Query 002260
Match_columns 946
No_of_seqs 275 out of 586
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 20:06:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002260.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002260hhsearch_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 4E-227 9E-232 1855.5 48.1 693 236-946 44-759 (759)
2 smart00435 TOPEUc DNA Topoisom 100.0 2E-130 5E-135 1068.2 35.2 375 542-919 1-391 (391)
3 cd03489 Topoisomer_IB_N_Ldtopo 100.0 1.4E-99 3E-104 767.1 21.5 211 402-614 1-212 (212)
4 cd03490 Topoisomer_IB_N_1 Topo 100.0 8.8E-99 2E-103 763.4 21.6 212 402-614 1-217 (217)
5 cd00660 Topoisomer_IB_N Topois 100.0 2.8E-98 6E-103 758.8 21.5 211 402-614 1-215 (215)
6 cd03488 Topoisomer_IB_N_htopoI 100.0 3E-98 7E-103 758.6 21.5 211 402-614 1-215 (215)
7 PF02919 Topoisom_I_N: Eukaryo 100.0 7.1E-97 2E-101 751.2 12.6 211 401-613 1-215 (215)
8 PHA03101 DNA topoisomerase typ 100.0 5.6E-65 1.2E-69 543.9 21.2 249 554-816 16-273 (314)
9 PF01028 Topoisom_I: Eukaryoti 100.0 8.5E-63 1.8E-67 512.6 12.9 228 616-843 2-233 (234)
10 cd00659 Topo_IB_C DNA topoisom 100.0 1.5E-55 3.3E-60 454.3 19.2 197 618-816 1-203 (218)
11 COG3569 Topoisomerase IB [DNA 100.0 5.8E-51 1.3E-55 434.0 -7.8 323 397-775 24-353 (354)
12 COG3569 Topoisomerase IB [DNA 100.0 1.6E-43 3.4E-48 377.3 12.1 275 518-823 13-306 (354)
13 PF14370 Topo_C_assoc: C-termi 100.0 1.6E-38 3.4E-43 276.5 -0.8 71 876-946 1-71 (71)
14 cd00397 DNA_BRE_C DNA breaking 96.7 0.0066 1.4E-07 56.8 7.8 123 656-812 14-156 (164)
15 PF00589 Phage_integrase: Phag 95.6 0.08 1.7E-06 50.3 9.4 106 656-775 20-141 (173)
16 cd00801 INT_P4 Bacteriophage P 95.1 0.071 1.5E-06 56.7 8.3 123 659-813 201-333 (357)
17 TIGR02224 recomb_XerC tyrosine 94.8 0.081 1.8E-06 54.4 7.3 118 660-811 132-267 (295)
18 PRK02436 xerD site-specific ty 94.8 0.065 1.4E-06 55.1 6.5 111 662-811 117-236 (245)
19 cd01193 INT_IntI IntI (E2) int 94.7 0.13 2.7E-06 51.8 8.2 119 660-811 89-232 (242)
20 cd01192 INT_P22_C P22-like int 94.5 0.18 4E-06 49.1 8.5 120 659-811 23-151 (177)
21 cd01188 INT_pAE1 pAE1 and rela 94.3 0.45 9.8E-06 46.9 11.0 121 657-811 26-164 (188)
22 cd01182 INT_REC_C DNA breaking 94.3 0.22 4.7E-06 45.7 8.3 123 658-813 16-155 (162)
23 cd01194 INT_Tn554A_C Tn544A an 94.2 0.29 6.2E-06 47.8 9.3 120 660-811 19-164 (186)
24 cd01189 INT_phiLC3_C phiLC3 ph 94.0 0.3 6.5E-06 47.3 8.9 119 661-810 25-174 (191)
25 cd01187 INT_SG4 INT_SG4, DNA b 93.7 0.76 1.7E-05 48.5 11.9 129 658-811 127-277 (299)
26 cd01186 INT_SG3_C INT_SG3, DNA 93.5 0.25 5.4E-06 49.0 7.5 117 661-811 28-156 (180)
27 PRK05084 xerS site-specific ty 93.1 0.41 8.8E-06 52.2 9.0 117 660-810 198-333 (357)
28 PRK09692 integrase; Provisiona 92.8 0.45 9.7E-06 53.5 9.2 139 661-831 237-386 (413)
29 cd00799 INT_Cre Cre recombinas 92.7 0.49 1.1E-05 49.6 8.7 123 660-811 119-265 (287)
30 cd01197 INT_FimBE_C FimB and F 92.6 0.24 5.2E-06 48.7 5.8 116 662-810 29-160 (180)
31 cd01185 INT_Tn4399 Tn4399 and 92.4 0.29 6.2E-06 51.5 6.6 111 668-811 160-277 (299)
32 cd01190 INT_SG5 INT_SG5, DNA b 92.2 1 2.2E-05 46.1 10.0 125 659-811 97-236 (260)
33 PRK00283 xerD site-specific ty 92.1 0.98 2.1E-05 47.0 10.0 118 660-811 137-273 (299)
34 TIGR02225 recomb_XerD tyrosine 92.0 0.95 2.1E-05 46.4 9.6 119 659-811 127-265 (291)
35 cd00796 INT_Rci Rci recombinas 92.0 0.28 6E-06 49.2 5.6 117 659-810 66-187 (206)
36 PRK09870 tyrosine recombinase; 92.0 0.41 8.9E-06 48.6 6.8 117 662-811 37-169 (200)
37 PHA03397 vlf-1 very late expre 91.8 0.5 1.1E-05 54.0 7.9 163 611-811 147-329 (363)
38 cd01183 INT_SG1_C INT_SG1, DNA 91.8 0.41 8.8E-06 47.7 6.4 121 659-810 28-186 (196)
39 PRK00236 xerC site-specific ty 90.3 1 2.2E-05 46.3 7.9 118 660-811 139-271 (297)
40 cd00798 INT_XerDC XerD and Xer 90.1 1.9 4.1E-05 43.8 9.5 117 661-811 131-265 (284)
41 cd01199 INT_Tn1545_C Tn1545-re 90.0 2.4 5.2E-05 41.8 9.9 124 659-812 23-183 (205)
42 PRK01287 xerC site-specific ty 89.8 0.71 1.5E-05 50.9 6.7 118 661-811 161-296 (358)
43 PRK09871 tyrosine recombinase; 89.8 0.73 1.6E-05 46.5 6.3 118 661-811 30-164 (198)
44 PF07106 TBPIP: Tat binding pr 88.9 2.6 5.6E-05 42.7 9.4 77 805-889 58-134 (169)
45 cd00800 INT_Lambda_C Lambda in 88.8 0.85 1.8E-05 44.2 5.7 99 658-773 20-134 (162)
46 cd01184 INT_SG2_C INT_SG2, DNA 87.5 3.3 7.2E-05 40.5 9.0 121 661-812 28-172 (181)
47 TIGR02249 integrase_gron integ 86.4 2.1 4.5E-05 45.8 7.4 117 661-810 120-289 (315)
48 KOG0981 DNA topoisomerase I [R 86.4 1.7 3.6E-05 52.3 7.1 116 724-843 566-700 (759)
49 cd00797 HP1_INT_C Phage HP1 in 84.1 4.2 9.1E-05 39.2 7.6 114 659-811 18-135 (158)
50 cd01191 INT_phiCTX_C phiCTX ph 83.2 2.8 6.1E-05 42.1 6.3 120 661-811 24-184 (196)
51 cd01195 INT_Tn544B_C Tn544B an 82.1 11 0.00023 37.8 9.9 123 659-811 22-176 (195)
52 cd01196 INT_VanD VanD integras 78.8 7.1 0.00015 41.0 7.7 116 660-811 110-238 (263)
53 PRK15417 integrase/recombinase 76.8 14 0.0003 40.8 9.5 57 661-732 135-191 (337)
54 cd01198 INT_ASSRA_C Archaeal s 75.0 18 0.00038 35.9 8.9 119 659-810 19-158 (186)
55 PF14282 FlxA: FlxA-like prote 73.3 12 0.00025 36.0 6.9 21 818-838 18-38 (106)
56 PHA02601 int integrase; Provis 70.0 11 0.00024 40.8 6.7 112 658-811 192-307 (333)
57 COG0582 XerC Integrase [DNA re 66.7 18 0.00039 34.9 6.7 53 668-734 153-206 (309)
58 PF09726 Macoilin: Transmembra 55.7 18 0.00039 45.0 5.6 77 819-896 488-570 (697)
59 PF05276 SH3BP5: SH3 domain-bi 43.0 1.1E+02 0.0024 33.8 8.5 53 790-842 145-207 (239)
60 COG3883 Uncharacterized protei 39.9 30 0.00064 38.7 3.7 55 816-887 49-103 (265)
61 PF12718 Tropomyosin_1: Tropom 39.4 53 0.0012 33.2 5.1 65 817-888 33-97 (143)
62 PRK06342 transcription elongat 39.4 61 0.0013 33.5 5.6 66 818-901 33-100 (160)
63 PF06476 DUF1090: Protein of u 39.2 3E+02 0.0066 27.2 10.1 50 790-847 42-91 (115)
64 PF14257 DUF4349: Domain of un 36.5 1E+02 0.0022 33.4 7.1 85 807-908 120-204 (262)
65 PF11336 DUF3138: Protein of u 36.4 92 0.002 37.2 7.0 34 814-847 20-53 (514)
66 PRK13729 conjugal transfer pil 36.1 91 0.002 37.6 7.0 50 821-887 71-120 (475)
67 KOG2289 Rhomboid family protei 34.8 15 0.00032 41.8 0.5 41 12-53 215-256 (316)
68 TIGR02680 conserved hypothetic 34.5 2.4E+02 0.0052 38.0 11.2 48 723-775 183-230 (1353)
69 KOG4253 Tryptophan-rich basic 33.3 31 0.00068 36.0 2.4 86 806-915 20-109 (175)
70 PRK10856 cytoskeletal protein 31.6 26 0.00057 39.8 1.7 23 414-436 290-317 (331)
71 PRK05892 nucleoside diphosphat 31.1 2.1E+02 0.0046 29.5 8.0 71 818-900 10-87 (158)
72 PF02388 FemAB: FemAB family; 30.7 58 0.0013 37.8 4.3 78 816-909 239-316 (406)
73 KOG0804 Cytoplasmic Zn-finger 30.3 74 0.0016 38.1 5.0 105 795-903 355-471 (493)
74 PF07106 TBPIP: Tat binding pr 28.1 1.3E+02 0.0029 30.5 5.9 99 747-848 31-138 (169)
75 PF15290 Syntaphilin: Golgi-lo 27.6 1.1E+02 0.0025 34.6 5.6 74 809-892 72-145 (305)
76 PF03962 Mnd1: Mnd1 family; I 27.5 1.3E+02 0.0029 31.7 5.9 17 746-762 27-44 (188)
77 PF09032 Siah-Interact_N: Siah 26.6 1.8E+02 0.0039 27.3 5.9 47 824-885 1-47 (79)
78 PF03026 CM1: Influenza C viru 26.0 33 0.00071 35.7 1.2 99 706-812 103-214 (235)
79 PF10779 XhlA: Haemolysin XhlA 25.8 1.8E+02 0.0039 26.0 5.7 47 822-885 2-48 (71)
80 PF01519 DUF16: Protein of unk 25.5 2.8E+02 0.006 27.4 7.1 52 816-884 50-101 (102)
81 PRK13182 racA polar chromosome 25.3 1.7E+02 0.0036 30.9 6.1 34 866-899 127-160 (175)
82 PF02403 Seryl_tRNA_N: Seryl-t 25.0 3E+02 0.0065 25.9 7.3 57 819-889 36-92 (108)
83 PRK09039 hypothetical protein; 23.6 2E+02 0.0042 33.1 6.8 38 809-846 127-164 (343)
84 PRK01885 greB transcription el 23.6 4.1E+02 0.0089 27.4 8.4 29 818-846 9-38 (157)
85 PF06810 Phage_GP20: Phage min 23.3 2.6E+02 0.0055 28.9 6.9 48 820-881 21-68 (155)
86 PF12835 Integrase_1: Integras 22.4 2.2E+02 0.0049 29.9 6.5 130 657-810 31-175 (187)
87 TIGR01010 BexC_CtrB_KpsE polys 22.0 1.2E+03 0.026 26.5 16.1 98 771-889 170-267 (362)
88 TIGR01461 greB transcription e 21.2 2.2E+02 0.0048 29.3 6.0 74 818-900 7-88 (156)
89 PF03961 DUF342: Protein of un 20.7 1.9E+02 0.0042 34.0 6.1 76 815-890 330-408 (451)
90 KOG0250 DNA repair protein RAD 20.2 2E+02 0.0043 37.8 6.5 84 812-905 654-738 (1074)
91 cd01390 HMGB-UBF_HMG-box HMGB- 20.1 2.1E+02 0.0046 23.8 4.7 52 462-521 11-62 (66)
No 1
>KOG0981 consensus DNA topoisomerase I [Replication, recombination and repair]
Probab=100.00 E-value=4.4e-227 Score=1855.49 Aligned_cols=693 Identities=56% Similarity=0.877 Sum_probs=619.4
Q ss_pred CCCCCCCcccccccC-CCCCCCCCCCCCCCCCCCccccccccCCCCccccccCCCCCCcCCCCCCCCCCCCCCCCCCCCC
Q 002260 236 PEDSDDEVPLSSRFP-KSNAGTSGAKPIDSDEKKPLASKVQQNGSTSRETQQKSSSVPVKRPLQKASSSGASSAKKPKVS 314 (946)
Q Consensus 236 ~dDSDDekPLssk~~-k~~~g~S~~~~~DSde~KPLask~~~Ngs~~~~~~~~~~~~~~kr~~~~~~~~~~~~~k~~~~~ 314 (946)
..+||++.|+|+-+. +.-+ .|...+..+++.+|+ +..++|.....+ ...+..+.+|++.+.+.+.+++.+....+
T Consensus 44 ~~~s~~~~p~s~~~~kk~~s-~s~~~~~~~ek~k~~--~~~~~~~~~~s~-~~~~~~~~~r~~kk~~~~~~~~~~e~~~~ 119 (759)
T KOG0981|consen 44 KSDSDDDKPESKTKKKKKES-GSDEDDLSIEKRKPS--NDSDKGKDVKSD-KEDDKVPGKRKLKKNSKSKQSSSKEDDDS 119 (759)
T ss_pred ccccccccchHHHhhhcccc-cCCcccCchhhcccc--cccccccccccc-ccccccccccccccccccCcccccCCccc
Confidence 478999999999998 4444 566777778888888 777788776544 35678999999999999999999999999
Q ss_pred CCccchhhceeeeecccc-----------cCCCCCCcccccccCCCCCCCCcccccccccccccCCchhhhhhhcccccc
Q 002260 315 DTSKEVKVKQVTVKVEKK-----------ADDDDHIPISQRMKNSAPSVKKSVTNTAKATKSVSSSSNKINKKTKKVIKN 383 (946)
Q Consensus 315 ~~~~~~~~~~~~~~~~~k-----------~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 383 (946)
++..+++.++.+.-.-.+ +++.| .++++ ..+..+..+.++...+..+.+ .....+.++..+.
T Consensus 120 ~~~~~~~~k~~~~~~~~~d~~~~~~~~vk~e~sd-----k~~k~-~~~~~~~~s~k~~~sk~~~~~-~~~~~~~~~~~k~ 192 (759)
T KOG0981|consen 120 ESEPSVKEKDVKPVKPKKDEKGKALKKVKEEDSD-----KDKKS-DLSNVKTKSAKPSASKLPAGA-RTEPKKKKKKAKD 192 (759)
T ss_pred ccCCCCchhhccccccccchhhhhhhhhhhcccc-----hhhhc-cccccCccccCcccccCcccC-cCCccccccccch
Confidence 999999999987332222 22222 22222 222222222122111111111 1112333444444
Q ss_pred cccCccccCCCCCCCCccccceeeeccccCCCCCC--CCcceEEEcCeeccCChhhHHHHHHHHHhcCCCCCChhhHHhh
Q 002260 384 SQYSKSTKMLPGSGDGQKKWTTLVHNGVIFPPPYL--PHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFREN 461 (946)
Q Consensus 384 ~~~~~~~~~~~~~~~g~~KW~tLeHnGv~FpP~Y~--P~~Vk~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~k~~F~~N 461 (946)
+.+.++..-++..+++++||+||+||||+|||||+ ||||+|||||+||+|||+|||||||||+||+|+|+++++||+|
T Consensus 193 e~e~~~kww~~e~~d~~~KW~tLeH~G~iFaPPYeplP~~Vk~~YdGkpv~L~~eaEEvAtfyA~mle~ey~tk~vF~~N 272 (759)
T KOG0981|consen 193 EEEDKWKWWEEEKGDDGVKWTTLEHNGPIFAPPYEPLPSGVKFYYDGKPVDLTPEAEEVATFYAAMLEHEYATKEVFRKN 272 (759)
T ss_pred hhhhhhhhcccccCCCccceeeeeecCcccCCCCcCCCCCceEEeCCccccCCHHHHHHHHHHHHHHhcchhccHHHHHH
Confidence 43332222234556677799999999999999999 8999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhC--CCCCccccCCCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccccEEEEcCceeeecCcccCC
Q 002260 462 FWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEP 539 (946)
Q Consensus 462 Ff~D~r~~l~--~~~~I~~~~kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg~~~vDG~kekVGNFrvEP 539 (946)
||+|||++|+ ++++|++|++||||+||+||++|+|+||+||+|||+++|+|+++++++|||||||||+|+||||||||
T Consensus 273 Ff~Dwrk~m~~~~~~~Ik~l~kCDFt~i~~yf~~~~E~rK~mskEEK~~iKeEkek~ee~y~~cilDG~kEkigNFriEP 352 (759)
T KOG0981|consen 273 FFNDWRKVMTVEEREVIKDLSKCDFTPIFEYFKEQKEKRKQMSKEEKLKIKEEKEKLEEKYGWCILDGHKEKIGNFRIEP 352 (759)
T ss_pred HHHHHHHHhhhhhhhhhccccccCCHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHcCeEEecCcHhhhcccccCC
Confidence 9999999999 57999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccCCCCCCCCCCCCCCCCCCchhhhccCCCCCCCCCCCCCCcceeeeCCCCcEEEEEecCCCCcceeeeeccCCchh
Q 002260 540 PGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSL 619 (946)
Q Consensus 540 PGLfRGRG~hPk~G~lKkRV~PedvtiNi~k~a~IPp~P~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L~ahs~w 619 (946)
||||||||+||+||+||+||+|+|||||||++++||+ |||||.|++|+|||+|||||+|+|+|+ ++++||||+|+|++
T Consensus 353 PgLFRGRG~HPKmG~lKrRI~Pedi~iN~gkda~iP~-pppGhkWkEVrHDNTVTWLa~W~e~i~-~~~KYi~L~~~Ssl 430 (759)
T KOG0981|consen 353 PGLFRGRGEHPKMGKLKRRIMPEDITINCGKDAPIPE-PPPGHKWKEVRHDNTVTWLASWTENIN-GSFKYIMLNPSSSL 430 (759)
T ss_pred CccccCCCCCCcccchhcccchhheEEecCCCCCCCC-CCCCCcccccccCCeeeeeeecccccC-CceeEEEecCcccc
Confidence 9999999999999999999999999999999999999 889999999999999999999999999 69999999999999
Q ss_pred hccccHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcC
Q 002260 620 KGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIP 699 (946)
Q Consensus 620 k~~rD~~Kferar~L~~~Lp~IR~~y~kDLksk~~~~RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~ 699 (946)
+|++|++|||+||+|..+|+.||++|++||++++|..||+|||+||||+||||+|||+++++||||||||||++||+|+|
T Consensus 431 KGesD~~KyE~ARrLk~~Id~IR~~Y~~d~ksk~m~~RQravAlY~IDklALRAGnEKdedeADTVGCCsLrvehV~l~p 510 (759)
T KOG0981|consen 431 KGESDKEKYETARRLKKYIDKIRATYTKDFKSKEMKVRQRAVALYFIDKLALRAGNEKDEDEADTVGCCSLRVEHVTLHP 510 (759)
T ss_pred cCchhHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhccCcccccccccccceeeeeeeeEeeC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CC-----eEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccCccCChhHHHHHHHhhCCCCccceecccchHH
Q 002260 700 PN-----KLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASI 774 (946)
Q Consensus 700 ~~-----~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LFd~Ldss~LN~yLkelm~glTAKdFRTynASv 774 (946)
++ +|.|||||||||||+|+|+|+++||+||..|++++.|||+|||+|+|+.||+||++||+|||||||||||||+
T Consensus 511 ~~~~~e~vv~FDFLGKDSIrYyN~VeVek~VyKnl~~F~~~K~~~ddLFDrLdt~~LN~hL~~lM~GLTAKVFRTYNASi 590 (759)
T KOG0981|consen 511 PNKGKEFVVEFDFLGKDSIRYYNEVEVEKRVYKNLKIFMEGKKPGDDLFDRLDTSSLNKHLQELMDGLTAKVFRTYNASI 590 (759)
T ss_pred ccccccceEEeeccCccceeeeeeccccHHHHHHHHHHhcCCCccchhhhhhchHHHHHHHHHHhccchhhhhhhcchhh
Confidence 65 5599999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCC-CCCHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 002260 775 TLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLM 853 (946)
Q Consensus 775 ta~~~L~~~~~-~~s~~eK~~~yn~AnreVAilCNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~ 853 (946)
|||++|..++. .+++++|++.||+|||+|||||||||+|||+|++||++|+++|+++++||.+++.+|.++++++.+.
T Consensus 591 TlqeqL~~lt~p~~~v~~KIl~YnrANr~VAIlCNHQR~v~K~h~~smekl~~kI~~~keql~e~~~~l~~ak~~~~~~- 669 (759)
T KOG0981|consen 591 TLQEQLDKLTNPDGNVAAKILSYNRANRTVAILCNHQRAVSKTHEKSMEKLAEKIKAKKEQLKEAEAELKSAKADEKKQ- 669 (759)
T ss_pred HHHHHHHhccCCCccHHHHHHHHhhccceeeeeecccccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc-
Confidence 99999999998 7899999999999999999999999999999999999999999999999999999999999998766
Q ss_pred CCcccccccCCCHHHHHHHHHHHHHHHHHHhhccccccccceeeeccccccccCccceeeecccccCCchhhccHhHHhh
Q 002260 854 KDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSLLAK 933 (946)
Q Consensus 854 ~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~keenK~vaLGTSKiNYlDPRItvAwcKr~~VPIeKif~Ktlr~K 933 (946)
.++++ ++ .+|+++++|++|++||++|++|++||||||||||||||||||||||||||||||+||||||||||||+|
T Consensus 670 ~~~~~--~k--~~Ek~~k~~~~l~eqi~kl~~q~~dkeenK~vALGTSKiNYiDPRitvawcKk~dVPiEKif~Kt~reK 745 (759)
T KOG0981|consen 670 EGSKE--KK--EVEKKEKKLERLEEQLKKLEIQMTDKEENKQVALGTSKLNYIDPRITVAWCKKHDVPIEKIFTKTLREK 745 (759)
T ss_pred ccccc--cc--cHHHHHHHHHHHHHHHHHHhhhccchhhcceeecccccccccCCceeeeehhccCCcHHHHhhHHHHHH
Confidence 33333 22 689999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccC-CCCCCC
Q 002260 934 FAWAMDV-DPEFRF 946 (946)
Q Consensus 934 F~WA~~~-~~d~~F 946 (946)
|+|||+| |++|+|
T Consensus 746 F~WA~d~~de~~~f 759 (759)
T KOG0981|consen 746 FAWAIDMADEEYRF 759 (759)
T ss_pred HHHHhhcCCcccCC
Confidence 9999998 699998
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=2.4e-130 Score=1068.23 Aligned_cols=375 Identities=64% Similarity=0.950 Sum_probs=351.6
Q ss_pred cccCCCCCCCCCCCCCCCCCCchhhhccCCCCCCCCCCCCCCcceeeeCCCCcEEEEEecCCCCcceeeeeccCCchhhc
Q 002260 542 LFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKG 621 (946)
Q Consensus 542 LfRGRG~hPk~G~lKkRV~PedvtiNi~k~a~IPp~P~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L~ahs~wk~ 621 (946)
||||||+||+||+||+||+||||||||+++++||+ |||||.|++|+||++|+|||+|+|+++ ++|+||||+|+|+|++
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-PPPGHKWKEVRHDNTVTWLASWKENIN-GSIKYVFLAASSSLKG 78 (391)
T ss_pred CCCCCCCCCCccccccccChhheEEecCCCCCCCc-cCCCCCcceeecCCCceEEEEeeccCC-CceeEEEECCCchhhh
Confidence 89999999999999999999999999999999999 679999999999999999999999999 7899999999999999
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCC
Q 002260 622 QSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPN 701 (946)
Q Consensus 622 ~rD~~Kferar~L~~~Lp~IR~~y~kDLksk~~~~RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~ 701 (946)
+||+.|||+|++|+.+||+||++|++||+++++.+||+||||||||.+|||||||+|+++|+||||||||++||++++++
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 99999999999999999999999999999999889999999999999999999999999999999999999999998679
Q ss_pred eEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccCccCChhHHHHHHHhhCCCCccceecccchHHHHHHHHh
Q 002260 702 KLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASITLDGMLN 781 (946)
Q Consensus 702 ~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LFd~Ldss~LN~yLkelm~glTAKdFRTynASvta~~~L~ 781 (946)
+|+|+|+|||||+|+++|.||++||++|+.|++++.||++||++|++++||+||+++|+|||||||||||||+||+++|.
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 99999999999999999999999999999999889999999999999999999999999999999999999999999999
Q ss_pred cCCC-CCCHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCCCCCCcc
Q 002260 782 KGTG-DGDVAVKIDVYQRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKG---KPPLMKDSD 857 (946)
Q Consensus 782 ~~~~-~~s~~eK~~~yn~AnreVAilCNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~---~~~~~~~~~ 857 (946)
+++. .+++++++..||+||++|||+|||||||||+|++||++|++||+++++|+++++.+|..++.. +.+. +...
T Consensus 239 ~~~~~~~s~~ek~~~yn~Anr~VAi~cnntraV~k~~~~~m~k~~~ki~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 317 (391)
T smart00435 239 ELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKL-KSKF 317 (391)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccchhhhh-hhhh
Confidence 9987 589999999999999999999999999999999999999999999999999999998765521 1100 0000
Q ss_pred ----------c--ccccCCCHHHHHHHHHHHHHHHHHHhhccccccccceeeeccccccccCccceeeeccccc
Q 002260 858 ----------G--KRKRNLAPEALERKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHE 919 (946)
Q Consensus 858 ----------~--~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~keenK~vaLGTSKiNYlDPRItvAwcKr~~ 919 (946)
+ ..+....+++.+++|+++++||++|++|++||||||+|||||||||||||||||||||+||
T Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~i~k~~~q~~~ke~nk~vaLgTSk~NY~DPRitvawck~~~ 391 (391)
T smart00435 318 ERDNEKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391 (391)
T ss_pred hhhhhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCeeeecccchhhccCCcceeEeecccC
Confidence 0 0112235678889999999999999999999999999999999999999999999999986
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=1.4e-99 Score=767.09 Aligned_cols=211 Identities=70% Similarity=1.246 Sum_probs=208.1
Q ss_pred ccceeeeccccCCCCCCCCcceEEEcCeeccCChhhHHHHHHHHHhcCCCCCChhhHHhhhHHHHHHHhCCCC-CccccC
Q 002260 402 KWTTLVHNGVIFPPPYLPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGKNH-VIQNLE 480 (946)
Q Consensus 402 KW~tLeHnGv~FpP~Y~P~~Vk~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~k~~F~~NFf~D~r~~l~~~~-~I~~~~ 480 (946)
||+|||||||+|||+|+||||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|++++ .|++|+
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 CCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccccEEEEcCceeeecCcccCCCccccCCCCCCCCCCCCCCCC
Q 002260 481 GCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQ 560 (946)
Q Consensus 481 kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg~~~vDG~kekVGNFrvEPPGLfRGRG~hPk~G~lKkRV~ 560 (946)
+|||++||+||++++|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+||+
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 CCchhhhccCCCCCCCCCCCCCCcceeeeCCCCcEEEEEecCCCCcceeeeecc
Q 002260 561 PSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (946)
Q Consensus 561 PedvtiNi~k~a~IPp~P~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L~ 614 (946)
||||||||+++++||+ ||+||+|++|+||++|||||+|+|+++ +||+|||||
T Consensus 161 PedVtINigkda~vP~-pp~Gh~WkeV~HDntVtWLA~W~enIn-~~~KYV~La 212 (212)
T cd03489 161 PEDITINIGKGAPIPE-CPAGHKWKEVKHDNTVTWLAMWRDPIA-GNFKYVMLA 212 (212)
T ss_pred hhheEEecCCCCCCCc-cCCCCCcceeecCCCceEEEEeEeccC-CceeEEEeC
Confidence 9999999999999999 459999999999999999999999999 899999996
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=8.8e-99 Score=763.37 Aligned_cols=212 Identities=49% Similarity=0.919 Sum_probs=208.1
Q ss_pred ccceeeeccccCCCCCCCCcceEEEcCeeccCChhhHHHHHHHHHhcCCCCCChhhHHhhhHHHHHHHhCCCC---Cccc
Q 002260 402 KWTTLVHNGVIFPPPYLPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGKNH---VIQN 478 (946)
Q Consensus 402 KW~tLeHnGv~FpP~Y~P~~Vk~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~k~~F~~NFf~D~r~~l~~~~---~I~~ 478 (946)
+|+|||||||+|||+|+||||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|++++ .|++
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 7999999999999999999999999999999999999999999999999999999999999999999997654 8999
Q ss_pred cCCCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccccEEEEcCceeeecCcccCCCccccCCCCCCCCCCCCCC
Q 002260 479 LEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKR 558 (946)
Q Consensus 479 ~~kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg~~~vDG~kekVGNFrvEPPGLfRGRG~hPk~G~lKkR 558 (946)
|++|||++||+||++++|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+|
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 CCCCchhhhccCCCCCCCCC--CCCCCcceeeeCCCCcEEEEEecCCCCcceeeeecc
Q 002260 559 IQPSDITINIGKDVPIPECP--IPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (946)
Q Consensus 559 V~PedvtiNi~k~a~IPp~P--~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L~ 614 (946)
|+||||||||+++++||+|| +|||+|++|+||++|||||+|+|+++ +||+||||+
T Consensus 161 V~PedVtINigkda~vP~~p~~~~GH~WkeV~HDntVtWLA~W~enIn-~~~KYV~Ls 217 (217)
T cd03490 161 IFPEDVILNISKDAPVPKVTNFMEGHSWKDIYHDNSVTWLAYYKDSIN-DQFKYMFLS 217 (217)
T ss_pred cChhheEEecCCCCCCCcCCCCCCCCccceeecCCCceEEEEeecCCC-CceeEEEeC
Confidence 99999999999999999986 59999999999999999999999999 799999995
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=2.8e-98 Score=758.81 Aligned_cols=211 Identities=69% Similarity=1.176 Sum_probs=206.3
Q ss_pred ccceeeeccccCCCCCCCC--cceEEEcCeeccCChhhHHHHHHHHHhcCCCCCChhhHHhhhHHHHHHHhC--CCCCcc
Q 002260 402 KWTTLVHNGVIFPPPYLPH--GVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLG--KNHVIQ 477 (946)
Q Consensus 402 KW~tLeHnGv~FpP~Y~P~--~Vk~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~k~~F~~NFf~D~r~~l~--~~~~I~ 477 (946)
||+|||||||+|||+|+|| ||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|+ .++.|+
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 7999999999999999955 999999999999999999999999999999999999999999999999995 469999
Q ss_pred ccCCCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccccEEEEcCceeeecCcccCCCccccCCCCCCCCCCCCC
Q 002260 478 NLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKK 557 (946)
Q Consensus 478 ~~~kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg~~~vDG~kekVGNFrvEPPGLfRGRG~hPk~G~lKk 557 (946)
+|++|||++||+||++|+|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+
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 CCCCCchhhhccCCCCCCCCCCCCCCcceeeeCCCCcEEEEEecCCCCcceeeeecc
Q 002260 558 RIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (946)
Q Consensus 558 RV~PedvtiNi~k~a~IPp~P~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L~ 614 (946)
||+||||||||+++++||+| |+||+|++|+||++|||||+|+|+++ +||+|||||
T Consensus 161 Rv~PedVtINigkda~vP~p-p~Gh~WkeV~HDntVtWLA~W~enIn-~~~KYV~La 215 (215)
T cd00660 161 RIMPEDITINIGKDAPVPEP-PAGHKWKEVRHDNTVTWLASWKENIN-GQFKYVMLA 215 (215)
T ss_pred ccChhhEEEecCCCCCCCcc-CCCCCcceeecCCCceEEEEeEeccC-CceeEEEeC
Confidence 99999999999999999995 58999999999999999999999999 899999996
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=3e-98 Score=758.60 Aligned_cols=211 Identities=59% Similarity=1.054 Sum_probs=206.6
Q ss_pred ccceeeeccccCCCCCC--CCcceEEEcCeeccCChhhHHHHHHHHHhcCCCCCChhhHHhhhHHHHHHHhCC--CCCcc
Q 002260 402 KWTTLVHNGVIFPPPYL--PHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGK--NHVIQ 477 (946)
Q Consensus 402 KW~tLeHnGv~FpP~Y~--P~~Vk~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~k~~F~~NFf~D~r~~l~~--~~~I~ 477 (946)
||+|||||||+|||+|+ ||||+|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|+. ++.|+
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 569999999999999999999999999999999999999999999999999954 68999
Q ss_pred ccCCCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccccEEEEcCceeeecCcccCCCccccCCCCCCCCCCCCC
Q 002260 478 NLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKK 557 (946)
Q Consensus 478 ~~~kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg~~~vDG~kekVGNFrvEPPGLfRGRG~hPk~G~lKk 557 (946)
+|++|||++||+||++|+|+||+||+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+
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 CCCCCchhhhccCCCCCCCCCCCCCCcceeeeCCCCcEEEEEecCCCCcceeeeecc
Q 002260 558 RIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLA 614 (946)
Q Consensus 558 RV~PedvtiNi~k~a~IPp~P~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L~ 614 (946)
||+||||||||+++++||+| |+||+|++|+||++|||||+|+|+++ +||+||||+
T Consensus 161 Rv~PedVtINigkda~vP~p-p~Gh~WkeV~HDntVtWLA~W~enIn-~~~KYV~La 215 (215)
T cd03488 161 RIMPEDIIINIGKDAKVPEP-PPGHKWKEVRHDNTVTWLASWTENIN-GSIKYVMLN 215 (215)
T ss_pred ccChhhEEEecCCCCCCCcc-CCCCCcceeecCCCceEEEEeEeccC-CceeEEEeC
Confidence 99999999999999999995 59999999999999999999999999 799999996
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=7.1e-97 Score=751.16 Aligned_cols=211 Identities=68% Similarity=1.192 Sum_probs=162.7
Q ss_pred cccceeeeccccCCCCCC--CCcceEEEcCeeccCChhhHHHHHHHHHhcCCCCCChhhHHhhhHHHHHHHhCCCC--Cc
Q 002260 401 KKWTTLVHNGVIFPPPYL--PHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGKNH--VI 476 (946)
Q Consensus 401 ~KW~tLeHnGv~FpP~Y~--P~~Vk~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~k~~F~~NFf~D~r~~l~~~~--~I 476 (946)
+||+|||||||+|||+|+ ||||+|+|||+||+|+|+|||||||||+||+|+|+++++||+|||+||+++|++.+ .|
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 599999999999999999 99999999999999999999999999999999999999999999999999999876 89
Q ss_pred cccCCCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccccEEEEcCceeeecCcccCCCccccCCCCCCCCCCCC
Q 002260 477 QNLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLK 556 (946)
Q Consensus 477 ~~~~kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg~~~vDG~kekVGNFrvEPPGLfRGRG~hPk~G~lK 556 (946)
++|++|||++||+||++++|+||+||+|||+++|+++++++++||||+|||++||||||||||||||||||+||+||+||
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 CCCCCCchhhhccCCCCCCCCCCCCCCcceeeeCCCCcEEEEEecCCCCcceeeeec
Q 002260 557 KRIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFL 613 (946)
Q Consensus 557 kRV~PedvtiNi~k~a~IPp~P~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L 613 (946)
+||+||||||||+++++||+|| |||+|++|+||++|||||+|+|+++ +|++||||
T Consensus 161 ~Ri~PedVtIN~~k~a~vP~pp-~Gh~Wk~V~HDntvtWLA~W~enI~-~~~KYV~L 215 (215)
T PF02919_consen 161 KRIYPEDVTINIGKDAPVPEPP-PGHKWKEVVHDNTVTWLASWTENIN-GQFKYVML 215 (215)
T ss_dssp ----GGGEEEE--TTS-----S-TT---SEEE--TTSS-SEEEEETTT-TEEEEEEB
T ss_pred cccChhhEEEeCCCCCCCCccc-CCCCcceeEeCCCceEEEEeEeccC-CceeEEeC
Confidence 9999999999999999999955 9999999999999999999999999 78999998
No 8
>PHA03101 DNA topoisomerase type I; Provisional
Probab=100.00 E-value=5.6e-65 Score=543.86 Aligned_cols=249 Identities=20% Similarity=0.252 Sum_probs=233.8
Q ss_pred CCCCCCCCCchhhhccCCCCCCCCCCCCCCcceee--e----CCCCcEEEEEecCCCCcceeeeeccCCchhhccccHHH
Q 002260 554 KLKKRIQPSDITINIGKDVPIPECPIPGESWKEVK--H----DNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREK 627 (946)
Q Consensus 554 ~lKkRV~PedvtiNi~k~a~IPp~P~pGhaWkdV~--h----D~~vhwlAtg~DaigRkQYkYv~L~ahs~wk~~rD~~K 627 (946)
..+++|.+++.++.+++.+.||| ||+||| + ++++|+||||+|++||+||+| ||.|++.|+..|
T Consensus 16 ~~~~~~~~~~~~~~RI~~LaIPP------Aw~dVwI~p~~~e~~~~hlQAtG~Da~GRKQYrY-----H~~W~~~R~~~K 84 (314)
T PHA03101 16 EFTNPVSDDNPTYEILKKVKIPP------HLTDVVVYEQTYEEALTGLIFVGSDSKGRKQYFY-----GKLHVKNRNANR 84 (314)
T ss_pred hhCCCCCCccHHHHHHHHcCCCC------CcceEEEeeccccCCCCceEEEeecCCCCeeeee-----CHHHHHHHHHHH
Confidence 35789999999999999999999 899999 5 489999999999999999999 999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCC-chHHHHHHHHHHhh-ccccCCcccccCCCceeeccCCCCceEEcCCCeEEE
Q 002260 628 YEKARKLKDYIHSIRAAYTKDFVSRDGT-RRQIAVATYLIDKL-ALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKF 705 (946)
Q Consensus 628 ferar~L~~~Lp~IR~~y~kDLksk~~~-~RqlAvAlyLIDkl-ALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~F 705 (946)
|+++.+|+++||+||++|.+||+.+++. ++++|++++|||.+ +||||||+|+++|+||||||||++||++. |+.|+|
T Consensus 85 f~r~~~f~~~LP~iR~~v~~dL~~~~~~~~kvlAavv~LLd~~~~iRvGne~Ya~~N~SyGltTLr~rHv~v~-g~~i~f 163 (314)
T PHA03101 85 DKIFVRVHNVIKKINCFIDKNIKIKKKNDVNFQLAVFLLMETSFFIRTGKMKYLKENETVGLLTLKNKHITIS-NDKILI 163 (314)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhccceecCCHhHHHhcCCccccccchhceEEE-CCEEEE
Confidence 9999999999999999999999988888 99999999999999 79999999999999999999999999999 699999
Q ss_pred EeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccCccCChhHHHHHHHhhCCCCccceecccchHHHHHHHHhc-CC
Q 002260 706 DFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASITLDGMLNK-GT 784 (946)
Q Consensus 706 dFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LFd~Ldss~LN~yLkelm~glTAKdFRTynASvta~~~L~~-~~ 784 (946)
+|+||+|++|..+|..|++|+++|+.|++.+.||++||+|+++++||+||++. ||||||||||+||++|+..|.. +.
T Consensus 164 ~F~GKsG~~~~~~i~dD~rL~~~v~~l~~~~~Pg~~LF~y~d~~~VN~Ylre~--~fTAKDFRTW~gTv~a~~~l~~~~~ 241 (314)
T PHA03101 164 KFVGKDKVSHEFVVHKSNRLYKPLLKLIDKTNPDDFLFNKLSERKVYKFMKQF--GIRLKDLRTYGVNYTFLYNFWTNVK 241 (314)
T ss_pred EEECCCCcEEEEEecccHHHHHHHHHHHcCCCChHHHhhcCCHHHHHHHHHhC--CCcceeecCchHHHHHHHHHHhhcc
Confidence 99999999999999966999999999988888999999999999999999996 9999999999999999999843 23
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHcCCCcccccc
Q 002260 785 GDGDVAVKIDVYQRANKEVAIICNHQRTVSKT 816 (946)
Q Consensus 785 ~~~s~~eK~~~yn~AnreVAilCNHQRaV~K~ 816 (946)
...+..+..+.++.|+++||..||||+|||++
T Consensus 242 ~~~~~~~~kk~i~~~i~~vA~~LGNTPaV~R~ 273 (314)
T PHA03101 242 SLDPLPSIKKLISLSIKQTAEIVGHTPSISKS 273 (314)
T ss_pred ccCChhHHHHHHHHHHHHHHHHhCCCHhhHHh
Confidence 34455667788999999999999999999997
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=8.5e-63 Score=512.56 Aligned_cols=228 Identities=32% Similarity=0.432 Sum_probs=207.5
Q ss_pred CchhhccccHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHHHHHhhccccCCcccccCCC-ceeeccCCCCc
Q 002260 616 SSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEAD-TVGCCTLKVGN 694 (946)
Q Consensus 616 hs~wk~~rD~~Kferar~L~~~Lp~IR~~y~kDLksk~~~~RqlAvAlyLIDklALRvGnEKy~~end-TvG~cTLR~eH 694 (946)
.+.|+++||+.||+++++|+.+||+||++|.+||++..+.+||+|+|+||||.++||||||+|+++|+ ||||||||++|
T Consensus 2 Ds~gRkQrd~~Kf~r~~~f~~~Lp~iR~~v~~dL~~~~~~~r~lA~a~~LlD~~~lRvGne~Y~~~n~ds~GltTLr~~H 81 (234)
T PF01028_consen 2 DSKGRKQRDEEKFDRARRFARALPKIRRRVRKDLRSGLPRERVLAVAVRLLDRTALRVGNEKYAEENGDSYGLTTLRVKH 81 (234)
T ss_dssp TTCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTCHHHHHHHHHHHHHHH------HHHHCCHHSHHHCCT-BGGG
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcchhHHHHHHHHHHhhheecCCcccccccCCCeeeCcCcHHH
Confidence 45666679999999999999999999999999995555559999999999999999999999998888 99999999999
Q ss_pred eEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccCccCChhHHHHHHHhhCCCCccceecccchHH
Q 002260 695 VECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASI 774 (946)
Q Consensus 695 Vkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LFd~Ldss~LN~yLkelm~glTAKdFRTynASv 774 (946)
|++.+++.|+|+|+||||++|+++|.||+.||++|+.|++++.||++||+.|++++||+||+++|+||||||||||+||+
T Consensus 82 v~~~~~~~i~f~F~GK~g~~~~~~v~~d~~l~~~l~~~~~~~~pg~~LF~~v~s~~vN~yL~~~~~~~TaKdFRTw~at~ 161 (234)
T PF01028_consen 82 VKLSGDNVIRFDFPGKSGVRQEITVRVDPRLAKNLKRLLRRKLPGDRLFHPVTSTDVNAYLREIMEDFTAKDFRTWNATV 161 (234)
T ss_dssp EEEETTCEEEEEEEEGGGEEEEEEEETTHHHHHHHHHHHTTTSTTSBTTTT--HHHHHHHHHHCTTTS-HHHHHHHHHHH
T ss_pred eeecCCcEEEEEeeCCCCeEEEEEEecCHHHHHHHHHHHhCCCChhhccCCCCHHHHHHHHHHhcCCCceeeeeeccHHH
Confidence 99997559999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCC---CCCCHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002260 775 TLDGMLNKGT---GDGDVAVKIDVYQRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLD 843 (946)
Q Consensus 775 ta~~~L~~~~---~~~s~~eK~~~yn~AnreVAilCNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~ 843 (946)
+|+++|.+.+ +..+..+++.+||.||++||++|||||+|||+|.-.+..++..++++++++++++++|+
T Consensus 162 ~a~~~L~~~~~~~~~~~~~~~~~~~~~a~~~VA~~LgnTpaV~r~sYi~p~v~~~~~~~~~~~~~~~~~~~~ 233 (234)
T PF01028_consen 162 LAAEALAKAPRVPPPESEKERKKAYNAAVKEVAELLGNTPAVCRKSYIHPRVLDLYIKELKEQIKELKKQLK 233 (234)
T ss_dssp HHHHHHHHHH--HHSSSHHHHHHHHHHHHHHHHHHHTSEHHHHHHHTSHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHhCCCccccchhhhCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999986 67899999999999999999999999999999999999999999999999999999886
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=1.5e-55 Score=454.30 Aligned_cols=197 Identities=48% Similarity=0.685 Sum_probs=189.9
Q ss_pred hhhccccHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC-chHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceE
Q 002260 618 SLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGT-RRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVE 696 (946)
Q Consensus 618 ~wk~~rD~~Kferar~L~~~Lp~IR~~y~kDLksk~~~-~RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVk 696 (946)
.|+..++..||+++.+|+.+||+||++|.+||++++++ ++|+|+|+||||.++||||||+|+++|+||||||||++||+
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 48999999999999999999999999999999999997 99999999999999999999999999999999999999999
Q ss_pred EcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccC-----ccCChhHHHHHHHhhCCCCccceecccc
Q 002260 697 CIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLF-----DKLDTAKLNAHLKELMPGLTAKVFRTYN 771 (946)
Q Consensus 697 l~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LF-----d~Ldss~LN~yLkelm~glTAKdFRTyn 771 (946)
+. |+.|+|+|+||||++|+++|..+++|+++|+.|++ +.||++|| +.|++++||+||+++|+||||||||||+
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 69999999999999999999933999999999976 69999999 6799999999999999999999999999
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCcccccc
Q 002260 772 ASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQRTVSKT 816 (946)
Q Consensus 772 ASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQRaV~K~ 816 (946)
||++|+..|.+.+...+..+++..|+.|+++||++||||++||+.
T Consensus 159 at~~a~~~L~~~~~~~~~~~~~~~i~~a~~~vA~~LgnTpav~r~ 203 (218)
T cd00659 159 ASLTALEQLARLPASLSLAEKKKAYNDANREVAILLNHTPAISKI 203 (218)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCCCcchhHH
Confidence 999999999988888899999999999999999999999999986
No 11
>COG3569 Topoisomerase IB [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.8e-51 Score=434.02 Aligned_cols=323 Identities=24% Similarity=0.256 Sum_probs=306.9
Q ss_pred CCCccccceeeeccccCCCCCC--CCcceEEEcCeeccCChhhHHHHHHHHHhcCCCCCChhhHHhhhHHHHHHHhCC--
Q 002260 397 GDGQKKWTTLVHNGVIFPPPYL--PHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFRENFWNDWRKLLGK-- 472 (946)
Q Consensus 397 ~~g~~KW~tLeHnGv~FpP~Y~--P~~Vk~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~k~~F~~NFf~D~r~~l~~-- 472 (946)
++|..+|+|+. |++|+|||. |.+++.+|+|++|.|+|+.||| |+.|++++|.|.+.| +|||++|-.+.++
T Consensus 24 epgirr~~~gk--gf~y~~Pdg~l~sd~~~~~ri~~l~lPPay~dV---wi~ld~~gHlqatg~-DargRkqyryhpew~ 97 (354)
T COG3569 24 EPGIRREKTGK--GFIYRPPDGPLVSDAKLLRRIAALALPPAYEDV---WICLDENGHLQATGR-DARGRKQYRYHPEWA 97 (354)
T ss_pred CcchhhhccCC--ceEecCCCCCCCccHHHHhcccccCCCcchhhh---eeecCccccccccch-hhhhhhhheeCchhh
Confidence 67888999999 999999999 5999999999999999999999 999999999999999 9999999998864
Q ss_pred --CCCccccCCCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhccccEEEEcCceeeecCcccCCCccccCCCCCC
Q 002260 473 --NHVIQNLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHP 550 (946)
Q Consensus 473 --~~~I~~~~kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg~~~vDG~kekVGNFrvEPPGLfRGRG~hP 550 (946)
..-|+.|.+|||+.++.+|....+++++++.+++++..++ .+|++||.+++|||| +||||+|-||
T Consensus 98 ~~r~~~K~~~l~~F~kalp~lrr~~~~~~~~~~~~~~~v~a~--------~~~lLD~~~~rVGN~-----~y~r~ngsyg 164 (354)
T COG3569 98 ALRDGIKYFSLVRFGKALPSLRRTIDADLRLPGLPKEKVVAA--------KVCLLDGARIRVGNF-----AYARDNGSYG 164 (354)
T ss_pred hcccchhHHHHHHHHHHhHHHHHHHHHhhcCCCccHHHHHHH--------HHHHhhhhHhhcccH-----HHhhccCCcC
Confidence 3459999999999999999999999999999999999877 899999999999999 9999999999
Q ss_pred CCCCCCCCCCCCchhhhccCCCCCCCCCCCCCCcceeeeCCCCcEEEEEecCCCCcceeeeeccCCchhhccccHHHHHH
Q 002260 551 KMGKLKKRIQPSDITINIGKDVPIPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEK 630 (946)
Q Consensus 551 k~G~lKkRV~PedvtiNi~k~a~IPp~P~pGhaWkdV~hD~~vhwlAtg~DaigRkQYkYv~L~ahs~wk~~rD~~Kfer 630 (946)
++|.+|++|.|++++||+....++ ||.|.++ .+|+.|++ .++++.|.-
T Consensus 165 ~TtllkRhV~~~~~ti~~~f~gk~------G~~~~~~--------------------l~~~rLaa--~L~~~~DLp---- 212 (354)
T COG3569 165 LTTLLKRHVDVEGSTIRFRFKGKS------GKEWKER--------------------LKDPRLAA--ILRGQLDLP---- 212 (354)
T ss_pred cccceeeeeccCCCEEEEEecCCc------chhhhhh--------------------hhhHHHHH--HHHHhhcCc----
Confidence 999999999999999999999864 9999987 79999999 899999977
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCC
Q 002260 631 ARKLKDYIHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGK 710 (946)
Q Consensus 631 ar~L~~~Lp~IR~~y~kDLksk~~~~RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGK 710 (946)
.+.|..+|+.++..+..|+++..+-.||.+++.|++|.+++|.|++.-+++++|+|||+++.+||++.+.....|+|+++
T Consensus 213 gr~Lf~y~D~~~~~~r~~s~~ln~ylr~~~g~~~sak~Frtw~Gt~~a~~~a~t~g~~s~~~~~v~~~~~~A~~Lgnt~a 292 (354)
T COG3569 213 GRKLFQYLDEDGRERRIDSKSLNAYLRQVTGAPFSAKDFRTWGGTLLAEEEADTVGCCSEAPELVSLVAAVAAVLGNTPA 292 (354)
T ss_pred hHHHHHhhcccCCcccCCchhHHHHHHHhcccceehhHHHhccCchHHHHHHhhhcchhcchhhhhhccchhhhccCCcc
Confidence 99999999999999999999888889999999999999999999999999999999999999999999889999999999
Q ss_pred CCeEEEEEEeeChhHHHHHHhhh-cCCCCCCccCccCChhHHHHHHHhhCCCCccceecccchHHH
Q 002260 711 DSIQYVNTVEVELPVYKAIGQFQ-TGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASIT 775 (946)
Q Consensus 711 dgir~~~tV~VD~~V~knLk~f~-k~K~Pgd~LFd~Ldss~LN~yLkelm~glTAKdFRTynASvt 775 (946)
.++++| |+|+||++...+. ..+.+|+.||++.... ||+|++.+|.+|++|+|||||||.|
T Consensus 293 isRr~Y----IhPqVf~~~~~~K~~~~~~g~~lr~r~~~~-L~~ee~~Ll~~L~~~~~~~~~~~~t 353 (354)
T COG3569 293 ISRRCY----IHPQVFDNYLIGKRLPKKSGRQLRDRARLE-LNKEEQRLLRFLEAKVRRRYRASKT 353 (354)
T ss_pred ccccce----ecHHHHhhhhhcccCcccchhHHHhhcccc-ccHHHHHHHhhhchhhhhhhhhhcc
Confidence 999999 6899999999997 5688999999999988 9999999999999999999999976
No 12
>COG3569 Topoisomerase IB [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.6e-43 Score=377.32 Aligned_cols=275 Identities=19% Similarity=0.238 Sum_probs=246.7
Q ss_pred ccccEEEEcCceeeecCcccCCCcccc---CCCCCCCCCCCCCCCCCCchhhhccCCCCCCCCCCCCCCcceee--eCCC
Q 002260 518 EKYMWAIVDGVKEKVGNFRVEPPGLFR---GRGEHPKMGKLKKRIQPSDITINIGKDVPIPECPIPGESWKEVK--HDNT 592 (946)
Q Consensus 518 ~~yg~~~vDG~kekVGNFrvEPPGLfR---GRG~hPk~G~lKkRV~PedvtiNi~k~a~IPp~P~pGhaWkdV~--hD~~ 592 (946)
|+-|||+|+.. -||+.| |+||. +.+-.+..+.+.+ .|.+++.+.||| +|.||| .|++
T Consensus 13 e~~~l~yv~d~----------epgirr~~~gkgf~-y~~Pdg~l~sd~~-~~~ri~~l~lPP------ay~dVwi~ld~~ 74 (354)
T COG3569 13 EEAGLKYVSDE----------EPGIRREKTGKGFI-YRPPDGPLVSDAK-LLRRIAALALPP------AYEDVWICLDEN 74 (354)
T ss_pred hhhcceeeccc----------CcchhhhccCCceE-ecCCCCCCCccHH-HHhcccccCCCc------chhhheeecCcc
Confidence 56788888875 689988 88886 3444456787655 677788888999 899999 9999
Q ss_pred CcEEEEEecCCCCcceeeeeccCCchhhccccHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC-chHHHHHHHHHHhhcc
Q 002260 593 VTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDGT-RRQIAVATYLIDKLAL 671 (946)
Q Consensus 593 vhwlAtg~DaigRkQYkYv~L~ahs~wk~~rD~~Kferar~L~~~Lp~IR~~y~kDLksk~~~-~RqlAvAlyLIDklAL 671 (946)
+|+||+|+|+.||+||+| ||.|.+.++..||....+|+++||.||+.++.||+..+.. ++++|.++.|||-..+
T Consensus 75 gHlqatg~DargRkqyry-----hpew~~~r~~~K~~~l~~F~kalp~lrr~~~~~~~~~~~~~~~v~a~~~~lLD~~~~ 149 (354)
T COG3569 75 GHLQATGRDARGRKQYRY-----HPEWAALRDGIKYFSLVRFGKALPSLRRTIDADLRLPGLPKEKVVAAKVCLLDGARI 149 (354)
T ss_pred ccccccchhhhhhhhhee-----CchhhhcccchhHHHHHHHHHHhHHHHHHHHHhhcCCCccHHHHHHHHHHHhhhhHh
Confidence 999999999999999999 9999999999999999999999999999999999999998 9999999999999999
Q ss_pred ccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccCccCC----
Q 002260 672 RAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLD---- 747 (946)
Q Consensus 672 RvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LFd~Ld---- 747 (946)
||||-.|++.|+|||+|||+.+||.+. +++|+|.|.||.|++|...+. +++|+.+|+.+ .+.||..||+|+|
T Consensus 150 rVGN~~y~r~ngsyg~TtllkRhV~~~-~~ti~~~f~gk~G~~~~~~l~-~~rLaa~L~~~--~DLpgr~Lf~y~D~~~~ 225 (354)
T COG3569 150 RVGNFAYARDNGSYGLTTLLKRHVDVE-GSTIRFRFKGKSGKEWKERLK-DPRLAAILRGQ--LDLPGRKLFQYLDEDGR 225 (354)
T ss_pred hcccHHHhhccCCcCcccceeeeeccC-CCEEEEEecCCcchhhhhhhh-hHHHHHHHHHh--hcCchHHHHHhhcccCC
Confidence 999999999999999999999999999 699999999999999999998 99999999999 7899999999987
Q ss_pred -----hhHHHHHHHhhC-CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCcccccc---hH
Q 002260 748 -----TAKLNAHLKELM-PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQRTVSKT---HS 818 (946)
Q Consensus 748 -----ss~LN~yLkelm-~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQRaV~K~---~~ 818 (946)
+.++|.||++.. .+|||||||||+||..+.+.+......+ -....+....+||..++++++||.. |-
T Consensus 226 ~~r~~s~~ln~ylr~~~g~~~sak~Frtw~Gt~~a~~~a~t~g~~s----~~~~~v~~~~~~A~~Lgnt~aisRr~YIhP 301 (354)
T COG3569 226 ERRIDSKSLNAYLRQVTGAPFSAKDFRTWGGTLLAEEEADTVGCCS----EAPELVSLVAAVAAVLGNTPAISRRCYIHP 301 (354)
T ss_pred cccCCchhHHHHHHHhcccceehhHHHhccCchHHHHHHhhhcchh----cchhhhhhccchhhhccCCccccccceecH
Confidence 899999999999 7999999999999999999987654433 1334567888999999999999996 34
Q ss_pred HHHHH
Q 002260 819 AQMSR 823 (946)
Q Consensus 819 ~~m~k 823 (946)
+..++
T Consensus 302 qVf~~ 306 (354)
T COG3569 302 QVFDN 306 (354)
T ss_pred HHHhh
Confidence 44444
No 13
>PF14370 Topo_C_assoc: C-terminal topoisomerase domain; 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=1.6e-38 Score=276.51 Aligned_cols=71 Identities=75% Similarity=1.212 Sum_probs=60.4
Q ss_pred HHHHHHHHhhccccccccceeeeccccccccCccceeeecccccCCchhhccHhHHhhccccccCCCCCCC
Q 002260 876 TNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSLLAKFAWAMDVDPEFRF 946 (946)
Q Consensus 876 ~~~~i~k~~~~~~~keenK~vaLGTSKiNYlDPRItvAwcKr~~VPIeKif~Ktlr~KF~WA~~~~~d~~F 946 (946)
+++||++|++|+++||+||+|||||||||||||||||||||+|||||||||+||||+||+|||++++||+|
T Consensus 1 ~~~ri~k~~~~~~~k~~~K~vaLgTSKiNYlDPRItvAWck~~~VPieKifsktlr~KF~WA~~~~~~~~F 71 (71)
T PF14370_consen 1 IKERIKKLELQLKDKEDNKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFSKTLREKFAWAMDVDEDFKF 71 (71)
T ss_dssp -HHHHHHHHHHHHHHHHTSCE-SHHHHHHTS-HHHHHHHHHHTT--GGGTS-HHHHHHTHHHCCS-TT---
T ss_pred ChHHHHHHHHHHHHHhhcceeecchhhhhhcCcHHHHHHHHHhCCcHHHHhhHHHHHhhhHHHcCCCCCCC
Confidence 47899999999999999999999999999999999999999999999999999999999999999999998
No 14
>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=96.66 E-value=0.0066 Score=56.82 Aligned_cols=123 Identities=20% Similarity=0.263 Sum_probs=87.1
Q ss_pred chHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeC-CCCeEEEEEEeeChhHHHHHHhhhc
Q 002260 656 RRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLG-KDSIQYVNTVEVELPVYKAIGQFQT 734 (946)
Q Consensus 656 ~RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlG-Kdgir~~~tV~VD~~V~knLk~f~k 734 (946)
....++++.|+-.+.+|.|. +|.|+.+||... ... +.|.+ |.+. ...+.+.+.+...|..++.
T Consensus 14 ~~~~~~~~~l~~~tG~R~~E-----------i~~l~~~~~~~~-~~~--~~i~~~K~~~--~~~i~i~~~~~~~l~~~~~ 77 (164)
T cd00397 14 PERLYLALLLLLATGLRISE-----------LCALRWSDIDLD-KRV--IHITGTKTKK--ERTVPLSEEALKLLKEYLK 77 (164)
T ss_pred ccHHHHHHHHHHHhCCCHHH-----------HhCCchhhhccc-cCE--EEEecCCCCC--eeEEecCHHHHHHHHHHHH
Confidence 35677788888889999985 788999999876 334 45555 8774 4566667877777777654
Q ss_pred CC----CCCCccCccC--------ChhHHHHHHHhhC--C-----CCccceecccchHHHHHHHHhcCCCCCCHHHHHHH
Q 002260 735 GK----KQNDDLFDKL--------DTAKLNAHLKELM--P-----GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDV 795 (946)
Q Consensus 735 ~K----~Pgd~LFd~L--------dss~LN~yLkelm--~-----glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~ 795 (946)
.- .+++.||... ....++.+++.++ . .++..+||-..||.++.... +
T Consensus 78 ~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~R~t~~t~~~~~g~-----~--------- 143 (164)
T cd00397 78 KRRPANGDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLRHTFASALLNAGL-----D--------- 143 (164)
T ss_pred HhccccCCCCceeecCCCCCccCCcHHHHHHHHHHHHHHcCCCCCCCCchHhHHHHHHHHHHcCC-----C---------
Confidence 32 4567888763 3557899999887 2 37888898888776544321 1
Q ss_pred HHHHHHHHHHHcCCCcc
Q 002260 796 YQRANKEVAIICNHQRT 812 (946)
Q Consensus 796 yn~AnreVAilCNHQRa 812 (946)
..++|.+|||...
T Consensus 144 ----~~~i~~~~gH~~~ 156 (164)
T cd00397 144 ----LEAVQDLLGHSSI 156 (164)
T ss_pred ----HHHHHHHhCCCcH
Confidence 5588999999654
No 15
>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=95.58 E-value=0.08 Score=50.31 Aligned_cols=106 Identities=15% Similarity=0.184 Sum_probs=74.3
Q ss_pred chHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEE-eeCCCCeEEEEEEeeChhHHHHHHhhhc
Q 002260 656 RRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFD-FLGKDSIQYVNTVEVELPVYKAIGQFQT 734 (946)
Q Consensus 656 ~RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~Fd-FlGKdgir~~~tV~VD~~V~knLk~f~k 734 (946)
.-..++++.|+=.+++|+|- +++|+.+||.+. ++.+.+. -.+|-+.. ..|.+.+.++..|+.++.
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 44556677777889999975 899999999888 5777774 45666666 666777999999998764
Q ss_pred C----CCCCCccCc-----cCChhHHHHHHHhhC-----C-CCccceecccchHHH
Q 002260 735 G----KKQNDDLFD-----KLDTAKLNAHLKELM-----P-GLTAKVFRTYNASIT 775 (946)
Q Consensus 735 ~----K~Pgd~LFd-----~Ldss~LN~yLkelm-----~-glTAKdFRTynASvt 775 (946)
. ..+.+.||. .++...++..++.++ + .+|..+||--.+|.+
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 3 356778883 567889999999887 2 577777774444433
No 16
>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=95.14 E-value=0.071 Score=56.73 Aligned_cols=123 Identities=12% Similarity=0.022 Sum_probs=87.7
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEe-eCCCCeEEEEEEeeChhHHHHHHhhhcCCC
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQTGKK 737 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k~K~ 737 (946)
...++.|+=.++||.|- +|.|+..||.+. ++.+.+.. .+|.+. ...|.+.+.+...|..++....
T Consensus 201 ~~~~~~l~~~tGlR~~E-----------i~~L~~~di~~~-~~~~~i~~~~~Kt~~--~r~vpl~~~~~~~l~~~~~~~~ 266 (357)
T cd00801 201 TRLALKLLLLTGVRPGE-----------LRGARWSEIDLE-NALWTIPAERMKTRR--PHRVPLSDQALALLEELRELSG 266 (357)
T ss_pred HHHHHHHHHHHCcChHh-----------HHcCcchhcccC-CCeEecchhhccCCC--CcccCCcHHHHHHHHHHHHHhC
Confidence 34445555569999984 899999999998 46666643 367663 3467778999999998876555
Q ss_pred CCCccCc-------cCChhHHHHHHHhhC--CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcC
Q 002260 738 QNDDLFD-------KLDTAKLNAHLKELM--PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICN 808 (946)
Q Consensus 738 Pgd~LFd-------~Ldss~LN~yLkelm--~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCN 808 (946)
+++.||. .++...++.+++.+. ..+|..+||-..||.++.. +. + ...|+.++|
T Consensus 267 ~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRHt~at~~~~~-----g~--~-----------~~~i~~~lG 328 (357)
T cd00801 267 HSEYVFPSRRDRGKPLSENTLNKALKRMGYLGEWTPHGLRRTARTWLNEL-----GF--P-----------PDVIERQLA 328 (357)
T ss_pred CCceEecCCCCCCCCCCHHHHHHHHHHcCCCCCcCcCchhHHHHHHHHHC-----CC--C-----------HHHHHHHhC
Confidence 5788884 456778999999987 5688888887766654432 11 1 246888899
Q ss_pred CCccc
Q 002260 809 HQRTV 813 (946)
Q Consensus 809 HQRaV 813 (946)
|.-..
T Consensus 329 Hs~~~ 333 (357)
T cd00801 329 HVLGG 333 (357)
T ss_pred CCCCC
Confidence 97543
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=94.77 E-value=0.081 Score=54.36 Aligned_cols=118 Identities=17% Similarity=0.231 Sum_probs=80.3
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC----
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG---- 735 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~---- 735 (946)
++++.|+-.+.+|+|. +|.|+.+||.+. ++.+.+. ||.+.. ..|.+.+.++..|..+++.
T Consensus 132 ~~~~~l~~~tG~R~~E-----------l~~l~~~di~~~-~~~~~i~--~k~~~~--r~vpl~~~~~~~l~~~~~~~~~~ 195 (295)
T TIGR02224 132 RAILELLYSSGLRVSE-----------LVGLDLDDLDLD-SGLVRVR--GKGNKE--RIVPFGSYAKDALQAYLEARREK 195 (295)
T ss_pred HHHHHHHHHhcchHHH-----------HhCCCchhcccC-cceEEEe--cCCCce--eEEECCHHHHHHHHHHHHHhhhc
Confidence 3456666678999985 889999999998 4676665 676654 4567789999999988651
Q ss_pred ---CCCCCccCc-----cCChhHHHHHHHhhC------CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q 002260 736 ---KKQNDDLFD-----KLDTAKLNAHLKELM------PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANK 801 (946)
Q Consensus 736 ---K~Pgd~LFd-----~Ldss~LN~yLkelm------~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr 801 (946)
..+++.||. .++...++..|+.++ .++|+.+||--.||..+. .+ .+ ..
T Consensus 196 ~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~~t~~~~-----~g--~~-----------~~ 257 (295)
T TIGR02224 196 LLASEGQDALFLNRRGGRLTPRGVQYRLQQLVAKAGLPKHVHPHALRHSFATHLLE-----NG--AD-----------LR 257 (295)
T ss_pred cchhcCCCeeEEeCCCCCCCHHHHHHHHHHHHHHcCCCCCcChHHHHHHHHHHHHH-----cC--CC-----------HH
Confidence 223336875 466778888888875 246777777444444332 11 11 34
Q ss_pred HHHHHcCCCc
Q 002260 802 EVAIICNHQR 811 (946)
Q Consensus 802 eVAilCNHQR 811 (946)
.||.++||.-
T Consensus 258 ~i~~~lGH~~ 267 (295)
T TIGR02224 258 AVQELLGHAS 267 (295)
T ss_pred HHHHHhcCCC
Confidence 7888999963
No 18
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed
Probab=94.76 E-value=0.065 Score=55.12 Aligned_cols=111 Identities=18% Similarity=0.202 Sum_probs=77.1
Q ss_pred HHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCc
Q 002260 662 ATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDD 741 (946)
Q Consensus 662 AlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~ 741 (946)
+++|+-.+.||+|- +|.|+.+||.+. .+.|.+ +|.+.. ..|.+.+.+...|+... ++..
T Consensus 117 ~~~ll~~tGlR~~E-----------l~~L~~~dId~~-~~~i~i---~k~~~~--R~vpl~~~l~~~L~~~~----~~~~ 175 (245)
T PRK02436 117 IALLILELGLTPSE-----------IAGLKVADIDLD-FQVLTI---EKAGGK--RVLTLPEALLPFLEAIL----NQTY 175 (245)
T ss_pred HHHHHHHcCCCHHH-----------HhcCcHHHcCcc-CCEEEE---cCCCce--eEEECCHHHHHHHHHHh----CCCe
Confidence 45566689999986 899999999988 577776 355443 46778899999999885 4567
Q ss_pred cCc----cCChhHHHHHHHhhC-----CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002260 742 LFD----KLDTAKLNAHLKELM-----PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (946)
Q Consensus 742 LFd----~Ldss~LN~yLkelm-----~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQR 811 (946)
||. .++...++..++.++ +.+|..+||=-.||.++.. + .+ ..+|+.++||.-
T Consensus 176 lF~~~g~~~~~~~~~~~~~~~~~~~gi~~~t~H~lRHtfat~~~~~-----g--~~-----------~~~l~~~lGH~~ 236 (245)
T PRK02436 176 LFEHKGKPYSRQWFFNQLKSFVKSIGYPGLSAQKLREQFILKQKEA-----G--KS-----------IYELARLLGLKS 236 (245)
T ss_pred eecCCCCcccHHHHHHHHHHHHHHcCCCCCCcchhHHHHHHHHHHc-----C--CC-----------HHHHHHHhCCCC
Confidence 885 345545555555543 5689999985555554422 1 12 456999999953
No 19
>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=94.67 E-value=0.13 Score=51.82 Aligned_cols=119 Identities=17% Similarity=0.225 Sum_probs=81.4
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCC---
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK--- 736 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K--- 736 (946)
.+++.|+=.+++|+|. ++.|+.+||.+. ++.+.+. .+|.+..+ .|.+.+.+...|+.++...
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 3455555568899986 788999999988 5787775 36766544 5666788888888775433
Q ss_pred ---CCCCccC-------------ccCChhHHHHHHHhhC--C----CCccceecccchHHHHHHHHhcCCCCCCHHHHHH
Q 002260 737 ---KQNDDLF-------------DKLDTAKLNAHLKELM--P----GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKID 794 (946)
Q Consensus 737 ---~Pgd~LF-------------d~Ldss~LN~yLkelm--~----glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~ 794 (946)
.+++.|| ..++...+|.+++.++ . .+|..+||-..||.. .+.+. +
T Consensus 154 ~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~s~h~lRht~at~l-----~~~~~--~------ 220 (242)
T cd01193 154 GRERPWQWLFPSTRRSRDPVERRHHLSERTLQRALKKAVEQAGIDKRVTPHTLRHSFATHL-----LEAGY--D------ 220 (242)
T ss_pred ccCCCCceecccCCCCcccccccCCCCHHHHHHHHHHHHHHcCCCCCCCcCcchHHHHHHH-----HHcCC--C------
Confidence 4566777 3466788999999886 2 467788885545433 22211 1
Q ss_pred HHHHHHHHHHHHcCCCc
Q 002260 795 VYQRANKEVAIICNHQR 811 (946)
Q Consensus 795 ~yn~AnreVAilCNHQR 811 (946)
...|+.++||..
T Consensus 221 -----~~~i~~~lGH~~ 232 (242)
T cd01193 221 -----IRTIQELLGHSD 232 (242)
T ss_pred -----HHHHHHHhCCCC
Confidence 247888889975
No 20
>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=94.45 E-value=0.18 Score=49.06 Aligned_cols=120 Identities=11% Similarity=0.007 Sum_probs=80.1
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEee-CCCCeEEEEEEeeChhHHHHHHhhhcCCC
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL-GKDSIQYVNTVEVELPVYKAIGQFQTGKK 737 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFl-GKdgir~~~tV~VD~~V~knLk~f~k~K~ 737 (946)
..+++.|+=.+.+|+|- ++.|+.+||.+. ++.+.+... +|.+..+ .|.+.+.+...|+.++. ..
T Consensus 23 ~~~~~~l~~~tG~R~~E-----------l~~l~~~did~~-~~~~~i~~~~~K~~~~r--~ipl~~~~~~~l~~~~~-~~ 87 (177)
T cd01192 23 LKPAVLFALNTGLRRSE-----------ILGLEWSQVDLD-NRVAWVRPATSKGGRAI--RVPLNDEALQVLKRQKA-GA 87 (177)
T ss_pred HHHHHHHHHHhCccHHH-----------HhcCchhhcccc-CCEEEEeccCCCCCCee--EecCCHHHHHHHHHHhc-cC
Confidence 34555666678899986 889999999887 477777663 5666543 57778999999999964 33
Q ss_pred CCCccCccCC-------hhHHHHHHHhhC-CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCC
Q 002260 738 QNDDLFDKLD-------TAKLNAHLKELM-PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNH 809 (946)
Q Consensus 738 Pgd~LFd~Ld-------ss~LN~yLkelm-~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNH 809 (946)
.+..||.... ...++.+++..- +++|..+||-..||.++.. + .+ ...|+.++||
T Consensus 88 ~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~at~l~~~-----g--~~-----------~~~i~~~lGH 149 (177)
T cd01192 88 HKPWVFAGAGGDPRIDSKTAWRQALQRAGISDFRWHDLRHTWASWLVQS-----G--VP-----------LYVLQELLGH 149 (177)
T ss_pred CCCeEeecCCCCcccchHHHHHHHHHHcCCCCCcchhhhHHHHHHHHHc-----C--CC-----------HHHHHHHhCC
Confidence 4566777544 222344444432 5778888887777754322 1 11 3468888999
Q ss_pred Cc
Q 002260 810 QR 811 (946)
Q Consensus 810 QR 811 (946)
.-
T Consensus 150 ~~ 151 (177)
T cd01192 150 SS 151 (177)
T ss_pred CC
Confidence 85
No 21
>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=94.32 E-value=0.45 Score=46.94 Aligned_cols=121 Identities=18% Similarity=0.310 Sum_probs=79.5
Q ss_pred hHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC-
Q 002260 657 RQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG- 735 (946)
Q Consensus 657 RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~- 735 (946)
+.++ +++|+-.+.+|.|. +|.|+..||.+. .+.+.+. .+|.+.. ..|.+.+.+...|..++..
T Consensus 26 ~~~~-~~~l~~~tGlR~~E-----------l~~l~~~di~~~-~~~i~i~-~~K~~~~--r~vpl~~~~~~~l~~~~~~~ 89 (188)
T cd01188 26 RDYA-ILLLLARLGLRAGE-----------VAALRLDDIDWR-TGTIRVR-QGKGGRV--TRLPLPAEVGAALADYLRDG 89 (188)
T ss_pred hHHH-HHHHHHHHCCCHHH-----------HHhCcccccCCC-CCeEEEE-eCCCCcc--eEEeCCHHHHHHHHHHHHhc
Confidence 3444 45555568899986 889999999987 4666664 2676654 4677789999888877543
Q ss_pred --CCCCCccCcc--------CChhHHHHHHHhhC--CC-----CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 002260 736 --KKQNDDLFDK--------LDTAKLNAHLKELM--PG-----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQR 798 (946)
Q Consensus 736 --K~Pgd~LFd~--------Ldss~LN~yLkelm--~g-----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~ 798 (946)
..+++.||-. ++...+|.+++.++ -| +|..+||--.||. |...+. +
T Consensus 90 ~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~-----l~~~g~--~---------- 152 (188)
T cd01188 90 RPATDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLATR-----LLRAGA--P---------- 152 (188)
T ss_pred CCCCCCCceeeeccCCcCCcccHHHHHHHHHHHHHHcCCCcCCCCcHHHHHHHHHH-----HHHcCC--C----------
Confidence 2345677742 36788998888887 23 4566666444443 322211 1
Q ss_pred HHHHHHHHcCCCc
Q 002260 799 ANKEVAIICNHQR 811 (946)
Q Consensus 799 AnreVAilCNHQR 811 (946)
...|+.++||+-
T Consensus 153 -~~~i~~~lGH~~ 164 (188)
T cd01188 153 -LKEIGDVLGHRS 164 (188)
T ss_pred -HHHHHHHhCCCC
Confidence 357888899974
No 22
>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=94.31 E-value=0.22 Score=45.72 Aligned_cols=123 Identities=15% Similarity=0.137 Sum_probs=84.3
Q ss_pred HHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCC-
Q 002260 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK- 736 (946)
Q Consensus 658 qlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K- 736 (946)
..++++.|+=.+.+|.+. ++.|...||... +..+.|.- .|.+.. ..+.+++.++..|..++...
T Consensus 16 ~~~~~~~l~~~~G~R~~e-----------i~~l~~~~v~~~-~~~~~i~~-~K~~~~--~~~~i~~~~~~~l~~~~~~~~ 80 (162)
T cd01182 16 RDRALILLLLYTGLRVSE-----------LLALRWSDIDLD-KGTITVRR-TKTGKE--RTVPLSPELAELLREYLELRR 80 (162)
T ss_pred HHHHHHHHHHHhCCCHHH-----------HhhhehhcccCc-CCEEEEEe-cCCCCc--eEEecCHHHHHHHHHHHHHhc
Confidence 445566666669999985 788999999987 34544442 366643 44566787888888887542
Q ss_pred ---CCCCccCccC-------ChhHHHHHHHhhC---C---CCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 002260 737 ---KQNDDLFDKL-------DTAKLNAHLKELM---P---GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRAN 800 (946)
Q Consensus 737 ---~Pgd~LFd~L-------dss~LN~yLkelm---~---glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~An 800 (946)
.++..||... +...++.+++.+. . ++|...||-..++.++...+ + .
T Consensus 81 ~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lR~~~~~~~~~~g~-------~-----------~ 142 (162)
T cd01182 81 PAPKPDDYLFPSRRGGPKRLTRRAVRRLLKKAGKRAGIPERLTPHDLRHTFATRLLEAGV-------P-----------L 142 (162)
T ss_pred ccCCCCCeEEEcCCCCCcccchHHHHHHHHHHHHHcCCCcccCcchhHHHHHHHHHHCCC-------C-----------H
Confidence 5677888764 3566888888887 2 68888888777775444221 1 5
Q ss_pred HHHHHHcCCCccc
Q 002260 801 KEVAIICNHQRTV 813 (946)
Q Consensus 801 reVAilCNHQRaV 813 (946)
.+||.+.||+...
T Consensus 143 ~~~~~~~gH~~~~ 155 (162)
T cd01182 143 EVIQELLGHSSIS 155 (162)
T ss_pred HHHHHHhCCCCHH
Confidence 5788888998654
No 23
>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=94.22 E-value=0.29 Score=47.76 Aligned_cols=120 Identities=17% Similarity=0.179 Sum_probs=81.1
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEee--------CCCCeEEEEEEeeChhHHHHHHh
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL--------GKDSIQYVNTVEVELPVYKAIGQ 731 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFl--------GKdgir~~~tV~VD~~V~knLk~ 731 (946)
.+++.|+-.+.+|.|. +|.|+.+||.+. ++.|.+.-. +|.+ ...+|.+.+.+...|..
T Consensus 19 ~~~~~l~~~tglR~~E-----------i~~L~~~di~~~-~~~i~i~~~~~~~~~~~~K~~--~~r~v~l~~~~~~~l~~ 84 (186)
T cd01194 19 KFLFALLYETGLRIGE-----------ALGLRIEDIDLA-ENQIWLVPREDNANGARAKSG--RERRIPVSQYLIDLYVD 84 (186)
T ss_pred HHHHHHHHHcCCChhh-----------hhccccceeecC-CCEEEEeecCCCcCcccccCC--CCceEEcCHHHHHHHHH
Confidence 4556666688999986 899999999988 466776543 2444 24466677888887777
Q ss_pred hhc-----CCCCCCccCc---------cCChhHHHHHHHhhC----CCCccceecccchHHHHHHHHhcCCCCCCHHHHH
Q 002260 732 FQT-----GKKQNDDLFD---------KLDTAKLNAHLKELM----PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKI 793 (946)
Q Consensus 732 f~k-----~K~Pgd~LFd---------~Ldss~LN~yLkelm----~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~ 793 (946)
++. ...++..||- .++...++.+++.++ ..+|..+||-..+|..+. .+. .
T Consensus 85 ~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lR~t~~t~~~~-----~g~--~----- 152 (186)
T cd01194 85 YVTEIYYLEELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGIDFTPHMFRHTHATELIR-----AGW--S----- 152 (186)
T ss_pred HHHHHcccccCCCCEEEEcCCCCCCCcccCHHHHHHHHHHHHHHcCCCCCccccchHHHHHHHH-----cCC--C-----
Confidence 643 1445667774 345677888888877 357888888766664322 211 1
Q ss_pred HHHHHHHHHHHHHcCCCc
Q 002260 794 DVYQRANKEVAIICNHQR 811 (946)
Q Consensus 794 ~~yn~AnreVAilCNHQR 811 (946)
.+.|+.++||.-
T Consensus 153 ------~~~i~~~~gH~~ 164 (186)
T cd01194 153 ------IEVVADRLGHAH 164 (186)
T ss_pred ------HHHHHHHhCCCC
Confidence 247888999975
No 24
>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=93.97 E-value=0.3 Score=47.32 Aligned_cols=119 Identities=18% Similarity=0.307 Sum_probs=76.6
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEE-----------ee-CCCCeEEEEEEeeChhHHHH
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFD-----------FL-GKDSIQYVNTVEVELPVYKA 728 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~Fd-----------Fl-GKdgir~~~tV~VD~~V~kn 728 (946)
+++.|+=.+.+|.+. ++.|+..+|... ...+.+. |. .|.+ .....|.|.+.+...
T Consensus 25 ~~~~l~~~~G~R~~E-----------i~~l~~~dv~~~-~~~~~~~~~~~~~~~~~~~~~~k~~-~~~~~v~i~~~~~~~ 91 (191)
T cd01189 25 LLILLLAYTGLRIGE-----------ALALTWSDIDFE-NNTITINKTWDYKTGGYIFKPPKTK-SSIRTIPLDKKTIAI 91 (191)
T ss_pred HHHHHHHHhccHHHH-----------HhhceecccCCc-CCEEEEEEEEEEcCCceEecCCccc-CcceeEecCHHHHHH
Confidence 333444448899986 778888888776 3444332 11 1322 233567788988888
Q ss_pred HHhhhcC---------CCCCCccCccCC-----hhHHHHHHHhhC-----CCCccceecccchHHHHHHHHhcCCCCCCH
Q 002260 729 IGQFQTG---------KKQNDDLFDKLD-----TAKLNAHLKELM-----PGLTAKVFRTYNASITLDGMLNKGTGDGDV 789 (946)
Q Consensus 729 Lk~f~k~---------K~Pgd~LFd~Ld-----ss~LN~yLkelm-----~glTAKdFRTynASvta~~~L~~~~~~~s~ 789 (946)
|..++.. ..+++.||...+ ...++.+++.++ ..+|..+||-..++.++.. .. +
T Consensus 92 l~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~s~h~lRht~~t~l~~~-----g~--~- 163 (191)
T cd01189 92 LKEYKKEQKKYLLGEINNDDELVFTNKGGKISTPSTINKRLKRICKKAGIPKITFHGLRHTHASLLLEA-----GV--S- 163 (191)
T ss_pred HHHHHHHHHHHhhcccCCCCCeEEeCCCCCCCCchhHHHHHHHHHHHcCCCCcceeccHHHHHHHHHHc-----CC--C-
Confidence 8887653 346678888654 478888888886 3478888886666644332 11 1
Q ss_pred HHHHHHHHHHHHHHHHHcCCC
Q 002260 790 AVKIDVYQRANKEVAIICNHQ 810 (946)
Q Consensus 790 ~eK~~~yn~AnreVAilCNHQ 810 (946)
...++.++||.
T Consensus 164 ----------~~~i~~~lgH~ 174 (191)
T cd01189 164 ----------IKYVSERLGHA 174 (191)
T ss_pred ----------HHHHHHHcCCC
Confidence 34788888984
No 25
>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=93.69 E-value=0.76 Score=48.46 Aligned_cols=129 Identities=18% Similarity=0.144 Sum_probs=89.3
Q ss_pred HHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC--
Q 002260 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-- 735 (946)
Q Consensus 658 qlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-- 735 (946)
...+++.|+-.+.+|+|- +|.|+.+||.+. ++.|.|. -+|.+..+ .|.+.+.+...|..++..
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 345678888899999986 899999999988 4666663 37877653 577889999999876421
Q ss_pred ----CCCCCccCcc-----CChh---HHHHHHHhhCC--------CCccceecccchHHHHHHHHhcCCCCCCHHHHHHH
Q 002260 736 ----KKQNDDLFDK-----LDTA---KLNAHLKELMP--------GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDV 795 (946)
Q Consensus 736 ----K~Pgd~LFd~-----Ldss---~LN~yLkelm~--------glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~ 795 (946)
..+++.||.. ++.. .+..+++.+.. .+|..+||-.-||.++...+. .+ .++.
T Consensus 192 ~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRHt~at~~l~~~~~-~g--~~~~----- 263 (299)
T cd01187 192 RLLPAPDSSAFFVSSRGGRLSYGGHRVFYALSREIGLRGWAQRGRGPRLHDLRHRFAVTRLTRWYR-AG--ADVE----- 263 (299)
T ss_pred hhccCCCCcceeeCCCCCCCCcccchHHHHHHHHhCcccCCCCCCCCCcccccHHHHHHHHHHHHH-cC--CChh-----
Confidence 2356778864 3345 78888888862 368888998777766543332 11 1211
Q ss_pred HHHHHHHHHHHcCCCc
Q 002260 796 YQRANKEVAIICNHQR 811 (946)
Q Consensus 796 yn~AnreVAilCNHQR 811 (946)
.....|+.++||..
T Consensus 264 --~~~~~v~~~lGH~~ 277 (299)
T cd01187 264 --RKLPVLATYLGHAN 277 (299)
T ss_pred --hhhHHHHHHcCCCC
Confidence 11368899999974
No 26
>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=93.45 E-value=0.25 Score=49.05 Aligned_cols=117 Identities=16% Similarity=0.145 Sum_probs=79.9
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCC
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQND 740 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd 740 (946)
+++.|+-.+.+|.|. ++.|+.+||... +.+.+. .+|-+. ...|.+.+.++..|+.++....+++
T Consensus 28 ~~~~l~~~tGlR~~E-----------l~~l~~~di~~~--~~i~i~-~~K~~~--~r~vpl~~~l~~~l~~~~~~~~~~~ 91 (180)
T cd01186 28 LLFLIGINTGLRISD-----------ILALKVKDVRGD--ERISIK-EKKTGK--RKRIYLNPILKEELLYYIKDLEENE 91 (180)
T ss_pred HHHHHHHHhhhHHHH-----------HHhcCHHHhCCC--CceEEE-EecCCc--eEEEEECHHHHHHHHHHHHhCCCcC
Confidence 456777788999986 788899988765 234443 256665 4567778999999999876555677
Q ss_pred ccCcc-------CChhHHHHHHHhhC--CC---CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcC
Q 002260 741 DLFDK-------LDTAKLNAHLKELM--PG---LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICN 808 (946)
Q Consensus 741 ~LFd~-------Ldss~LN~yLkelm--~g---lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCN 808 (946)
.||.. ++...++.+++.++ -| +|..+||--.|| .|...+. ....|+.++|
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 88864 56778999998877 33 566666654444 3333221 2357788889
Q ss_pred CCc
Q 002260 809 HQR 811 (946)
Q Consensus 809 HQR 811 (946)
|..
T Consensus 154 H~~ 156 (180)
T cd01186 154 HSS 156 (180)
T ss_pred CCC
Confidence 953
No 27
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=93.07 E-value=0.41 Score=52.22 Aligned_cols=117 Identities=19% Similarity=0.184 Sum_probs=82.9
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCC---
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK--- 736 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K--- 736 (946)
.+++.|+-.+.||+|- ||.|+.+||.+. ++.|.+ .+|.+..+ .|.+.+.+...|..++...
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 3456677789999986 899999999987 476665 47877655 5666788888888775321
Q ss_pred ----CCCCccCc--------cCChhHHHHHHHhhC--CC--CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 002260 737 ----KQNDDLFD--------KLDTAKLNAHLKELM--PG--LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRAN 800 (946)
Q Consensus 737 ----~Pgd~LFd--------~Ldss~LN~yLkelm--~g--lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~An 800 (946)
.+.+.||- .++...++..++.+. .| +|..+||-..||.++.. +. + .
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 23455773 466778999998885 23 78889997777755432 11 1 2
Q ss_pred HHHHHHcCCC
Q 002260 801 KEVAIICNHQ 810 (946)
Q Consensus 801 reVAilCNHQ 810 (946)
..|+.++||.
T Consensus 324 ~~i~~~lGH~ 333 (357)
T PRK05084 324 VLVADQLGHT 333 (357)
T ss_pred HHHHHHcCCC
Confidence 5899999996
No 28
>PRK09692 integrase; Provisional
Probab=92.84 E-value=0.45 Score=53.53 Aligned_cols=139 Identities=11% Similarity=0.061 Sum_probs=89.8
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEe-eCCCCeEEEEEEeeChhHHHHHHhhhcCCCCC
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQTGKKQN 739 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k~K~Pg 739 (946)
.+++|+=.+.+|+|. +|.|+.++|.+. ...+++.- ..|.+. ...|.+.+.+...|+.+.....++
T Consensus 237 ~~~~lll~TG~R~gE-----------l~~l~W~diD~~-~~~~~I~~~~~K~~~--~r~VpL~~~~~~~L~~~~~~~~~~ 302 (413)
T PRK09692 237 CLFMWQLLTITRPAE-----------AAEARWEEIDIE-AQEWKIPAARMKMNR--DHTVPLSDEALAILEMMKPLSGNR 302 (413)
T ss_pred HHHHHHHHHCcchHH-----------HhcCchHHhccC-CCeEEechhhccCCC--CeeccChHHHHHHHHHHHHhcCCC
Confidence 344555579999997 899999999998 47776643 234332 246888899999998885433455
Q ss_pred CccCcc-------CChhHHHHHHHhhC-CC-CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002260 740 DDLFDK-------LDTAKLNAHLKELM-PG-LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (946)
Q Consensus 740 d~LFd~-------Ldss~LN~yLkelm-~g-lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQ 810 (946)
+.||.. ++...+|..|+.+- ++ +|..+||-..||.++. .+. + ...|+.++||.
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 678853 45677888888764 44 5789999777665432 111 1 24788888996
Q ss_pred -cccccchHHHHHHHHHHHHHH
Q 002260 811 -RTVSKTHSAQMSRLTEKIEDL 831 (946)
Q Consensus 811 -RaV~K~~~~~m~kl~~ki~~l 831 (946)
..+...+=...+-+.++.+.+
T Consensus 365 ~~~~~~~~Y~r~~y~~err~~~ 386 (413)
T PRK09692 365 DKNEVRRAYNRSDYLEQRRPMM 386 (413)
T ss_pred CCCchHHHHHHHHHHHHHHHHH
Confidence 344333223444455555444
No 29
>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=92.67 E-value=0.49 Score=49.55 Aligned_cols=123 Identities=15% Similarity=0.084 Sum_probs=82.1
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEee-CCCCe---EEEEEEee-ChhHHHHHHhhhc
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL-GKDSI---QYVNTVEV-ELPVYKAIGQFQT 734 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFl-GKdgi---r~~~tV~V-D~~V~knLk~f~k 734 (946)
.+++.|+-.+.+|+|- ++.|+.+||.+..++.+.+... +|.+. .....+.. +..+...|..++.
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 4567777889999986 8899999999983266666554 66633 44444431 1246666666543
Q ss_pred C-CCCCCccCcc-----------CChhHHHHHHHhhC--C-----CCccceecccchHHHHHHHHhcCCCCCCHHHHHHH
Q 002260 735 G-KKQNDDLFDK-----------LDTAKLNAHLKELM--P-----GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDV 795 (946)
Q Consensus 735 ~-K~Pgd~LFd~-----------Ldss~LN~yLkelm--~-----glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~ 795 (946)
. ..+++.||.. +++..+|..|+.++ - .+|..+||-..||.++.. +. +
T Consensus 188 ~~~~~~~~lF~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~gi~~~~~~~H~lRht~at~l~~~-----g~--~------- 253 (287)
T cd00799 188 AARIPKGPLFRRIDRWGVLGPGALSDNSLNRILKRLAEAAGLRSGSWSGHSLRRGFATEAARA-----GY--S------- 253 (287)
T ss_pred HhCCCCCceeEEecCCCCcCCCCCCHHHHHHHHHHHHHHcCCCcccccccccchhHHHHHHHc-----CC--C-------
Confidence 2 4567788853 56788999999986 2 368888997777755432 11 1
Q ss_pred HHHHHHHHHHHcCCCc
Q 002260 796 YQRANKEVAIICNHQR 811 (946)
Q Consensus 796 yn~AnreVAilCNHQR 811 (946)
...|+.++||..
T Consensus 254 ----~~~i~~~lGH~~ 265 (287)
T cd00799 254 ----LLEIMRQGRWRS 265 (287)
T ss_pred ----HHHHHHHcCCCC
Confidence 356888999975
No 30
>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=92.57 E-value=0.24 Score=48.66 Aligned_cols=116 Identities=15% Similarity=0.212 Sum_probs=79.5
Q ss_pred HHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC-----C
Q 002260 662 ATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-----K 736 (946)
Q Consensus 662 AlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-----K 736 (946)
++.|+-.+.+|+|. ++.|+.++|.+. .+.+.+.- +|.+.. ..+.+.+.+...|+.++.. .
T Consensus 29 ~~~l~~~tGlR~~E-----------i~~L~~~did~~-~~~l~v~~-~K~~~~--~~~pi~~~~~~~l~~~~~~~~~~~~ 93 (180)
T cd01197 29 LMLLMFRHGLRVSE-----------ACGLKLSDIDLE-SRQIYIRR-LKGGFS--TTHPLRDDELEALKNWLEIRAWKGL 93 (180)
T ss_pred HHHHHHHhCCcHHH-----------HHcCcHHHhCCC-CCeEEEEe-cCCCcc--ceeECCHHHHHHHHHHHHHhccCCC
Confidence 34566677899986 788999999987 47777663 355443 3566778888888887643 2
Q ss_pred CCCCccC-----ccCChhHHHHHHHhhC--CC----CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Q 002260 737 KQNDDLF-----DKLDTAKLNAHLKELM--PG----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAI 805 (946)
Q Consensus 737 ~Pgd~LF-----d~Ldss~LN~yLkelm--~g----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAi 805 (946)
.+++.|| ..++...+++.++.+. .| +|..+||-..||.++. .+. + ...|+.
T Consensus 94 ~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~H~lRht~~t~l~~-----~g~--~-----------~~~i~~ 155 (180)
T cd01197 94 PDSDWIFLSRRGGPLSRQQVYKLIRRLGAQAGLSIKVHPHMLRHACGYALAN-----QGA--D-----------TRLIQD 155 (180)
T ss_pred CCCCeEEeCCCCCcCCHHHHHHHHHHHHHHcCCCCCCCcchhhhHHHHHHHH-----cCC--C-----------HHHHHH
Confidence 3456777 4577889999999986 34 5677888766664332 211 1 346888
Q ss_pred HcCCC
Q 002260 806 ICNHQ 810 (946)
Q Consensus 806 lCNHQ 810 (946)
+.||+
T Consensus 156 ~lGH~ 160 (180)
T cd01197 156 YLGHR 160 (180)
T ss_pred HhCCC
Confidence 89997
No 31
>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=92.42 E-value=0.29 Score=51.49 Aligned_cols=111 Identities=16% Similarity=0.152 Sum_probs=77.4
Q ss_pred hhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEe-eCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccCccC
Q 002260 668 KLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKL 746 (946)
Q Consensus 668 klALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LFd~L 746 (946)
.+.+|+|- +|.|+.+||.+...+...+.+ .+|.+.. ..|.+.+.+...|..+... +++.||-.+
T Consensus 160 ~tGlR~~E-----------i~~L~~~did~~~~g~~~i~~~~~K~~~~--r~ipl~~~~~~~l~~~~~~--~~~~lf~~~ 224 (299)
T cd01185 160 FTGLRYSD-----------IKKLTWEEIVEDSDGEKWIRKRRQKTKVE--VYIPLLDEALQILGKYPDE--KEGLVFPLL 224 (299)
T ss_pred HHcccHHH-----------HHhcCHHHceECCCCCEEEEEeecccCCc--ccccCcHHHHHHHHHhcCC--CCCcCcCCC
Confidence 47899986 789999999987422233333 4566644 4566678899999988543 677899999
Q ss_pred ChhHHHHHHHhhC--C----CCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002260 747 DTAKLNAHLKELM--P----GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (946)
Q Consensus 747 dss~LN~yLkelm--~----glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQR 811 (946)
....++.+++.+. . ++|..+||-..||.++. .+. + ...|+.++||.-
T Consensus 225 ~~~~~~~~~~~~~~~~gi~~~~~~H~lRht~at~l~~-----~g~--~-----------~~~i~~~lGH~~ 277 (299)
T cd01185 225 KNSNMNKPLKEWAKLAGIKKHITFHCARHTFATLQLL-----SGG--P-----------IETVSKMLGHTN 277 (299)
T ss_pred CHHHHHHHHHHHHHHcCCCCCCccccchHHHHHHHHH-----cCC--C-----------HHHHHHHhCCCc
Confidence 9888999998886 2 46778888766665442 211 1 146888899974
No 32
>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=92.20 E-value=1 Score=46.15 Aligned_cols=125 Identities=16% Similarity=0.158 Sum_probs=79.7
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCC-
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKK- 737 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~- 737 (946)
..++++|+=.+.+|.|. ++.|+.+||.+.. + ..+...||.+.. .+|.+.+.+...|..+.....
T Consensus 97 ~~~~~~l~~~tGlR~~E-----------i~~L~~~di~~~~-~-~~~~~~~k~~~~--r~vpl~~~~~~~l~~~~~~~~~ 161 (260)
T cd01190 97 DRAMLLFLYNTGARVSE-----------ATGLKVDDLQLDP-P-AQVRLIGKGRKE--RTVPLWRSTAAALRAWLRERGL 161 (260)
T ss_pred HHHHHHHHHHhCccHHH-----------HHcCCHHHhccCC-C-cEEEEecCCCcc--eeEECCHHHHHHHHHHHHhcCC
Confidence 34577777888999986 7789999999874 3 233345776544 467778999999988865443
Q ss_pred --CCCccCcc-----CChhHHHHHHHhhC--CC-----CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Q 002260 738 --QNDDLFDK-----LDTAKLNAHLKELM--PG-----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEV 803 (946)
Q Consensus 738 --Pgd~LFd~-----Ldss~LN~yLkelm--~g-----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreV 803 (946)
+.+.||.. ++...++..++.++ .| +..+.|.++..=.|++..|.+.+. + ...|
T Consensus 162 ~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~~g~--~-----------~~~i 228 (260)
T cd01190 162 HAEDEPLFVNRRGEPMTRFGVTYLLRKHAAKAAATAPTLATKRISPHVLRHTTAMHLLQSGV--D-----------IVVI 228 (260)
T ss_pred CCCCCeeeecCCCCcCcHHHHHHHHHHHHHHhcccccccccCCCCchHHHHHHHHHHHHcCC--C-----------HHHH
Confidence 66778864 55677888887765 11 122334333333455555543321 2 2357
Q ss_pred HHHcCCCc
Q 002260 804 AIICNHQR 811 (946)
Q Consensus 804 AilCNHQR 811 (946)
+.+.||.-
T Consensus 229 ~~~lGH~~ 236 (260)
T cd01190 229 ALWLGHAS 236 (260)
T ss_pred HHHcCCCc
Confidence 77889973
No 33
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=92.13 E-value=0.98 Score=46.95 Aligned_cols=118 Identities=19% Similarity=0.224 Sum_probs=79.5
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC----
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG---- 735 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~---- 735 (946)
.++++|+=.+++|.|. +|.|+.++|.+. ++.+.+. +|.+..+ .|.+.+.+...|..++..
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 4556666678999986 889999999988 5777665 7877654 566678888888887522
Q ss_pred ---CCCCCccCcc-----CChhHHHHHHHhhC-------CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Q 002260 736 ---KKQNDDLFDK-----LDTAKLNAHLKELM-------PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRAN 800 (946)
Q Consensus 736 ---K~Pgd~LFd~-----Ldss~LN~yLkelm-------~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~An 800 (946)
..+.+.||-. ++...++..|+.+. +++|..+||--.||.++ ..+. + .
T Consensus 201 ~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~-----~~g~--~-----------~ 262 (299)
T PRK00283 201 LLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHVLRHAFATHLL-----NHGA--D-----------L 262 (299)
T ss_pred cCCCCCCCceeecCCCCcCCHHHHHHHHHHHHHHhCCCccCCCchHHHHHHHHHHH-----HcCC--C-----------H
Confidence 2344667753 45667888888764 24566667654444433 2211 1 3
Q ss_pred HHHHHHcCCCc
Q 002260 801 KEVAIICNHQR 811 (946)
Q Consensus 801 reVAilCNHQR 811 (946)
.+|+.++||..
T Consensus 263 ~~i~~~lGH~~ 273 (299)
T PRK00283 263 RVVQELLGHSD 273 (299)
T ss_pred HHHHHHhCCCC
Confidence 58889999964
No 34
>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=92.01 E-value=0.95 Score=46.39 Aligned_cols=119 Identities=19% Similarity=0.234 Sum_probs=79.0
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCC--
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK-- 736 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K-- 736 (946)
.++++.|+=.+++|+|. ++.|+..+|.+. .+.+. ..+|.+..+ .|.+.+.+...|..++...
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 45556666678999986 788999999887 45555 678887654 5666789898888764321
Q ss_pred -------CCCCccCc-----cCChhHHHHHHHhhC--CC----CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHH
Q 002260 737 -------KQNDDLFD-----KLDTAKLNAHLKELM--PG----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQR 798 (946)
Q Consensus 737 -------~Pgd~LFd-----~Ldss~LN~yLkelm--~g----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~ 798 (946)
.+++.||- .++...++.+++.+. .| +|..+||- ++...|...+. +
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 15667884 456677888888875 23 46666763 44444433221 2
Q ss_pred HHHHHHHHcCCCc
Q 002260 799 ANKEVAIICNHQR 811 (946)
Q Consensus 799 AnreVAilCNHQR 811 (946)
...++.+.||.-
T Consensus 254 -~~~i~~~~GH~~ 265 (291)
T TIGR02225 254 -LRVVQELLGHAD 265 (291)
T ss_pred -HHHHHHHhCCCC
Confidence 137888889964
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=91.98 E-value=0.28 Score=49.22 Aligned_cols=117 Identities=16% Similarity=0.180 Sum_probs=80.1
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCC
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQ 738 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~P 738 (946)
..++++|+=.+.+|.|. +|.|+.++|.+. .+.|.+. .+|.+.. ..|.+.+.+...|+.+... .+
T Consensus 66 ~~~~~~l~~~tGlR~~E-----------~~~l~~~did~~-~~~i~i~-~~K~~~~--r~ipl~~~~~~~l~~~~~~-~~ 129 (206)
T cd00796 66 LPVIILLALETAMRRGE-----------ILSLRWEQVDLK-KRVAHLP-DTKNGTS--RDVPLSKRAVALLQMLPKV-PD 129 (206)
T ss_pred hHHHHHHHHHhcccHHH-----------HHcCcHHHcCcc-cCEEEEe-cCcCCCc--ceecCCHHHHHHHHHhhhc-CC
Confidence 45567777788999985 889999999887 4676664 2555543 3577788999999988543 46
Q ss_pred CCccCccCChhHHHHHHHhhC-----CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002260 739 NDDLFDKLDTAKLNAHLKELM-----PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (946)
Q Consensus 739 gd~LFd~Ldss~LN~yLkelm-----~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQ 810 (946)
++.||. ++...++.+++.++ +++|..+||-..||.++.. +. -...|+.+.||.
T Consensus 130 ~~~lf~-~~~~~~~~~~~~~~~~~g~~~~~~H~lRht~~t~l~~~-----g~-------------~~~~i~~~lGH~ 187 (206)
T cd00796 130 DGPVFP-ITSDSVDAAFRRAKERAGLEDLHFHDLRHEATSRLFEK-----GL-------------SIMEVASISGHR 187 (206)
T ss_pred CCceec-CCCccHHHHHHHHHHHcCCCCCchHhhHhHHHHHHHHc-----CC-------------CHHHHHHHhCCC
Confidence 677885 34556777777776 3567777776666643321 11 134778888986
No 36
>PRK09870 tyrosine recombinase; Provisional
Probab=91.97 E-value=0.41 Score=48.65 Aligned_cols=117 Identities=12% Similarity=0.106 Sum_probs=82.0
Q ss_pred HHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC-----C
Q 002260 662 ATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG-----K 736 (946)
Q Consensus 662 AlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~-----K 736 (946)
++.|+-.+.+|+|. ++.|+.++|.+. .+.|.+. ..|.+.. ..|.+.+.+...|..+... .
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 44555668999987 899999999987 4777765 3344433 3567778888888777532 2
Q ss_pred CCCCccCc-----cCChhHHHHHHHhhC-----C-CCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Q 002260 737 KQNDDLFD-----KLDTAKLNAHLKELM-----P-GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAI 805 (946)
Q Consensus 737 ~Pgd~LFd-----~Ldss~LN~yLkelm-----~-glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAi 805 (946)
.+++.||- .++...+|..++.+. + .+|..+||-..||.++..- .+ ...|+.
T Consensus 102 ~~~~~lf~~~~g~~~s~~~~~~~~k~~~~~~gi~~~~t~H~lRht~at~l~~~G-------~~-----------~~~i~~ 163 (200)
T PRK09870 102 AESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMG-------ID-----------TRLIQD 163 (200)
T ss_pred CCCCceeeCCCCCcCCHHHHHHHHHHHHHHcCCCCCCCCccccchHHHHHHHcC-------CC-----------HHHHHH
Confidence 34567783 577889999998875 2 5788999998888755421 11 347778
Q ss_pred HcCCCc
Q 002260 806 ICNHQR 811 (946)
Q Consensus 806 lCNHQR 811 (946)
++||.-
T Consensus 164 ~LGH~s 169 (200)
T PRK09870 164 YLGHRN 169 (200)
T ss_pred HHCCCC
Confidence 888854
No 37
>PHA03397 vlf-1 very late expression factor 1; Provisional
Probab=91.79 E-value=0.5 Score=54.03 Aligned_cols=163 Identities=19% Similarity=0.140 Sum_probs=98.5
Q ss_pred eeccCCchhhccccHHHHHHHHHHHHHHHHHHHHHHHhhc--CCCCC----chHHHHHHHHHHhhccccCCcccccCCCc
Q 002260 611 VFLAASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFV--SRDGT----RRQIAVATYLIDKLALRAGNEKDDDEADT 684 (946)
Q Consensus 611 v~L~ahs~wk~~rD~~Kferar~L~~~Lp~IR~~y~kDLk--sk~~~----~RqlAvAlyLIDklALRvGnEKy~~endT 684 (946)
|+|...-..+..+...| -..|.+.|.+|...+.+... ..... .---++++.||-.+.||+|.
T Consensus 147 v~lp~dk~~k~~k~~~k---~i~l~~~i~~ll~~i~~~~~~~~~~~~~~~~~~Rd~aif~lLl~TGLRISE--------- 214 (363)
T PHA03397 147 VMLPRDKELKNIRAKEK---NIVLKDIIDPVLNYIEKKIKYLNSNYVHNRGLIRGAIVFCIILGTGLRITE--------- 214 (363)
T ss_pred ccCCccHHHHHHHhhhc---chhHHHHHHHHHHHHHHHhhhccchhcccchhHHHHHHHHHHHHHHHHHHH---------
Confidence 66665555554444433 33466888888888877665 33222 12335667788889999986
Q ss_pred eeeccCCCCceEE--cCCCeEEEE-eeCCCCeEEEEEEeeChh----HHHHHHhhhcCCCCCCccCccCCh----hHHHH
Q 002260 685 VGCCTLKVGNVEC--IPPNKLKFD-FLGKDSIQYVNTVEVELP----VYKAIGQFQTGKKQNDDLFDKLDT----AKLNA 753 (946)
Q Consensus 685 vG~cTLR~eHVkl--~~~~~V~Fd-FlGKdgir~~~tV~VD~~----V~knLk~f~k~K~Pgd~LFd~Lds----s~LN~ 753 (946)
+|.|+.+||.+ . .+.|.+. ..||.+..+.+-+. .. +-..|..+. ..| ..+|-...+ ..++.
T Consensus 215 --l~~Lk~eDId~~~~-~g~I~I~gi~tKg~K~R~VpLs--~~~~~~L~~~L~~y~--~~~-~~~~is~~~~~~~~~~kk 286 (363)
T PHA03397 215 --ARQITLDDLNKLIK-KGEHKVNNINLKRKKSRFNYLN--CIKKKPLELAREIYQ--KHP-TLLKISKNSSTPFKDFKR 286 (363)
T ss_pred --HHCCCHHHcchhhc-CCEEEEecccCCCCceeEEEeC--hHHHHHHHHHHHHHh--cCc-hhcccCCCchHHHHHHHH
Confidence 89999999995 5 4788887 67888876665553 33 333344332 222 222322222 35666
Q ss_pred HHHhhC-CC--CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002260 754 HLKELM-PG--LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (946)
Q Consensus 754 yLkelm-~g--lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQR 811 (946)
+++.+. ++ +|...||=..||.++.. +.+ ...|+.+.||.-
T Consensus 287 i~kkAGI~~~~itpH~LRHTFAt~Ll~~-------Gvd-----------L~~IqklLGHsS 329 (363)
T PHA03397 287 LLEEAGVEMDRPRSNMIRHYLASNMYNS-------GVP-----------LQKVSKLMNHES 329 (363)
T ss_pred HHHHcCCCCCCCCCcccHHHHHHHHHHC-------CCC-----------HHHHHHHcCCCC
Confidence 666665 33 78888885555544322 122 348889999964
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=91.75 E-value=0.41 Score=47.68 Aligned_cols=121 Identities=17% Similarity=0.170 Sum_probs=78.3
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcC-CCeEEEEee-CCCCeEEEEEEeeChhHHHHHHhhhcCC
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIP-PNKLKFDFL-GKDSIQYVNTVEVELPVYKAIGQFQTGK 736 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~-~~~V~FdFl-GKdgir~~~tV~VD~~V~knLk~f~k~K 736 (946)
..+++.|+-.+.||+|- ++.|+.++|.+.. +....+.+. +|.+.. ..|.+.+.+...|+.++...
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 44556777788999986 8999999998763 122334444 777654 46778899999998876421
Q ss_pred --------CCCCccCcc---------CChhHHHHHHHhhC-------------------CCCccceecccchHHHHHHHH
Q 002260 737 --------KQNDDLFDK---------LDTAKLNAHLKELM-------------------PGLTAKVFRTYNASITLDGML 780 (946)
Q Consensus 737 --------~Pgd~LFd~---------Ldss~LN~yLkelm-------------------~glTAKdFRTynASvta~~~L 780 (946)
.+++.||.. ++...++..++.++ ..+|..+||--.||.++.
T Consensus 95 ~~~~~~~~~~~~~lF~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~--- 171 (196)
T cd01183 95 GLPPEPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAAADRLQADGFEEDAAQLRAASTHWLRHTHASHDLA--- 171 (196)
T ss_pred CCCCCCCCCCCCceeeccccccCCCCCCHHHHHHHHHHHHHHHHHHHHhccChhHHHhhcccchHHHHHHHHHHHHH---
Confidence 134567754 44667777766542 356777787666555442
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002260 781 NKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (946)
Q Consensus 781 ~~~~~~~s~~eK~~~yn~AnreVAilCNHQ 810 (946)
.+. + ...|+.++||.
T Consensus 172 --~G~--~-----------~~~i~~~lGH~ 186 (196)
T cd01183 172 --AGV--P-----------LEHVQDNLGHA 186 (196)
T ss_pred --cCC--C-----------HHHHHHHhCCC
Confidence 111 1 34688888985
No 39
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=90.28 E-value=1 Score=46.28 Aligned_cols=118 Identities=21% Similarity=0.267 Sum_probs=78.4
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC----
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG---- 735 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~---- 735 (946)
.+++.|+-.+.+|+|. +++|+.+||.+. ++.+.+. +|.+.. ..|.+.+.+...|..++..
T Consensus 139 ~~~~~l~~~tG~R~~E-----------i~~L~~~~i~~~-~~~~~i~--~k~~~~--r~vpl~~~~~~~l~~~~~~~~~~ 202 (297)
T PRK00236 139 RAILELLYGSGLRLSE-----------LVGLDIDDLDLA-SGTLRVL--GKGNKE--RTVPLGRAAREALEAYLALRPLF 202 (297)
T ss_pred HHHHHHHHHccchHHH-----------HHhccHHHhccC-CceEEEE--ecCCce--EEEECcHHHHHHHHHHHHHccCc
Confidence 3455566678999986 889999999987 4666664 666654 4566678888888877543
Q ss_pred CCCCCccCcc-----CChhHHHHHHHhhC-----C-CCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHH
Q 002260 736 KKQNDDLFDK-----LDTAKLNAHLKELM-----P-GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVA 804 (946)
Q Consensus 736 K~Pgd~LFd~-----Ldss~LN~yLkelm-----~-glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVA 804 (946)
..+++.||-. ++...+++.++.++ . ++|..+||=..|| .|...+. + ...++
T Consensus 203 ~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~H~lRht~~t-----~l~~~g~--~-----------~~~i~ 264 (297)
T PRK00236 203 LPDDDALFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFAT-----HLLESGG--D-----------LRAVQ 264 (297)
T ss_pred CccCCceeecCCCCCCChhHHHHHHHHHHHHcCCCCCcCcHHHHHHHHH-----HHHHcCC--C-----------HHHHH
Confidence 2367788853 56677777777775 2 5677777733333 3322211 2 23688
Q ss_pred HHcCCCc
Q 002260 805 IICNHQR 811 (946)
Q Consensus 805 ilCNHQR 811 (946)
.++||.-
T Consensus 265 ~~lGH~~ 271 (297)
T PRK00236 265 ELLGHAS 271 (297)
T ss_pred HHhCCCc
Confidence 8999963
No 40
>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=90.05 E-value=1.9 Score=43.81 Aligned_cols=117 Identities=20% Similarity=0.254 Sum_probs=75.1
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCC----
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK---- 736 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K---- 736 (946)
+++.|+-.+.+|.|. +|.|+..||.+. ++.+.+. +|.+..+ .|.+.+.+...|+.++...
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 344455568999975 788999999987 4666655 8887654 4566788888888875421
Q ss_pred ---CCCCccCc-----cCChhHHHHHHHhhC--C----CCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Q 002260 737 ---KQNDDLFD-----KLDTAKLNAHLKELM--P----GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKE 802 (946)
Q Consensus 737 ---~Pgd~LFd-----~Ldss~LN~yLkelm--~----glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anre 802 (946)
..++.||- .++...++..++.++ . ++|..+||-..| ..|...+. +. ..
T Consensus 195 ~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~h~lR~t~a-----t~l~~~g~--~~-----------~~ 256 (284)
T cd00798 195 LKVGDSDALFLNQRGKRLSRRGVWKILKEYARRAGIEKKISPHTLRHSFA-----THLLENGA--DL-----------RA 256 (284)
T ss_pred ccCCCCCceeecCCCCCCCHHHHHHHHHHHHHHhCCCcCCChHHHHHHHH-----HHHHHcCC--CH-----------HH
Confidence 23455663 456677888777765 2 467777774444 34433222 21 35
Q ss_pred HHHHcCCCc
Q 002260 803 VAIICNHQR 811 (946)
Q Consensus 803 VAilCNHQR 811 (946)
++.++||..
T Consensus 257 i~~~~GH~~ 265 (284)
T cd00798 257 VQELLGHAS 265 (284)
T ss_pred HHHHhCCCc
Confidence 777788864
No 41
>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=90.01 E-value=2.4 Score=41.81 Aligned_cols=124 Identities=16% Similarity=0.164 Sum_probs=74.3
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEee----C----------CCCeEEEEEEeeChh
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFL----G----------KDSIQYVNTVEVELP 724 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFl----G----------Kdgir~~~tV~VD~~ 724 (946)
..+++.|+-.+.+|+|- ++.|+.+||.+. ...|.+.-. + ........+|.+.+.
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 44566677789999985 888999999887 355555421 0 000011347888899
Q ss_pred HHHHHHhhhcC---------CCCCCccCccCC------hhHHHHHHHhhC-----C---CCccceecccchHHHHHHHHh
Q 002260 725 VYKAIGQFQTG---------KKQNDDLFDKLD------TAKLNAHLKELM-----P---GLTAKVFRTYNASITLDGMLN 781 (946)
Q Consensus 725 V~knLk~f~k~---------K~Pgd~LFd~Ld------ss~LN~yLkelm-----~---glTAKdFRTynASvta~~~L~ 781 (946)
+...|+.++.. ..+.+.||.... ...++..++.++ + .+|...||-.-||. |.
T Consensus 91 ~~~~l~~~~~~~~~~~~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~~t~-----~~ 165 (205)
T cd01199 91 AVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKGNPLDLGPINSKILSKFLKDLGSQSKKHVTTHIFRHTHISF-----LA 165 (205)
T ss_pred HHHHHHHHHHHHHhhhhcccCCCCceEEecCCCCEeccchHHHHHHHHHHHHcCCCcCCCcceecchHHHHHH-----HH
Confidence 99999888653 224566776433 233555555443 1 55666666444443 32
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHcCCCcc
Q 002260 782 KGTGDGDVAVKIDVYQRANKEVAIICNHQRT 812 (946)
Q Consensus 782 ~~~~~~s~~eK~~~yn~AnreVAilCNHQRa 812 (946)
..+. ....|+.+.||.-.
T Consensus 166 ~~g~-------------~~~~i~~~lGH~~~ 183 (205)
T cd01199 166 EEGV-------------PLKAIMDRVGHSDG 183 (205)
T ss_pred HcCC-------------CHHHHHHHhCCCch
Confidence 2211 13578888999653
No 42
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=89.84 E-value=0.71 Score=50.86 Aligned_cols=118 Identities=18% Similarity=0.262 Sum_probs=80.3
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC-----
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG----- 735 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~----- 735 (946)
+++.|+-.+.||+|. +|.|+..+|.+. ++.|.+. .||.+..+ .|.+.+.+...|+.++..
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 345566668899986 899999999987 4777765 47776554 466678888877776432
Q ss_pred --CCCCCccCc-----cCChhHHHHHHHhhC--CC----CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Q 002260 736 --KKQNDDLFD-----KLDTAKLNAHLKELM--PG----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKE 802 (946)
Q Consensus 736 --K~Pgd~LFd-----~Ldss~LN~yLkelm--~g----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anre 802 (946)
..+++.||- .++...|+..++.++ .| +|..+||-..||.++. .+. + ...
T Consensus 226 ~~~~~~~~lF~~~~g~~i~~~~i~~~~~~~~~~agi~~~~t~H~lRHt~at~l~~-----~G~--~-----------~~~ 287 (358)
T PRK01287 226 AVRPDSGALFVAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLE-----NGA--D-----------TRH 287 (358)
T ss_pred ccCCCCCceEEeCCCCcCCHHHHHHHHHHHHHHhCCCCCCCcccchHHHHHHHHH-----cCC--C-----------HHH
Confidence 235566885 356788888887765 23 5667888766664332 211 2 238
Q ss_pred HHHHcCCCc
Q 002260 803 VAIICNHQR 811 (946)
Q Consensus 803 VAilCNHQR 811 (946)
|+.++||.-
T Consensus 288 v~~~LGH~s 296 (358)
T PRK01287 288 IQAILGHAK 296 (358)
T ss_pred HHHHhCCCc
Confidence 899999987
No 43
>PRK09871 tyrosine recombinase; Provisional
Probab=89.80 E-value=0.73 Score=46.48 Aligned_cols=118 Identities=9% Similarity=0.137 Sum_probs=81.9
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC-----
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG----- 735 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~----- 735 (946)
+++.|+-.+.+|+|- ++.|+.++|.+. .+.|.+.- +|.+..+ .|.+.+.+...|..+...
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 446666779999986 889999999987 47777653 4655543 456678888888776432
Q ss_pred -CCCCCccCc-----cCChhHHHHHHHhhC------CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Q 002260 736 -KKQNDDLFD-----KLDTAKLNAHLKELM------PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEV 803 (946)
Q Consensus 736 -K~Pgd~LFd-----~Ldss~LN~yLkelm------~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreV 803 (946)
..+.+.||- .++...++..|+.+. +.+|..+||-..||.++.. +. + ...|
T Consensus 95 ~~~~~~~lF~~~~g~~~~~~~~~~~lk~~~~~~~~~~~~~~H~LRHT~at~l~~~-----G~--~-----------~~~i 156 (198)
T PRK09871 95 GADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAER-----GA--D-----------TRLI 156 (198)
T ss_pred CCCCCCCeEecCCCCCccHHHHHHHHHHHHHhcCcCCCCCCcccchHHHHHHHHc-----CC--C-----------HHHH
Confidence 134556884 567888998888874 3578899998777754432 11 1 2478
Q ss_pred HHHcCCCc
Q 002260 804 AIICNHQR 811 (946)
Q Consensus 804 AilCNHQR 811 (946)
+.++||.-
T Consensus 157 ~~~lGH~s 164 (198)
T PRK09871 157 QDYLGHRN 164 (198)
T ss_pred HHHhCCCC
Confidence 88899975
No 44
>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=88.89 E-value=2.6 Score=42.74 Aligned_cols=77 Identities=16% Similarity=0.319 Sum_probs=50.1
Q ss_pred HHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHh
Q 002260 805 IICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKME 884 (946)
Q Consensus 805 ilCNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~ 884 (946)
|+|=+|...+.--...|..|...|..|+.++.+++.+.+.+...-. .....+|.+.+...|+.++++|..|+
T Consensus 58 iY~~~Q~~~~~~s~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~--------~L~~~~t~~el~~~i~~l~~e~~~l~ 129 (169)
T PF07106_consen 58 IYFANQDELEVPSPEELAELDAEIKELREELAELKKEVKSLEAELA--------SLSSEPTNEELREEIEELEEEIEELE 129 (169)
T ss_pred EEeeCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 4454555544333456788888888888888888877765542221 12334667788888888888888887
Q ss_pred hcccc
Q 002260 885 RDMKT 889 (946)
Q Consensus 885 ~~~~~ 889 (946)
..+..
T Consensus 130 ~kL~~ 134 (169)
T PF07106_consen 130 EKLEK 134 (169)
T ss_pred HHHHH
Confidence 66653
No 45
>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=88.79 E-value=0.85 Score=44.17 Aligned_cols=99 Identities=14% Similarity=0.111 Sum_probs=70.1
Q ss_pred HHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCC
Q 002260 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKK 737 (946)
Q Consensus 658 qlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~ 737 (946)
.+..++.|+-.+.+|+|. +|.|+.+||... .+.+ -.+|.+.. ..|.+.+.+...|..+.....
T Consensus 20 ~~~~~~~l~~~tGlR~~E-----------~~~l~~~di~~~---~~~i-~~~K~~~~--r~vpl~~~~~~~l~~~~~~~~ 82 (162)
T cd00800 20 WLRCAMDLALLTGQRVGD-----------VLRMKWSDIDDD---GLHI-EQSKTGAK--LAIPLSPSLREVIERCRDLSR 82 (162)
T ss_pred HHHHHHHHHHHHcCCHHH-----------HHhCcHHHccCC---eEEE-EecCcCCe--eEEECCHHHHHHHHHHHhhcc
Confidence 455667788889999987 888999998743 3444 24565443 457778999999998854332
Q ss_pred -CCCccCcc------CChhHHHHHHHhhC-----C----CCccceecccchH
Q 002260 738 -QNDDLFDK------LDTAKLNAHLKELM-----P----GLTAKVFRTYNAS 773 (946)
Q Consensus 738 -Pgd~LFd~------Ldss~LN~yLkelm-----~----glTAKdFRTynAS 773 (946)
+++.||.. ++...++.+++.+. + .++..+||...+|
T Consensus 83 ~~~~~vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~H~lRht~~t 134 (162)
T cd00800 83 VSSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTFHDIRAKAAS 134 (162)
T ss_pred cCCceEEEcCCCCCCcCcchHHHHHHHHHHhcccccCCCCCchhhHHHHHHH
Confidence 56778854 66788999998874 2 5678888875544
No 46
>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=87.52 E-value=3.3 Score=40.52 Aligned_cols=121 Identities=14% Similarity=0.130 Sum_probs=74.1
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeC-------CCCeEEEEEEeeChhHHHH-HHhh
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLG-------KDSIQYVNTVEVELPVYKA-IGQF 732 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlG-------Kdgir~~~tV~VD~~V~kn-Lk~f 732 (946)
.++.|+=.+.+|+|. ++.|+.++|.+.. +.+.+.+.. |.+. -...|.+.+.+... |..+
T Consensus 28 ~~~~l~~~tGlR~~E-----------i~~l~~~di~~~~-~~~~i~~~~~~~~~~~K~~~-~~r~vpl~~~~~~~~l~~~ 94 (181)
T cd01184 28 WLPLLGLYTGARVNE-----------IAQLQVDDIREED-GVPCIDITNDDEDQSLKNAA-SRRTIPVHPELIELGFLDY 94 (181)
T ss_pred HHHHHHHHHCCCHHH-----------HhcccHHHeeeeC-CeEEEEeecchhccCCCCCC-CcccccCCHHHHHccHHHH
Confidence 344455567899986 7889999999873 555554432 2222 14577788888887 6554
Q ss_pred hcC--CCCCCccCccC-------ChhHHHHHHHhhC-------CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHH
Q 002260 733 QTG--KKQNDDLFDKL-------DTAKLNAHLKELM-------PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVY 796 (946)
Q Consensus 733 ~k~--K~Pgd~LFd~L-------dss~LN~yLkelm-------~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~y 796 (946)
++. ..+.+.||-.. ....++++++.++ .++|..+||--.||.++. ...
T Consensus 95 ~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~H~lRht~at~~~~-----~g~----------- 158 (181)
T cd01184 95 VEARRAAGHKRLFPDLPAGKTGGYGSAVSKWFSRYLKKLGLKDKGKSFHSFRHTFITELRN-----AGV----------- 158 (181)
T ss_pred HHHHHccCCceecccccccCCCCchHHHHHHHHHHHHHhcCCCCccchhhhHHHHHHHHHH-----cCC-----------
Confidence 332 24566788753 2345666666654 356788888555554432 111
Q ss_pred HHHHHHHHHHcCCCcc
Q 002260 797 QRANKEVAIICNHQRT 812 (946)
Q Consensus 797 n~AnreVAilCNHQRa 812 (946)
-...|+.++||.-.
T Consensus 159 --~~~~i~~~lgHs~~ 172 (181)
T cd01184 159 --SRELIAAIMGHEEG 172 (181)
T ss_pred --CHHHHHHhcCCCCC
Confidence 13578888899754
No 47
>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=86.36 E-value=2.1 Score=45.81 Aligned_cols=117 Identities=15% Similarity=0.231 Sum_probs=78.0
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcC-----
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTG----- 735 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~----- 735 (946)
++++|+=.+.||+|- +|.|+.+||.+. ++.|.+. .+|.+.. .+|.+.+.+...|+..+..
T Consensus 120 ~~v~ll~~tGlR~~E-----------~~~L~~~did~~-~~~i~v~-~~K~~~~--r~vpl~~~~~~~L~~~~~~~~~~~ 184 (315)
T TIGR02249 120 LIAKLLYGSGMRLME-----------CLRLRIQDIDFD-YGEIRIR-QGKGGKD--RTVTLPKELIPPLREQIELARAYH 184 (315)
T ss_pred HHHHHHHHcCCCHHH-----------HHhccHHhcccC-CCeEEEE-eCCCCce--eEEecCHHHHHHHHHHHHHHHhhh
Confidence 345555568899986 899999999998 5888776 4677654 4567778888777664321
Q ss_pred -------------------C-------CCCCccCc----------------cCChhHHHHHHHhhC-----C-CCcccee
Q 002260 736 -------------------K-------KQNDDLFD----------------KLDTAKLNAHLKELM-----P-GLTAKVF 767 (946)
Q Consensus 736 -------------------K-------~Pgd~LFd----------------~Ldss~LN~yLkelm-----~-glTAKdF 767 (946)
+ .+.+.||- .++...++..++.++ + .+|..+|
T Consensus 185 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~g~~~~~~~~~~~~~~~~k~~~~~~gi~~~~~~H~l 264 (315)
T TIGR02249 185 EADLAEGYGGVYLPHALARKYPNAPKEWGWQYLFPSHRLSRDPESGVIRRHHINETTIQRAVRRAVERAGIEKPVTCHTL 264 (315)
T ss_pred ccchhhccccccchhhhhhcccccccCCCceeeeecccccccccccccccCCcCHHHHHHHHHHHHHHcCCCCCcccccc
Confidence 0 11234663 256677888888875 2 4788899
Q ss_pred cccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCC
Q 002260 768 RTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQ 810 (946)
Q Consensus 768 RTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQ 810 (946)
|--.||.++. .+. + ...|+.++||.
T Consensus 265 RHt~at~l~~-----~g~--~-----------~~~i~~~LGH~ 289 (315)
T TIGR02249 265 RHSFATHLLE-----SGA--D-----------IRTVQELLGHS 289 (315)
T ss_pred cHHHHHHHHH-----cCC--C-----------HHHHHHHhCCC
Confidence 9655555543 221 1 25788899996
No 48
>KOG0981 consensus DNA topoisomerase I [Replication, recombination and repair]
Probab=86.36 E-value=1.7 Score=52.27 Aligned_cols=116 Identities=20% Similarity=0.348 Sum_probs=59.7
Q ss_pred hHHHHHHhhhcCCCCCCccCccCC-hhHHHHHHHhhC---CCCccceecccch-HHHHHHHHhcCCC--C-------CCH
Q 002260 724 PVYKAIGQFQTGKKQNDDLFDKLD-TAKLNAHLKELM---PGLTAKVFRTYNA-SITLDGMLNKGTG--D-------GDV 789 (946)
Q Consensus 724 ~V~knLk~f~k~K~Pgd~LFd~Ld-ss~LN~yLkelm---~glTAKdFRTynA-Svta~~~L~~~~~--~-------~s~ 789 (946)
.|-+.|+.||.+ -..-+|.-++ +-.|-.-|..+. ..+.+|.. .||. +.+.+ .|..... . ...
T Consensus 566 ~LN~hL~~lM~G--LTAKVFRTYNASiTlqeqL~~lt~p~~~v~~KIl-~YnrANr~VA-IlCNHQR~v~K~h~~smekl 641 (759)
T KOG0981|consen 566 SLNKHLQELMDG--LTAKVFRTYNASITLQEQLDKLTNPDGNVAAKIL-SYNRANRTVA-ILCNHQRAVSKTHEKSMEKL 641 (759)
T ss_pred HHHHHHHHHhcc--chhhhhhhcchhhHHHHHHHhccCCCccHHHHHH-HHhhccceee-eeecccccCCccHHHHHHHH
Confidence 366678888543 2345788888 556788888887 46777876 3442 22221 1111111 1 123
Q ss_pred HHHHHHHHHHHHHHHHHc-----CCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002260 790 AVKIDVYQRANKEVAIIC-----NHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLD 843 (946)
Q Consensus 790 ~eK~~~yn~AnreVAilC-----NHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~ 843 (946)
++|+.+....+.+.-.-+ .|..----.--..|++++.+|+.|++||..++.++.
T Consensus 642 ~~kI~~~keql~e~~~~l~~ak~~~~~~~~~~~~k~~Ek~~k~~~~l~eqi~kl~~q~~ 700 (759)
T KOG0981|consen 642 AEKIKAKKEQLKEAEAELKSAKADEKKQEGSKEKKEVEKKEKKLERLEEQLKKLEIQMT 700 (759)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccccccccccccccHHHHHHHHHHHHHHHHHHhhhcc
Confidence 444443333332222211 111111001112678888888888888887766554
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=84.08 E-value=4.2 Score=39.24 Aligned_cols=114 Identities=18% Similarity=0.183 Sum_probs=76.5
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCC
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQ 738 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~P 738 (946)
+..++.|+=.+++|+|. ++.|+..+|. .+.+.+. .+|.+.. ..|.+.+.+...|+... .
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 33444455568899885 7788888874 2444443 3676653 56777899999998773 3
Q ss_pred CCccCccCChhHHHHHHHhhC----CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002260 739 NDDLFDKLDTAKLNAHLKELM----PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (946)
Q Consensus 739 gd~LFd~Ldss~LN~yLkelm----~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQR 811 (946)
++.||-.++...++.+++.+. .++|..+||--.||.++. .+. + ...|+.++||.-
T Consensus 77 ~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~~t~l~~-----~g~--~-----------~~~i~~~lGH~~ 135 (158)
T cd00797 77 RGGLFPDLYYESFRHIWKRAKIELPKGQATHILRHTFASHFMM-----NGG--N-----------IATLQHILGHAT 135 (158)
T ss_pred cCCCCCCcChHHHHHHHHHHHHHhCCCCccccchhHHHHHHHH-----cCC--C-----------HHHHHHHhCCCC
Confidence 567898777778888888885 468888888655554332 111 1 357788889863
No 50
>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=83.16 E-value=2.8 Score=42.06 Aligned_cols=120 Identities=14% Similarity=0.053 Sum_probs=73.0
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEe--------eCCCCeEEEEEEeeChhHHHHHHhh
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDF--------LGKDSIQYVNTVEVELPVYKAIGQF 732 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdF--------lGKdgir~~~tV~VD~~V~knLk~f 732 (946)
.+++|+=.+.||+|- |++|+.+||.+. +..|.+.= .+|..- ....|.+.+.+...|...
T Consensus 24 ~~~~l~~~tGlR~~E-----------~~~L~~~did~~-~~~~~i~~~~~~~~~~~~kt~~-~~r~vpl~~~~~~~l~~~ 90 (196)
T cd01191 24 NLWEFAVFTGLRPSE-----------LIALAWEDVDLE-RGTVYVRRALVRGIFKVPKTKA-GTRDVDLNPPALAALKEQ 90 (196)
T ss_pred HHHHHHHHHCCCHHH-----------HHhCcHHhcCcc-CCeEEEEeeeecccccCCCcCC-CeEEEeCCHHHHHHHHHH
Confidence 456666668999986 899999999887 46666531 123321 234577789988888764
Q ss_pred hcC--------------------CCCCCccCccCC--------hhHHHHHHHhhC-----CCCccceecccchHHHHHHH
Q 002260 733 QTG--------------------KKQNDDLFDKLD--------TAKLNAHLKELM-----PGLTAKVFRTYNASITLDGM 779 (946)
Q Consensus 733 ~k~--------------------K~Pgd~LFd~Ld--------ss~LN~yLkelm-----~glTAKdFRTynASvta~~~ 779 (946)
... ..+.+.||...+ ...++..++.++ +.+|.-+||-..||.++.
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lF~~~~~g~~~~~~~~~~~~~~~~~~~~~gi~~~~~H~lRht~at~l~~-- 168 (196)
T cd01191 91 AKLTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGIRYRNPYQMRHTFASWMLT-- 168 (196)
T ss_pred HHHhhcccccchhhcccccccccCCCceEEEecCCCCCcCCchhHHHHHHHHHHHHHcCCCcCCcccchHHHHHHHHH--
Confidence 321 123456774321 234555555554 345677777666655442
Q ss_pred HhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002260 780 LNKGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (946)
Q Consensus 780 L~~~~~~~s~~eK~~~yn~AnreVAilCNHQR 811 (946)
.+. + ...|+.++||+.
T Consensus 169 ---~g~--~-----------~~~i~~~lGH~~ 184 (196)
T cd01191 169 ---AGA--N-----------PAFIADQMGHKS 184 (196)
T ss_pred ---CCC--C-----------HHHHHHHhCCCc
Confidence 111 1 357888899987
No 51
>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=82.07 E-value=11 Score=37.79 Aligned_cols=123 Identities=15% Similarity=0.142 Sum_probs=74.9
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcC--CCeEEEEe-eCCCCeEEEEEEeeChhHHHHHHhhhcC
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIP--PNKLKFDF-LGKDSIQYVNTVEVELPVYKAIGQFQTG 735 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~--~~~V~FdF-lGKdgir~~~tV~VD~~V~knLk~f~k~ 735 (946)
+..++.|+-.+.+|+|- ++.|+..++.... ...+.+.. .+|.+ .....|.+.+.+...|+.+...
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 44566777888899985 5566665543221 12333322 35554 1334677889999998877531
Q ss_pred --------CCCCCccCcc---------CChhHHHHHHHhhC--CC----------CccceecccchHHHHHHHHhcCCCC
Q 002260 736 --------KKQNDDLFDK---------LDTAKLNAHLKELM--PG----------LTAKVFRTYNASITLDGMLNKGTGD 786 (946)
Q Consensus 736 --------K~Pgd~LFd~---------Ldss~LN~yLkelm--~g----------lTAKdFRTynASvta~~~L~~~~~~ 786 (946)
..+.+.||.. ++...+|..++.+. .| ++..+||=..||.+++ .+.
T Consensus 90 ~~~~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~-----~g~- 163 (195)
T cd01195 90 TKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYHFHAHAFRHTVATRMIN-----NGM- 163 (195)
T ss_pred HHHHhccCCCCCceEeeccCCCCCCCcCcHHHHHHHHHHHHHHcCCccCCCCEeeccchhhhhHHHHHHHH-----cCC-
Confidence 2356678854 66778998888875 23 4666677555554432 211
Q ss_pred CCHHHHHHHHHHHHHHHHHHcCCCc
Q 002260 787 GDVAVKIDVYQRANKEVAIICNHQR 811 (946)
Q Consensus 787 ~s~~eK~~~yn~AnreVAilCNHQR 811 (946)
+ ...|+.++||..
T Consensus 164 -~-----------~~~i~~~lGH~~ 176 (195)
T cd01195 164 -P-----------IHIIQKFLGHES 176 (195)
T ss_pred -C-----------HHHHHHHhCCCC
Confidence 1 237888999964
No 52
>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=78.78 E-value=7.1 Score=40.97 Aligned_cols=116 Identities=13% Similarity=0.100 Sum_probs=76.4
Q ss_pred HHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCC-CC
Q 002260 660 AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGK-KQ 738 (946)
Q Consensus 660 AvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K-~P 738 (946)
-++++|+-.+.||+|. +|.|+.+||.+. .+.+ .+|.+.. ..|.+.+.+...|..++... ..
T Consensus 110 ~~~~~l~~~tGlR~~E-----------~~~L~~~di~~~---~~~i--~~K~~~~--r~i~l~~~~~~~l~~~~~~~~~~ 171 (263)
T cd01196 110 YFVVWFLAATGARVSE-----------LIHIKVEHVQTG---YADI--YSKGGKI--RRLYIPKNLRVEALKWLKELNLD 171 (263)
T ss_pred HHHHHHHHHhCCCHHH-----------HhcCcHHHHhCC---eeEE--eecCCce--eEEecCHHHHHHHHHHHHHcCCC
Confidence 3467777778999986 899999999753 2333 3666544 34667787777776665432 34
Q ss_pred CCccCc-----cCChhHHHHHHHhhC--CC-----CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Q 002260 739 NDDLFD-----KLDTAKLNAHLKELM--PG-----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAII 806 (946)
Q Consensus 739 gd~LFd-----~Ldss~LN~yLkelm--~g-----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAil 806 (946)
.+.||. .++...++.+++.+. -| ++..+||--.||.++.. + .+ ...|+.+
T Consensus 172 ~~~lf~~~~g~~~~~~~~~~~~~~~~~~~gi~~~~~~~H~lRHt~at~~~~~-----g--~~-----------~~~i~~~ 233 (263)
T cd01196 172 SGYIFLNRFGKPITARGIAQQLKNYAAKYKMNPRVVYPHSFRHLFAKNFLAK-----Y--ND-----------LALLADL 233 (263)
T ss_pred CCceeeeCCCCcCcHHHHHHHHHHHHHHhCCCCCCCCchhhHHHHHHHHHHc-----C--CC-----------HHHHHHH
Confidence 567884 577888999888874 23 56777876555544321 1 12 3568888
Q ss_pred cCCCc
Q 002260 807 CNHQR 811 (946)
Q Consensus 807 CNHQR 811 (946)
.||.-
T Consensus 234 lGH~~ 238 (263)
T cd01196 234 MGHES 238 (263)
T ss_pred hCCCC
Confidence 88864
No 53
>PRK15417 integrase/recombinase; Provisional
Probab=76.76 E-value=14 Score=40.83 Aligned_cols=57 Identities=12% Similarity=0.134 Sum_probs=41.5
Q ss_pred HHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhh
Q 002260 661 VATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQF 732 (946)
Q Consensus 661 vAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f 732 (946)
+++.|+-.+.||+|- +|.|+.++|.+. ++.|.+. .||.+..+ .|.+.+.+...|+..
T Consensus 135 ~~~~ll~~TGlR~sE-----------l~~L~~~dId~~-~~~i~v~-~~K~~k~R--~vpl~~~~~~~L~~~ 191 (337)
T PRK15417 135 LFAQLLYGTGMRISE-----------GLQLRVKDLDFD-HGTIIVR-EGKGSKDR--ALMLPESLAPSLREQ 191 (337)
T ss_pred HHHHHHHHcCCcHHH-----------HHhcchhhccCC-CCeEEEE-eCCCCCce--eeeCCHHHHHHHHHH
Confidence 455677789999986 899999999988 4776664 37766544 466677777766553
No 54
>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=75.05 E-value=18 Score=35.86 Aligned_cols=119 Identities=15% Similarity=0.049 Sum_probs=68.7
Q ss_pred HHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeC-CCCeEEEEEEeeChhHHHHHHhhhcC--
Q 002260 659 IAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLG-KDSIQYVNTVEVELPVYKAIGQFQTG-- 735 (946)
Q Consensus 659 lAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlG-Kdgir~~~tV~VD~~V~knLk~f~k~-- 735 (946)
.-++++|+=.+.+|+|- ++.|+.+||.+. +..|.+.-.+ |.+.++ +..+..+...+......
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 34667888889999986 899999999988 4677776542 333332 22244444444444322
Q ss_pred CCCCCccCccC-----ChhH----HHHHHHhhC---------CCCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHH
Q 002260 736 KKQNDDLFDKL-----DTAK----LNAHLKELM---------PGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQ 797 (946)
Q Consensus 736 K~Pgd~LFd~L-----dss~----LN~yLkelm---------~glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn 797 (946)
..+.+.||-.. +... ++.+++.+- ..+|.-+||---||..+.. +. +
T Consensus 84 ~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~H~lRHt~at~l~~~-----g~--~--------- 147 (186)
T cd01198 84 TSPADALFIGTQDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRHFFTTWLRRR-----GG--D--------- 147 (186)
T ss_pred CCCCCceEEecCCCcccchhHHHHHHHHHHHhcccccccccccCcCcccchhHHHHHHHHc-----CC--C---------
Confidence 23556777532 2233 444444442 2466677776555554422 11 1
Q ss_pred HHHHHHHHHcCCC
Q 002260 798 RANKEVAIICNHQ 810 (946)
Q Consensus 798 ~AnreVAilCNHQ 810 (946)
...|..+.||.
T Consensus 148 --~~~i~~llGH~ 158 (186)
T cd01198 148 --RGVVQELRGDS 158 (186)
T ss_pred --HHHHHHHhCCC
Confidence 35677788996
No 55
>PF14282 FlxA: FlxA-like protein
Probab=73.34 E-value=12 Score=36.01 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 002260 818 SAQMSRLTEKIEDLKGVLKDL 838 (946)
Q Consensus 818 ~~~m~kl~~ki~~lk~~~~~~ 838 (946)
+.+++.|+.+|..|..+|.+|
T Consensus 18 ~~~I~~L~~Qi~~Lq~ql~~l 38 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQEQLQEL 38 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 556666666666666666555
No 56
>PHA02601 int integrase; Provisional
Probab=69.96 E-value=11 Score=40.79 Aligned_cols=112 Identities=21% Similarity=0.208 Sum_probs=75.7
Q ss_pred HHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHhhhcCCC
Q 002260 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKK 737 (946)
Q Consensus 658 qlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~f~k~K~ 737 (946)
.+++++.|+=.+.+|.|- +|.|+.++|. .+.|.+. .+|.+- ...|.+.+.++..|..-
T Consensus 192 ~~~~~~~l~~~TG~R~~E-----------i~~L~~~did---~~~~~~~-~~K~~~--~r~Vpl~~~~~~~L~~~----- 249 (333)
T PHA02601 192 DLGLIAKICLATGARWSE-----------AETLKRSQIS---PYKITFV-KTKGKK--NRTVPISEELYKMLPKR----- 249 (333)
T ss_pred hHHHHHHHHHHcCCCHHH-----------HHhCCHHHcC---cCeEEEE-ECCCCc--eeEEECCHHHHHHHHhc-----
Confidence 455667777788999986 8888888885 2444432 456553 46678889998887642
Q ss_pred CCCccCccCChhHHHHHHHhhC-C---CCccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCc
Q 002260 738 QNDDLFDKLDTAKLNAHLKELM-P---GLTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQR 811 (946)
Q Consensus 738 Pgd~LFd~Ldss~LN~yLkelm-~---glTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQR 811 (946)
.+.||... ...++.+++.+- + ++|..+||=-.||.++.. +. -...|+.++||.-
T Consensus 250 -~~~~f~~~-~~~~~~~~~~~~~~~~~~~~~H~lRHt~at~l~~~-----G~-------------~~~~i~~~lGH~~ 307 (333)
T PHA02601 250 -RGRLFKDA-YESFERAVKRAGIDLPEGQATHVLRHTFASHFMMN-----GG-------------NILVLQRILGHAT 307 (333)
T ss_pred -CCCcChhH-HHHHHHHHHHhCCCCCCCCcCchhhHHHHHHHHHc-----CC-------------CHHHHHHHhCCCC
Confidence 34577543 467888888774 2 678888987777765442 11 1368888999963
No 57
>COG0582 XerC Integrase [DNA replication, recombination, and repair]
Probab=66.66 E-value=18 Score=34.93 Aligned_cols=53 Identities=11% Similarity=0.088 Sum_probs=36.2
Q ss_pred hhccccCCcccccCCCceeeccCCCCceEEcCCCeEEEEeeC-CCCeEEEEEEeeChhHHHHHHhhhc
Q 002260 668 KLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLG-KDSIQYVNTVEVELPVYKAIGQFQT 734 (946)
Q Consensus 668 klALRvGnEKy~~endTvG~cTLR~eHVkl~~~~~V~FdFlG-Kdgir~~~tV~VD~~V~knLk~f~k 734 (946)
.+.+|+|- ++.|+.+|+.+. ...+.+.-.. |.+. ...+.+.+.+...|.....
T Consensus 153 ~tG~R~~E-----------~~~l~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~ 206 (309)
T COG0582 153 LTGLRVSE-----------LLGLRWSDIDLE-NGTIWIRGTKTKGRK--ERRVPLSEQALEALKKYLL 206 (309)
T ss_pred HhcccHHH-----------HHhCcHhhcccc-cCeEEEeccccCCCC--ceEEecCHHHHHHHHHHHH
Confidence 79999876 889999999988 3555444443 2333 3445556888887777753
No 58
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=55.74 E-value=18 Score=45.04 Aligned_cols=77 Identities=16% Similarity=0.329 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC------cccccccCCCHHHHHHHHHHHHHHHHHHhhccccccc
Q 002260 819 AQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKD------SDGKRKRNLAPEALERKMAQTNAKIEKMERDMKTKED 892 (946)
Q Consensus 819 ~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~------~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~kee 892 (946)
++|+-|+.||.+.+.++..++++|...++.+... .. ......+.-..|.++.+...++..|.+|+.+++.+||
T Consensus 488 q~l~~LEkrL~eE~~~R~~lEkQL~eErk~r~~e-e~~aar~~~~~~~~r~e~~e~~r~r~~~lE~E~~~lr~elk~kee 566 (697)
T PF09726_consen 488 QSLQQLEKRLAEERRQRASLEKQLQEERKARKEE-EEKAARALAQAQATRQECAESCRQRRRQLESELKKLRRELKQKEE 566 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH-HHhhhhccccchhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577778888888888888888776443332110 00 0001122234588999999999999999999999988
Q ss_pred ccee
Q 002260 893 LKTV 896 (946)
Q Consensus 893 nK~v 896 (946)
-...
T Consensus 567 ~~~~ 570 (697)
T PF09726_consen 567 QIRE 570 (697)
T ss_pred HHHH
Confidence 6544
No 59
>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=43.03 E-value=1.1e+02 Score=33.81 Aligned_cols=53 Identities=21% Similarity=0.396 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHc-CCCcccccc---------hHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002260 790 AVKIDVYQRANKEVAIIC-NHQRTVSKT---------HSAQMSRLTEKIEDLKGVLKDLRVDL 842 (946)
Q Consensus 790 ~eK~~~yn~AnreVAilC-NHQRaV~K~---------~~~~m~kl~~ki~~lk~~~~~~~~~l 842 (946)
......|+.|...|+.|- -|.|+|-|+ |..+|+....+|..|+.++..+|...
T Consensus 145 ~~~~~~~~~ae~~v~~Lek~lkr~I~KSrPYfe~K~~~~~~l~~~k~~v~~Le~~v~~aK~~Y 207 (239)
T PF05276_consen 145 QRRARIYNEAEQRVQQLEKKLKRAIKKSRPYFELKAKFNQQLEEQKEKVEELEAKVKQAKSRY 207 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678999999999986 899999776 55666666666666666666665444
No 60
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.87 E-value=30 Score=38.66 Aligned_cols=55 Identities=16% Similarity=0.393 Sum_probs=31.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhcc
Q 002260 816 THSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDM 887 (946)
Q Consensus 816 ~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~ 887 (946)
.++..++.|..+|+.+..++.+++.+.++.+. ..++++++|+.++++|....--+
T Consensus 49 ~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~-----------------eik~l~~eI~~~~~~I~~r~~~l 103 (265)
T COG3883 49 NIQNEIESLDNQIEEIQSKIDELQKEIDQSKA-----------------EIKKLQKEIAELKENIVERQELL 103 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666666666666666666666655554431 12455566666666665544333
No 61
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=39.43 E-value=53 Score=33.22 Aligned_cols=65 Identities=25% Similarity=0.393 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhccc
Q 002260 817 HSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMK 888 (946)
Q Consensus 817 ~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~ 888 (946)
.+..+.-|+.|+..|..++..+...|..++..-. .........|.+.++|..|++.++..+..+.
T Consensus 33 ~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~le-------e~~~~~~~~E~l~rriq~LEeele~ae~~L~ 97 (143)
T PF12718_consen 33 KEQEITSLQKKNQQLEEELDKLEEQLKEAKEKLE-------ESEKRKSNAEQLNRRIQLLEEELEEAEKKLK 97 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------hHHHHHHhHHHHHhhHHHHHHHHHHHHHHHH
Confidence 5677788888888888888888877776653221 1112223457777888888877777665543
No 62
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=39.38 E-value=61 Score=33.54 Aligned_cols=66 Identities=14% Similarity=0.223 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhccccccccce
Q 002260 818 SAQMSRLTEKIEDLKGVLKDLRV--DLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMKTKEDLKT 895 (946)
Q Consensus 818 ~~~m~kl~~ki~~lk~~~~~~~~--~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~keenK~ 895 (946)
...+++|++.++.|+.++++++. +|..++ . ....++.+|..|+.+|...++-- .....-.
T Consensus 33 ~~G~~~L~~El~~L~~~i~~Ar~~GDlsEak---------------~--~~~~~e~rI~~L~~~L~~A~Ii~-~~~~~d~ 94 (160)
T PRK06342 33 EAGLKALEDQLAQARAAYEAAQAIEDVNERR---------------R--QMARPLRDLRYLAARRRTAQLMP-DPASTDV 94 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCChhHHH---------------H--HHHHHHHHHHHHHHHHccCEEEC-CCCCCCE
Confidence 46788888888888876666632 122211 0 01345677888888888877742 2234567
Q ss_pred eeeccc
Q 002260 896 VALGTS 901 (946)
Q Consensus 896 vaLGTS 901 (946)
|.+|+-
T Consensus 95 V~~Gs~ 100 (160)
T PRK06342 95 VAFGST 100 (160)
T ss_pred EEeCcE
Confidence 888863
No 63
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=39.24 E-value=3e+02 Score=27.22 Aligned_cols=50 Identities=16% Similarity=0.277 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002260 790 AVKIDVYQRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKK 847 (946)
Q Consensus 790 ~eK~~~yn~AnreVAilCNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~ 847 (946)
..++.-.+.|..+|=..|.+- ..+...+.+|.+++.++.+.+.+|..++.
T Consensus 42 ~~rv~GLe~AL~~v~~~Ctd~--------~l~~e~q~ki~~~~~kV~ere~eL~eA~~ 91 (115)
T PF06476_consen 42 QHRVAGLEKALEEVKAHCTDE--------GLKAERQQKIAEKQQKVAEREAELKEAQA 91 (115)
T ss_pred HHHHHHHHHHHHHHHhhcCCc--------hhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456777899999999999873 44567788899999999999999988763
No 64
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=36.52 E-value=1e+02 Score=33.39 Aligned_cols=85 Identities=21% Similarity=0.293 Sum_probs=60.0
Q ss_pred cCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhc
Q 002260 807 CNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERD 886 (946)
Q Consensus 807 CNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~ 886 (946)
..++..-......++.-++.+|+.++.++.+|..-|++++.-. ..-.++.+|.+++.+|+.++.|
T Consensus 120 v~~~~~~~~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka~~~~---------------d~l~ie~~L~~v~~eIe~~~~~ 184 (262)
T PF14257_consen 120 VTSRNISSEDVTEQYVDLEARLKNLEAEEERLLELLEKAKTVE---------------DLLEIERELSRVRSEIEQLEGQ 184 (262)
T ss_pred eeeeeccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHH---------------HHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555677888899999999999999988877776543100 1236778888888888888877
Q ss_pred cccccccceeeeccccccccCc
Q 002260 887 MKTKEDLKTVALGTSKINYLDP 908 (946)
Q Consensus 887 ~~~keenK~vaLGTSKiNYlDP 908 (946)
+.. =...|++.|=.|++--|
T Consensus 185 ~~~--l~~~v~~sti~i~l~~~ 204 (262)
T PF14257_consen 185 LKY--LDDRVDYSTITISLYEP 204 (262)
T ss_pred HHH--HHHhhceEEEEEEEEec
Confidence 765 33456777766666554
No 65
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=36.43 E-value=92 Score=37.25 Aligned_cols=34 Identities=18% Similarity=0.360 Sum_probs=27.6
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 002260 814 SKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKK 847 (946)
Q Consensus 814 ~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~ 847 (946)
.-+-..+|+.|+.++..|+.|..||+..|.....
T Consensus 20 a~a~a~~i~~L~~ql~aLq~~v~eL~~~laa~~~ 53 (514)
T PF11336_consen 20 AAATADQIKALQAQLQALQDQVNELRAKLAAKPA 53 (514)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3456688999999999999999999998865433
No 66
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=36.14 E-value=91 Score=37.56 Aligned_cols=50 Identities=10% Similarity=0.227 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhcc
Q 002260 821 MSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDM 887 (946)
Q Consensus 821 m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~ 887 (946)
++..+.+.++|+++|..+++++....+. .+.++.+|+.+++.+..|+.|+
T Consensus 71 LteqQ~kasELEKqLaaLrqElq~~saq-----------------~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 71 TTEMQVTAAQMQKQYEEIRRELDVLNKQ-----------------RGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh-----------------hhhHHHHHHHHHHHHHHHHHHH
Confidence 4556778888888888887777644321 1344567777777777777776
No 67
>KOG2289 consensus Rhomboid family proteins [Signal transduction mechanisms]
Probab=34.82 E-value=15 Score=41.78 Aligned_cols=41 Identities=24% Similarity=0.342 Sum_probs=28.8
Q ss_pred hhhhhh-hccccCceEEEEeecceecccccccceeeeeccCCC
Q 002260 12 VKLLQM-CINCNFGTLIFVRNWCHIHANIVSGGIMAVEASSKP 53 (946)
Q Consensus 12 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~ 53 (946)
..++.+ |+||.+|.+.++|||-||++- ++|=.+...+...|
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 68
>TIGR02680 conserved hypothetical protein TIGR02680. Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.
Probab=34.47 E-value=2.4e+02 Score=38.02 Aligned_cols=48 Identities=17% Similarity=0.230 Sum_probs=32.8
Q ss_pred hhHHHHHHhhhcCCCCCCccCccCChhHHHHHHHhhCCCCccceecccchHHH
Q 002260 723 LPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASIT 775 (946)
Q Consensus 723 ~~V~knLk~f~k~K~Pgd~LFd~Ldss~LN~yLkelm~glTAKdFRTynASvt 775 (946)
..+++.+..+...+.+ ..++++.|.++|++.+++++-=+.++..-++.
T Consensus 183 ~~l~~~l~~lr~P~Ls-----~~~~~~~l~~~l~~~l~~l~~~~i~~l~e~~~ 230 (1353)
T TIGR02680 183 AALLDLLIQLRQPQLS-----KKPDEGVLSDALTEALPPLDDDELTDVADALE 230 (1353)
T ss_pred HHHHHHHHHHcCCCCC-----CCCChHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3466666666444433 25778899999999998888777666555543
No 69
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=33.28 E-value=31 Score=36.02 Aligned_cols=86 Identities=26% Similarity=0.336 Sum_probs=53.5
Q ss_pred HcCCCcccccchHHHHHH----HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHH
Q 002260 806 ICNHQRTVSKTHSAQMSR----LTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIE 881 (946)
Q Consensus 806 lCNHQRaV~K~~~~~m~k----l~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~ 881 (946)
.||--|++--.|.-.|.. ..+|-.+..+|+.++|++|..... .++ =.+-++++.+|+
T Consensus 20 ~~nk~r~l~~s~~i~~s~~~nkdakk~~q~~~ei~dmKqelnavs~------------------qD~-fAkwaRlnRKi~ 80 (175)
T KOG4253|consen 20 GCNKLRILLPSFSIFMSRVGNKDAKKESQKVAEIQDMKQELNAVSM------------------QDN-FAKWARLNRKIN 80 (175)
T ss_pred hhhHhheecchhhhhhhcccchhHHHHHHHHHHHHHHHHHHhhhhh------------------HHH-HHHHHHHHHHHH
Confidence 488888887777766644 444455556666666666654320 011 134555566666
Q ss_pred HHhhccccccccceeeeccccccccCccceeeec
Q 002260 882 KMERDMKTKEDLKTVALGTSKINYLDPRITVAWC 915 (946)
Q Consensus 882 k~~~~~~~keenK~vaLGTSKiNYlDPRItvAwc 915 (946)
+|...++..-+|++.-.+|=|. -|||+|-
T Consensus 81 kl~~ele~qs~n~~~q~~~~K~-----vlSv~f~ 109 (175)
T KOG4253|consen 81 KLDKELETQSKNKTAQAHLHKW-----VLSVAFY 109 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHH
Confidence 6666666667888888888876 5666654
No 70
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=31.55 E-value=26 Score=39.83 Aligned_cols=23 Identities=39% Similarity=0.745 Sum_probs=20.4
Q ss_pred CCCCC-----CCcceEEEcCeeccCChh
Q 002260 414 PPPYL-----PHGVKMLYKGKEVNLTPE 436 (946)
Q Consensus 414 pP~Y~-----P~~Vk~~YdGkpv~L~p~ 436 (946)
-+||. |.+|.|.|+|+||+|++.
T Consensus 290 ~~p~~v~iG~~~~v~i~~nG~~vdl~~~ 317 (331)
T PRK10856 290 QAPYKLKIGAPAAVQIQYQGKPVDLSRF 317 (331)
T ss_pred CceEEEEEcCCCceEEEECCEEccCCcc
Confidence 46776 899999999999999985
No 71
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=31.13 E-value=2.1e+02 Score=29.48 Aligned_cols=71 Identities=13% Similarity=0.158 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCC-------CHHHHHHHHHHHHHHHHHHhhccccc
Q 002260 818 SAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNL-------APEALERKMAQTNAKIEKMERDMKTK 890 (946)
Q Consensus 818 ~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~-------~~e~~~k~i~~~~~~i~k~~~~~~~k 890 (946)
.+.+++|++.++.|+.++.++-+.+..|...- ....|. ..-.++.+|..|+.+|...++- .
T Consensus 10 ~eg~~~L~~EL~~L~~~r~~i~~~i~~Ar~~G---------DlsENaey~aak~~q~~~e~RI~~L~~~L~~A~ii---~ 77 (158)
T PRK05892 10 PAARDHLEAELARLRARRDRLAVEVNDRGMIG---------DHGDQAEAIQRADELARLDDRINELDRRLRTGPTP---W 77 (158)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCC---------CcchhhhHHHHHHHHHHHHHHHHHHHHHHHhCEEe---c
Confidence 35678899888888876666655665544211 111111 1234566777777777766553 2
Q ss_pred cccceeeecc
Q 002260 891 EDLKTVALGT 900 (946)
Q Consensus 891 eenK~vaLGT 900 (946)
.+...|.+|+
T Consensus 78 ~~~~~V~~Gs 87 (158)
T PRK05892 78 SGSETLPGGT 87 (158)
T ss_pred CCCCEEEcCc
Confidence 2446788886
No 72
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=30.68 E-value=58 Score=37.79 Aligned_cols=78 Identities=23% Similarity=0.336 Sum_probs=51.6
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhccccccccce
Q 002260 816 THSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMKTKEDLKT 895 (946)
Q Consensus 816 ~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~keenK~ 895 (946)
.+.+.++.++++|+.++.++.+|+..|....+.+ + ....++.++++++.+|..++.-+....+.
T Consensus 239 ~~~~~~~~l~~~~~~~~~~i~~l~~~l~~~~k~~-----------~---k~~~~~~q~~~~~k~~~~~~~~~~~~~~~-- 302 (406)
T PF02388_consen 239 NGKEYLESLQEKLEKLEKEIEKLEEKLEKNPKKK-----------N---KLKELEEQLASLEKRIEEAEELIAEYGDE-- 302 (406)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHHHHH-THHH-----------H---HHHHHHHHHHHHHHHHHHHHHHHHHH-SE--
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcchh-----------h---HHHHHHHHHHHHHHHHHHHHHHHHhcCCc--
Confidence 5778888899999999999888888776543100 1 13567788888888888887665443333
Q ss_pred eeeccccccccCcc
Q 002260 896 VALGTSKINYLDPR 909 (946)
Q Consensus 896 vaLGTSKiNYlDPR 909 (946)
|.|+.+-+-+-.-.
T Consensus 303 ~~la~~l~~~~g~~ 316 (406)
T PF02388_consen 303 IPLAGALFIYYGDE 316 (406)
T ss_dssp EEEEEEEEEEETTE
T ss_pred ceEEEEEEEEECCE
Confidence 66666555444433
No 73
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=30.32 E-value=74 Score=38.06 Aligned_cols=105 Identities=18% Similarity=0.212 Sum_probs=59.0
Q ss_pred HHHHHHHHHHH---HcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCccccccc-----CCCH
Q 002260 795 VYQRANKEVAI---ICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKR-----NLAP 866 (946)
Q Consensus 795 ~yn~AnreVAi---lCNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~-----~~~~ 866 (946)
.|+....++-. ..+..+++-+.-+.-|+++++|++.+..++.+++..=+.+.++.... -++.++ .-..
T Consensus 355 ~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~E~n~~l~knq~vw----~~kl~~~~e~~~~~~ 430 (493)
T KOG0804|consen 355 YYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKEEREENKKLIKNQDVW----RGKLKELEEREKEAL 430 (493)
T ss_pred HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH----HHHHHHHHHHHHHHH
Confidence 34444444433 45666777778888899999999999999888774333333222110 011100 0112
Q ss_pred HHHHHHHHHHHHHHHHHhhccccccccc----eeeeccccc
Q 002260 867 EALERKMAQTNAKIEKMERDMKTKEDLK----TVALGTSKI 903 (946)
Q Consensus 867 e~~~k~i~~~~~~i~k~~~~~~~keenK----~vaLGTSKi 903 (946)
...+.+|.-|+|||..|-..+....+.| .|.=||--|
T Consensus 431 ~s~d~~I~dLqEQlrDlmf~le~qqklk~dt~eIqegtI~~ 471 (493)
T KOG0804|consen 431 GSKDEKITDLQEQLRDLMFFLEAQQKLKSDTDEIQEGTILI 471 (493)
T ss_pred HHHHHHHHHHHHHHHhHheehhhhhhhhcchhhhcCceeec
Confidence 3445566667777766655555555554 666665433
No 74
>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=28.09 E-value=1.3e+02 Score=30.54 Aligned_cols=99 Identities=17% Similarity=0.275 Sum_probs=46.3
Q ss_pred ChhHHHHHHHhhC--CCCccceec---ccchHHHHHHHHhcCCCCC--CHHHHHHHHHHHHHHHHHHcCCCcccccchHH
Q 002260 747 DTAKLNAHLKELM--PGLTAKVFR---TYNASITLDGMLNKGTGDG--DVAVKIDVYQRANKEVAIICNHQRTVSKTHSA 819 (946)
Q Consensus 747 dss~LN~yLkelm--~glTAKdFR---TynASvta~~~L~~~~~~~--s~~eK~~~yn~AnreVAilCNHQRaV~K~~~~ 819 (946)
.=+.|-+.|..+. ..|..|+|= -|.+. |..+...+... .....+.....-+.++...|.+-++--++...
T Consensus 31 ~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~---Q~~~~~~s~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~ 107 (169)
T PF07106_consen 31 GKTAVQKALDSLVEEGKIVEKEYGKQKIYFAN---QDELEVPSPEELAELDAEIKELREELAELKKEVKSLEAELASLSS 107 (169)
T ss_pred cHHHHHHHHHHHHhCCCeeeeeecceEEEeeC---ccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3577888888888 678888762 23222 33332222211 11111222222222222223222222222222
Q ss_pred HH--HHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 002260 820 QM--SRLTEKIEDLKGVLKDLRVDLDRAKKG 848 (946)
Q Consensus 820 ~m--~kl~~ki~~lk~~~~~~~~~l~~~k~~ 848 (946)
++ +.|...|..|+.++..++..|..++.+
T Consensus 108 ~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~ 138 (169)
T PF07106_consen 108 EPTNEELREEIEELEEEIEELEEKLEKLRSG 138 (169)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 22 446666666776666666666666543
No 75
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=27.63 E-value=1.1e+02 Score=34.63 Aligned_cols=74 Identities=20% Similarity=0.311 Sum_probs=36.9
Q ss_pred CCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhccc
Q 002260 809 HQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMK 888 (946)
Q Consensus 809 HQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~ 888 (946)
|-||--|--+..++--...|++|+.||.+++.+--.-. + . .....++.....+.|.+|++-|+.|...+-
T Consensus 72 HLkakLkes~~~l~dRetEI~eLksQL~RMrEDWIEEE-----C-H----RVEAQLALKEARkEIkQLkQvieTmrssL~ 141 (305)
T PF15290_consen 72 HLKAKLKESENRLHDRETEIDELKSQLARMREDWIEEE-----C-H----RVEAQLALKEARKEIKQLKQVIETMRSSLA 141 (305)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH-----H-H----HHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 44554444444444455567777777776665432100 0 0 000001112223567777777777777766
Q ss_pred cccc
Q 002260 889 TKED 892 (946)
Q Consensus 889 ~kee 892 (946)
+||.
T Consensus 142 ekDk 145 (305)
T PF15290_consen 142 EKDK 145 (305)
T ss_pred hhhh
Confidence 6643
No 76
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=27.53 E-value=1.3e+02 Score=31.73 Aligned_cols=17 Identities=24% Similarity=0.438 Sum_probs=13.1
Q ss_pred CChhHHHHHHHhhC-CCC
Q 002260 746 LDTAKLNAHLKELM-PGL 762 (946)
Q Consensus 746 Ldss~LN~yLkelm-~gl 762 (946)
|.+-.|-++|+.|+ +|+
T Consensus 27 I~~~~VKdvlq~LvDDgl 44 (188)
T PF03962_consen 27 IVSMSVKDVLQSLVDDGL 44 (188)
T ss_pred CchhhHHHHHHHHhcccc
Confidence 77788888888887 554
No 77
>PF09032 Siah-Interact_N: Siah interacting protein, N terminal ; InterPro: IPR015120 The N-terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N-terminal domain []. ; PDB: 1YSM_A 2A26_C 2A25_B 1X5M_A.
Probab=26.64 E-value=1.8e+02 Score=27.32 Aligned_cols=47 Identities=26% Similarity=0.495 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhh
Q 002260 824 LTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMER 885 (946)
Q Consensus 824 l~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~ 885 (946)
|.++|++|+.+|.||+.=|..++... --+.|...|.+++..|.+++.
T Consensus 1 ~~~~i~eL~~Dl~El~~Ll~~a~R~r---------------Vk~~L~~ei~klE~eI~~~~~ 47 (79)
T PF09032_consen 1 MSEQIEELQLDLEELKSLLEQAKRKR---------------VKDLLTNEIRKLETEIKKLKE 47 (79)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTTCC---------------HHHHHHHHHHHHHHHHHHCHH
T ss_pred ChhHHHHHHHHHHHHHHHHHHhhHHH---------------HHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999887777664221 136778888999999998876
No 78
>PF03026 CM1: Influenza C virus M1 protein; InterPro: IPR004271 This family represents the matrix protein, M1, of Influenza C virus. The M1 protein is the product of a spliced mRNA. Small quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein (see IPR004267 from INTERPRO).; GO: 0019028 viral capsid
Probab=26.05 E-value=33 Score=35.71 Aligned_cols=99 Identities=23% Similarity=0.304 Sum_probs=49.8
Q ss_pred EeeCCCCeEEEEEEeeChhHHHHHHhhhcCCCCCCccCccCChhHHHHHHH-----------hhC-CCCcccee-cccch
Q 002260 706 DFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLK-----------ELM-PGLTAKVF-RTYNA 772 (946)
Q Consensus 706 dFlGKdgir~~~tV~VD~~V~knLk~f~k~K~Pgd~LFd~Ldss~LN~yLk-----------elm-~glTAKdF-RTynA 772 (946)
||+|-.++-.-...+ |.++...+... -+.|+|---| +.-..+.+||+ .+. .|-||=-. -.-.|
T Consensus 103 dflgvesmmkmrafr-ddqimemveev--ydhpddytpd-irigtitawlrcknkkseryrsnvsesgrtalkihevrka 178 (235)
T PF03026_consen 103 DFLGVESMMKMRAFR-DDQIMEMVEEV--YDHPDDYTPD-IRIGTITAWLRCKNKKSERYRSNVSESGRTALKIHEVRKA 178 (235)
T ss_pred chhhHHHHHHHHhhh-hHHHHHHHHHH--hcCCccCCCC-eeeeehhhhhhhcccchHHHhhcccccchhhhHHHHHHHH
Confidence 677766655555555 77777777776 3455543211 22333444443 222 33333111 11122
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCcc
Q 002260 773 SITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQRT 812 (946)
Q Consensus 773 Svta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQRa 812 (946)
| |+...++.++ ...|-.+..++--...||||||+=.
T Consensus 179 s-tamneiagit---glgeealslqrqteslailcnhtfg 214 (235)
T PF03026_consen 179 S-TAMNEIAGIT---GLGEEALSLQRQTESLAILCNHTFG 214 (235)
T ss_pred H-HHHHHHhccc---cccHHHHHHHhhhhHHHHHHccccc
Confidence 2 2223333322 2234455667777889999999743
No 79
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=25.80 E-value=1.8e+02 Score=26.01 Aligned_cols=47 Identities=21% Similarity=0.388 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhh
Q 002260 822 SRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMER 885 (946)
Q Consensus 822 ~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~ 885 (946)
+.++++|..++..+..+...++.+... .+..+.+|..+.++|.+++.
T Consensus 2 ~~i~e~l~~ie~~l~~~~~~i~~lE~~-----------------~~~~e~~i~~~~~~l~~I~~ 48 (71)
T PF10779_consen 2 QDIKEKLNRIETKLDNHEERIDKLEKR-----------------DAANEKDIKNLNKQLEKIKS 48 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHHH
Confidence 445566666665555554444433211 13445567777777777653
No 80
>PF01519 DUF16: Protein of unknown function DUF16; InterPro: IPR002862 Proteins that contain this domain are of unknown function. It appears to be confined to proteins from Mycoplasma pneumoniae [].; PDB: 2BA2_C.
Probab=25.48 E-value=2.8e+02 Score=27.39 Aligned_cols=52 Identities=25% Similarity=0.482 Sum_probs=41.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHh
Q 002260 816 THSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKME 884 (946)
Q Consensus 816 ~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~ 884 (946)
.+++|+.+|.+.++.+-+|++++..+.+.. | -+.+.+.+.+..+..||.+||
T Consensus 50 ~qgeqI~kL~e~V~~QGEqIkel~~e~k~q------------g-----ktL~~I~~~L~~inkRLD~~E 101 (102)
T PF01519_consen 50 AQGEQINKLTEKVDKQGEQIKELQVEQKAQ------------G-----KTLQLILKTLQSINKRLDKME 101 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------H-----HHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------H-----HHHHHHHHHHHHHHHHHhhcc
Confidence 688889999999999999999887776621 1 134777888899999999886
No 81
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=25.27 E-value=1.7e+02 Score=30.89 Aligned_cols=34 Identities=18% Similarity=0.191 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhccccccccceeeec
Q 002260 866 PEALERKMAQTNAKIEKMERDMKTKEDLKTVALG 899 (946)
Q Consensus 866 ~e~~~k~i~~~~~~i~k~~~~~~~keenK~vaLG 899 (946)
.|.+-++|.+|+++|.+++-.....+.-.+++=+
T Consensus 127 ~ee~~~~l~~le~~~~~~e~~~~~~~~~~~~~~~ 160 (175)
T PRK13182 127 MEEMLERLQKLEARLKKLEPIYITPDTEPTYERE 160 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccCCccccccccc
Confidence 3677789999999999998777777665555544
No 82
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=25.02 E-value=3e+02 Score=25.86 Aligned_cols=57 Identities=19% Similarity=0.398 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhcccc
Q 002260 819 AQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMKT 889 (946)
Q Consensus 819 ~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~ 889 (946)
.+...++.+++.|+.+..++-+.+..+++.. ...+.+..++..++++|..++.++..
T Consensus 36 ~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~--------------~~~~~l~~e~~~lk~~i~~le~~~~~ 92 (108)
T PF02403_consen 36 QERRELQQELEELRAERNELSKEIGKLKKAG--------------EDAEELKAEVKELKEEIKELEEQLKE 92 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCHTT--------------CCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHhhCc--------------ccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555666655555555555544322 12355555666666666666555443
No 83
>PRK09039 hypothetical protein; Validated
Probab=23.61 E-value=2e+02 Score=33.09 Aligned_cols=38 Identities=29% Similarity=0.392 Sum_probs=27.6
Q ss_pred CCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 002260 809 HQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAK 846 (946)
Q Consensus 809 HQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k 846 (946)
.+++....-..++..|+.+|+.|+.|+..++..|..++
T Consensus 127 ~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae 164 (343)
T PRK09039 127 SEKQVSARALAQVELLNQQIAALRRQLAALEAALDASE 164 (343)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444445678888999999999988888887665
No 84
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=23.57 E-value=4.1e+02 Score=27.38 Aligned_cols=29 Identities=14% Similarity=0.173 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHh
Q 002260 818 SAQMSRLTEKIEDLKG-VLKDLRVDLDRAK 846 (946)
Q Consensus 818 ~~~m~kl~~ki~~lk~-~~~~~~~~l~~~k 846 (946)
...+++|++.++.|+. .+.++-+.+..+.
T Consensus 9 ~~g~~~L~~EL~~L~~~~r~e~~~~i~~Ar 38 (157)
T PRK01885 9 REGYARLKQELDYLWREERPEVTQKVSWAA 38 (157)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence 3567888988888875 4556656666654
No 85
>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length. The function of this family is unknown.; GO: 0005198 structural molecule activity
Probab=23.28 E-value=2.6e+02 Score=28.87 Aligned_cols=48 Identities=23% Similarity=0.371 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHH
Q 002260 820 QMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIE 881 (946)
Q Consensus 820 ~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~ 881 (946)
....+.+.++.++.||.++...|+.+++.. ...|.++++|+.|+..++
T Consensus 21 ~~~~~~~e~~~~k~ql~~~d~~i~~Lk~~~--------------~d~eeLk~~i~~lq~~~~ 68 (155)
T PF06810_consen 21 KVDKVKEERDNLKTQLKEADKQIKDLKKSA--------------KDNEELKKQIEELQAKNK 68 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--------------CCHHHHHHHHHHHHHHHH
Confidence 445556777788888888877777776421 235777788888777777
No 86
>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=22.43 E-value=2.2e+02 Score=29.87 Aligned_cols=130 Identities=18% Similarity=0.129 Sum_probs=75.1
Q ss_pred hHHHHHHHHHHhhccccCCcccccCCCceeeccCCCCceE----E-cCCCeEEEEeeCCCCeEEEEEEeeChhHHHHHHh
Q 002260 657 RQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVE----C-IPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQ 731 (946)
Q Consensus 657 RqlAvAlyLIDklALRvGnEKy~~endTvG~cTLR~eHVk----l-~~~~~V~FdFlGKdgir~~~tV~VD~~V~knLk~ 731 (946)
.-+|+++.|...|.||.= | ++.|+..+.+ + .+++.|.+.+-+|.|..+.+.|.-...+...|..
T Consensus 31 ~~~a~~l~Lq~~fGLR~~-E----------a~~l~~~~~~w~~~l~~~~~~~~v~~gtKGGr~R~v~I~~~~~~~~~L~~ 99 (187)
T PF12835_consen 31 PRVAAALELQRAFGLRRE-E----------ALKLRPSLATWEKALERGDETLRVVVGTKGGRPREVPILDSEKQREALER 99 (187)
T ss_pred hhhHHHHHHHHHhCCCHH-H----------HHhccHhhhhHHHHHhcCCCceEEeecCCCCCcceecCCCcHHHHHHHHH
Confidence 347888899999999982 2 3444444441 1 1257888999999999999988524666666665
Q ss_pred hhc-CCCCCCccCccCChhHHHHHHHhhC-----CC----CccceecccchHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Q 002260 732 FQT-GKKQNDDLFDKLDTAKLNAHLKELM-----PG----LTAKVFRTYNASITLDGMLNKGTGDGDVAVKIDVYQRANK 801 (946)
Q Consensus 732 f~k-~K~Pgd~LFd~Ldss~LN~yLkelm-----~g----lTAKdFRTynASvta~~~L~~~~~~~s~~eK~~~yn~Anr 801 (946)
-.. ....+..|+.. ..++.+++.+. -| .++.-+|=.-|--.+.+.+ ..+ ..|-.|..
T Consensus 100 a~~~~~~~~~~li~~---~~l~~~~~~~~~~~~k~gl~~~~~~HGLRh~YAqery~~l~----~~G------~~~~~a~~ 166 (187)
T PF12835_consen 100 AAAVARERNGSLIPK---YSLKQALRRYRYALRKLGLTGSTGFHGLRHAYAQERYEELQ----AQG------FSYKEALA 166 (187)
T ss_pred HHHHhcccCCcccCc---cCHHHHHHHHHHHHHHcCCCcCCCchhHHHHHHHHHHHHHH----HCC------CCHHHHHH
Confidence 321 12234455552 22444443332 24 3455555433333333333 222 12446888
Q ss_pred HHHHHcCCC
Q 002260 802 EVAIICNHQ 810 (946)
Q Consensus 802 eVAilCNHQ 810 (946)
.|+.-++|=
T Consensus 167 ~VS~eLGHG 175 (187)
T PF12835_consen 167 QVSQELGHG 175 (187)
T ss_pred HHHHHhcCC
Confidence 999999993
No 87
>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family. This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.
Probab=22.01 E-value=1.2e+03 Score=26.47 Aligned_cols=98 Identities=13% Similarity=0.180 Sum_probs=56.6
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 002260 771 NASITLDGMLNKGTGDGDVAVKIDVYQRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKP 850 (946)
Q Consensus 771 nASvta~~~L~~~~~~~s~~eK~~~yn~AnreVAilCNHQRaV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~ 850 (946)
.+...+.++|.+ -...+..|-.++..+=+-...+. -+.+.......|..|+.|+.+++.+|..+..--.
T Consensus 170 ~a~~fl~~ql~~---------~~~~l~~ae~~l~~fr~~~~~~d--~~~~~~~~~~~i~~L~~~l~~~~~~l~~l~~~~~ 238 (362)
T TIGR01010 170 DTIAFAENEVKE---------AEQRLNATKAELLKYQIKNKVFD--PKAQSSAQLSLISTLEGELIRVQAQLAQLRSITP 238 (362)
T ss_pred HHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHhCCCcC--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 344455666643 33444555556666554444442 2334445556677777777777777765542111
Q ss_pred CCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhcccc
Q 002260 851 PLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMKT 889 (946)
Q Consensus 851 ~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~ 889 (946)
...+.+-.++.+++.++.+|.+...++..
T Consensus 239 ----------~~~P~v~~l~~~i~~l~~~i~~e~~~i~~ 267 (362)
T TIGR01010 239 ----------EQNPQVPSLQARIKSLRKQIDEQRNQLSG 267 (362)
T ss_pred ----------CCCCchHHHHHHHHHHHHHHHHHHHHhhc
Confidence 12345667778888888888877665554
No 88
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=21.17 E-value=2.2e+02 Score=29.27 Aligned_cols=74 Identities=12% Similarity=0.160 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCCCCCCcccccccCCC-------HHHHHHHHHHHHHHHHHHhhcccc
Q 002260 818 SAQMSRLTEKIEDLKG-VLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLA-------PEALERKMAQTNAKIEKMERDMKT 889 (946)
Q Consensus 818 ~~~m~kl~~ki~~lk~-~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~-------~e~~~k~i~~~~~~i~k~~~~~~~ 889 (946)
...+++|++.++.|+. .+-++-+.+..+...- ....|.. ...++.+|..|+.+|...++--.+
T Consensus 7 ~~G~~~L~~El~~L~~~~r~~~~~~i~~Ar~~G---------DlsENaeY~aak~~~~~le~rI~~L~~~L~~A~iid~~ 77 (156)
T TIGR01461 7 PEGYEKLKQELNYLWREERPEVTQKVTWAASLG---------DRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYS 77 (156)
T ss_pred HHHHHHHHHHHHHHHhcccHHHHHHHHHHHHcC---------CcchhhhhHHHHHHHHHHHHHHHHHHHHHhcCEEeCCC
Confidence 3567888988888874 5666666666654211 1111111 134555666666666665543222
Q ss_pred ccccceeeecc
Q 002260 890 KEDLKTVALGT 900 (946)
Q Consensus 890 keenK~vaLGT 900 (946)
......|.+|+
T Consensus 78 ~~~~~~V~~Gs 88 (156)
T TIGR01461 78 PQQEGKVFFGA 88 (156)
T ss_pred CCCCCEEecCe
Confidence 22345777775
No 89
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=20.67 E-value=1.9e+02 Score=33.98 Aligned_cols=76 Identities=18% Similarity=0.339 Sum_probs=42.5
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCccccc--cc-CCCHHHHHHHHHHHHHHHHHHhhccccc
Q 002260 815 KTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKR--KR-NLAPEALERKMAQTNAKIEKMERDMKTK 890 (946)
Q Consensus 815 K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~--~~-~~~~e~~~k~i~~~~~~i~k~~~~~~~k 890 (946)
....+.++.|.+.++.++.++.+++..|..+++.+.......+-.. .+ .....++..+++++++++..|+.++...
T Consensus 330 ~~l~~~~~~l~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~l~~~l~~~ 408 (451)
T PF03961_consen 330 PELKEKLEELEEELEELKEELEKLKKNLKKLKKLKKQGKLPPEKKEQLKKLKEKKKELKEELKELKEELKELKEELERS 408 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4455677888888888888888888887766653321100000000 00 0123455666666666666666555554
No 90
>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]
Probab=20.19 E-value=2e+02 Score=37.84 Aligned_cols=84 Identities=15% Similarity=0.214 Sum_probs=47.6
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcccccccCCCHHHHHHHHHHHHHHHHHHhhcccccc
Q 002260 812 TVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALERKMAQTNAKIEKMERDMKTKE 891 (946)
Q Consensus 812 aV~K~~~~~m~kl~~ki~~lk~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~e~~~k~i~~~~~~i~k~~~~~~~ke 891 (946)
-++.+++.+++.|+.-+..++.++.+|..++.++++.-... ++ ....+..++.+++.+|.+....|+.=+
T Consensus 654 ~~~~s~d~~ie~le~e~~~l~~~~~~l~~~~~~~e~~l~e~--------~~--~~~~l~~~~~q~~~~~~~~~~em~el~ 723 (1074)
T KOG0250|consen 654 VDEFSFDDEIEDLEREASRLQKEILELENQRREAEKNLEEL--------EK--KLRELSEHIEQIKRRIRKKRAEMTELK 723 (1074)
T ss_pred ccchhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HH--HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45788899988888888888888888877777665321100 00 123344455555555555555544433
Q ss_pred cc-ceeeeccccccc
Q 002260 892 DL-KTVALGTSKINY 905 (946)
Q Consensus 892 en-K~vaLGTSKiNY 905 (946)
.+ -.-++-|+++|=
T Consensus 724 n~~e~~~~~~~~~~~ 738 (1074)
T KOG0250|consen 724 NTAEEKQVDISKLED 738 (1074)
T ss_pred hhhhhhhcchhhhHH
Confidence 32 234455555553
No 91
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=20.15 E-value=2.1e+02 Score=23.85 Aligned_cols=52 Identities=31% Similarity=0.392 Sum_probs=34.7
Q ss_pred hHHHHHHHhCCCCCccccCCCCcHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhcccc
Q 002260 462 FWNDWRKLLGKNHVIQNLEGCDFKPIYDWHQEQKEKKKQMSSEEKKALKEEKNKQEEKYM 521 (946)
Q Consensus 462 Ff~D~r~~l~~~~~I~~~~kcDF~~I~~~~~~~ke~kk~~skeEKk~~K~ek~~~e~~yg 521 (946)
|+.+++..+...+. .+.|..|...+ .+.-++||.+||+.-.+..++..+.|.
T Consensus 11 f~~~~r~~~~~~~p-----~~~~~~i~~~~---~~~W~~ls~~eK~~y~~~a~~~~~~y~ 62 (66)
T cd01390 11 FSQEQRPKLKKENP-----DASVTEVTKIL---GEKWKELSEEEKKKYEEKAEKDKERYE 62 (66)
T ss_pred HHHHHHHHHHHHCc-----CCCHHHHHHHH---HHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 66666666543321 25666665544 567799999999988777777666664
Done!