EEeCCHHHHHHHHHHHHhcCCCCC
Confidence 45666668899987 899999999987 4566554 26766544 677789999888877532 234
Q ss_pred CCcccc--------cCChhHHHHHHHhhCC--C-----CcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Q 002904 739 NDDLFD--------KLDTAKLNAHLKELMP--G-----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEV 803 (868)
Q Consensus 739 Gd~LFd--------~L~ss~LN~yLkelM~--g-----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~V 803 (868)
++.||- .++...+|.+++.++. | +|+.+||---|| .|...+.. ...|
T Consensus 95 ~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at-----~l~~~g~~-------------~~~i 156 (188)
T cd01188 95 SRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLAT-----RLLRAGAP-------------LKEI 156 (188)
T ss_pred CCceeeeccCCcCCcccHHHHHHHHHHHHHHcCCCcCCCCcHHHHHHHHH-----HHHHcCCC-------------HHHH
Confidence 567883 2478899999998882 3 455566643334 33322211 3567
Q ss_pred HHHcCCCc
Q 002904 804 AIICNHQR 811 (868)
Q Consensus 804 AilCNHqR 811 (868)
+.+++|.-
T Consensus 157 ~~~lGH~~ 164 (188)
T cd01188 157 GDVLGHRS 164 (188)
T ss_pred HHHhCCCC
Confidence 78888864
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=94.39 E-value=0.14 Score=53.80 Aligned_cols=122 Identities=12% Similarity=0.035 Sum_probs=86.1
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEe-eCCCCeEEEEEEeeChHHHHHHHhhhcCCC
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQTGKK 737 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k~K~ 737 (868)
...++.|+=.+.||.|- +|.|+.+||.+. ++.+.+.. .+|.+.. ..|.+.+.+...|..+.....
T Consensus 201 ~~~~~~l~~~tGlR~~E-----------i~~L~~~di~~~-~~~~~i~~~~~Kt~~~--r~vpl~~~~~~~l~~~~~~~~ 266 (357)
T cd00801 201 TRLALKLLLLTGVRPGE-----------LRGARWSEIDLE-NALWTIPAERMKTRRP--HRVPLSDQALALLEELRELSG 266 (357)
T ss_pred HHHHHHHHHHHCcChHh-----------HHcCcchhcccC-CCeEecchhhccCCCC--cccCCcHHHHHHHHHHHHHhC
Confidence 34445555569999985 899999999998 56666543 3676643 367778999999998875545
Q ss_pred CCCcccc-------cCChhHHHHHHHhhC--CCCcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcC
Q 002904 738 QNDDLFD-------KLDTAKLNAHLKELM--PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICN 808 (868)
Q Consensus 738 PGd~LFd-------~L~ss~LN~yLkelM--~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCN 808 (868)
+++.||. .++...++.+++.+. ..+|..+||-.-||.++. .+.+ ...|+.+++
T Consensus 267 ~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRHt~at~~~~-----~g~~-------------~~~i~~~lG 328 (357)
T cd00801 267 HSEYVFPSRRDRGKPLSENTLNKALKRMGYLGEWTPHGLRRTARTWLNE-----LGFP-------------PDVIERQLA 328 (357)
T ss_pred CCceEecCCCCCCCCCCHHHHHHHHHHcCCCCCcCcCchhHHHHHHHHH-----CCCC-------------HHHHHHHhC
Confidence 5788994 466788999999987 468888888776665443 2111 235777888
Q ss_pred CCcc
Q 002904 809 HQRT 812 (868)
Q Consensus 809 HqR~ 812 (868)
|.-.
T Consensus 329 Hs~~ 332 (357)
T cd00801 329 HVLG 332 (357)
T ss_pred CCCC
Confidence 8653
No 21
>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=93.54 E-value=0.37 Score=43.69 Aligned_cols=123 Identities=16% Similarity=0.125 Sum_probs=83.4
Q ss_pred HHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC--
Q 002904 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-- 735 (868)
Q Consensus 658 qlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-- 735 (868)
..++++.|+=.+.+|.+. ++.|..+||... +..+.|.- .|.+..+ .+.+++.++..|..+...
T Consensus 16 ~~~~~~~l~~~~G~R~~e-----------i~~l~~~~v~~~-~~~~~i~~-~K~~~~~--~~~i~~~~~~~l~~~~~~~~ 80 (162)
T cd01182 16 RDRALILLLLYTGLRVSE-----------LLALRWSDIDLD-KGTITVRR-TKTGKER--TVPLSPELAELLREYLELRR 80 (162)
T ss_pred HHHHHHHHHHHhCCCHHH-----------HhhhehhcccCc-CCEEEEEe-cCCCCce--EEecCHHHHHHHHHHHHHhc
Confidence 455566666679999976 788999999887 34444432 3666444 466678788888888754
Q ss_pred --CCCCCccccc-------CChhHHHHHHHhhC---C---CCcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 002904 736 --KKQNDDLFDK-------LDTAKLNAHLKELM---P---GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRAN 800 (868)
Q Consensus 736 --K~PGd~LFd~-------L~ss~LN~yLkelM---~---glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~An 800 (868)
..++..||.. ++...++.+++.+. . ++|...||-..++.++..- .. .
T Consensus 81 ~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lR~~~~~~~~~~g-----~~-------------~ 142 (162)
T cd01182 81 PAPKPDDYLFPSRRGGPKRLTRRAVRRLLKKAGKRAGIPERLTPHDLRHTFATRLLEAG-----VP-------------L 142 (162)
T ss_pred ccCCCCCeEEEcCCCCCcccchHHHHHHHHHHHHHcCCCcccCcchhHHHHHHHHHHCC-----CC-------------H
Confidence 2567788865 34677888888887 2 5788888877777544321 11 4
Q ss_pred HHHHHHcCCCccc
Q 002904 801 KEVAIICNHQRTV 813 (868)
Q Consensus 801 r~VAilCNHqR~V 813 (868)
.+||.+.+|....
T Consensus 143 ~~~~~~~gH~~~~ 155 (162)
T cd01182 143 EVIQELLGHSSIS 155 (162)
T ss_pred HHHHHHhCCCCHH
Confidence 5677777887543
No 22
>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=93.53 E-value=0.35 Score=46.62 Aligned_cols=119 Identities=10% Similarity=0.006 Sum_probs=78.3
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEee-CCCCeEEEEEEeeChHHHHHHHhhhcCCCC
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL-GKDSIQYVNTVEVELPVYKAIGQFQTGKKQ 738 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFl-GKdgir~~~tV~VD~~V~knLk~f~k~K~P 738 (868)
.+++.|+=.+.+|+|- ++.|+.+||.+. ++.+.+... +|.+..+ .|.+.+.+...|+.+.. ...
T Consensus 24 ~~~~~l~~~tG~R~~E-----------l~~l~~~did~~-~~~~~i~~~~~K~~~~r--~ipl~~~~~~~l~~~~~-~~~ 88 (177)
T cd01192 24 KPAVLFALNTGLRRSE-----------ILGLEWSQVDLD-NRVAWVRPATSKGGRAI--RVPLNDEALQVLKRQKA-GAH 88 (177)
T ss_pred HHHHHHHHHhCccHHH-----------HhcCchhhcccc-CCEEEEeccCCCCCCee--EecCCHHHHHHHHHHhc-cCC
Confidence 4555666678899987 889999999887 567777663 5666554 57778999999999985 234
Q ss_pred CCcccccCCh---hHHHHHHHhhC-----CCCcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002904 739 NDDLFDKLDT---AKLNAHLKELM-----PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (868)
Q Consensus 739 Gd~LFd~L~s---s~LN~yLkelM-----~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCNHq 810 (868)
+..||..... ..++..++.++ +++|...||-..||.++.. +. + ...|+.+++|.
T Consensus 89 ~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~at~l~~~-----g~--~-----------~~~i~~~lGH~ 150 (177)
T cd01192 89 KPWVFAGAGGDPRIDSKTAWRQALQRAGISDFRWHDLRHTWASWLVQS-----GV--P-----------LYVLQELLGHS 150 (177)
T ss_pred CCeEeecCCCCcccchHHHHHHHHHHcCCCCCcchhhhHHHHHHHHHc-----CC--C-----------HHHHHHHhCCC
Confidence 5677854321 12333344444 4678888887776754321 11 1 34677788887
Q ss_pred c
Q 002904 811 R 811 (868)
Q Consensus 811 R 811 (868)
-
T Consensus 151 ~ 151 (177)
T cd01192 151 S 151 (177)
T ss_pred C
Confidence 4
No 23
>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=92.94 E-value=0.39 Score=47.15 Aligned_cols=116 Identities=16% Similarity=0.157 Sum_probs=79.2
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCC
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQND 740 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd 740 (868)
+++.|+-.+.+|.|. ++.|+.+||.+. ..+.+. .+|-+.. ..|.+.+.++..|+.+.....+.+
T Consensus 28 ~~~~l~~~tGlR~~E-----------l~~l~~~di~~~--~~i~i~-~~K~~~~--r~vpl~~~l~~~l~~~~~~~~~~~ 91 (180)
T cd01186 28 LLFLIGINTGLRISD-----------ILALKVKDVRGD--ERISIK-EKKTGKR--KRIYLNPILKEELLYYIKDLEENE 91 (180)
T ss_pred HHHHHHHHhhhHHHH-----------HHhcCHHHhCCC--CceEEE-EecCCce--EEEEECHHHHHHHHHHHHhCCCcC
Confidence 457777789999987 888999988766 234443 2566654 467788999999999885445677
Q ss_pred ccccc-------CChhHHHHHHHhhC--CC---CcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcC
Q 002904 741 DLFDK-------LDTAKLNAHLKELM--PG---LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICN 808 (868)
Q Consensus 741 ~LFd~-------L~ss~LN~yLkelM--~g---lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCN 808 (868)
.||.. ++...++.+++.++ -| +|..+||--.|| .|...+. ....|+.+++
T Consensus 92 ~lf~~~~~~~~~~~~~~~~~~~k~~~~~~gi~~~~~H~lRht~at-----~l~~~g~-------------~~~~i~~~lG 153 (180)
T cd01186 92 YLFQSRKGGNRPITRQQAYRILKKAAEQVGIDNIGTHTLRKTFGY-----HYYKQTK-------------DIALLMEIFN 153 (180)
T ss_pred ceEEecCCCCCCccHHHHHHHHHHHHHHcCCCcccccccHHHHHH-----HHHHcCC-------------CHHHHHHHhC
Confidence 88843 77888999999887 24 455556554444 4433221 2346777788
Q ss_pred CC
Q 002904 809 HQ 810 (868)
Q Consensus 809 Hq 810 (868)
|.
T Consensus 154 H~ 155 (180)
T cd01186 154 HS 155 (180)
T ss_pred CC
Confidence 85
No 24
>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=92.92 E-value=0.63 Score=44.84 Aligned_cols=120 Identities=17% Similarity=0.170 Sum_probs=81.0
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEee--------CCCCeEEEEEEeeChHHHHHHHh
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL--------GKDSIQYVNTVEVELPVYKAIGQ 731 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFl--------GKdgir~~~tV~VD~~V~knLk~ 731 (868)
.+++.|+-.+.+|.|. +|.|+.+||.+. +..|.+.-. +|.+. ..+|.+.+.+...|..
T Consensus 19 ~~~~~l~~~tglR~~E-----------i~~L~~~di~~~-~~~i~i~~~~~~~~~~~~K~~~--~r~v~l~~~~~~~l~~ 84 (186)
T cd01194 19 KFLFALLYETGLRIGE-----------ALGLRIEDIDLA-ENQIWLVPREDNANGARAKSGR--ERRIPVSQYLIDLYVD 84 (186)
T ss_pred HHHHHHHHHcCCChhh-----------hhccccceeecC-CCEEEEeecCCCcCcccccCCC--CceEEcCHHHHHHHHH
Confidence 4556667789999986 899999999988 566666543 24442 3467778888887777
Q ss_pred hhc-----CCCCCCcccc---------cCChhHHHHHHHhhC----CCCcceeeccccchHHHHHHHhcCCCCCCHHHHH
Q 002904 732 FQT-----GKKQNDDLFD---------KLDTAKLNAHLKELM----PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKI 793 (868)
Q Consensus 732 f~k-----~K~PGd~LFd---------~L~ss~LN~yLkelM----~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~ 793 (868)
+.. ...++..||- .++...++.+++.++ ..+|..+||-..++.. ...+.+
T Consensus 85 ~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lR~t~~t~~-----~~~g~~------- 152 (186)
T cd01194 85 YVTEIYYLEELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGIDFTPHMFRHTHATEL-----IRAGWS------- 152 (186)
T ss_pred HHHHHcccccCCCCEEEEcCCCCCCCcccCHHHHHHHHHHHHHHcCCCCCccccchHHHHHH-----HHcCCC-------
Confidence 642 1455677883 356778898998887 2477778887666633 222211
Q ss_pred HHHHHHHHHHHHHcCCCc
Q 002904 794 DVYQRANKEVAIICNHQR 811 (868)
Q Consensus 794 ~~yn~Anr~VAilCNHqR 811 (868)
.+.|+.+++|.-
T Consensus 153 ------~~~i~~~~gH~~ 164 (186)
T cd01194 153 ------IEVVADRLGHAH 164 (186)
T ss_pred ------HHHHHHHhCCCC
Confidence 247788888874
No 25
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=92.90 E-value=0.75 Score=47.25 Aligned_cols=99 Identities=19% Similarity=0.230 Sum_probs=69.4
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC----
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG---- 735 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~---- 735 (868)
.++++|+=.++||.|. +|.|+.++|.+. ++.+.+. +|.+..+ .|.+.+.+...|..+...
T Consensus 137 ~~~~~l~~~tGlR~~E-----------~~~L~~~di~~~-~~~~~i~--~k~~~~r--~vpl~~~~~~~l~~~~~~~~~~ 200 (299)
T PRK00283 137 RAMLELLYATGLRVSE-----------LVGLTLDDVSLR-QGVVRVT--GKGNKER--LVPLGEEAVYAIERYLERGRPA 200 (299)
T ss_pred HHHHHHHHHhCCcHHH-----------HHcCcHHHcCcC-CCEEEEe--ccCCCee--eeeCCHHHHHHHHHHHHhcccc
Confidence 4556677778999987 889999999988 5676665 7877654 566788888888887521
Q ss_pred ---CCCCCcccc-----cCChhHHHHHHHhhC-------CCCcceeeccccchH
Q 002904 736 ---KKQNDDLFD-----KLDTAKLNAHLKELM-------PGLTAKVFRTYNASI 774 (868)
Q Consensus 736 ---K~PGd~LFd-----~L~ss~LN~yLkelM-------~glTAKdFRTynASv 774 (868)
..+.+.||- .++...++..|+.+. +++|..+||--.||.
T Consensus 201 ~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~ 254 (299)
T PRK00283 201 LLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHVLRHAFATH 254 (299)
T ss_pred cCCCCCCCceeecCCCCcCCHHHHHHHHHHHHHHhCCCccCCCchHHHHHHHHH
Confidence 234567884 366778888888875 245666666444443
No 26
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=92.84 E-value=0.42 Score=52.06 Aligned_cols=118 Identities=18% Similarity=0.257 Sum_probs=80.7
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-----
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG----- 735 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~----- 735 (868)
+++.|+-.+.||+|. +|.|+.++|.+. +..|.+. .||.+..+ .|.+...+...|+.+...
T Consensus 161 ~~~~ll~~tGlR~~E-----------~~~L~~~did~~-~~~i~i~-~~K~~~~R--~vpl~~~~~~~L~~~~~~~r~~~ 225 (358)
T PRK01287 161 ALLELLWSTGIRRGE-----------LARLDLYDVDAS-RGVVTVR-QGKGNKDR--VVPVGERALAWLQRYLQDVRPQL 225 (358)
T ss_pred HHHHHHHHhCCCHHH-----------HHcCCHHhcCcc-CCeEEEe-eCCCCCCC--cccCCHHHHHHHHHHHHHhchhc
Confidence 346666678899987 899999999887 5666664 47877655 466778888777766421
Q ss_pred --CCCCCcccc-----cCChhHHHHHHHhhC--CC----CcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Q 002904 736 --KKQNDDLFD-----KLDTAKLNAHLKELM--PG----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKE 802 (868)
Q Consensus 736 --K~PGd~LFd-----~L~ss~LN~yLkelM--~g----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~ 802 (868)
..+++.||- .++...|+..++.++ -| +|..+||-.-||.++ +.+. + ...
T Consensus 226 ~~~~~~~~lF~~~~g~~i~~~~i~~~~~~~~~~agi~~~~t~H~lRHt~at~l~-----~~G~--~-----------~~~ 287 (358)
T PRK01287 226 AVRPDSGALFVAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQML-----ENGA--D-----------TRH 287 (358)
T ss_pred ccCCCCCceEEeCCCCcCCHHHHHHHHHHHHHHhCCCCCCCcccchHHHHHHHH-----HcCC--C-----------HHH
Confidence 235567884 477888998888775 23 466777776666433 2221 1 237
Q ss_pred HHHHcCCCc
Q 002904 803 VAIICNHQR 811 (868)
Q Consensus 803 VAilCNHqR 811 (868)
|+.+++|.-
T Consensus 288 v~~~LGH~s 296 (358)
T PRK01287 288 IQAILGHAK 296 (358)
T ss_pred HHHHhCCCc
Confidence 888889876
No 27
>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=92.58 E-value=0.87 Score=46.06 Aligned_cols=125 Identities=17% Similarity=0.171 Sum_probs=80.3
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCC-
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKK- 737 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~- 737 (868)
..++++|+-.+.+|.|- ++.|+.+||.+..+ ..+-..||.+..+ +|.+.+.+...|..+.....
T Consensus 97 ~~~~~~l~~~tGlR~~E-----------i~~L~~~di~~~~~--~~~~~~~k~~~~r--~vpl~~~~~~~l~~~~~~~~~ 161 (260)
T cd01190 97 DRAMLLFLYNTGARVSE-----------ATGLKVDDLQLDPP--AQVRLIGKGRKER--TVPLWRSTAAALRAWLRERGL 161 (260)
T ss_pred HHHHHHHHHHhCccHHH-----------HHcCCHHHhccCCC--cEEEEecCCCcce--eEECCHHHHHHHHHHHHhcCC
Confidence 34577888889999987 78899999998743 2333457765544 67788999999988865432
Q ss_pred --CCCcccc-----cCChhHHHHHHHhhCC--C-----CcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Q 002904 738 --QNDDLFD-----KLDTAKLNAHLKELMP--G-----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEV 803 (868)
Q Consensus 738 --PGd~LFd-----~L~ss~LN~yLkelM~--g-----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~V 803 (868)
+.+.||. .++...++..++.++. | +..+.|.++..=.|+...|.+.+.+ ...|
T Consensus 162 ~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~~g~~-------------~~~i 228 (260)
T cd01190 162 HAEDEPLFVNRRGEPMTRFGVTYLLRKHAAKAAATAPTLATKRISPHVLRHTTAMHLLQSGVD-------------IVVI 228 (260)
T ss_pred CCCCCeeeecCCCCcCcHHHHHHHHHHHHHHhcccccccccCCCCchHHHHHHHHHHHHcCCC-------------HHHH
Confidence 6677884 3677788888887751 2 1233444444444555555443221 1246
Q ss_pred HHHcCCCc
Q 002904 804 AIICNHQR 811 (868)
Q Consensus 804 AilCNHqR 811 (868)
+.+.+|.-
T Consensus 229 ~~~lGH~~ 236 (260)
T cd01190 229 ALWLGHAS 236 (260)
T ss_pred HHHcCCCc
Confidence 66678863
No 28
>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=91.93 E-value=2 Score=41.10 Aligned_cols=103 Identities=17% Similarity=0.336 Sum_probs=67.1
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEE-----------ee-CCCCeEEEEEEeeChHHHH
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFD-----------FL-GKDSIQYVNTVEVELPVYK 727 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~Fd-----------Fl-GKdgir~~~tV~VD~~V~k 727 (868)
.+++.|+=.+.+|.+. ++.|+..+|... ...+.+. |. .|.+ .....|.+.+.+..
T Consensus 24 ~~~~~l~~~~G~R~~E-----------i~~l~~~dv~~~-~~~~~~~~~~~~~~~~~~~~~~k~~-~~~~~v~i~~~~~~ 90 (191)
T cd01189 24 KLLILLLAYTGLRIGE-----------ALALTWSDIDFE-NNTITINKTWDYKTGGYIFKPPKTK-SSIRTIPLDKKTIA 90 (191)
T ss_pred HHHHHHHHHhccHHHH-----------HhhceecccCCc-CCEEEEEEEEEEcCCceEecCCccc-CcceeEecCHHHHH
Confidence 3444444458899987 788888888766 3343332 11 1332 23346778888888
Q ss_pred HHHhhhcC---------CCCCCccccc-----CChhHHHHHHHhhC-----CCCcceeeccccchHH
Q 002904 728 AIGQFQTG---------KKQNDDLFDK-----LDTAKLNAHLKELM-----PGLTAKVFRTYNASIT 775 (868)
Q Consensus 728 nLk~f~k~---------K~PGd~LFd~-----L~ss~LN~yLkelM-----~glTAKdFRTynASvt 775 (868)
.|..+... ..+++.||.. ++...++.+++.++ ..+|.-+||-.-++.+
T Consensus 91 ~l~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~s~h~lRht~~t~l 157 (191)
T cd01189 91 ILKEYKKEQKKYLLGEINNDDELVFTNKGGKISTPSTINKRLKRICKKAGIPKITFHGLRHTHASLL 157 (191)
T ss_pred HHHHHHHHHHHHhhcccCCCCCeEEeCCCCCCCCchhHHHHHHHHHHHcCCCCcceeccHHHHHHHH
Confidence 88887753 3466788865 34578999999886 2477888886666643
No 29
>PRK09692 integrase; Provisional
Probab=91.74 E-value=1 Score=50.14 Aligned_cols=153 Identities=11% Similarity=0.053 Sum_probs=95.7
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEe-eCCCCeEEEEEEeeChHHHHHHHhhhcCCCCC
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQTGKKQN 739 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k~K~PG 739 (868)
.+++|+=.+.+|+|. +|.|+.++|.+. ...+.+.= ..|.+.. ..|.+.+.+...|+.+.....++
T Consensus 237 ~~~~lll~TG~R~gE-----------l~~l~W~diD~~-~~~~~I~~~~~K~~~~--r~VpL~~~~~~~L~~~~~~~~~~ 302 (413)
T PRK09692 237 CLFMWQLLTITRPAE-----------AAEARWEEIDIE-AQEWKIPAARMKMNRD--HTVPLSDEALAILEMMKPLSGNR 302 (413)
T ss_pred HHHHHHHHHCcchHH-----------HhcCchHHhccC-CCeEEechhhccCCCC--eeccChHHHHHHHHHHHHhcCCC
Confidence 345555579999998 899999999988 56666542 2343332 36888999999998886433456
Q ss_pred Cccccc-------CChhHHHHHHHhhC-CC-CcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002904 740 DDLFDK-------LDTAKLNAHLKELM-PG-LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (868)
Q Consensus 740 d~LFd~-------L~ss~LN~yLkelM-~g-lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCNHq 810 (868)
+.||.. ++...+|..|+.+- ++ +|..+||-..||.++. .+. + ...|+.++||.
T Consensus 303 ~~vF~~~~~~~~~~~~~~~~~~lk~~g~~~~~~~H~lRhT~aT~l~~-----~G~--~-----------~~~i~~~LGH~ 364 (413)
T PRK09692 303 EFIFPSRIKPNQPMNSQTVNAALKRAGLGGVLVSHGLRSIASTALNE-----QGF--P-----------PDVIEAALAHV 364 (413)
T ss_pred CeEecCCCCCCCCCCHHHHHHHHHHhCCCCCcCCCCcHHHHHHHHHh-----cCC--C-----------HHHHHHHcCCC
Confidence 788842 56778999888763 33 5789999766664432 221 1 23677778996
Q ss_pred -cccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 002904 811 -RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGK 849 (868)
Q Consensus 811 -R~V~K~~~~sm~kl~~ki~~lk~q~~~~~~~l~~~k~~~ 849 (868)
..+...+=...+-+.++.+.++.+ -..|..+..++
T Consensus 365 ~~~~~~~~Y~r~~y~~err~~~~~w----~~~l~~~~~~~ 400 (413)
T PRK09692 365 DKNEVRRAYNRSDYLEQRRPMMQWW----ADFVMAADSGS 400 (413)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHH----HHHHHHHhcCC
Confidence 333322223444455555555443 33455555554
No 30
>TIGR02225 recomb_XerD tyrosine recombinase XerD. 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 model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK.
Probab=91.62 E-value=1.1 Score=45.43 Aligned_cols=118 Identities=19% Similarity=0.245 Sum_probs=78.7
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-C-
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-K- 736 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-K- 736 (868)
.++++.|+-.+.+|+|- ++.|+..+|.+. .+.+. ..+|.+..+ .|.+.+.+...|..+... .
T Consensus 127 ~~~~~~l~~~tG~R~~E-----------~~~L~~~di~~~-~~~i~--~~~k~~~~r--~ipl~~~~~~~l~~~~~~~~~ 190 (291)
T TIGR02225 127 DRAMLELLYATGLRVSE-----------LVGLRLEDVNLD-EGFVR--VRGKGNKER--LVPLGEEAIEALERYLKEARP 190 (291)
T ss_pred HHHHHHHHHHhCCCHHH-----------HHcCcHHHhCcC-CCeEE--EecCCCcce--EEecCHHHHHHHHHHHHHhhh
Confidence 45556666778999987 789999999887 45554 678887765 567788989888876531 1
Q ss_pred -------CCCCcccc-----cCChhHHHHHHHhhC--CC----CcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHH
Q 002904 737 -------KQNDDLFD-----KLDTAKLNAHLKELM--PG----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQR 798 (868)
Q Consensus 737 -------~PGd~LFd-----~L~ss~LN~yLkelM--~g----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~ 798 (868)
.+++.||- .++...++.+++.+. .| +|..+||- |+...|...+. +
T Consensus 191 ~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~h~lRh-----t~~t~~~~~g~--~---------- 253 (291)
T TIGR02225 191 LLLKKKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRH-----SFATHLLENGA--D---------- 253 (291)
T ss_pred cccccccCCCCceeecCCCCcCCHHHHHHHHHHHHHHhCCCCCcCchHHHH-----HHHHHHHHcCC--C----------
Confidence 15667883 467788899998875 24 45666663 44444433222 1
Q ss_pred HHHHHHHHcCCC
Q 002904 799 ANKEVAIICNHQ 810 (868)
Q Consensus 799 Anr~VAilCNHq 810 (868)
...++.+.+|.
T Consensus 254 -~~~i~~~~GH~ 264 (291)
T TIGR02225 254 -LRVVQELLGHA 264 (291)
T ss_pred -HHHHHHHhCCC
Confidence 13677777885
No 31
>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=90.91 E-value=1.8 Score=44.92 Aligned_cols=123 Identities=15% Similarity=0.091 Sum_probs=81.2
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEee-CCCCe---EEEEEEee-ChHHHHHHHhhhc
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL-GKDSI---QYVNTVEV-ELPVYKAIGQFQT 734 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFl-GKdgi---r~~~tV~V-D~~V~knLk~f~k 734 (868)
.+++.|+-.+.+|+|- ++.|+.+||.+..++.+.+... +|.+. .....+.. ...+...|+.++.
T Consensus 119 ~~~~~l~~~tGlR~~E-----------i~~L~~~did~~~~~~~~i~i~~~K~~~~~~~~~~~ip~~~~~~~~~l~~~~~ 187 (287)
T cd00799 119 LALLLLGFAGLLRRSE-----------LVRLRWEDLTFTDGGGLLVTLRRSKTDQSGLGVLKLIPPLTTCPVRALERWLE 187 (287)
T ss_pred HHHHHHHHHhhhhHHH-----------HHhhhHhheEEccCCCEEEEeccCCcCcCCCCeEEecCCcccCHHHHHHHHHH
Confidence 4567788889999987 8899999999984255666554 66633 44444431 1245666666553
Q ss_pred C-CCCCCcccc-----------cCChhHHHHHHHhhCC--C-----CcceeeccccchHHHHHHHhcCCCCCCHHHHHHH
Q 002904 735 G-KKQNDDLFD-----------KLDTAKLNAHLKELMP--G-----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDV 795 (868)
Q Consensus 735 ~-K~PGd~LFd-----------~L~ss~LN~yLkelM~--g-----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~ 795 (868)
. ..+++.||. .+++..+|..|+.++. | +|..+||-..||..+. .+.+
T Consensus 188 ~~~~~~~~lF~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~gi~~~~~~~H~lRht~at~l~~-----~g~~--------- 253 (287)
T cd00799 188 AARIPKGPLFRRIDRWGVLGPGALSDNSLNRILKRLAEAAGLRSGSWSGHSLRRGFATEAAR-----AGYS--------- 253 (287)
T ss_pred HhCCCCCceeEEecCCCCcCCCCCCHHHHHHHHHHHHHHcCCCcccccccccchhHHHHHHH-----cCCC---------
Confidence 2 357778884 2678889999999862 3 6788888777665443 2111
Q ss_pred HHHHHHHHHHHcCCCc
Q 002904 796 YQRANKEVAIICNHQR 811 (868)
Q Consensus 796 yn~Anr~VAilCNHqR 811 (868)
...|+.+.+|..
T Consensus 254 ----~~~i~~~lGH~~ 265 (287)
T cd00799 254 ----LLEIMRQGRWRS 265 (287)
T ss_pred ----HHHHHHHcCCCC
Confidence 246777888864
No 32
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=90.84 E-value=1.1 Score=45.49 Aligned_cols=93 Identities=22% Similarity=0.309 Sum_probs=66.7
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC----
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG---- 735 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~---- 735 (868)
.+++.|+-.+.+|+|. +|+|+.+||.+. ++.+.+ .+|.+..+ .|.+.+.+...|..+...
T Consensus 139 ~~~~~l~~~tG~R~~E-----------i~~L~~~~i~~~-~~~~~i--~~k~~~~r--~vpl~~~~~~~l~~~~~~~~~~ 202 (297)
T PRK00236 139 RAILELLYGSGLRLSE-----------LVGLDIDDLDLA-SGTLRV--LGKGNKER--TVPLGRAAREALEAYLALRPLF 202 (297)
T ss_pred HHHHHHHHHccchHHH-----------HHhccHHHhccC-CceEEE--EecCCceE--EEECcHHHHHHHHHHHHHccCc
Confidence 3455666778999987 889999999987 566665 46666544 566788888888877642
Q ss_pred CCCCCcccc-----cCChhHHHHHHHhhC-----C-CCcceeec
Q 002904 736 KKQNDDLFD-----KLDTAKLNAHLKELM-----P-GLTAKVFR 768 (868)
Q Consensus 736 K~PGd~LFd-----~L~ss~LN~yLkelM-----~-glTAKdFR 768 (868)
..+++.||- .++...++..++.++ + ++|..+||
T Consensus 203 ~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~H~lR 246 (297)
T PRK00236 203 LPDDDALFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLR 246 (297)
T ss_pred CccCCceeecCCCCCCChhHHHHHHHHHHHHcCCCCCcCcHHHH
Confidence 236778884 367778888888886 2 46666776
No 33
>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=90.80 E-value=0.54 Score=48.88 Aligned_cols=94 Identities=16% Similarity=0.152 Sum_probs=68.2
Q ss_pred hcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEe-eCCCCeEEEEEEeeChHHHHHHHhhhcCCCCCCcccccC
Q 002904 668 KLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKL 746 (868)
Q Consensus 668 klALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k~K~PGd~LFd~L 746 (868)
.+.+|+|- +|.|+.+||.+...+...+.+ .+|.+..+ .|.+.+.+...|+.+.. .+++.||-.+
T Consensus 160 ~tGlR~~E-----------i~~L~~~did~~~~g~~~i~~~~~K~~~~r--~ipl~~~~~~~l~~~~~--~~~~~lf~~~ 224 (299)
T cd01185 160 FTGLRYSD-----------IKKLTWEEIVEDSDGEKWIRKRRQKTKVEV--YIPLLDEALQILGKYPD--EKEGLVFPLL 224 (299)
T ss_pred HHcccHHH-----------HHhcCHHHceECCCCCEEEEEeecccCCcc--cccCcHHHHHHHHHhcC--CCCCcCcCCC
Confidence 47899887 889999999987422233333 46666444 56667889999998874 3678899988
Q ss_pred ChhHHHHHHHhhC------CCCcceeeccccchHHH
Q 002904 747 DTAKLNAHLKELM------PGLTAKVFRTYNASITL 776 (868)
Q Consensus 747 ~ss~LN~yLkelM------~glTAKdFRTynASvta 776 (868)
....++.+++.+. .++|..+||-..||.++
T Consensus 225 ~~~~~~~~~~~~~~~~gi~~~~~~H~lRht~at~l~ 260 (299)
T cd01185 225 KNSNMNKPLKEWAKLAGIKKHITFHCARHTFATLQL 260 (299)
T ss_pred CHHHHHHHHHHHHHHcCCCCCCccccchHHHHHHHH
Confidence 8888999999886 14677788876666543
No 34
>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=90.40 E-value=0.49 Score=45.30 Aligned_cols=99 Identities=14% Similarity=0.106 Sum_probs=71.1
Q ss_pred HHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCC-
Q 002904 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK- 736 (868)
Q Consensus 658 qlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K- 736 (868)
.+.+++.|+-.+.+|+|. +|.|+.+||... .+.+ -.+|.+..+ .|.+.+.+...|..+....
T Consensus 20 ~~~~~~~l~~~tGlR~~E-----------~~~l~~~di~~~---~~~i-~~~K~~~~r--~vpl~~~~~~~l~~~~~~~~ 82 (162)
T cd00800 20 WLRCAMDLALLTGQRVGD-----------VLRMKWSDIDDD---GLHI-EQSKTGAKL--AIPLSPSLREVIERCRDLSR 82 (162)
T ss_pred HHHHHHHHHHHHcCCHHH-----------HHhCcHHHccCC---eEEE-EecCcCCee--EEECCHHHHHHHHHHHhhcc
Confidence 455667788889999987 889999998743 4444 245655443 5778899999999887432
Q ss_pred CCCCccccc------CChhHHHHHHHhhC-----C----CCcceeeccccch
Q 002904 737 KQNDDLFDK------LDTAKLNAHLKELM-----P----GLTAKVFRTYNAS 773 (868)
Q Consensus 737 ~PGd~LFd~------L~ss~LN~yLkelM-----~----glTAKdFRTynAS 773 (868)
.+++.||.. ++...++.+++.+. + .++..+||...+|
T Consensus 83 ~~~~~vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~H~lRht~~t 134 (162)
T cd00800 83 VSSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTFHDIRAKAAS 134 (162)
T ss_pred cCCceEEEcCCCCCCcCcchHHHHHHHHHHhcccccCCCCCchhhHHHHHHH
Confidence 256788843 77888999999885 2 4677888876544
No 35
>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=90.13 E-value=0.45 Score=47.19 Aligned_cols=100 Identities=14% Similarity=0.154 Sum_probs=70.7
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCC
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQ 738 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~P 738 (868)
..++++|+=.+.+|.|. +|.|+.++|.+. .+.|.+. .+|.+..+ .|.+.+.+...|+.+... .+
T Consensus 66 ~~~~~~l~~~tGlR~~E-----------~~~l~~~did~~-~~~i~i~-~~K~~~~r--~ipl~~~~~~~l~~~~~~-~~ 129 (206)
T cd00796 66 LPVIILLALETAMRRGE-----------ILSLRWEQVDLK-KRVAHLP-DTKNGTSR--DVPLSKRAVALLQMLPKV-PD 129 (206)
T ss_pred hHHHHHHHHHhcccHHH-----------HHcCcHHHcCcc-cCEEEEe-cCcCCCcc--eecCCHHHHHHHHHhhhc-CC
Confidence 45567777788999986 889999999887 4566654 25555433 577788999999988743 36
Q ss_pred CCcccccCChhHHHHHHHhhC-----CCCcceeeccccchHH
Q 002904 739 NDDLFDKLDTAKLNAHLKELM-----PGLTAKVFRTYNASIT 775 (868)
Q Consensus 739 Gd~LFd~L~ss~LN~yLkelM-----~glTAKdFRTynASvt 775 (868)
++.||. ++...++.+++.++ +++|.-+||-..||.+
T Consensus 130 ~~~lf~-~~~~~~~~~~~~~~~~~g~~~~~~H~lRht~~t~l 170 (206)
T cd00796 130 DGPVFP-ITSDSVDAAFRRAKERAGLEDLHFHDLRHEATSRL 170 (206)
T ss_pred CCceec-CCCccHHHHHHHHHHHcCCCCCchHhhHhHHHHHH
Confidence 677885 34556787888776 2456677776665543
No 36
>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=90.08 E-value=2.3 Score=41.46 Aligned_cols=123 Identities=18% Similarity=0.199 Sum_probs=72.7
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEee----C----------CCCeEEEEEEeeChH
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL----G----------KDSIQYVNTVEVELP 724 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFl----G----------Kdgir~~~tV~VD~~ 724 (868)
..+++.|+-.+.+|+|- ++.|+.+||.+. ...|.+.-. + ........+|.+.+.
T Consensus 23 ~~~~~~l~~~tG~R~~E-----------i~~L~~~di~~~-~~~i~v~~~~~~~~~~~~~~~~~~~k~~~~~r~v~l~~~ 90 (205)
T cd01199 23 YADILEFLFLTGMRIGE-----------LLALQEKDIDFE-NKLINIDGTLDSHTGKEENGYKDTPKTKSSIRTISLSER 90 (205)
T ss_pred HHHHHHHHHHhCChHHH-----------HhcCchhhccCC-CCEEEEEeeEeeccCCCCceeecCCCCCCCceEEecCHH
Confidence 34566677789999986 889999999887 445554321 0 001111336888999
Q ss_pred HHHHHHhhhcC---------CCCCCccccc-----CC-hhHHHHHHHhhC----C----CCcceeeccccchHHHHHHHh
Q 002904 725 VYKAIGQFQTG---------KKQNDDLFDK-----LD-TAKLNAHLKELM----P----GLTAKVFRTYNASITLDGMLN 781 (868)
Q Consensus 725 V~knLk~f~k~---------K~PGd~LFd~-----L~-ss~LN~yLkelM----~----glTAKdFRTynASvta~~~L~ 781 (868)
+...|+.+... ..+.+.||.. ++ ...++..++.++ . .+|...||-.-|| .|.
T Consensus 91 ~~~~l~~~~~~~~~~~~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~~t-----~~~ 165 (205)
T cd01199 91 AVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKGNPLDLGPINSKILSKFLKDLGSQSKKHVTTHIFRHTHIS-----FLA 165 (205)
T ss_pred HHHHHHHHHHHHHhhhhcccCCCCceEEecCCCCEeccchHHHHHHHHHHHHcCCCcCCCcceecchHHHHH-----HHH
Confidence 99999888753 2255678843 32 344555555543 1 4566666644444 333
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002904 782 KGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (868)
Q Consensus 782 ~~~~~~s~~eK~~~yn~Anr~VAilCNHqR 811 (868)
..+. ....|+.+.+|.-
T Consensus 166 ~~g~-------------~~~~i~~~lGH~~ 182 (205)
T cd01199 166 EEGV-------------PLKAIMDRVGHSD 182 (205)
T ss_pred HcCC-------------CHHHHHHHhCCCc
Confidence 3221 1346777888864
No 37
>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=89.94 E-value=0.58 Score=45.46 Aligned_cols=99 Identities=15% Similarity=0.209 Sum_probs=70.4
Q ss_pred HHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-----C
Q 002904 662 ATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-----K 736 (868)
Q Consensus 662 AlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-----K 736 (868)
++.|+-.+.+|+|. ++.|+.++|.+. ...+.+.- +|.+..+ .+.+.+.+...|+.++.. .
T Consensus 29 ~~~l~~~tGlR~~E-----------i~~L~~~did~~-~~~l~v~~-~K~~~~~--~~pi~~~~~~~l~~~~~~~~~~~~ 93 (180)
T cd01197 29 LMLLMFRHGLRVSE-----------ACGLKLSDIDLE-SRQIYIRR-LKGGFST--THPLRDDELEALKNWLEIRAWKGL 93 (180)
T ss_pred HHHHHHHhCCcHHH-----------HHcCcHHHhCCC-CCeEEEEe-cCCCccc--eeECCHHHHHHHHHHHHHhccCCC
Confidence 35666778899987 888999999987 56666653 4555433 567788888888887632 2
Q ss_pred CCCCccc-----ccCChhHHHHHHHhhC--CC----CcceeeccccchHH
Q 002904 737 KQNDDLF-----DKLDTAKLNAHLKELM--PG----LTAKVFRTYNASIT 775 (868)
Q Consensus 737 ~PGd~LF-----d~L~ss~LN~yLkelM--~g----lTAKdFRTynASvt 775 (868)
.+++.|| ..++...++..++.+. .| +|..+||-..||.+
T Consensus 94 ~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~H~lRht~~t~l 143 (180)
T cd01197 94 PDSDWIFLSRRGGPLSRQQVYKLIRRLGAQAGLSIKVHPHMLRHACGYAL 143 (180)
T ss_pred CCCCeEEeCCCCCcCCHHHHHHHHHHHHHHcCCCCCCCcchhhhHHHHHH
Confidence 3556788 4578899999999986 34 45677777655543
No 38
>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=89.39 E-value=1.5 Score=43.23 Aligned_cols=105 Identities=17% Similarity=0.216 Sum_probs=70.2
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCC-CeEEEEee-CCCCeEEEEEEeeChHHHHHHHhhhcCC
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPP-NKLKFDFL-GKDSIQYVNTVEVELPVYKAIGQFQTGK 736 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~-~~V~FdFl-GKdgir~~~tV~VD~~V~knLk~f~k~K 736 (868)
..+++.|+-.+.||+|- ++.|+.++|.+..+ ....+.+. +|.+.. .+|.+.+.+...|+.+....
T Consensus 28 ~~~l~~l~~~tGlR~~E-----------l~~L~~~did~~~~~~~~~i~i~~~K~~~~--r~vpl~~~~~~~L~~~~~~~ 94 (196)
T cd01183 28 LLFLLALLYSTGLRISE-----------LAAATGPDLEAFVQGGGWWLYVPVGKGGKE--RRVPVSDELLAALARYRQAR 94 (196)
T ss_pred HHHHHHHHHHccChHHH-----------HHcccccccccccCCCceEEEEecCCCCCc--eEEeCCHHHHHHHHHHHHHc
Confidence 34557777889999987 89999999988731 22334444 777654 36778999999998876421
Q ss_pred --------CCCCccccc---------CChhHHHHHHHhhC-------------------CCCcceeeccccchHHH
Q 002904 737 --------KQNDDLFDK---------LDTAKLNAHLKELM-------------------PGLTAKVFRTYNASITL 776 (868)
Q Consensus 737 --------~PGd~LFd~---------L~ss~LN~yLkelM-------------------~glTAKdFRTynASvta 776 (868)
.+++.||.. ++...++..++.++ ..+|..+||--.||.++
T Consensus 95 ~~~~~~~~~~~~~lF~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~ 170 (196)
T cd01183 95 GLPPEPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAAADRLQADGFEEDAAQLRAASTHWLRHTHASHDL 170 (196)
T ss_pred CCCCCCCCCCCCceeeccccccCCCCCCHHHHHHHHHHHHHHHHHHHHhccChhHHHhhcccchHHHHHHHHHHHH
Confidence 134568843 45677777777653 24677777766666544
No 39
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=89.30 E-value=1.4 Score=47.56 Aligned_cols=117 Identities=19% Similarity=0.184 Sum_probs=83.3
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCC---
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK--- 736 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K--- 736 (868)
.+++.|+-.+.||+|- ||.|+.+||.+. +..|.+ .+|.+..+ .|.+.+.+...|..+....
T Consensus 198 ~~i~~ll~~tGlR~~E-----------~~~L~~~did~~-~~~l~v--~~K~~~~r--~vpl~~~~~~~l~~~~~~~~~~ 261 (357)
T PRK05084 198 LAIIALILGSGLRVSE-----------LVNLDLSDLNLK-QMTIDV--TRKGGKRD--SVNIAPFALPYLEEYLKIRASR 261 (357)
T ss_pred HHHHHHHHHhCCCHHH-----------HHcCCHHHcCcC-CCEEEE--EecCCcee--EEEECHHHHHHHHHHHHHhhhh
Confidence 3446677889999987 999999999987 566655 47887665 5666888888887765321
Q ss_pred ----CCCCcccc--------cCChhHHHHHHHhhC--CC--CcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 002904 737 ----KQNDDLFD--------KLDTAKLNAHLKELM--PG--LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRAN 800 (868)
Q Consensus 737 ----~PGd~LFd--------~L~ss~LN~yLkelM--~g--lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~An 800 (868)
.+.+.||- .++...++..++.+. -| +|..+||-..||..+.. +. + .
T Consensus 262 ~~~~~~~~~lF~~~~~~~~~~~~~~~i~~~~~~~~~~~gi~~~~H~lRHt~at~l~~~-----g~--~-----------~ 323 (357)
T PRK05084 262 YKAEKQEKALFLTKYRGKPNRISARAIEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-----TK--D-----------Q 323 (357)
T ss_pred ccCCCCCcceEeecCCCCCCCCCHHHHHHHHHHHHHHcCCCCCcccccHHHHHHHHHc-----CC--C-----------H
Confidence 23456772 477788999999886 23 78888888777754432 11 1 2
Q ss_pred HHHHHHcCCC
Q 002904 801 KEVAIICNHQ 810 (868)
Q Consensus 801 r~VAilCNHq 810 (868)
..|+.+++|.
T Consensus 324 ~~i~~~lGH~ 333 (357)
T PRK05084 324 VLVADQLGHT 333 (357)
T ss_pred HHHHHHcCCC
Confidence 5788889996
No 40
>PRK09870 tyrosine recombinase; Provisional
Probab=89.29 E-value=0.93 Score=45.57 Aligned_cols=101 Identities=12% Similarity=0.148 Sum_probs=73.4
Q ss_pred HHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-----C
Q 002904 662 ATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-----K 736 (868)
Q Consensus 662 AlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-----K 736 (868)
++.|+-.+.+|+|. ++.|+.++|.+. ...|.+. ..|.+.. ..|.+.+.+...|..+... .
T Consensus 37 ~~~l~~~tGlR~~E-----------i~~L~~~did~~-~~~l~i~-~~k~~~~--~~vpl~~~~~~~l~~~~~~~~~~~~ 101 (200)
T PRK09870 37 LTLLCFIHGFRASE-----------ICRLRISDIDLK-AKCIYIH-RLKKGFS--TTHPLLNKEIQALKNWLSIRTSYPH 101 (200)
T ss_pred HHHHHHHhCCcHHH-----------HHcccHHHcCCC-CCeEEEE-ECCCCcc--eEEECCHHHHHHHHHHHHhcccCCC
Confidence 45566678999988 899999999987 5666664 3344433 3567788888888777532 2
Q ss_pred CCCCccc-----ccCChhHHHHHHHhhC-----C-CCcceeeccccchHHHH
Q 002904 737 KQNDDLF-----DKLDTAKLNAHLKELM-----P-GLTAKVFRTYNASITLD 777 (868)
Q Consensus 737 ~PGd~LF-----d~L~ss~LN~yLkelM-----~-glTAKdFRTynASvta~ 777 (868)
.+++.|| ..++...+|..|+.+. + .+|..+||-..||.++.
T Consensus 102 ~~~~~lf~~~~g~~~s~~~~~~~~k~~~~~~gi~~~~t~H~lRht~at~l~~ 153 (200)
T PRK09870 102 AESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALAN 153 (200)
T ss_pred CCCCceeeCCCCCcCCHHHHHHHHHHHHHHcCCCCCCCCccccchHHHHHHH
Confidence 3456788 3588899999999885 2 47889999988887553
No 41
>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=88.65 E-value=3 Score=41.85 Aligned_cols=97 Identities=20% Similarity=0.255 Sum_probs=65.8
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-----
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG----- 735 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~----- 735 (868)
+++.|+-.+.+|.|. +|.|+..||.+. +..+.+. +|.+..+ .|.+.+.+...|+.+...
T Consensus 131 ~~~~l~~~tG~R~~E-----------i~~l~~~di~~~-~~~~~i~--~k~~~~~--~vpl~~~~~~~l~~~~~~~~~~~ 194 (284)
T cd00798 131 ALLELLYSTGLRVSE-----------LVGLKLSDVDLS-RGLIRVR--GKGNKER--IVPLGETAVEALQRYLEVRRPLL 194 (284)
T ss_pred HHHHHHHHhCchHHH-----------HHhCchHhhccc-CCeEEEE--ecCCCce--EEEeCHHHHHHHHHHHHHccccc
Confidence 344555568999975 788999999987 4565555 8887655 566678888888887642
Q ss_pred --CCCCCccc-----ccCChhHHHHHHHhhC--C----CCcceeeccccch
Q 002904 736 --KKQNDDLF-----DKLDTAKLNAHLKELM--P----GLTAKVFRTYNAS 773 (868)
Q Consensus 736 --K~PGd~LF-----d~L~ss~LN~yLkelM--~----glTAKdFRTynAS 773 (868)
...++.|| ..++...+|..++.++ . ++|.-+||-.-||
T Consensus 195 ~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~h~lR~t~at 245 (284)
T cd00798 195 LKVGDSDALFLNQRGKRLSRRGVWKILKEYARRAGIEKKISPHTLRHSFAT 245 (284)
T ss_pred ccCCCCCceeecCCCCCCCHHHHHHHHHHHHHHhCCCcCCChHHHHHHHHH
Confidence 12345677 3467778888888776 1 4566677644443
No 42
>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=86.14 E-value=4.1 Score=39.42 Aligned_cols=103 Identities=13% Similarity=0.083 Sum_probs=63.5
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeC-------CCCeEEEEEEeeChHHHHH-HHhh
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLG-------KDSIQYVNTVEVELPVYKA-IGQF 732 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlG-------Kdgir~~~tV~VD~~V~kn-Lk~f 732 (868)
.++.|+=.+.+|+|. ++.|+.++|.+. ...+.+.+.. |.+. -...|.+.+.+... |..+
T Consensus 28 ~~~~l~~~tGlR~~E-----------i~~l~~~di~~~-~~~~~i~~~~~~~~~~~K~~~-~~r~vpl~~~~~~~~l~~~ 94 (181)
T cd01184 28 WLPLLGLYTGARVNE-----------IAQLQVDDIREE-DGVPCIDITNDDEDQSLKNAA-SRRTIPVHPELIELGFLDY 94 (181)
T ss_pred HHHHHHHHHCCCHHH-----------HhcccHHHeeee-CCeEEEEeecchhccCCCCCC-CcccccCCHHHHHccHHHH
Confidence 444555668899987 788999999987 3444444332 3222 13577888888887 5554
Q ss_pred hcC--CCCCCccccc-------CChhHHHHHHHhhC-------CCCcceeeccccchHHH
Q 002904 733 QTG--KKQNDDLFDK-------LDTAKLNAHLKELM-------PGLTAKVFRTYNASITL 776 (868)
Q Consensus 733 ~k~--K~PGd~LFd~-------L~ss~LN~yLkelM-------~glTAKdFRTynASvta 776 (868)
.+. ..+.+.||-. +....++++++.++ .++|..+||--.||.++
T Consensus 95 ~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~H~lRht~at~~~ 154 (181)
T cd01184 95 VEARRAAGHKRLFPDLPAGKTGGYGSAVSKWFSRYLKKLGLKDKGKSFHSFRHTFITELR 154 (181)
T ss_pred HHHHHccCCceecccccccCCCCchHHHHHHHHHHHHHhcCCCCccchhhhHHHHHHHHH
Confidence 322 2456778854 23455666666654 24677778765555443
No 43
>PHA03397 vlf-1 very late expression factor 1; Provisional
Probab=85.76 E-value=2.1 Score=48.68 Aligned_cols=145 Identities=19% Similarity=0.118 Sum_probs=85.0
Q ss_pred eeccCCchhhcCccHHHHHHHHHHHHHHHHHHHHHHHhcc--CCCC-C---chHHHHHHHHHHhcccccCCCCCccCCCc
Q 002904 611 VFLAASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFV--SRDG-T---RRQIAVATYLIDKLALRAGNEKDDDEADT 684 (868)
Q Consensus 611 vyl~ahs~wk~~rD~~Kyerar~Lk~~Lp~IR~~y~kDLk--sk~~-~---~RqlAvAlyLIDklALRvGNEKy~deadT 684 (868)
|+|-..-..+..+.. ++-..|.+.|.+|...+.+... .... . .---++++.||-.+.||+|.
T Consensus 147 v~lp~dk~~k~~k~~---~k~i~l~~~i~~ll~~i~~~~~~~~~~~~~~~~~~Rd~aif~lLl~TGLRISE--------- 214 (363)
T PHA03397 147 VMLPRDKELKNIRAK---EKNIVLKDIIDPVLNYIEKKIKYLNSNYVHNRGLIRGAIVFCIILGTGLRITE--------- 214 (363)
T ss_pred ccCCccHHHHHHHhh---hcchhHHHHHHHHHHHHHHHhhhccchhcccchhHHHHHHHHHHHHHHHHHHH---------
Confidence 444333344433333 3344466888888888877665 3322 2 11235667888899999987
Q ss_pred eeeccCCCCceEE--cCCCeEEEE-eeCCCCeEEEEEEeeChHHH----HHHHhhhcCCCCCCcccccCCh----hHHHH
Q 002904 685 VGCCTLKVGNVEC--IPPNKLKFD-FLGKDSIQYVNTVEVELPVY----KAIGQFQTGKKQNDDLFDKLDT----AKLNA 753 (868)
Q Consensus 685 vG~cTLR~eHV~l--~~~~~V~Fd-FlGKdgir~~~tV~VD~~V~----knLk~f~k~K~PGd~LFd~L~s----s~LN~ 753 (868)
+|.|+.+||.+ . .+.|.+. +.||.+..+..-+ ...+. ..|..+. +.+ ..+|-...+ ..++.
T Consensus 215 --l~~Lk~eDId~~~~-~g~I~I~gi~tKg~K~R~VpL--s~~~~~~L~~~L~~y~--~~~-~~~~is~~~~~~~~~~kk 286 (363)
T PHA03397 215 --ARQITLDDLNKLIK-KGEHKVNNINLKRKKSRFNYL--NCIKKKPLELAREIYQ--KHP-TLLKISKNSSTPFKDFKR 286 (363)
T ss_pred --HHCCCHHHcchhhc-CCEEEEecccCCCCceeEEEe--ChHHHHHHHHHHHHHh--cCc-hhcccCCCchHHHHHHHH
Confidence 89999999995 5 5678777 6788887665444 43333 3344443 223 222322222 25566
Q ss_pred HHHhhC-CC--CcceeeccccchHH
Q 002904 754 HLKELM-PG--LTAKVFRTYNASIT 775 (868)
Q Consensus 754 yLkelM-~g--lTAKdFRTynASvt 775 (868)
+++.+. ++ +|.-.||=..||..
T Consensus 287 i~kkAGI~~~~itpH~LRHTFAt~L 311 (363)
T PHA03397 287 LLEEAGVEMDRPRSNMIRHYLASNM 311 (363)
T ss_pred HHHHcCCCCCCCCCcccHHHHHHHH
Confidence 666664 22 67777885556543
No 44
>PRK09871 tyrosine recombinase; Provisional
Probab=84.80 E-value=2 Score=42.92 Aligned_cols=101 Identities=9% Similarity=0.122 Sum_probs=72.4
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-----
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG----- 735 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~----- 735 (868)
+++.|+-.+.+|+|- ++.|+.++|.+. .+.|.+.- +|.+..+ .|.+.+.+...|..+...
T Consensus 30 ~l~~l~~~tGlR~sE-----------l~~L~~~did~~-~~~i~i~~-~K~~~~~--~vpl~~~~~~~l~~~~~~~~~~~ 94 (198)
T PRK09871 30 CLILLAYRHGMRISE-----------LLDLHYQDLDLN-EGRINIRR-LKNGFST--VHPLRFDEREAVERWTQERANWK 94 (198)
T ss_pred HHHHHHHHhCCcHHH-----------HHcCCHHhcCcc-CCeEEEEe-cCCCccc--eecCCHHHHHHHHHHHHhhhccC
Confidence 446777789999987 889999999987 56676643 4666544 456678888888776531
Q ss_pred -CCCCCcccc-----cCChhHHHHHHHhhC------CCCcceeeccccchHHH
Q 002904 736 -KKQNDDLFD-----KLDTAKLNAHLKELM------PGLTAKVFRTYNASITL 776 (868)
Q Consensus 736 -K~PGd~LFd-----~L~ss~LN~yLkelM------~glTAKdFRTynASvta 776 (868)
..+.+.||- .++...++..|+.+. +.+|..+||-..||.++
T Consensus 95 ~~~~~~~lF~~~~g~~~~~~~~~~~lk~~~~~~~~~~~~~~H~LRHT~at~l~ 147 (198)
T PRK09871 95 GADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELA 147 (198)
T ss_pred CCCCCCCeEecCCCCCccHHHHHHHHHHHHHhcCcCCCCCCcccchHHHHHHH
Confidence 134556883 478888999988874 35788899888777543
No 45
>TIGR02249 integrase_gron integron integrase. 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 (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), 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.
Probab=84.51 E-value=2.9 Score=44.23 Aligned_cols=101 Identities=15% Similarity=0.209 Sum_probs=69.0
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-----
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG----- 735 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~----- 735 (868)
++++|+=.+.||+|- +|.|+.+||.+. ++.|.+. .+|.+..+ +|.+.+.+...|+.....
T Consensus 120 ~~v~ll~~tGlR~~E-----------~~~L~~~did~~-~~~i~v~-~~K~~~~r--~vpl~~~~~~~L~~~~~~~~~~~ 184 (315)
T TIGR02249 120 LIAKLLYGSGMRLME-----------CLRLRIQDIDFD-YGEIRIR-QGKGGKDR--TVTLPKELIPPLREQIELARAYH 184 (315)
T ss_pred HHHHHHHHcCCCHHH-----------HHhccHHhcccC-CCeEEEE-eCCCCcee--EEecCHHHHHHHHHHHHHHHhhh
Confidence 345666678999987 899999999998 6788775 46776543 577788888777654310
Q ss_pred -------------------C-------CCCCcccc----------------cCChhHHHHHHHhhC-----C-CCcceee
Q 002904 736 -------------------K-------KQNDDLFD----------------KLDTAKLNAHLKELM-----P-GLTAKVF 767 (868)
Q Consensus 736 -------------------K-------~PGd~LFd----------------~L~ss~LN~yLkelM-----~-glTAKdF 767 (868)
+ .+.+.||- .++...++.+++.++ + .+|.-+|
T Consensus 185 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~g~~~~~~~~~~~~~~~~k~~~~~~gi~~~~~~H~l 264 (315)
T TIGR02249 185 EADLAEGYGGVYLPHALARKYPNAPKEWGWQYLFPSHRLSRDPESGVIRRHHINETTIQRAVRRAVERAGIEKPVTCHTL 264 (315)
T ss_pred ccchhhccccccchhhhhhcccccccCCCceeeeecccccccccccccccCCcCHHHHHHHHHHHHHHcCCCCCcccccc
Confidence 0 11235662 256778899888875 2 3688888
Q ss_pred ccccchHHH
Q 002904 768 RTYNASITL 776 (868)
Q Consensus 768 RTynASvta 776 (868)
|--.||.++
T Consensus 265 RHt~at~l~ 273 (315)
T TIGR02249 265 RHSFATHLL 273 (315)
T ss_pred cHHHHHHHH
Confidence 865555544
No 46
>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=81.41 E-value=16 Score=36.23 Aligned_cols=123 Identities=15% Similarity=0.135 Sum_probs=73.7
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcC--CCeEEEEe-eCCCCeEEEEEEeeChHHHHHHHhhhc-
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIP--PNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQT- 734 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~--~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k- 734 (868)
+..++.|+-.+.+|+|- ++.|+.+++.... ...+.+.. .+|.+ .....|.+.+.+...|+.+..
T Consensus 22 ~~~~~~l~~~tGlR~~E-----------i~~L~~~~~~~~~~~~~~~~~~~~~~K~~-~~~r~vpl~~~~~~~l~~~~~~ 89 (195)
T cd01195 22 IIPMTMIVQETGMRISD-----------LLTLKKNCLLEDKDGDFFYKYYQCIWKTK-IKEHIIPISKKVALLIKVREDK 89 (195)
T ss_pred HHHHHHHHHHhCCCHHH-----------HHcCCccccccCCCCCceEEEEeecCcCC-CcCccccCCHHHHHHHHHHHHH
Confidence 34566778888899876 5666665553221 12333322 35554 123367789999999887753
Q ss_pred -------CCCCCCccccc---------CChhHHHHHHHhhC--CC----------CcceeeccccchHHHHHHHhcCCCC
Q 002904 735 -------GKKQNDDLFDK---------LDTAKLNAHLKELM--PG----------LTAKVFRTYNASITLDGMLNKGTGD 786 (868)
Q Consensus 735 -------~K~PGd~LFd~---------L~ss~LN~yLkelM--~g----------lTAKdFRTynASvta~~~L~~~~~~ 786 (868)
...+.+.||.. ++...+|..++.+. -| ++.-+||=..||. |...+.
T Consensus 90 ~~~~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~-----l~~~g~- 163 (195)
T cd01195 90 TKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYHFHAHAFRHTVATR-----MINNGM- 163 (195)
T ss_pred HHHHhccCCCCCceEeeccCCCCCCCcCcHHHHHHHHHHHHHHcCCccCCCCEeeccchhhhhHHHHH-----HHHcCC-
Confidence 12356678843 67788999998876 23 4555666544553 333221
Q ss_pred CCHHHHHHHHHHHHHHHHHHcCCCc
Q 002904 787 GDVAVKIDVYQRANKEVAIICNHQR 811 (868)
Q Consensus 787 ~s~~eK~~~yn~Anr~VAilCNHqR 811 (868)
+ ...|+.+++|..
T Consensus 164 -~-----------~~~i~~~lGH~~ 176 (195)
T cd01195 164 -P-----------IHIIQKFLGHES 176 (195)
T ss_pred -C-----------HHHHHHHhCCCC
Confidence 1 236788888864
No 47
>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=80.00 E-value=7.1 Score=38.77 Aligned_cols=119 Identities=14% Similarity=0.053 Sum_probs=72.2
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEe--------eCCCC-eEEEEEEeeChHHHHHHHh
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF--------LGKDS-IQYVNTVEVELPVYKAIGQ 731 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdF--------lGKdg-ir~~~tV~VD~~V~knLk~ 731 (868)
.+++|+=.+.||+|- |++|+.+||.+. ...|.+.= .+|.. .. ..|.+.+++...|..
T Consensus 24 ~~~~l~~~tGlR~~E-----------~~~L~~~did~~-~~~~~i~~~~~~~~~~~~kt~~~~--r~vpl~~~~~~~l~~ 89 (196)
T cd01191 24 NLWEFAVFTGLRPSE-----------LIALAWEDVDLE-RGTVYVRRALVRGIFKVPKTKAGT--RDVDLNPPALAALKE 89 (196)
T ss_pred HHHHHHHHHCCCHHH-----------HHhCcHHhcCcc-CCeEEEEeeeecccccCCCcCCCe--EEEeCCHHHHHHHHH
Confidence 456666678999987 899999999987 45655531 12332 22 357778999888876
Q ss_pred hhcC--------------------CCCCCcccccC--------ChhHHHHHHHhhC-----CCCcceeeccccchHHHHH
Q 002904 732 FQTG--------------------KKQNDDLFDKL--------DTAKLNAHLKELM-----PGLTAKVFRTYNASITLDG 778 (868)
Q Consensus 732 f~k~--------------------K~PGd~LFd~L--------~ss~LN~yLkelM-----~glTAKdFRTynASvta~~ 778 (868)
.... ..+.+.||..- +...++..++.++ +.+|.-+||-..||.++
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lF~~~~~g~~~~~~~~~~~~~~~~~~~~~gi~~~~~H~lRht~at~l~-- 167 (196)
T cd01191 90 QAKLTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGIRYRNPYQMRHTFASWML-- 167 (196)
T ss_pred HHHHhhcccccchhhcccccccccCCCceEEEecCCCCCcCCchhHHHHHHHHHHHHHcCCCcCCcccchHHHHHHHH--
Confidence 4321 12356677321 1234566666665 24466677766665444
Q ss_pred HHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002904 779 MLNKGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (868)
Q Consensus 779 ~L~~~~~~~s~~eK~~~yn~Anr~VAilCNHqR 811 (868)
+.+. + ...|+.+++|+.
T Consensus 168 ---~~g~--~-----------~~~i~~~lGH~~ 184 (196)
T cd01191 168 ---TAGA--N-----------PAFIADQMGHKS 184 (196)
T ss_pred ---HCCC--C-----------HHHHHHHhCCCc
Confidence 2211 1 356778888886
No 48
>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=78.04 E-value=6.9 Score=40.54 Aligned_cols=99 Identities=12% Similarity=0.100 Sum_probs=67.2
Q ss_pred HHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcC-CCC
Q 002904 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-KKQ 738 (868)
Q Consensus 660 AvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-K~P 738 (868)
-++++|+-.+.||+|. +|.|+.+||.+. .+.+ .+|.+..+ .|.+.+.+...|..+... ...
T Consensus 110 ~~~~~l~~~tGlR~~E-----------~~~L~~~di~~~---~~~i--~~K~~~~r--~i~l~~~~~~~l~~~~~~~~~~ 171 (263)
T cd01196 110 YFVVWFLAATGARVSE-----------LIHIKVEHVQTG---YADI--YSKGGKIR--RLYIPKNLRVEALKWLKELNLD 171 (263)
T ss_pred HHHHHHHHHhCCCHHH-----------HhcCcHHHHhCC---eeEE--eecCCcee--EEecCHHHHHHHHHHHHHcCCC
Confidence 3467777789999987 999999999764 3333 36665543 466777777766666533 234
Q ss_pred CCcccc-----cCChhHHHHHHHhhC--CC-----CcceeeccccchHHH
Q 002904 739 NDDLFD-----KLDTAKLNAHLKELM--PG-----LTAKVFRTYNASITL 776 (868)
Q Consensus 739 Gd~LFd-----~L~ss~LN~yLkelM--~g-----lTAKdFRTynASvta 776 (868)
.+.||. .++...++.+++.+. -| ++..+||---||.++
T Consensus 172 ~~~lf~~~~g~~~~~~~~~~~~~~~~~~~gi~~~~~~~H~lRHt~at~~~ 221 (263)
T cd01196 172 SGYIFLNRFGKPITARGIAQQLKNYAAKYKMNPRVVYPHSFRHLFAKNFL 221 (263)
T ss_pred CCceeeeCCCCcCcHHHHHHHHHHHHHHhCCCCCCCCchhhHHHHHHHHH
Confidence 567883 578888999998875 13 566777755555443
No 49
>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=77.03 E-value=8 Score=36.88 Aligned_cols=96 Identities=19% Similarity=0.173 Sum_probs=66.3
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCCC
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQ 738 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~P 738 (868)
+..++.|+=.+++|+|. ++.|+..+|. .+.+.+. .+|.+.. .+|.+.+.+...|+... .
T Consensus 18 ~~~~~~l~~~tG~R~~E-----------i~~l~~~di~---~~~~~~~-~~K~~~~--r~ipl~~~~~~~l~~~~----~ 76 (158)
T cd00797 18 LKDVAILCLDTGARWGE-----------ALGLKAEDIQ---EGRVTFW-KTKSGKS--RTVPISERVAAMLKRRR----M 76 (158)
T ss_pred HHHHHHHHHHhcCCHHH-----------HhcCCHHHcc---cCeEEEE-ecCCCCc--eEeeCCHHHHHHHHHHh----h
Confidence 33444455578899875 7788888874 2344443 3677654 46778899999888765 3
Q ss_pred CCcccccCChhHHHHHHHhhC----CCCcceeeccccchHH
Q 002904 739 NDDLFDKLDTAKLNAHLKELM----PGLTAKVFRTYNASIT 775 (868)
Q Consensus 739 Gd~LFd~L~ss~LN~yLkelM----~glTAKdFRTynASvt 775 (868)
++.||-.++...++.+++.+. .++|..+||--.||..
T Consensus 77 ~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~~t~l 117 (158)
T cd00797 77 RGGLFPDLYYESFRHIWKRAKIELPKGQATHILRHTFASHF 117 (158)
T ss_pred cCCCCCCcChHHHHHHHHHHHHHhCCCCccccchhHHHHHH
Confidence 567897777778888888885 4678888886555543
No 50
>PRK15417 integrase/recombinase; Provisional
Probab=76.28 E-value=15 Score=40.19 Aligned_cols=56 Identities=13% Similarity=0.152 Sum_probs=41.5
Q ss_pred HHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHh
Q 002904 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQ 731 (868)
Q Consensus 661 vAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~ 731 (868)
+++.|+-.+.||+|- +|.|+.++|.+. ++.|.+. .||.+..+ .|.+.+.+...|+.
T Consensus 135 ~~~~ll~~TGlR~sE-----------l~~L~~~dId~~-~~~i~v~-~~K~~k~R--~vpl~~~~~~~L~~ 190 (337)
T PRK15417 135 LFAQLLYGTGMRISE-----------GLQLRVKDLDFD-HGTIIVR-EGKGSKDR--ALMLPESLAPSLRE 190 (337)
T ss_pred HHHHHHHHcCCcHHH-----------HHhcchhhccCC-CCeEEEE-eCCCCCce--eeeCCHHHHHHHHH
Confidence 455777889999987 899999999988 5666653 37776554 46667777776654
No 51
>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=71.67 E-value=24 Score=34.44 Aligned_cols=103 Identities=15% Similarity=0.020 Sum_probs=59.1
Q ss_pred HHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEee-CCCCeEEEEEEeeChHHHHHHHhhhcC--
Q 002904 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL-GKDSIQYVNTVEVELPVYKAIGQFQTG-- 735 (868)
Q Consensus 659 lAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFl-GKdgir~~~tV~VD~~V~knLk~f~k~-- 735 (868)
.-++++|+=.+.||+|- ++.|+.+||.+. ...|.+.-. +|.+.++ |..+..+...+......
T Consensus 19 ~~~~~~ll~~tGlR~~E-----------l~~L~~~did~~-~~~i~i~~~k~k~~~r~---v~~~~~~~~~~~~~~~~~~ 83 (186)
T cd01198 19 ERAVIVGLAKTGIRRGE-----------LINLDRRDVNLD-KPTLYLKPASNKRSNRT---LFPDLETELFRWLAIRPRT 83 (186)
T ss_pred HHHHHHHHHHhCchHHH-----------HhCCeecccccc-CCEEEEcCCCCCCCcee---ecchHHHHHHHHHHhcccc
Confidence 34668888899999986 899999999988 566666654 2333333 22244444444444322
Q ss_pred CCCCCccccc-----CChhH----HHHHHHhhC---------CCCcceeeccccchHHH
Q 002904 736 KKQNDDLFDK-----LDTAK----LNAHLKELM---------PGLTAKVFRTYNASITL 776 (868)
Q Consensus 736 K~PGd~LFd~-----L~ss~----LN~yLkelM---------~glTAKdFRTynASvta 776 (868)
..+.+.||-. ++... ++.+++.+- ..+|.-+||---||..+
T Consensus 84 ~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~H~lRHt~at~l~ 142 (186)
T cd01198 84 TSPADALFIGTQDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRHFFTTWLR 142 (186)
T ss_pred CCCCCceEEecCCCcccchhHHHHHHHHHHHhcccccccccccCcCcccchhHHHHHHH
Confidence 2355678832 33333 444444442 13566666655555443
No 52
>KOG0981 consensus DNA topoisomerase I [Replication, recombination and repair]
Probab=55.93 E-value=28 Score=42.15 Aligned_cols=117 Identities=19% Similarity=0.325 Sum_probs=61.4
Q ss_pred hHHHHHHHhhhcCCCCCCcccccCC-hhHHHHHHHhhC---CCCcceeeccccch-HHHHHHHhcC---CCCC------C
Q 002904 723 LPVYKAIGQFQTGKKQNDDLFDKLD-TAKLNAHLKELM---PGLTAKVFRTYNAS-ITLDGMLNKG---TGDG------D 788 (868)
Q Consensus 723 ~~V~knLk~f~k~K~PGd~LFd~L~-ss~LN~yLkelM---~glTAKdFRTynAS-vta~~~L~~~---~~~~------s 788 (868)
..|-+.|+.|| ..-..-+|.-.+ +-.|-.-|..+. +.+.+|.. .||.. .+. ..|... .... .
T Consensus 565 ~~LN~hL~~lM--~GLTAKVFRTYNASiTlqeqL~~lt~p~~~v~~KIl-~YnrANr~V-AIlCNHQR~v~K~h~~smek 640 (759)
T KOG0981|consen 565 SSLNKHLQELM--DGLTAKVFRTYNASITLQEQLDKLTNPDGNVAAKIL-SYNRANRTV-AILCNHQRAVSKTHEKSMEK 640 (759)
T ss_pred HHHHHHHHHHh--ccchhhhhhhcchhhHHHHHHHhccCCCccHHHHHH-HHhhcccee-eeeecccccCCccHHHHHHH
Confidence 45677888998 334456786655 445777788777 35788877 45532 221 112111 1111 2
Q ss_pred HHHHHHHHHHHHHHHHHHc-----CCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002904 789 VAVKIDVYQRANKEVAIIC-----NHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLD 843 (868)
Q Consensus 789 ~~eK~~~yn~Anr~VAilC-----NHqR~V~K~~~~sm~kl~~ki~~lk~q~~~~~~~l~ 843 (868)
.++|+.+....+.+.-.-+ .|..----.--..|++++.+|+.|++||..|+.++.
T Consensus 641 l~~kI~~~keql~e~~~~l~~ak~~~~~~~~~~~~k~~Ek~~k~~~~l~eqi~kl~~q~~ 700 (759)
T KOG0981|consen 641 LAEKIKAKKEQLKEAEAELKSAKADEKKQEGSKEKKEVEKKEKKLERLEEQLKKLEIQMT 700 (759)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccccccccccccccHHHHHHHHHHHHHHHHHHhhhcc
Confidence 2344443333322221111 222111111122778888888888888888876654
No 53
>PF09266 VirDNA-topo-I_N: Viral DNA topoisomerase I, N-terminal; InterPro: IPR015346 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents a domain foundpredominantly found in viral DNA topoisomerase I, a type IB enzyme. This domain assumes a beta(2)-alpha-beta-alpha-beta(2) fold, with a left-handed crossover between strands beta2 and beta3 []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change; PDB: 3IGC_A 2H7G_X 2H7F_X 1VCC_A.
Probab=42.63 E-value=6.1 Score=34.52 Aligned_cols=28 Identities=21% Similarity=0.259 Sum_probs=17.4
Q ss_pred cccccCCChhHHhccCCCCCCCCCCCCCCcceee
Q 002904 555 LKKRIQPSDITINIGKDVPIPECPIPGESWKEVK 588 (868)
Q Consensus 555 lK~RI~PdditInrik~l~IPP~P~~GhaWkeV~ 588 (868)
++.+|.-|+.+.++++...||+ ..+||.
T Consensus 14 ~~~~v~~~n~~yeIlk~~KiP~------HLtdV~ 41 (58)
T PF09266_consen 14 YTNPVPDDNPTYEILKKYKIPS------HLTDVI 41 (58)
T ss_dssp S-SB--TT-THHHHHHH----T------T-EEEE
T ss_pred hCCCCCCccHHHHHHHHcCCCc------ccceEE
Confidence 6788988999999999999999 899996
No 54
>COG0582 XerC Integrase [DNA replication, recombination, and repair]
Probab=42.53 E-value=39 Score=32.25 Aligned_cols=88 Identities=16% Similarity=0.166 Sum_probs=52.0
Q ss_pred hcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeC-CCCeEEEEEEeeChHHHHHHHhhhcCCCCCC-ccccc
Q 002904 668 KLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLG-KDSIQYVNTVEVELPVYKAIGQFQTGKKQND-DLFDK 745 (868)
Q Consensus 668 klALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlG-Kdgir~~~tV~VD~~V~knLk~f~k~K~PGd-~LFd~ 745 (868)
.+.+|+|- ++.|+.+|+.+. ...+.+.-.. |.+..+ .+.+.+.+...|....... +.. .||..
T Consensus 153 ~tG~R~~E-----------~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~-~~~~~~~~~ 217 (309)
T COG0582 153 LTGLRVSE-----------LLGLRWSDIDLE-NGTIWIRGTKTKGRKER--RVPLSEQALEALKKYLLIR-RPREYLFLS 217 (309)
T ss_pred HhcccHHH-----------HHhCcHhhcccc-cCeEEEeccccCCCCce--EEecCHHHHHHHHHHHHHh-cchhhhccc
Confidence 78999877 899999999988 3444444333 233333 4666788888887776321 221 56644
Q ss_pred CCh----------hHHHHHHHhhC--CC---Ccceeec-cc
Q 002904 746 LDT----------AKLNAHLKELM--PG---LTAKVFR-TY 770 (868)
Q Consensus 746 L~s----------s~LN~yLkelM--~g---lTAKdFR-Ty 770 (868)
... ..++.-+...+ .| +|..+|| ||
T Consensus 218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~ 258 (309)
T COG0582 218 LRGPRLSRSALTINRLLRARAKAAKEAGIRKITPHGLRHTF 258 (309)
T ss_pred cccCCCchHHHHHHHHHHHHHHHHHhcCCCccccchhHHHH
Confidence 221 12223222332 23 7899998 66
No 55
>PHA02601 int integrase; Provisional
Probab=41.86 E-value=60 Score=34.86 Aligned_cols=111 Identities=20% Similarity=0.179 Sum_probs=73.9
Q ss_pred HHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhhhcCCC
Q 002904 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKK 737 (868)
Q Consensus 658 qlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~ 737 (868)
.+.+++.|+=.+.+|.|- +|.|+.++|.. +.|.+. .+|.+- ...|.+.+.++..|..-
T Consensus 192 ~~~~~~~l~~~TG~R~~E-----------i~~L~~~did~---~~~~~~-~~K~~~--~r~Vpl~~~~~~~L~~~----- 249 (333)
T PHA02601 192 DLGLIAKICLATGARWSE-----------AETLKRSQISP---YKITFV-KTKGKK--NRTVPISEELYKMLPKR----- 249 (333)
T ss_pred hHHHHHHHHHHcCCCHHH-----------HHhCCHHHcCc---CeEEEE-ECCCCc--eeEEECCHHHHHHHHhc-----
Confidence 455667777788999987 88899888852 344332 456553 34688889998887642
Q ss_pred CCCcccccCChhHHHHHHHhhC-C---CCcceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002904 738 QNDDLFDKLDTAKLNAHLKELM-P---GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (868)
Q Consensus 738 PGd~LFd~L~ss~LN~yLkelM-~---glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~VAilCNHq 810 (868)
.+.||... ...++.+++.+- + ++|..+||=-.||.+++. +. -...|+.+++|.
T Consensus 250 -~~~~f~~~-~~~~~~~~~~~~~~~~~~~~~H~lRHt~at~l~~~-----G~-------------~~~~i~~~lGH~ 306 (333)
T PHA02601 250 -RGRLFKDA-YESFERAVKRAGIDLPEGQATHVLRHTFASHFMMN-----GG-------------NILVLQRILGHA 306 (333)
T ss_pred -CCCcChhH-HHHHHHHHHHhCCCCCCCCcCchhhHHHHHHHHHc-----CC-------------CHHHHHHHhCCC
Confidence 34577543 467888888764 2 578888887777765441 11 135777888885
No 56
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=38.06 E-value=12 Score=42.01 Aligned_cols=41 Identities=24% Similarity=0.342 Sum_probs=28.7
Q ss_pred hhhhhh-hccccCceEEEEeecceecccccccceeeeeccCCC
Q 002904 12 VKLLQM-CINCNFGTLIFVRNWCHIHANIVSGGIMAVEASSKP 53 (868)
Q Consensus 12 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~ 53 (868)
..++.+ |+||.+|.+.++|||-||++- ++|=.+...+...|
T Consensus 215 ~~ll~Ii~i~l~~G~~~~~~~~~h~gg~-~~G~~~~fil~~~g 256 (316)
T KOG2289|consen 215 RTLLIIIFINLDLGFAPYVDNFAHIGGL-LAGFLLGFVLHIGG 256 (316)
T ss_pred HHHHHHHHHHHhhccccceecccccccc-CCCcchhHHhhhcc
Confidence 345666 999999999999999999863 34433444444443
No 57
>PF05276 SH3BP5: SH3 domain-binding protein 5 (SH3BP5); InterPro: IPR007940 The SH3 domain-binding protein inhibits the auto and transphophorylation of BTK and acts as a negative regulator of BTK-related signalling in B cells.
Probab=26.46 E-value=1.4e+02 Score=32.60 Aligned_cols=54 Identities=20% Similarity=0.392 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHHHHc-CCCcccccc---------hHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002904 790 AVKIDVYQRANKEVAIIC-NHQRTVSKT---------HSAQMSRLTEKIEDLKGVLKDLRVDLD 843 (868)
Q Consensus 790 ~eK~~~yn~Anr~VAilC-NHqR~V~K~---------~~~sm~kl~~ki~~lk~q~~~~~~~l~ 843 (868)
......|+.|...|..|- -|.|+|-|+ |...|+....+|..|+.++..+|....
T Consensus 145 ~~~~~~~~~ae~~v~~Lek~lkr~I~KSrPYfe~K~~~~~~l~~~k~~v~~Le~~v~~aK~~Y~ 208 (239)
T PF05276_consen 145 QRRARIYNEAEQRVQQLEKKLKRAIKKSRPYFELKAKFNQQLEEQKEKVEELEAKVKQAKSRYS 208 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677999999999987 899999875 667777788888888888777776443
No 58
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=24.38 E-value=4.9e+02 Score=26.22 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=26.2
Q ss_pred HcCCCcccccchHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 002904 806 ICNHQRTVSKTHSAQM--SRLTEKIEDLKGVLKDLRVDLDRAKKGKP 850 (868)
Q Consensus 806 lCNHqR~V~K~~~~sm--~kl~~ki~~lk~q~~~~~~~l~~~k~~~~ 850 (868)
.|.+-++--+....++ +.|...|..|+.++..++..|..++.+..
T Consensus 94 ~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~ 140 (169)
T PF07106_consen 94 EVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSK 140 (169)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 3444444333333333 33667777777777777777777766543
No 59
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=22.02 E-value=1e+02 Score=31.10 Aligned_cols=22 Identities=14% Similarity=0.309 Sum_probs=16.6
Q ss_pred CChhHHHHHHHhhC--CCCcceee
Q 002904 746 LDTAKLNAHLKELM--PGLTAKVF 767 (868)
Q Consensus 746 L~ss~LN~yLkelM--~glTAKdF 767 (868)
+.=+.|-+.|..|. +-|+.|+|
T Consensus 30 ~~K~~v~k~Ld~L~~~g~i~~K~~ 53 (169)
T PF07106_consen 30 VGKTAVQKALDSLVEEGKIVEKEY 53 (169)
T ss_pred ccHHHHHHHHHHHHhCCCeeeeee
Confidence 44577888888888 46888877
No 60
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=22.01 E-value=54 Score=36.98 Aligned_cols=23 Identities=39% Similarity=0.745 Sum_probs=19.9
Q ss_pred CCCCC-----CCcceEEEcCEeccCChh
Q 002904 414 PPPYL-----PHGVKMLYKGKEVNLTPE 436 (868)
Q Consensus 414 pp~Y~-----P~~V~~~YdGkpv~L~p~ 436 (868)
-+||. |.+|.|+|+|+||+|++.
T Consensus 290 ~~p~~v~iG~~~~v~i~~nG~~vdl~~~ 317 (331)
T PRK10856 290 QAPYKLKIGAPAAVQIQYQGKPVDLSRF 317 (331)
T ss_pred CceEEEEEcCCCceEEEECCEEccCCcc
Confidence 45676 799999999999999975
No 61
>PF12835 Integrase_1: Integrase; InterPro: IPR024456 Phage integrase proteins 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 [, ]. This entry represents the catalytic domain from a family of putative prophage DNA-binding integrases.
Probab=20.75 E-value=2.3e+02 Score=29.43 Aligned_cols=129 Identities=18% Similarity=0.117 Sum_probs=73.5
Q ss_pred HHHHHHHHHHhcccccCCCCCccCCCceeeccCCCCceE----E-cCCCeEEEEeeCCCCeEEEEEEeeChHHHHHHHhh
Q 002904 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVE----C-IPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQF 732 (868)
Q Consensus 658 qlAvAlyLIDklALRvGNEKy~deadTvG~cTLR~eHV~----l-~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f 732 (868)
-+|+++.|...|-||.= | ++.|+..+.+ + ..++.|.+.|-+|.|..+...|.-...+...|..-
T Consensus 32 ~~a~~l~Lq~~fGLR~~------E-----a~~l~~~~~~w~~~l~~~~~~~~v~~gtKGGr~R~v~I~~~~~~~~~L~~a 100 (187)
T PF12835_consen 32 RVAAALELQRAFGLRRE------E-----ALKLRPSLATWEKALERGDETLRVVVGTKGGRPREVPILDSEKQREALERA 100 (187)
T ss_pred hhHHHHHHHHHhCCCHH------H-----HHhccHhhhhHHHHHhcCCCceEEeecCCCCCcceecCCCcHHHHHHHHHH
Confidence 46888899999999972 2 3444444441 1 12468889999999999988875246666666653
Q ss_pred hcC-CCCCCcccccCChhHHHHHHHhhC-----CCC----cceeeccccchHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Q 002904 733 QTG-KKQNDDLFDKLDTAKLNAHLKELM-----PGL----TAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKE 802 (868)
Q Consensus 733 ~k~-K~PGd~LFd~L~ss~LN~yLkelM-----~gl----TAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr~ 802 (868)
..- ...+..|+. ...|+.+++.+. -|| |+.-+|=.-| ++...++...+- .|-.|...
T Consensus 101 ~~~~~~~~~~li~---~~~l~~~~~~~~~~~~k~gl~~~~~~HGLRh~YA----qery~~l~~~G~------~~~~a~~~ 167 (187)
T PF12835_consen 101 AAVARERNGSLIP---KYSLKQALRRYRYALRKLGLTGSTGFHGLRHAYA----QERYEELQAQGF------SYKEALAQ 167 (187)
T ss_pred HHHhcccCCcccC---ccCHHHHHHHHHHHHHHcCCCcCCCchhHHHHHH----HHHHHHHHHCCC------CHHHHHHH
Confidence 211 233445555 222444443332 244 3555554333 333333322221 13468889
Q ss_pred HHHHcCCC
Q 002904 803 VAIICNHQ 810 (868)
Q Consensus 803 VAilCNHq 810 (868)
|+.-++|=
T Consensus 168 VS~eLGHG 175 (187)
T PF12835_consen 168 VSQELGHG 175 (187)
T ss_pred HHHHhcCC
Confidence 99999983
Done!