Query psy12447
Match_columns 551
No_of_seqs 212 out of 1678
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 19:31:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12447.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12447hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0969|consensus 100.0 1.3E-81 2.9E-86 664.4 17.1 411 6-551 56-489 (1066)
2 PTZ00166 DNA polymerase delta 100.0 9.7E-75 2.1E-79 670.7 39.9 423 9-551 27-481 (1054)
3 PF03104 DNA_pol_B_exo1: DNA p 100.0 7.3E-51 1.6E-55 421.4 21.2 316 59-509 1-325 (325)
4 cd05777 DNA_polB_delta_exo DED 100.0 1.9E-44 4.1E-49 355.8 19.8 214 242-551 3-222 (230)
5 PRK05762 DNA polymerase II; Re 100.0 2E-42 4.3E-47 394.6 21.8 330 24-551 3-347 (786)
6 cd05778 DNA_polB_zeta_exo inac 100.0 3.1E-41 6.7E-46 332.5 20.1 213 244-550 2-231 (231)
7 KOG0970|consensus 100.0 3.8E-35 8.1E-40 321.7 21.5 390 21-550 329-749 (1429)
8 cd05780 DNA_polB_Kod1_like_exo 100.0 3.3E-34 7.3E-39 275.9 18.0 188 244-551 1-194 (195)
9 cd05779 DNA_polB_epsilon_exo D 100.0 4.1E-34 8.9E-39 275.6 17.4 197 245-549 1-203 (204)
10 cd05784 DNA_polB_II_exo DEDDy 100.0 2.9E-33 6.4E-38 267.8 16.1 154 339-550 32-193 (193)
11 PRK05761 DNA polymerase I; Rev 100.0 2.5E-33 5.5E-38 317.9 16.1 294 28-549 20-334 (787)
12 TIGR00592 pol2 DNA polymerase 100.0 1.3E-31 2.8E-36 315.9 30.4 368 50-551 321-721 (1172)
13 cd05776 DNA_polB_alpha_exo ina 100.0 6E-33 1.3E-37 274.3 8.3 217 244-551 1-225 (234)
14 cd05781 DNA_polB_B3_exo DEDDy 100.0 6.9E-32 1.5E-36 257.8 15.1 178 244-551 1-187 (188)
15 cd05785 DNA_polB_like2_exo Unc 100.0 1.5E-31 3.2E-36 259.1 14.4 190 242-549 5-206 (207)
16 COG0417 PolB DNA polymerase el 100.0 1.9E-30 4.2E-35 296.0 22.9 324 50-550 7-348 (792)
17 KOG0968|consensus 100.0 4.8E-31 1.1E-35 289.4 13.2 225 242-549 654-885 (1488)
18 cd05160 DEDDy_DNA_polB_exo DED 100.0 5.2E-30 1.1E-34 247.6 16.2 195 248-550 1-199 (199)
19 PHA02528 43 DNA polymerase; Pr 100.0 9.4E-30 2E-34 289.4 15.8 213 243-551 103-323 (881)
20 KOG1798|consensus 100.0 8E-29 1.7E-33 276.4 21.5 329 50-546 68-444 (2173)
21 PHA03036 DNA polymerase; Provi 100.0 2.2E-29 4.7E-34 284.1 15.8 222 243-551 157-474 (1004)
22 cd05783 DNA_polB_B1_exo DEDDy 100.0 4.8E-29 1E-33 240.9 14.2 188 242-550 1-202 (204)
23 PHA02524 43A DNA polymerase su 100.0 7.6E-28 1.6E-32 256.2 16.1 208 244-550 104-322 (498)
24 smart00486 POLBc DNA polymeras 99.9 1.7E-26 3.7E-31 250.5 17.8 211 244-551 1-219 (471)
25 TIGR00592 pol2 DNA polymerase 99.9 2.5E-26 5.3E-31 271.3 6.1 245 152-550 154-424 (1172)
26 cd05782 DNA_polB_like1_exo Unc 99.8 6.4E-19 1.4E-23 171.1 12.9 131 354-551 74-208 (208)
27 KOG0969|consensus 99.5 6E-15 1.3E-19 158.8 0.9 140 290-476 317-471 (1066)
28 PHA03334 putative DNA polymera 99.4 1E-13 2.2E-18 158.2 6.6 191 347-551 320-554 (1545)
29 PF10108 DNA_pol_B_exo2: Predi 99.1 3.5E-10 7.5E-15 108.6 10.9 126 356-548 35-165 (209)
30 PF13482 RNase_H_2: RNase_H su 98.3 1.4E-06 3.1E-11 81.1 6.2 90 357-532 42-132 (164)
31 PTZ00166 DNA polymerase delta 97.8 1.1E-05 2.4E-10 95.5 3.7 129 290-465 309-452 (1054)
32 COG3359 Predicted exonuclease 97.7 0.00027 5.8E-09 68.6 10.2 92 356-533 141-238 (278)
33 cd05777 DNA_polB_delta_exo DED 97.4 0.00011 2.4E-09 72.7 4.1 120 292-458 52-184 (230)
34 cd05778 DNA_polB_zeta_exo inac 97.4 0.00017 3.7E-09 71.4 4.9 114 298-459 68-194 (231)
35 PRK06309 DNA polymerase III su 97.2 0.0024 5.2E-08 63.3 11.0 47 351-399 59-105 (232)
36 cd06125 DnaQ_like_exo DnaQ-lik 97.2 0.0019 4.2E-08 54.8 8.2 35 365-400 35-69 (96)
37 PRK08517 DNA polymerase III su 97.1 0.0036 7.8E-08 62.9 10.6 44 352-399 128-171 (257)
38 PRK05601 DNA polymerase III su 97.1 0.0059 1.3E-07 63.8 12.0 41 354-398 108-148 (377)
39 PRK06310 DNA polymerase III su 97.0 0.0047 1E-07 61.9 10.8 46 352-400 68-113 (250)
40 cd06138 ExoI_N N-terminal DEDD 97.0 0.0062 1.3E-07 58.0 11.0 43 356-399 67-109 (183)
41 cd06136 TREX1_2 DEDDh 3'-5' ex 97.0 0.013 2.8E-07 55.5 13.1 39 361-399 84-123 (177)
42 TIGR01405 polC_Gram_pos DNA po 96.9 0.0025 5.5E-08 76.4 8.9 44 352-399 251-294 (1213)
43 PRK06063 DNA polymerase III su 96.9 0.0099 2.1E-07 61.6 12.1 44 352-399 75-118 (313)
44 PRK06807 DNA polymerase III su 96.9 0.0023 4.9E-08 66.2 6.9 44 352-399 69-112 (313)
45 PRK05711 DNA polymerase III su 96.8 0.015 3.3E-07 57.8 12.2 41 354-398 69-109 (240)
46 TIGR01406 dnaQ_proteo DNA poly 96.8 0.017 3.6E-07 57.0 12.1 39 356-398 67-105 (225)
47 cd06130 DNA_pol_III_epsilon_li 96.7 0.022 4.8E-07 52.2 11.3 40 356-399 62-101 (156)
48 PRK07883 hypothetical protein; 96.5 0.017 3.6E-07 64.6 11.4 45 352-400 76-120 (557)
49 PRK07942 DNA polymerase III su 96.5 0.038 8.3E-07 54.7 12.8 41 358-399 75-117 (232)
50 cd06131 DNA_pol_III_epsilon_Ec 96.5 0.037 8E-07 51.5 11.6 42 354-399 64-105 (167)
51 PRK06195 DNA polymerase III su 96.4 0.027 5.9E-07 58.2 11.3 44 352-399 61-104 (309)
52 cd06127 DEDDh DEDDh 3'-5' exon 96.4 0.031 6.7E-07 50.6 10.2 39 356-398 64-102 (159)
53 COG2176 PolC DNA polymerase II 96.3 0.016 3.4E-07 67.5 9.4 110 242-400 417-526 (1444)
54 PRK07740 hypothetical protein; 96.3 0.038 8.3E-07 55.1 11.2 37 352-392 122-158 (244)
55 TIGR01407 dinG_rel DnaQ family 96.2 0.011 2.3E-07 69.7 7.5 44 352-399 61-104 (850)
56 smart00479 EXOIII exonuclease 96.0 0.13 2.8E-06 47.5 12.9 42 355-399 64-105 (169)
57 PRK08074 bifunctional ATP-depe 96.0 0.013 2.8E-07 69.5 7.5 44 352-399 65-108 (928)
58 PRK09146 DNA polymerase III su 95.9 0.071 1.5E-06 53.1 11.0 39 354-396 112-150 (239)
59 TIGR00573 dnaq exonuclease, DN 95.9 0.059 1.3E-06 52.8 10.3 41 353-397 69-109 (217)
60 PHA02524 43A DNA polymerase su 95.8 0.01 2.2E-07 64.7 4.7 50 300-367 169-218 (498)
61 PRK07748 sporulation inhibitor 95.6 0.14 3E-06 49.8 11.6 47 351-400 72-118 (207)
62 PRK07247 DNA polymerase III su 95.6 0.028 6.1E-07 54.1 6.5 37 351-390 64-100 (195)
63 PRK07246 bifunctional ATP-depe 95.4 0.028 6E-07 65.7 6.7 39 352-394 67-105 (820)
64 cd06134 RNaseT DEDDh 3'-5' exo 95.0 0.33 7.2E-06 46.4 11.9 41 358-399 80-126 (189)
65 PRK11779 sbcB exonuclease I; P 94.9 0.13 2.9E-06 56.1 9.8 37 357-394 77-113 (476)
66 cd06144 REX4_like DEDDh 3'-5' 94.7 0.11 2.4E-06 47.8 7.2 36 351-390 57-92 (152)
67 cd06137 DEDDh_RNase DEDDh 3'-5 94.5 0.23 5E-06 46.1 9.0 31 488-518 106-140 (161)
68 PRK05168 ribonuclease T; Provi 94.4 0.23 5E-06 48.4 9.2 42 357-399 91-138 (211)
69 TIGR01298 RNaseT ribonuclease 94.2 0.75 1.6E-05 44.4 12.3 42 357-399 82-129 (200)
70 PRK05359 oligoribonuclease; Pr 94.0 0.43 9.4E-06 45.4 10.0 44 355-399 76-122 (181)
71 TIGR03491 RecB family nuclease 93.7 0.5 1.1E-05 51.7 11.1 96 356-532 326-426 (457)
72 cd06133 ERI-1_3'hExo_like DEDD 93.3 0.41 8.9E-06 44.6 8.4 46 352-399 69-114 (176)
73 COG0847 DnaQ DNA polymerase II 92.8 0.73 1.6E-05 45.6 9.8 39 359-400 82-120 (243)
74 cd05776 DNA_polB_alpha_exo ina 92.4 0.13 2.9E-06 50.9 3.9 49 302-368 73-121 (234)
75 cd06145 REX1_like DEDDh 3'-5' 91.9 0.68 1.5E-05 42.5 7.7 31 357-390 61-91 (150)
76 PRK00448 polC DNA polymerase I 91.9 0.16 3.6E-06 62.2 4.5 43 354-400 482-524 (1437)
77 PRK09145 DNA polymerase III su 91.9 0.72 1.6E-05 44.5 8.2 41 352-396 92-132 (202)
78 cd05779 DNA_polB_epsilon_exo D 90.9 0.34 7.4E-06 47.0 4.8 54 296-367 57-111 (204)
79 PRK09182 DNA polymerase III su 90.6 0.33 7.1E-06 49.8 4.7 32 243-279 34-65 (294)
80 cd06135 Orn DEDDh 3'-5' exonuc 89.7 2.4 5.1E-05 39.9 9.4 44 354-398 71-117 (173)
81 PHA02528 43 DNA polymerase; Pr 87.7 0.4 8.7E-06 56.3 3.2 49 302-368 169-217 (881)
82 PRK06722 exonuclease; Provisio 84.9 0.75 1.6E-05 46.9 3.1 46 351-400 70-115 (281)
83 cd05784 DNA_polB_II_exo DEDDy 84.1 1.3 2.8E-05 42.6 4.2 89 244-367 1-89 (193)
84 PHA03036 DNA polymerase; Provi 83.9 0.54 1.2E-05 55.4 1.7 63 287-368 214-279 (1004)
85 PF03104 DNA_pol_B_exo1: DNA p 82.0 0.87 1.9E-05 46.9 2.3 59 291-367 201-260 (325)
86 PF01612 DNA_pol_A_exo1: 3'-5' 80.6 0.72 1.6E-05 42.6 1.0 30 361-393 65-95 (176)
87 PF00929 RNase_T: Exonuclease; 73.2 3.9 8.5E-05 36.6 3.7 35 356-393 67-101 (164)
88 PF03337 Pox_F12L: Poxvirus F1 65.4 40 0.00087 38.1 9.9 158 159-396 128-297 (651)
89 KOG0968|consensus 61.3 23 0.00049 42.3 7.2 134 49-183 47-201 (1488)
90 cd06149 ISG20 DEDDh 3'-5' exon 56.0 25 0.00054 32.4 5.5 34 353-390 59-92 (157)
91 cd05160 DEDDy_DNA_polB_exo DED 42.8 30 0.00065 32.9 4.0 50 300-367 52-101 (199)
92 PRK07983 exodeoxyribonuclease 42.8 14 0.00031 36.1 1.8 17 373-390 73-89 (219)
93 PTZ00315 2'-phosphotransferase 41.5 37 0.0008 38.1 4.8 44 351-395 123-174 (582)
94 PHA03334 putative DNA polymera 37.6 2.9 6.2E-05 50.5 -4.7 180 303-497 323-557 (1545)
95 smart00486 POLBc DNA polymeras 30.3 55 0.0012 35.2 4.0 54 296-367 54-107 (471)
96 PRK05755 DNA polymerase I; Pro 29.2 4E+02 0.0086 31.8 11.2 29 360-391 357-386 (880)
97 cd05780 DNA_polB_Kod1_like_exo 25.4 72 0.0016 30.4 3.4 45 305-367 50-94 (195)
98 TIGR00215 lpxB lipid-A-disacch 24.6 1.2E+02 0.0027 32.1 5.3 42 361-403 77-118 (385)
99 PHA02952 EEV maturation protei 23.9 1.9E+02 0.0041 32.9 6.6 45 349-394 245-293 (648)
100 COG5018 KapD Inhibitor of the 21.2 1.1E+02 0.0024 28.8 3.5 113 247-400 5-122 (210)
101 cd05785 DNA_polB_like2_exo Unc 20.3 89 0.0019 30.2 2.9 41 309-367 56-96 (207)
No 1
>KOG0969|consensus
Probab=100.00 E-value=1.3e-81 Score=664.41 Aligned_cols=411 Identities=57% Similarity=0.965 Sum_probs=368.0
Q ss_pred ccCcCCCCCCCCCCCCCCceEEEEEEEEEEeCCCCCCCCCCCCCCccEEEEEeecCCCcEEEEEEeceeeEEEEeCCCCC
Q psy12447 6 TSDKWSRAPPPELNPKEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEF 85 (551)
Q Consensus 6 ~~~~w~~~~~~~~~~~~~~~~f~~~d~d~~~~~~~~~~~~~~~~~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~~~~ 85 (551)
.++.|.||++|.++|.+..+.||++|++.|...+ ......+|++|+||.|.+|.|||+|||||.||||+++|.++
T Consensus 56 ~~~~w~Rp~~p~~~p~~~~i~fqq~~~e~y~~~~-----~~~~~~~pvvr~fGvT~~G~sv~~~v~gf~pyfYv~ap~g~ 130 (1066)
T KOG0969|consen 56 EHSRWARPALPALDPIKNDIEFQQIDIEFYVENG-----SGTSGSVPVVRLFGVTKEGNSVCCHVHGFFPYFYVEAPNGF 130 (1066)
T ss_pred ccccccCCCCCccCcccccceEEEeehhhhccCC-----CcccCCCceEEEeeeccCCCeEEEEEecccceEEecCCCCC
Confidence 3578999999999999999999999999997533 23456789999999999999999999999999999999999
Q ss_pred ChhHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEeeeeeeecCCCcccEEEEEccc------------CC---CcC
Q psy12447 86 NSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITESV------------FP---TFP 150 (551)
Q Consensus 86 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k~~lygy~~~~~~~flKI~~~~------------~~---~l~ 150 (551)
.++++..+...|+..+.. ..+..+++|++..+|||++..+.+|+||+... .+ ...
T Consensus 131 ~~e~i~~~~~~l~~~~~~----------~av~~ve~~~k~~l~~~~g~~k~~f~kit~~lP~~~~~~r~~lergv~~~~~ 200 (1066)
T KOG0969|consen 131 GPEHIGKFQQALDVKVTA----------HAVDHVEVVSKESLYGYQGDTKQPFLKITVTLPRMVAAARRLLERGVFISGK 200 (1066)
T ss_pred CHHHHHHHHHHHHHHHHH----------hHHHHHHHHhhhhhheecCCCCceeEEEecccHHHHHHhHHHHHhccccccc
Confidence 999999888888766532 14567889999999999998899999999421 01 011
Q ss_pred --CCcccccccCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCC
Q psy12447 151 --THTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVST 228 (551)
Q Consensus 151 --~~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~ 228 (551)
...+++||+||+|.+|||+|.+|.||+|++++.++|..+. .+.|.|++|+++.+.+
T Consensus 201 ~~~~~~~~yEsNi~f~lrfmvd~~iVG~~wi~lp~gk~~~~~---------~~~s~cqlEv~v~y~~------------- 258 (1066)
T KOG0969|consen 201 GEKVGFTTYESNIDFVLRFMVDCDIVGMNWIELPAGKYRIRD---------NRVSRCQLEVSVNYKD------------- 258 (1066)
T ss_pred CcceeeeEecCCccEEEEEEecCccccceeEEeccchheecc---------chhcccceEEEEeecc-------------
Confidence 1346899999999999999999999999999999998763 3799999999999999
Q ss_pred CcccccCCCCCcccccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeee
Q psy12447 229 DDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICC 308 (551)
Q Consensus 229 ~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~ 308 (551)
+++++++++|..+||+++|||||||.+++|.||.|+.|||++|+..+...|..+
T Consensus 259 --lishp~eG~w~~~APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~------------------------ 312 (1066)
T KOG0969|consen 259 --LISHPAEGEWSKIAPLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENE------------------------ 312 (1066)
T ss_pred --cccccccCcccccccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCc------------------------
Confidence 678888899999999999999999999999999999999999997765555443
Q ss_pred cchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChH
Q psy12447 309 KTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFP 388 (551)
Q Consensus 309 ~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~ 388 (551)
|+.+++|++++|.++.|++|++|.+|++||..|..+|++.|||+|+|||+.+||+|
T Consensus 313 ------------------------pf~rnvf~l~~capI~G~~V~~~~~e~elL~~W~~firevDPDvI~GYNi~nFDiP 368 (1066)
T KOG0969|consen 313 ------------------------PFVRNVFTLKTCAPIVGSNVHSYETEKELLESWRKFIREVDPDVIIGYNICNFDIP 368 (1066)
T ss_pred ------------------------hHHHhhhcccCcCCCCCceeEEeccHHHHHHHHHHHHHhcCCCeEecccccccccc
Confidence 78888999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccc
Q psy12447 389 YLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFI 468 (551)
Q Consensus 389 yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~ 468 (551)
||++||+.||+..|..|||+++.. ..|.|+.+
T Consensus 369 Yll~RA~~L~Ie~Fp~LGRikn~~------------------------------------------------s~irDttf 400 (1066)
T KOG0969|consen 369 YLLNRAKTLGIENFPYLGRIKNSR------------------------------------------------SVIRDSTF 400 (1066)
T ss_pred eecChHhhcCcccccccceecccc------------------------------------------------eeeecccc
Confidence 999999999999999999987643 23445678
Q ss_pred cccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc------ccc
Q psy12447 469 QSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP------KSN 542 (551)
Q Consensus 469 ~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~------~D~ 542 (551)
+|+++|.|+.+.+.|.||+.+||+.++++++||+||+|+.|+.||||++|+|+++.-|+++.+++.+.|+| |||
T Consensus 401 SSkq~GtRetK~v~I~GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siItdLQng~~~TRRRlA~YCLkDA 480 (1066)
T KOG0969|consen 401 SSKQYGTRETKEVNIDGRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQTRRRLAVYCLKDA 480 (1066)
T ss_pred chhhcCcccceEEeecceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchhhhhcCcHHHHHHHHHHHhhhh
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999 999
Q ss_pred ccccccCCC
Q psy12447 543 AAPLRYSPK 551 (551)
Q Consensus 543 ~l~~rl~~~ 551 (551)
+||+|||+|
T Consensus 481 YLPlRLlek 489 (1066)
T KOG0969|consen 481 YLPLRLLEK 489 (1066)
T ss_pred cchHHHHHH
Confidence 999999975
No 2
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=100.00 E-value=9.7e-75 Score=670.71 Aligned_cols=423 Identities=44% Similarity=0.768 Sum_probs=354.3
Q ss_pred cCCCCCCCCCCCCCCceEEEEEEEEEE------eCCCCCCCCCCCCCCccEEEEEeecCCCcEEEEEEeceeeEEEEeCC
Q psy12447 9 KWSRAPPPELNPKEDKIVFQQISIEHY------TGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAP 82 (551)
Q Consensus 9 ~w~~~~~~~~~~~~~~~~f~~~d~d~~------~~~~~~~~~~~~~~~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~ 82 (551)
.|.|+|.|+.. ....|.||++|+||+ .+.|.++.++.....+|+|||||+|++|+|||||||||+|||||++|
T Consensus 27 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pvIRlFGvTe~G~SV~v~V~gF~PYFYV~~p 105 (1054)
T PTZ00166 27 SKLRRPLPPIS-LQKDLVFFQLDADYTEKDDKSQGNPHNTVSGVRHVEVPIIRLYGVTKEGHSVLVNVHNFFPYFYIEAP 105 (1054)
T ss_pred HhccCCCCccc-ccCCceEEEEeeeccccccccccCccccCCCccCCCceEEEEEEecCCCCEEEEEEeCCceEEEEecC
Confidence 47788865533 567899999999998 66666677777788999999999999999999999999999999999
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEeeeeeeecCCCcccEEEEEcccC-----------CCcC-
Q psy12447 83 KEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITESVF-----------PTFP- 150 (551)
Q Consensus 83 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k~~lygy~~~~~~~flKI~~~~~-----------~~l~- 150 (551)
+++.++++..+...|+..+..... .......+.++++|+|+++|||+++++.+|+||+.... ..+.
T Consensus 106 ~~~~~~~~~~~~~~L~~~l~~~~~--~~~~~~~V~~VeiV~k~sl~gY~~~~~~~flKIt~~~P~~v~klR~~Le~g~~~ 183 (1054)
T PTZ00166 106 PNFLPEDSQKLKRELNAQLSEQSQ--FKKYQNTVLDIEIVKKESLMYYKGNGEKDFLKITVQLPKMVPRLRSLIESGVVV 183 (1054)
T ss_pred CCCCHHHHHHHHHHHHHHHhhccc--ccccCCceEEEEEEEeeeeceeCCCCceeEEEEEEcCHHHHHHHHHHHHcCCcc
Confidence 999888888888888775533110 01233578999999999999999766899999994221 1100
Q ss_pred -------CCcccccccCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcc
Q psy12447 151 -------THTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEE 223 (551)
Q Consensus 151 -------~~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~ 223 (551)
...+++||+||+|++|||+|++|.||+|+++++++|.++... .+.|+|++|++|++++|
T Consensus 184 ~~~~~~~~~~~~vyEsnI~f~lRFmID~~I~g~~Wi~i~~~~~~~~~~~-------~~~s~c~~E~~~~~~~l------- 249 (1054)
T PTZ00166 184 CGGGWDGIRLFQTYESNVPFVLRFLIDNNITGGSWLTLPKGKYKIRPPK-------KKTSTCQIEVDCSYEDL------- 249 (1054)
T ss_pred cccccccccccceeecCCCHHHHHHhccCCCceeEEEecCcceeecccc-------cCCCcceEEEEEehhhe-------
Confidence 123689999999999999999999999999998887765432 37899999999999884
Q ss_pred cccCCCcccccCCCCCcccccCceeEEEEEEeccCCC-CCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccC
Q psy12447 224 IDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKG-IFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVG 302 (551)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~~-~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~ 302 (551)
.+++++.+|.++|||+||||||||.++.+ .||+|+.|||+|||+++...|...
T Consensus 250 --------~~~~~~~~~~~~pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~------------------ 303 (1054)
T PTZ00166 250 --------IPLPPEGEYLTIAPLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEE------------------ 303 (1054)
T ss_pred --------eecccccccCCCCCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCcc------------------
Confidence 44444556778999999999999999877 499999999999999876655432
Q ss_pred ceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecc
Q psy12447 303 SQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNI 382 (551)
Q Consensus 303 ~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi 382 (551)
.|+.+.+|+++.|.++.|..|..|++|++||.+|+++|+.+|||||+|||+
T Consensus 304 -----------------------------~~~~r~vftl~~c~~i~g~~V~~f~sE~eLL~~f~~~I~~~DPDII~GYNi 354 (1054)
T PTZ00166 304 -----------------------------EPLTKFIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVDPDFLTGYNI 354 (1054)
T ss_pred -----------------------------CCcceEEEecCccccCCCceEEEeCCHHHHHHHHHHHHHhcCCCEEEecCC
Confidence 144566888888998899999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccc
Q psy12447 383 QNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSV 462 (551)
Q Consensus 383 ~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~ 462 (551)
.+||||||++||+.||+..|..|||++......
T Consensus 355 ~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~----------------------------------------------- 387 (1054)
T PTZ00166 355 INFDLPYLLNRAKALKLNDFKYLGRIKSTRSVI----------------------------------------------- 387 (1054)
T ss_pred cCCcHHHHHHHHHHhCCCchhhcCcccCCCccc-----------------------------------------------
Confidence 999999999999999999888899986543111
Q ss_pred cccccccccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---
Q psy12447 463 IKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP--- 539 (551)
Q Consensus 463 i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~--- 539 (551)
++..++++++|.++...+.++||+++|+|++++++++|+||+|++||+|+||++|+++++++|++||.+++..+++
T Consensus 388 -~~~~~~~~~~g~~~~~~~~i~GR~~iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~ 466 (1054)
T PTZ00166 388 -KDSKFSSKQMGTRESKEINIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAV 466 (1054)
T ss_pred -cccccccccccccccceeEeeeEEEEEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHH
Confidence 1123455678877777899999999999999999999999999999999999999999999999999988887766
Q ss_pred ---cccccccccCCC
Q psy12447 540 ---KSNAAPLRYSPK 551 (551)
Q Consensus 540 ---~D~~l~~rl~~~ 551 (551)
+||.|+++||.|
T Consensus 467 Y~l~Da~L~~~L~~k 481 (1054)
T PTZ00166 467 YCLKDAILPLRLLDK 481 (1054)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999864
No 3
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=100.00 E-value=7.3e-51 Score=421.36 Aligned_cols=316 Identities=37% Similarity=0.640 Sum_probs=230.6
Q ss_pred ecCCCcEEEEEEeceeeEEEEeCCCCCChhHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEe-eeeeeecCCCccc
Q psy12447 59 VTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQK-QTVFGFWGEELEN 137 (551)
Q Consensus 59 ~te~G~svcv~V~gf~PYFYv~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k-~~lygy~~~~~~~ 137 (551)
.|++|++|||+|+||+||||+.+++......+.. .++.. +. ......+++++.|+| +++|||+.+ ...
T Consensus 1 ~t~~g~svcv~v~~f~pyfYv~~~~~~~~~~~~~---~~~~~----~~---~~~~~~~~~~~~V~r~~~~~~y~~~-~~~ 69 (325)
T PF03104_consen 1 MTEDGKSVCVRVHGFRPYFYVLPPESDSPKDLEQ---FIEQL----LR---KKFKIDVFKIEKVKRKKSFYGYDGK-EEP 69 (325)
T ss_dssp -ECTSEEEEEEEST--EEEEEEESSGGGHHHHTT---HEEHH----EE---TTEEEEEEEEEEEEEEEESSEETTE-EEE
T ss_pred CCCCCCEEEEEEcCCCEEEEEECCCCccHHHHHH---HHHHH----hh---hccCCceEEEEEEEeeeeeccCCCC-Cce
Confidence 4789999999999999999999887644322211 11000 11 123467899999999 999999975 455
Q ss_pred EEEEEcccCC-------CcCCCcccccccCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEE
Q psy12447 138 FLKITESVFP-------TFPTHTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEID 210 (551)
Q Consensus 138 flKI~~~~~~-------~l~~~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~ 210 (551)
|+||+..... .+.+..+++||+||++++|||+|++|.|++|+++++..... ..+.|+|+.|+.
T Consensus 70 ~lkV~~~~~~~~~~~~~~l~~~~~~~~e~~i~~~~rfl~~~~i~~~~wi~i~~~~~~~----------~~~~s~~~~e~~ 139 (325)
T PF03104_consen 70 FLKVYFSSPRDVRKLRDNLKKTFFKVYEADIPPLERFLIDRNIRGPGWIKIKNPSKPV----------KDRVSWCDIEFS 139 (325)
T ss_dssp EEEEEESSTTHHHHHHHHHHHTEEEEESTSS-HHHHHHHHTTHCTTEEEEEETTECHH----------HHHTCTCSCECE
T ss_pred EEEEEECcHHHHHHHHHHHHhccchhhccCCCHHHheeeecCcccceeeecccccccc----------cccccccccccc
Confidence 9999954322 12235679999999999999999999999999998751111 136899999999
Q ss_pred EEcCcccCCCCcccccCCCcccccCCCCCcccccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCccccccc
Q psy12447 211 VSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKN 290 (551)
Q Consensus 211 v~~~~I~n~~~~~~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~ 290 (551)
+...++.. .... ...|++++|||||||.+.++.||++..|+|+|||++++..+...
T Consensus 140 ~~~~~~~~---------------~~~~---~~~p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~------ 195 (325)
T PF03104_consen 140 VDYSNLKP---------------LPDE---SIPPPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSE------ 195 (325)
T ss_dssp CCHHHHEC---------------HTSS---SSGGGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEE------
T ss_pred cccccccc---------------cccc---ccccccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccC------
Confidence 88877322 1111 11299999999999999988899999999999999987554221
Q ss_pred ccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCcc-CcEEeEcCCHHHHHHHHHHHH
Q psy12447 291 VFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIV-GSQVICCKTETELLDKWSAFI 369 (551)
Q Consensus 291 ~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~-g~~V~~~~~E~~LL~~f~~~i 369 (551)
+..+..|+++.|+... +..|..|++|++||.+|+++|
T Consensus 196 ------------------------------------------~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i 233 (325)
T PF03104_consen 196 ------------------------------------------PYRRKVFTLGSCDSIEDNVEVIYFDSEKELLEAFLDII 233 (325)
T ss_dssp ------------------------------------------TTEEEEEECSCSCCTTCTTEEEEESSHHHHHHHHHHHH
T ss_pred ------------------------------------------CCceEEEEecCCCCCCCCcEEEEECCHHHHHHHHHHHH
Confidence 2334567888877776 899999999999999999999
Q ss_pred HhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCcccccccccc
Q psy12447 370 RELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKN 449 (551)
Q Consensus 370 ~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~ 449 (551)
+++|||||+|||+.+|||+||.+||+.||++.+...++.......+.
T Consensus 234 ~~~dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~~~~--------------------------------- 280 (325)
T PF03104_consen 234 QEYDPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFGRLK--------------------------------- 280 (325)
T ss_dssp HHHS-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEEEEE---------------------------------
T ss_pred HhcCCcEEEEecccCCCHHHHHHHHHHhCccccccccccccceeEEe---------------------------------
Confidence 99999999999999999999999999999876544333221110000
Q ss_pred ccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHH
Q psy12447 450 FTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSV 509 (551)
Q Consensus 450 ~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V 509 (551)
...+.+.++|.+....+.++||++||+|+++|+.++|+||+|++|
T Consensus 281 ---------------~~~~~~~~~~~~~~~~~~~~Gr~~~D~~~~~~~~~~l~sY~L~~V 325 (325)
T PF03104_consen 281 ---------------RKKWPSSANGSRKFSRIDIPGRLVLDLYRLARKDYKLDSYSLDNV 325 (325)
T ss_dssp ---------------EEESEECTCCCTTEEEEEETTSEEEEHHHHHHHHS--SS-SHHHH
T ss_pred ---------------ecccccccCCCcceeEEEECCChHhHHHHHHHhhCCCCCCCCCCC
Confidence 001112224555566789999999999999999999999999997
No 4
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=100.00 E-value=1.9e-44 Score=355.81 Aligned_cols=214 Identities=62% Similarity=1.004 Sum_probs=183.7
Q ss_pred cccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHH
Q psy12447 242 KVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 321 (551)
Q Consensus 242 ~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~ 321 (551)
++||+++|||||||.+.+|.||+|+.|+|+|||+++...+...
T Consensus 3 ~~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~------------------------------------- 45 (230)
T cd05777 3 KIAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGE------------------------------------- 45 (230)
T ss_pred CCCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCC-------------------------------------
Confidence 4799999999999999988899999999999999976555432
Q ss_pred HHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCc
Q psy12447 322 IRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKN 401 (551)
Q Consensus 322 ~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~ 401 (551)
+..+.+|+++.|.++.|..|..|++|++||.+|+++|+++|||||+|||+.+||||||.+||+.+|++.
T Consensus 46 -----------~~~~~~~~l~~~~~~~~~~v~~~~~E~eLL~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~ 114 (230)
T cd05777 46 -----------PFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNT 114 (230)
T ss_pred -----------CceeEEEEeCCCCCCCCCEEEEECCHHHHHHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCcc
Confidence 223446777777788888999999999999999999999999999999999999999999999999998
Q ss_pred ccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceee
Q psy12447 402 FTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTI 481 (551)
Q Consensus 402 ~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~ 481 (551)
|..+||.+......+. ..+.++++|.+....+
T Consensus 115 ~~~lgR~~~~~~~~~~------------------------------------------------~~~~~~~~g~~~~~~~ 146 (230)
T cd05777 115 FPFLGRIKNIKSTIKD------------------------------------------------TTFSSKQMGTRETKEI 146 (230)
T ss_pred ccccccccCCceeEeC------------------------------------------------CcccccccccccceEE
Confidence 8889998654311110 1233455776666678
Q ss_pred eeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc------cccccccccCCC
Q psy12447 482 NFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP------KSNAAPLRYSPK 551 (551)
Q Consensus 482 ~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~------~D~~l~~rl~~~ 551 (551)
.++||+++|+|++++++++|+||+|++||+++||++|+++++++|.+||.+++..+++ +||.|+++||.|
T Consensus 147 ~i~GR~~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~k 222 (230)
T cd05777 147 NIEGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDK 222 (230)
T ss_pred EEcCEEeeeHHHHHHHhcCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999988776655 999999999865
No 5
>PRK05762 DNA polymerase II; Reviewed
Probab=100.00 E-value=2e-42 Score=394.60 Aligned_cols=330 Identities=20% Similarity=0.220 Sum_probs=231.6
Q ss_pred ceEEEEEEEEEEeCCCCCCCCCCCCCCccEEEEEeecCCCcEEEEEEeceeeEEEEeCCCCCChhHHHHHHHHHHHHHHH
Q psy12447 24 KIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIA 103 (551)
Q Consensus 24 ~~~f~~~d~d~~~~~~~~~~~~~~~~~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~~~~~~~~~~~~~~~l~~~l~~ 103 (551)
.+.++++|++|... +++|+|++||+|++|.++||++.+|+||||+..+.... . ..+..
T Consensus 3 ~~~~~lL~~~~~~~-----------~~~~vi~l~g~t~~G~~~~v~~~~~~~yFy~~~~~~~~---~----~~~~~---- 60 (786)
T PRK05762 3 LQQGFILTRHYRDT-----------PGGPEVELWLATDEGPRVVLLDPQFRPYFIPAEQDERA---E----SLLAG---- 60 (786)
T ss_pred ceEEEEEeeEEEEE-----------CCeEEEEEEEEcCCCCEEEEECCCCcEEEEEeCchhhh---H----HHHhh----
Confidence 47899999999873 36799999999999999999999999999998543211 1 11110
Q ss_pred HhccCcccccceEEEEEEEEeeeeeeecCCCcccEEEEEcc-------cCCCcCCCcccccccCcchhhhhhhhCCCCcc
Q psy12447 104 DMRGNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITES-------VFPTFPTHTYKAFESNIDFDIRFMVDNDIVGC 176 (551)
Q Consensus 104 ~~~~~~~~~~~~i~~ie~V~k~~lygy~~~~~~~flKI~~~-------~~~~l~~~~~~vyEa~I~~~~rFliD~~I~g~ 176 (551)
. ....++.+..+ .|.+ +++..++.. ....++..++++||+||+|..|||+|++|.|+
T Consensus 61 -~---------~~~~~~~~~l~---~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~i~EaDI~~~~R~lid~~i~~~ 124 (786)
T PRK05762 61 -E---------IGVRLSPLALK---DFHR---RPVLGLYCRQHRQLTRLPKRLREGGVDVYEADIRFPERYLMERFITPC 124 (786)
T ss_pred -c---------ccceeecccee---cccC---CeeeEEEeccHHHHHHHHHHHHHcCCeEEECCCChhHhheeeCCCCCc
Confidence 0 00233333223 3332 234444421 12234457789999999999999999999999
Q ss_pred eEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCCCcccccCCCCCcccccCceeEEEEEEec
Q psy12447 177 NWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECA 256 (551)
Q Consensus 177 ~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~ 256 (551)
+|+.+... ..+++.++. ..+| . +...+ .|++++|||||||.
T Consensus 125 ~w~~~~~~-----------------~~~~~~~~~--~~~i---------------~---~~~~~--~p~lrvlsfDIE~~ 165 (786)
T PRK05762 125 VWFSGEVE-----------------QYTTDGVLR--NARL---------------K---PAPDY--RPPLKVVSLDIETS 165 (786)
T ss_pred EEEEEEee-----------------ccccceeEE--ecce---------------e---eCCCC--CCCCeEEEEEEEEc
Confidence 99987521 112344432 2331 1 11123 39999999999998
Q ss_pred cCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceee
Q psy12447 257 GRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVK 336 (551)
Q Consensus 257 ~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~ 336 (551)
+. ++|++|++. +.... .+
T Consensus 166 ~~---------~~i~sI~~~----~~~~~----~v--------------------------------------------- 183 (786)
T PRK05762 166 NK---------GELYSIGLE----GCGQR----PV--------------------------------------------- 183 (786)
T ss_pred CC---------CceEEeeec----CCCCC----eE---------------------------------------------
Confidence 64 268888864 21110 11
Q ss_pred eeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccc
Q psy12447 337 NVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIK 416 (551)
Q Consensus 337 ~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~ 416 (551)
+.++.+....+.-|..|.+|++||.+|+++|+++|||||+|||+.+||||||.+||+.+|++. .+||.....
T Consensus 184 --i~ig~~~~~~~~~v~~~~sE~~LL~~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~--~~GR~~~~~---- 255 (786)
T PRK05762 184 --IMLGPPNGEALDFLEYVADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPL--RLGRDGSEL---- 255 (786)
T ss_pred --EEEECCCCCCcceEEEcCCHHHHHHHHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCc--ccCcCCCcc----
Confidence 222222221112277899999999999999999999999999999999999999999999974 488754321
Q ss_pred hhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHH
Q psy12447 417 DSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLL 496 (551)
Q Consensus 417 ~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~ 496 (551)
.+... .+......+.++||+++|+|.++|
T Consensus 256 --------------------------------------------------~~~~~-~~~~~~~~~~i~GRv~lDl~~~~k 284 (786)
T PRK05762 256 --------------------------------------------------EWREH-PFRSGYGFASVPGRLVLDGIDALK 284 (786)
T ss_pred --------------------------------------------------ccccC-CCCCCcceEEEeeEEEEEHHHHHH
Confidence 00000 011122357899999999999999
Q ss_pred HHc-cCCCCCHHHHHHHhhccCCCCCCh----hhHHHHHhcCCCCCcc---cccccccccCCC
Q psy12447 497 REY-KLRSYTLNSVSYHFLQEQKEDVQH----SIISDLQIALLQPSDP---KSNAAPLRYSPK 551 (551)
Q Consensus 497 ~~~-kl~sYsL~~V~~~~Lg~~k~~~~~----~~i~~~~~~~~~~~~~---~D~~l~~rl~~~ 551 (551)
+.. +++||+|++||+++||++|+..+. ++|.++|.++....+. +||.|+++|+.|
T Consensus 285 ~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~k 347 (786)
T PRK05762 285 SATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEK 347 (786)
T ss_pred HhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 976 999999999999999999976544 7899999977655555 999999999863
No 6
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=100.00 E-value=3.1e-41 Score=332.46 Aligned_cols=213 Identities=24% Similarity=0.338 Sum_probs=172.0
Q ss_pred cCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHH
Q psy12447 244 APLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIR 323 (551)
Q Consensus 244 p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~ 323 (551)
+.|++|||||||.++++.||+|+.|||++|++++..++..... ......+
T Consensus 2 ~~l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~------------~~~~~~~------------------ 51 (231)
T cd05778 2 QHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFIL------------DANKVGV------------------ 51 (231)
T ss_pred CceEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccc------------cccceeE------------------
Confidence 4689999999999999999999999999999997654433210 0000011
Q ss_pred HhCCCCccCceeeeeeecCCC---------CCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHH
Q psy12447 324 TMGQGASENIFVKNVFTLNTC---------APIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRA 394 (551)
Q Consensus 324 ~~~~~~~~~p~~~~~f~~~~~---------~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~ 394 (551)
+|..+.| ..+.|+.|..|++|++||.+|+++|+.+|||||+|||+.+||||||++||
T Consensus 52 --------------l~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra 117 (231)
T cd05778 52 --------------IIVDELKSNASNGRIRSGLSGIPVEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERA 117 (231)
T ss_pred --------------EEEcCccchhhhhccccCCCCCeEEEeCCHHHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHH
Confidence 1222222 24567899999999999999999999999999999999999999999999
Q ss_pred HHcCCCcc-cccccccccccccchhhhhhhcccccccccccccCCCcccccccccccccccccccccccccccccccccc
Q psy12447 395 KHLGVKNF-TFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQM 473 (551)
Q Consensus 395 ~~l~i~~~-~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~ 473 (551)
+.+++..| ..+||++...... . .-.++++
T Consensus 118 ~~l~~~~~~~~lgR~~~~~~~~---------~-----------------------------------------~~~~~~~ 147 (231)
T cd05778 118 AALGIDDLLDEISRVPSDSNGK---------F-----------------------------------------GDRDDEW 147 (231)
T ss_pred HHhCCcchhhhccCCCCCCccc---------c-----------------------------------------ccccccc
Confidence 99999887 7899987643100 0 0001346
Q ss_pred CcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCC-CCCcc------ccccccc
Q psy12447 474 GKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALL-QPSDP------KSNAAPL 546 (551)
Q Consensus 474 g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~-~~~~~------~D~~l~~ 546 (551)
|.+..+.+.++||+++|+|+.+|++++|+||||++||+++||++|+++++++|++||+++. ..|++ +||.|++
T Consensus 148 g~~~~~~~~i~GRi~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l 227 (231)
T cd05778 148 GYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNL 227 (231)
T ss_pred ccccCCceEEeeEEEeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHH
Confidence 7666678999999999999999999999999999999999999999999999999998654 55666 9999999
Q ss_pred ccCC
Q psy12447 547 RYSP 550 (551)
Q Consensus 547 rl~~ 550 (551)
+||.
T Consensus 228 ~Ll~ 231 (231)
T cd05778 228 EILD 231 (231)
T ss_pred HhhC
Confidence 9985
No 7
>KOG0970|consensus
Probab=100.00 E-value=3.8e-35 Score=321.75 Aligned_cols=390 Identities=20% Similarity=0.301 Sum_probs=270.1
Q ss_pred CCCceEEEEEEEEEEeCCCCCCCCCCCCCCccEEEEEee----cCCCcEEEEEEeceeeEEEEeC-CCCCC--------h
Q psy12447 21 KEDKIVFQQISIEHYTGEPIPGMPGSQLKPVPIVRMFGV----TMEGNSVCCHVHGFSPYLYVSA-PKEFN--------S 87 (551)
Q Consensus 21 ~~~~~~f~~~d~d~~~~~~~~~~~~~~~~~~pvI~lfG~----te~G~svcv~V~gf~PYFYv~~-~~~~~--------~ 87 (551)
..+.++|+|+|+-.... +.-..|.|||+ ++++.||||.|.|.....|+.+ +..+. +
T Consensus 329 e~~~l~f~wlDaYee~~-----------~~~g~l~LFGKVk~~~~t~~Sccv~V~ni~R~lyflPR~~~l~~~~~e~~~~ 397 (1429)
T KOG0970|consen 329 EDGSLRFFWLDAYEEVY-----------KAPGTLYLFGKVKLSGDTYVSCCVVVKNICRVLYFLPRPIKLSAAVGEDSIP 397 (1429)
T ss_pred ccceEEEEEehhhHHHh-----------CCCceEEEEeeeeccCCCceEEEEEEcCeeeEEEecccccccccccCCccch
Confidence 45679999999643321 11278999999 3468999999999999888765 32222 1
Q ss_pred hHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEeeeeeeecC---CCcccEEEEEcc-----cCCCcCCCcc-cccc
Q psy12447 88 THCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFGFWG---EELENFLKITES-----VFPTFPTHTY-KAFE 158 (551)
Q Consensus 88 ~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k~~lygy~~---~~~~~flKI~~~-----~~~~l~~~~~-~vyE 158 (551)
+-..++..++...+... ....-++.+.|++. |.|+- ....+|++|... +..++.+..| ++|.
T Consensus 398 ~s~~dv~~E~~~~l~~k-------~~~~~fk~k~v~~~--yafe~~dvp~~~dyLeV~y~~~~p~LP~Dlkgdsfshvfg 468 (1429)
T KOG0970|consen 398 ESKRDVYKEVGSLLSNK-------LGLTEFKSKPVKKN--YAFELPDVPMKSDYLEVLYSYETPKLPSDLKGDSFSHVFG 468 (1429)
T ss_pred hhHHHHHHHHHHHHHhh-------hhhhHhhhhhhhhh--hccccCCCCCCCcceEEeccccCCCCccccccchHHHHhc
Confidence 12233344443333322 22234666777777 55652 335788999843 2234555666 8999
Q ss_pred cCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCCCcccccCCCC
Q psy12447 159 SNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEG 238 (551)
Q Consensus 159 a~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~~~~~~~~ 238 (551)
+|..+++||+++|+|+|+||+++.+.. .+ ....|||++||.|.-++- +....+.
T Consensus 469 t~tn~lE~fll~rKimGPCWlkv~~~s---~~--------~~~~SwCk~Ev~v~sP~n---------------I~~~~~~ 522 (1429)
T KOG0970|consen 469 TNTNPLERFLLSRKIMGPCWLKVKGYS---DP--------PRNASWCKVEVTVKSPQN---------------ITVVCSK 522 (1429)
T ss_pred cCccHHHHHHHhccccCceEEEeecCC---CC--------CCCccceeeEEEecCCcc---------------eEEeecC
Confidence 999999999999999999999998643 11 246899999999986662 1111111
Q ss_pred CcccccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCccccc--CceeeeecchhhHHH
Q psy12447 239 EWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIV--GSQVICCKTETELLD 316 (551)
Q Consensus 239 ~~~~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~--~~~v~~~~~e~~~~~ 316 (551)
. .++|||++||+.|+|.. .|..+.++|+|||+.+++.-. |+..+|-+ +.+....-
T Consensus 523 ~-a~~Ppl~llsL~i~T~~----N~k~~~~Eiv~is~l~~~~~~-----------id~p~p~~~~~~~~c~l~------- 579 (1429)
T KOG0970|consen 523 K-APPPPLTLLSLNIRTSM----NPKQNKNEIVMISMLCFHNFS-----------IDKPAPAPAFPRHFCVLT------- 579 (1429)
T ss_pred C-CCCCCeeEEEeeeeehh----ccccchhhhhhhhhhhccccc-----------ccCCCCCCcccCcceeEe-------
Confidence 1 45899999999999987 455667999999988754322 11112111 11110000
Q ss_pred HHHHHHHHhCCCCccCceeeeeeecCCCCC--ccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHH
Q psy12447 317 KWSAFIRTMGQGASENIFVKNVFTLNTCAP--IVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRA 394 (551)
Q Consensus 317 ~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~--~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~ 394 (551)
+|. ...|+++.... -....|..+++|++||..|+..++..|||+|+|||+.+|++..|..|+
T Consensus 580 ---------------rP~-~~~fP~g~~ela~~k~~~v~~~~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~ 643 (1429)
T KOG0970|consen 580 ---------------RPP-GTSFPLGLKELAKQKLSKVVLHNSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRL 643 (1429)
T ss_pred ---------------cCC-CCcCCchHHHHHHhccCceEEecCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHH
Confidence 011 11344332110 122358999999999999999999999999999999999999999999
Q ss_pred HHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccC
Q psy12447 395 KHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMG 474 (551)
Q Consensus 395 ~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g 474 (551)
..+++++|+.+||+++.. ..+ +| .++.+|
T Consensus 644 ~~~Kip~WS~IgRLrrS~---~~k------fg------------------------------------------~~s~~~ 672 (1429)
T KOG0970|consen 644 HALKIPNWSSIGRLRRSW---PPK------FG------------------------------------------RSSSFG 672 (1429)
T ss_pred HHhcCcchhhhhhhhhcc---ccc------cC------------------------------------------Cccccc
Confidence 999999999999997641 000 11 011244
Q ss_pred cccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc-----cccccccccC
Q psy12447 475 KRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP-----KSNAAPLRYS 549 (551)
Q Consensus 475 ~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~-----~D~~l~~rl~ 549 (551)
. ...+.|||++|+=...+...+..||+|.+++++.|+..+.++...+|.++|......... +|+.+.++||
T Consensus 673 e----~~~~aGRl~CD~~~~a~~lik~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s~~L~~ll~~~~~d~~~~l~i~ 748 (1429)
T KOG0970|consen 673 E----FFIIAGRLMCDLNLAARELIKAQSYSLSELSQQILKEERKEINANEIPKMYEDSKSLTYLLEHTITDAELILQIM 748 (1429)
T ss_pred c----cccccceEEeehHHHHHhhhccccccHHHHHHHHHhhhcccCCHhHhhhhccChHHHHHHHHHHhHHHHHHHHHH
Confidence 3 244999999999555566678999999999999999988889999999999987762111 9999999987
Q ss_pred C
Q psy12447 550 P 550 (551)
Q Consensus 550 ~ 550 (551)
.
T Consensus 749 ~ 749 (1429)
T KOG0970|consen 749 F 749 (1429)
T ss_pred H
Confidence 4
No 8
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=100.00 E-value=3.3e-34 Score=275.92 Aligned_cols=188 Identities=33% Similarity=0.468 Sum_probs=151.4
Q ss_pred cCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHH
Q psy12447 244 APLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIR 323 (551)
Q Consensus 244 p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~ 323 (551)
|++++++|||||.+.+| ||+|..|+|+|||++. .+... +++
T Consensus 1 p~l~i~~fDIEt~~~~g-~p~~~~d~Ii~Is~~~--~~~~~------~~~------------------------------ 41 (195)
T cd05780 1 EDLKILSFDIEVLNHEG-EPNPEKDPIIMISFAD--EGGNK------VIT------------------------------ 41 (195)
T ss_pred CCceEEEEEEEecCCCC-CCCCCCCcEEEEEEec--CCCce------EEE------------------------------
Confidence 78999999999998876 8999999999999864 11111 111
Q ss_pred HhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCccc
Q psy12447 324 TMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFT 403 (551)
Q Consensus 324 ~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~ 403 (551)
+..++. ..|..|.+|++||.+|+++|+++|||+|+|||+.+||||||.+||..+|++.
T Consensus 42 -----------------~~~~~~---~~v~~~~~E~~lL~~F~~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~-- 99 (195)
T cd05780 42 -----------------WKKFDL---PFVEVVKTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIEL-- 99 (195)
T ss_pred -----------------ecCCCC---CeEEEeCCHHHHHHHHHHHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCC--
Confidence 111111 1577899999999999999999999999999999999999999999999973
Q ss_pred ccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeee
Q psy12447 404 FLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINF 483 (551)
Q Consensus 404 ~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i 483 (551)
.+||..... .+ ..+|.+ ....+
T Consensus 100 ~~~r~~~~~------------------------------------------------------~~--~~~g~~--~~~~i 121 (195)
T cd05780 100 DLGRDGSEI------------------------------------------------------KI--QRGGFN--NASEI 121 (195)
T ss_pred ccccCCCce------------------------------------------------------eE--eeccee--eeecc
Confidence 466653211 00 113332 24578
Q ss_pred eceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc------cccccccccCCC
Q psy12447 484 EGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP------KSNAAPLRYSPK 551 (551)
Q Consensus 484 ~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~------~D~~l~~rl~~~ 551 (551)
.||+++|+|+++++.++++||+|++||+++||.+|+++++++|.++|.+++ .+++ +||+|+++||++
T Consensus 122 ~Gr~~lDl~~~~~~~~~l~sy~L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~-~~~~l~~Y~~~D~~lt~~L~~~ 194 (195)
T cd05780 122 KGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGE-NLERLFRYSMEDAKYTYEIGKE 194 (195)
T ss_pred CCeEEEeHHHHHHhhCCCCcCcHHHHHHHHhCCCCCcCCHHHHHHHHhCCC-chHHHHHHhHHHHHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999875 3333 999999999864
No 9
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=100.00 E-value=4.1e-34 Score=275.60 Aligned_cols=197 Identities=25% Similarity=0.272 Sum_probs=152.6
Q ss_pred CceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHH
Q psy12447 245 PLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRT 324 (551)
Q Consensus 245 ~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~ 324 (551)
++++|||||||.+.++.||+|+.|+|+|||+++...|... ..+.+....+
T Consensus 1 ~lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~-----------~~~~~~~~~~------------------- 50 (204)
T cd05779 1 DPRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLI-----------VNREIVSEDI------------------- 50 (204)
T ss_pred CceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEE-----------eccccccccc-------------------
Confidence 5899999999998777899999999999999875433211 0011110000
Q ss_pred hCCCCccCceeeeeeecCCCCCccC-cEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCccc
Q psy12447 325 MGQGASENIFVKNVFTLNTCAPIVG-SQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFT 403 (551)
Q Consensus 325 ~~~~~~~~p~~~~~f~~~~~~~~~g-~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~ 403 (551)
..|....|..+.+ ..|+.|++|++||.+|+++++++|||+|+|||+.+||||||.+||+.+|++...
T Consensus 51 ------------~~~~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~ 118 (204)
T cd05779 51 ------------EDFEYTPKPEYEGPFKVFNEPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEE 118 (204)
T ss_pred ------------ccccccCCCCCCCceEEecCCCHHHHHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchh
Confidence 0122333444433 578889999999999999999999999999999999999999999999986533
Q ss_pred ccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeee
Q psy12447 404 FLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINF 483 (551)
Q Consensus 404 ~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i 483 (551)
.+||... ..| ...+
T Consensus 119 ~~g~~~~-------------------------------------------------------------~~~-----~~~~ 132 (204)
T cd05779 119 EIGFRKD-------------------------------------------------------------SEG-----EYKS 132 (204)
T ss_pred hhCeEec-------------------------------------------------------------CCC-----eEEe
Confidence 3332100 011 2456
Q ss_pred eceeeeeHHHHHHHHccC--CCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---cccccccccC
Q psy12447 484 EGRVCFDLLFVLLREYKL--RSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPLRYS 549 (551)
Q Consensus 484 ~GR~~lDl~~~~~~~~kl--~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~rl~ 549 (551)
+||+++|+|.++++...+ .+|+|++||+++||++|.++++.+|.++|.++++..+. +||+++++|.
T Consensus 133 ~gr~~iDl~~~~~~~~~l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 133 RYIIHMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLY 203 (204)
T ss_pred ccEEEEEhHHHHHHhhcCCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCcHHHHhccHHHHHHHHHHh
Confidence 899999999999997654 69999999999999999999999999999998876666 9999999875
No 10
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=100.00 E-value=2.9e-33 Score=267.76 Aligned_cols=154 Identities=25% Similarity=0.263 Sum_probs=126.3
Q ss_pred eecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchh
Q psy12447 339 FTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDS 418 (551)
Q Consensus 339 f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~ 418 (551)
+.++.+....|..|..|++|++||.+|+++++++|||||+|||+.+||||||.+||+.+|++. .+||.+...
T Consensus 32 ~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~--~~gR~~~~~------ 103 (193)
T cd05784 32 LMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPL--RLGRGGSPL------ 103 (193)
T ss_pred EEECCCCCCCCCEEEEECCHHHHHHHHHHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCc--ccccCCCcc------
Confidence 444445555677899999999999999999999999999999999999999999999999975 577765421
Q ss_pred hhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHH-
Q psy12447 419 FIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLR- 497 (551)
Q Consensus 419 f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~- 497 (551)
.+. ..|.+......++||+++|+|.++|+
T Consensus 104 ------------------------------------------------~~~--~~g~~~~~~~~i~GR~~~D~~~~~k~~ 133 (193)
T cd05784 104 ------------------------------------------------NWR--QSGKPGQGFLSLPGRVVLDGIDALKTA 133 (193)
T ss_pred ------------------------------------------------ccc--cCCcCCcceEEEeeEEEEEhHHHHHHc
Confidence 000 01222234689999999999999987
Q ss_pred HccCCCCCHHHHHHHhhccCCCCCC----hhhHHHHHhcCCCCCcc---cccccccccCC
Q psy12447 498 EYKLRSYTLNSVSYHFLQEQKEDVQ----HSIISDLQIALLQPSDP---KSNAAPLRYSP 550 (551)
Q Consensus 498 ~~kl~sYsL~~V~~~~Lg~~k~~~~----~~~i~~~~~~~~~~~~~---~D~~l~~rl~~ 550 (551)
.++|.||+|++||+++||++|.+++ +.+|.++|.+++...+. +||.|++|||+
T Consensus 134 ~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 134 TYHFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDKLALARYNLQDCELVWRIFE 193 (193)
T ss_pred cCCCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhC
Confidence 6899999999999999999998765 45999999988765555 99999999985
No 11
>PRK05761 DNA polymerase I; Reviewed
Probab=100.00 E-value=2.5e-33 Score=317.87 Aligned_cols=294 Identities=21% Similarity=0.271 Sum_probs=200.9
Q ss_pred EEEEEEEEeCCCCCCCCCCCCCCccEEEEEeecCCCcEEEEEEe-ceeeEEEEeCCCCCChhHHHHHHHHHHHHHHHHhc
Q psy12447 28 QQISIEHYTGEPIPGMPGSQLKPVPIVRMFGVTMEGNSVCCHVH-GFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMR 106 (551)
Q Consensus 28 ~~~d~d~~~~~~~~~~~~~~~~~~pvI~lfG~te~G~svcv~V~-gf~PYFYv~~~~~~~~~~~~~~~~~l~~~l~~~~~ 106 (551)
+++|++|... .++|+|+|||++ +|..+.+... ||+||||+..+++. +.+ .+ ..
T Consensus 20 ~lld~~Y~~~-----------~~~~vi~l~~~~-~~~~~~~~d~~gfkPYfy~~~~~~~----~~~---~~------~~- 73 (787)
T PRK05761 20 YLLSVDYDGK-----------LGKAVVKLYDPE-TGKIYKWYDRTGHKPYFLTDLDPDE----IDK---IP------KI- 73 (787)
T ss_pred eEEEEEEecc-----------CCeeEEEEEecC-CCeEEEEEcCCCCCCeEEecCChHH----HHh---hh------hh-
Confidence 6999998762 478999999995 6765555554 59999999865431 111 00 00
Q ss_pred cCcccccceEEEEEEEEeeeeeeecCCCcccEEEEEcccC---CCcCC---CcccccccCcchhhhhhhhCCCCcceEEE
Q psy12447 107 GNKDEIQEAVLMVEIVQKQTVFGFWGEELENFLKITESVF---PTFPT---HTYKAFESNIDFDIRFMVDNDIVGCNWIE 180 (551)
Q Consensus 107 ~~~~~~~~~i~~ie~V~k~~lygy~~~~~~~flKI~~~~~---~~l~~---~~~~vyEa~I~~~~rFliD~~I~g~~Wi~ 180 (551)
.....+..++.|++.+.|+|+ ..+++||+.... +.++. ..+++|||||+|+.|||+|++|.||+|+.
T Consensus 74 ----~~~~~~~~~e~~~~~~~~~~~---~~~~~kI~~~~p~~v~~~r~~~~~~~~~~EaDI~f~~RyliD~~i~~~~~~~ 146 (787)
T PRK05761 74 ----LRHPSFDHLEIVEKYDGLRDK---KVKVTKIVVKDPLAVRRLRLSVRDIPRAWEADIKYEFRYIYDNGLIPGMPYD 146 (787)
T ss_pred ----hcCCCeeeEEEEEEEeccCCC---cceEEEEEECCHHHHHHHHHHHHhhhhheeCCCChHHheEEeCCCCCCceEE
Confidence 012357789999999988774 689999995432 22211 11689999999999999999999999999
Q ss_pred eCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCCCcccccCCCCCcccccCceeEEEEEEeccCC-
Q psy12447 181 IPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRK- 259 (551)
Q Consensus 181 i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~- 259 (551)
+....+... ...|+.|+...+...+.... +...+. ....|++++|||||||.+..
T Consensus 147 ~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~--------~~~~l~----~~~~P~lk~lsfDIE~~~~~~ 202 (787)
T PRK05761 147 VKNGLESVE------------PEILVEEIKKAFKDERKLAE--------DWLPIF----EAPIPKIKRIAIDIEVYTPAK 202 (787)
T ss_pred ecccccccc------------cccccccccccchhhhhhhh--------hhhhhc----cCCCCCcceEEEEEEeccCcC
Confidence 976543221 12255555443322000000 000000 12469999999999998753
Q ss_pred CCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeee
Q psy12447 260 GIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVF 339 (551)
Q Consensus 260 ~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f 339 (551)
|.||+
T Consensus 203 g~~P~--------------------------------------------------------------------------- 207 (787)
T PRK05761 203 GRIPD--------------------------------------------------------------------------- 207 (787)
T ss_pred CCCCC---------------------------------------------------------------------------
Confidence 33332
Q ss_pred ecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhh
Q psy12447 340 TLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSF 419 (551)
Q Consensus 340 ~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f 419 (551)
++|++||.+|+++|+++||||+ ||+.+||||||.+||+.+|++.. .++|.
T Consensus 208 ----------------~~E~eLL~~f~~~i~~~dPdi~--yN~~~FDlPYL~~Ra~~lgi~~~-~~~~~----------- 257 (787)
T PRK05761 208 ----------------DSEKELLAELFDIILEYPPVVT--FNGDNFDLPYLYNRALKLGIPKE-EIPIE----------- 257 (787)
T ss_pred ----------------CCHHHHHHHHHHHHHhcCCEEE--EcCCcchHHHHHHHHHHhCCCch-hcccc-----------
Confidence 4899999999999999999985 99999999999999999998642 12221
Q ss_pred hhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHH--
Q psy12447 420 IQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLR-- 497 (551)
Q Consensus 420 ~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~-- 497 (551)
.|. |+.++|++..++.
T Consensus 258 -----------------------------------------------------~~~---------~~~~iDl~~~~~~~~ 275 (787)
T PRK05761 258 -----------------------------------------------------PGR---------AGIHIDLYKFFQNKA 275 (787)
T ss_pred -----------------------------------------------------cCC---------CceEEechhheeecc
Confidence 010 2335666665542
Q ss_pred --------HccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---cccccccccC
Q psy12447 498 --------EYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPLRYS 549 (551)
Q Consensus 498 --------~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~rl~ 549 (551)
.+++++|+|++||+++||++|.+++ .+|.++ +....+. +||.|+++|+
T Consensus 276 ~~~y~~~~~~~~~~ysL~~Va~~~Lg~~K~~~~-~~i~~~---~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 276 VRSYAFYGKYRHREARLDAVGRALLGISKVELE-TNISEL---DLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred eeeeeccceeecccCChHHHHHHHhCCCccccc-cccccc---CHHHHHHHHHHHHHHHHHHH
Confidence 2456799999999999999999997 566542 3323333 9999999984
No 12
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.3e-31 Score=315.88 Aligned_cols=368 Identities=20% Similarity=0.276 Sum_probs=250.1
Q ss_pred CccEEEEEeecCCCcEEEEEEecee-eEEEEeCCCCCChh---HHH---HHHH-HHHHHHHHHhccCcccccceEEEEEE
Q psy12447 50 PVPIVRMFGVTMEGNSVCCHVHGFS-PYLYVSAPKEFNST---HCR---AFKE-ALNRAIIADMRGNKDEIQEAVLMVEI 121 (551)
Q Consensus 50 ~~pvI~lfG~te~G~svcv~V~gf~-PYFYv~~~~~~~~~---~~~---~~~~-~l~~~l~~~~~~~~~~~~~~i~~ie~ 121 (551)
..+++.+||+...|.+||+.+.|+. ..|+++.+...... .+. .+.. .++ .++..+.+ .+..-++.+.
T Consensus 321 ~~G~~~lfGr~~~~~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le-~vs~~~lg----~~k~dv~~k~ 395 (1172)
T TIGR00592 321 KLGVVLLFGRDVDHVSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLE-FVSELALG----YKKEKFRAKP 395 (1172)
T ss_pred CCCeEEEecccCCceeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHH-HHHHHHhh----cCcCceeeEE
Confidence 3478999998767899999999976 66778776532211 111 1111 111 11111110 1122355566
Q ss_pred EEeeeeeeecCC-----CcccEEEEEccc------CC----CcCCCc-ccccccCcchhhhhhhhCCCCcceEEEeCCCe
Q psy12447 122 VQKQTVFGFWGE-----ELENFLKITESV------FP----TFPTHT-YKAFESNIDFDIRFMVDNDIVGCNWIEIPPGK 185 (551)
Q Consensus 122 V~k~~lygy~~~-----~~~~flKI~~~~------~~----~l~~~~-~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~ 185 (551)
|.+. |.+... ....++++.... .+ .+.+.. .++|+++....+|||++++++|+||+.+....
T Consensus 396 I~~~--~~~~~~~~~v~y~~~~lkv~y~l~~~~~~l~~l~~~~~g~~~~~vf~~n~g~~erfll~rki~gp~WL~i~~p~ 473 (1172)
T TIGR00592 396 IAKK--YEFEAPDIDAPYSSEYLEVTYELGKEFAPMEALPSDLKGQTFWHVFGSNTGNLERFLLLRKIKGPCWLAVKGPD 473 (1172)
T ss_pred ehhh--ccCCCCccCCcCCcceEEEEEccCccchhhhhhhhhccCCcchheeccCHHHHHHHHhcCCCCCCceEEeCCCc
Confidence 6665 333321 234667777332 11 122333 47999999999999999999999999997643
Q ss_pred eEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCCCcccccCCCCCcccccCceeEEEEEEeccCCCCCCCC
Q psy12447 186 WQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDP 265 (551)
Q Consensus 186 ~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~~~fP~~ 265 (551)
.. . ..+.|+|.+|+.+..+.. +.. +.+..+||+++|+|+||+ .+|..
T Consensus 474 ~~--~--------~~~~S~c~yEga~v~~p~---------------v~~---g~~~~~pPl~vLdFsi~S-----lyPsi 520 (1172)
T TIGR00592 474 EL--E--------YPRRSWCKYEGGYVKPPN---------------VEK---GLDKTPPPLVVLDFSMKS-----LNPSI 520 (1172)
T ss_pred cc--C--------cCCccccceEEEEecCcc---------------ccc---cccCCCCCeEEEEeeeEE-----ecCcc
Confidence 21 1 124789999999876551 111 123347999999999993 48999
Q ss_pred CCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCC-
Q psy12447 266 NHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTC- 344 (551)
Q Consensus 266 ~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~- 344 (551)
..++|+|||+++......++. .++.+.. +..+. +. .| ....|+++..
T Consensus 521 ~~~~nl~iS~~v~~~~~~d~~--------~~~~~~~---~~~~~------------------~~--~~-~~~~~p~~~~~ 568 (1172)
T TIGR00592 521 IRNEIVSIPDTLHREFALDKP--------PPEPPYD---VHPCV------------------GT--RP-KDCSFPLDLKG 568 (1172)
T ss_pred ccCceEEEEEEEeecccccCC--------CCCCccc---eEEEE------------------EE--cc-CCCCCCchhhh
Confidence 889999999998654322110 0000000 00000 00 00 0012233221
Q ss_pred --CCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhh
Q psy12447 345 --APIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQS 422 (551)
Q Consensus 345 --~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s 422 (551)
..+.+..|..|.+|++||.+|++.++.+|||+++|||+.+|||+||.+||..++++.|+.+||+++..
T Consensus 569 ~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~---------- 638 (1172)
T TIGR00592 569 EFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSP---------- 638 (1172)
T ss_pred hhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCC----------
Confidence 22345679999999999999999999999999999999999999999999999999999999875421
Q ss_pred hcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHHHccCC
Q psy12447 423 KQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLR 502 (551)
Q Consensus 423 ~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~ 502 (551)
.+|.+ ....+.||+++|+|..+++.+++.
T Consensus 639 -------------------------------------------------~~~~~--~~~~~~Grl~~D~~~~~k~~~~~~ 667 (1172)
T TIGR00592 639 -------------------------------------------------KFGRR--FGERTCGRMICDVEISAKELIRCK 667 (1172)
T ss_pred -------------------------------------------------Ccccc--ccceECCEEEEEHHHHHHHHhCcC
Confidence 01221 123499999999999999999999
Q ss_pred CCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc------cccccccccCCC
Q psy12447 503 SYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP------KSNAAPLRYSPK 551 (551)
Q Consensus 503 sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~------~D~~l~~rl~~~ 551 (551)
||+|++||+++||++|.++++.+|.++|..+. .+++ +||.|+++||.|
T Consensus 668 sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~-~~~~~~~y~~~Da~l~~~L~~~ 721 (1172)
T TIGR00592 668 SYDLSELVQQILKTERKVIPIDNINNMYSESS-SLTYLLEHTWKDAMFILQIMCE 721 (1172)
T ss_pred CCCHHHHHHHHhCCCCcccCHHHHHHHHhCcH-HHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999533 3444 999999999853
No 13
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=99.98 E-value=6e-33 Score=274.32 Aligned_cols=217 Identities=20% Similarity=0.238 Sum_probs=158.2
Q ss_pred cCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCce--eeeecchhhHHHHHHHH
Q psy12447 244 APLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQ--VICCKTETELLDKWSAF 321 (551)
Q Consensus 244 p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~--v~~~~~e~~~~~~~~~~ 321 (551)
|||++||+.|.|..+ +..+++||+|||+++++.-..++. .+....+ .+..
T Consensus 1 Ppl~v~sls~~T~~n----~k~~~~EI~~iS~~~~~~~~~d~~-----------~~~~~~~~~~~~~------------- 52 (234)
T cd05776 1 PPLTVMSLSIKTVLN----SKTNKNEIVMISMLVHRNVSLDKP-----------TPPPPFQSHTCTL------------- 52 (234)
T ss_pred CCeEEEEEEeEEEec----CcCCcchhheehHHHhcCCCCCCC-----------CCCcccccceEEE-------------
Confidence 899999999999863 444579999999998654333211 1100000 0000
Q ss_pred HHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCc
Q psy12447 322 IRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKN 401 (551)
Q Consensus 322 ~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~ 401 (551)
.+ +.+++ ..|. ....+....+..|..|++|++||.+|+++|+++|||||+|||+.+|||+||++||+.+|++.
T Consensus 53 ~r-~~~~~-~~~~-----~~~~~~~~~~~~v~~~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ 125 (234)
T cd05776 53 TR-PLGRS-PPPD-----LFEKNAKKKKTKVRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPH 125 (234)
T ss_pred Ee-CCCCC-CCCc-----hHHHHHHhcCCcEEEeCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCc
Confidence 00 00000 0010 00011223456799999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceee
Q psy12447 402 FTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTI 481 (551)
Q Consensus 402 ~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~ 481 (551)
|+++||++....+.+ ..++++ ....
T Consensus 126 ws~iGR~~~~~~~~~---------------------------------------------------~~~~~~----~~~~ 150 (234)
T cd05776 126 WSRIGRLKRSVWPKK---------------------------------------------------KGGGKF----GERE 150 (234)
T ss_pred cccccccccccCccc---------------------------------------------------cccccc----cccc
Confidence 999999876421100 001111 1246
Q ss_pred eeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc------cccccccccCCC
Q psy12447 482 NFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP------KSNAAPLRYSPK 551 (551)
Q Consensus 482 ~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~------~D~~l~~rl~~~ 551 (551)
.+.||+++|+|..+|+.++++||+|++||+++||++|.++++++|.++|.+ +..+.+ +||.|+++||.|
T Consensus 151 ~~~GRl~~D~~~~~k~~~~~~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~-~~~l~~l~~y~~~Da~l~~~L~~k 225 (234)
T cd05776 151 LTAGRLLCDTYLSAKELIRCKSYDLTELSQQVLGIERQDIDPEEILNMYND-SESLLKLLEHTEKDAYLILQLMFK 225 (234)
T ss_pred cccCchhhccHHHHHHHhCCCCCChHHHHHHHhCcCcccCCHHHHHHHHhC-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999999999999999999999999999999999997 444444 999999999864
No 14
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=99.97 E-value=6.9e-32 Score=257.81 Aligned_cols=178 Identities=28% Similarity=0.408 Sum_probs=141.1
Q ss_pred cCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHH
Q psy12447 244 APLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIR 323 (551)
Q Consensus 244 p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~ 323 (551)
|+|++|||||||.+..+ ||+|+.|+|+|||++. .+|...
T Consensus 1 p~l~~l~fDIEt~~~~g-fp~~~~d~Ii~Is~~~-~~g~~~--------------------------------------- 39 (188)
T cd05781 1 PDLKTLAFDIEVYSKYG-TPNPRRDPIIVISLAT-SNGDVE--------------------------------------- 39 (188)
T ss_pred CCceEEEEEEEecCCCC-CCCCCCCCEEEEEEEe-CCCCEE---------------------------------------
Confidence 78999999999997766 9999999999999874 111100
Q ss_pred HhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCccc
Q psy12447 324 TMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFT 403 (551)
Q Consensus 324 ~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~ 403 (551)
+| ...+.+|++||.+|+++|+++|||+|+|||+.+||||||.+||+.+|++.
T Consensus 40 --------------~~------------~~~~~~E~~lL~~F~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~-- 91 (188)
T cd05781 40 --------------FI------------LAEGLDDRKIIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKL-- 91 (188)
T ss_pred --------------EE------------EecCCCHHHHHHHHHHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCc--
Confidence 01 12357999999999999999999999999999999999999999999974
Q ss_pred ccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeee
Q psy12447 404 FLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINF 483 (551)
Q Consensus 404 ~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i 483 (551)
.+||..... ...+.+| .+.+
T Consensus 92 ~~gr~~~~~-------------------------------------------------------~~~~~~~-----~~~i 111 (188)
T cd05781 92 DVGRRGGSE-------------------------------------------------------PSTGVYG-----HYSI 111 (188)
T ss_pred ccccCCCcc-------------------------------------------------------cccCCcc-----eEee
Confidence 455532210 0011233 3789
Q ss_pred eceeeeeHHHHHHHHccCCCCCHHHHHHHhhcc----CCCCCChhhHHHHHhcCC--CCCcc---cccccccccCCC
Q psy12447 484 EGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQE----QKEDVQHSIISDLQIALL--QPSDP---KSNAAPLRYSPK 551 (551)
Q Consensus 484 ~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~----~k~~~~~~~i~~~~~~~~--~~~~~---~D~~l~~rl~~~ 551 (551)
+||+++|+|.++++..++.+|+|++||++ ||. .|.++++.+|.++|.++. ...++ +||.++++|+++
T Consensus 112 ~Gr~~iDl~~~~~~~~~l~~y~L~~Va~~-Lg~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 112 TGRLNVDLYDFAEEIPEVKVKTLENVAEY-LGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred eeEEEEEhHHHHHhhCCCCCCCHHHHHHH-HCCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999984 886 466789999999998732 12222 999999999865
No 15
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=99.97 E-value=1.5e-31 Score=259.14 Aligned_cols=190 Identities=27% Similarity=0.335 Sum_probs=145.1
Q ss_pred cccCceeEEEEEEeccCCCCC-CC--CCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHH
Q psy12447 242 KVAPLRILSFDIECAGRKGIF-PD--PNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKW 318 (551)
Q Consensus 242 ~~p~l~ils~DIE~~~~~~~f-P~--~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~ 318 (551)
..|+|++|||||||.+..+.| |+ +..|+|+|||+... .+. +
T Consensus 5 ~~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~-~~~-~---------------------------------- 48 (207)
T cd05785 5 TFDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDN-RGW-E---------------------------------- 48 (207)
T ss_pred CCCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccC-CCc-e----------------------------------
Confidence 368999999999999987654 54 56799999997521 110 0
Q ss_pred HHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcC
Q psy12447 319 SAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLG 398 (551)
Q Consensus 319 ~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~ 398 (551)
..+. ..+.+|++||.+|+++++++|||||+|||+.+||||||.+||+.+|
T Consensus 49 ------------------~~~~------------~~~~~E~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~ 98 (207)
T cd05785 49 ------------------EVLH------------AEDAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHG 98 (207)
T ss_pred ------------------eeec------------cCCCCHHHHHHHHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhC
Confidence 0110 1268999999999999999999999999999999999999999999
Q ss_pred CCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccc
Q psy12447 399 VKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKREN 478 (551)
Q Consensus 399 i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~ 478 (551)
++. .+||...... .+ ......+.|.+..
T Consensus 99 ~~~--~~~r~~~~~~-~~-------------------------------------------------~~~~~~~~~~~~~ 126 (207)
T cd05785 99 VPL--AIGRDGSIPR-QR-------------------------------------------------PSRFRFAERLIDY 126 (207)
T ss_pred CCc--ccccCCCcce-Ee-------------------------------------------------ecccccccccccc
Confidence 975 4666543210 00 0000000111122
Q ss_pred eeeeeeceeeeeHHHHHHH----HccCCCCCHHHHHHHh--hccCCCCCChhhHHHHHhcCCCCCcc---cccccccccC
Q psy12447 479 KTINFEGRVCFDLLFVLLR----EYKLRSYTLNSVSYHF--LQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPLRYS 549 (551)
Q Consensus 479 ~~~~i~GR~~lDl~~~~~~----~~kl~sYsL~~V~~~~--Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~rl~ 549 (551)
..+.++||+++|+|.++++ .++|+||+|++||+++ +|++|.++++.+|.++|.++....+. +||.++++|.
T Consensus 127 ~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~~~k~d~~~~~I~~l~~~~~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 127 PRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLASPDRTYIDGRQIAEVWRSDPARLLAYALDDVRETEGLA 206 (207)
T ss_pred ceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhcccCCCcCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHhh
Confidence 4678999999999999997 5689999999999997 67889999999999999998755555 9999999874
No 16
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=99.97 E-value=1.9e-30 Score=295.96 Aligned_cols=324 Identities=29% Similarity=0.406 Sum_probs=231.5
Q ss_pred CccEEEEEeecCCCcEEEEEEeceeeEEEEeCCCCCChhHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEeeeeee
Q psy12447 50 PVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFG 129 (551)
Q Consensus 50 ~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k~~lyg 129 (551)
+.|++++||.+++|.+++..+.+|.||||+..+.......+.. .... .........+.+.....++
T Consensus 7 ~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~---~~~~~~~~~~~~~~~~~~~ 72 (792)
T COG0417 7 GFPLVRIFGDTDSGKSVVKLVATFRPYFYVTLDNSRPEDYVLK-----------ILNR---RLDDVLELEEVENVPDPYL 72 (792)
T ss_pred CceEEEEeeecCCCCEEEEEecCCCCcEEEecCCCcccchhhh-----------hccc---cccccceeeeeeeeecccc
Confidence 4699999999999999999999999999999886511111100 0000 0011122222334443333
Q ss_pred ecCCCcccEEEEEcccC---CCc-------CCCcccccccCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCC
Q psy12447 130 FWGEELENFLKITESVF---PTF-------PTHTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNR 199 (551)
Q Consensus 130 y~~~~~~~flKI~~~~~---~~l-------~~~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~ 199 (551)
. .+....||+.... +.+ ......+||+||+|..|||+|++|.+|.|+.++.......
T Consensus 73 ~---~~~~~~~i~~~~p~~v~~~r~~~~~~~~~~~~i~e~dI~~~~r~~~d~~i~~~~~~~~~~~~~~~~---------- 139 (792)
T COG0417 73 G---REVEVLKIYARDPQAVRKLREKVKRELEGVVDIFEADIPFAMRYLIDKGIRPMVWVSVDVEDIGSI---------- 139 (792)
T ss_pred C---CcccceeeEecCHHHHHHHHHHHhhhhhccceEeecCCCcchheeeecCCCCceEEEeeeccccch----------
Confidence 2 4677889985321 111 1345689999999999999999999999998874211100
Q ss_pred CccccceeEEEEEcCcccCCCCcccccCCCcccccCCCCCcccccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeec
Q psy12447 200 PCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCIS 279 (551)
Q Consensus 200 ~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~~~~~~~~~~~~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~ 279 (551)
.... . . ..+...|+|++|||||||.+..+.+|++..|+|++|++....
T Consensus 140 -~~~~--~-------~----------------------~~~~~~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~ 187 (792)
T COG0417 140 -HSLF--L-------E----------------------HREDVRPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEA 187 (792)
T ss_pred -hhcc--c-------c----------------------cccCcCCCceEEEEEEEEecCCCCCCCccCCceEEEEEEecc
Confidence 0000 0 0 112347999999999999999999999999999999988532
Q ss_pred cCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHH
Q psy12447 280 QGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTET 359 (551)
Q Consensus 280 ~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~ 359 (551)
.+... +. ..+....+..|.++.+|.
T Consensus 188 ~~~~~------------~~-------------------------------------------~~~~~~~~~~v~~~~~e~ 212 (792)
T COG0417 188 EGGLI------------EV-------------------------------------------FIYTSGEGFSVEVVISEA 212 (792)
T ss_pred CCCcc------------cc-------------------------------------------ccccCCCCceeEEecCHH
Confidence 22110 00 001223445599999999
Q ss_pred HHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCC
Q psy12447 360 ELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNS 439 (551)
Q Consensus 360 ~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~ 439 (551)
+||.+|..++..+|||||+|||+++||||||.+||..+|++.+ +||.......
T Consensus 213 e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~--~gr~~~~~~~------------------------- 265 (792)
T COG0417 213 ELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLR--LGRDGSELRV------------------------- 265 (792)
T ss_pred HHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCcc--ccccccccce-------------------------
Confidence 9999999999999999999999999999999999999999874 7776543200
Q ss_pred ccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHH-HHccCCCCCHHHHHHHhhccCC
Q psy12447 440 DRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLL-REYKLRSYTLNSVSYHFLQEQK 518 (551)
Q Consensus 440 ~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~-~~~kl~sYsL~~V~~~~Lg~~k 518 (551)
.. .|. ..-.||+++|+|..++ +..++.+|+|++|+.++|++.|
T Consensus 266 ----------------------------~~---~~~-----~~~~Gr~~iDl~~~~~~~~~~~~~ysl~~v~~~~l~~~k 309 (792)
T COG0417 266 ----------------------------RK---SGF-----SSQVGRLHIDLYPALRRRPLNLKSYSLEAVSEALLGEGK 309 (792)
T ss_pred ----------------------------ee---ccc-----ccccceEEEecHHHHhhhhcccccccHHHHHHHhccccc
Confidence 00 111 0011999999999999 6999999999999999999988
Q ss_pred -CCCChhhHHHHHhcCCCCCcc------cccccccccCC
Q psy12447 519 -EDVQHSIISDLQIALLQPSDP------KSNAAPLRYSP 550 (551)
Q Consensus 519 -~~~~~~~i~~~~~~~~~~~~~------~D~~l~~rl~~ 550 (551)
.++....+.++|........+ +|+.|+++++.
T Consensus 310 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~ 348 (792)
T COG0417 310 REDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILL 348 (792)
T ss_pred ccccCccchhhccccCccchhHHHHHHHHHHHHHHHHHH
Confidence 788888888888766644333 99999998864
No 17
>KOG0968|consensus
Probab=99.97 E-value=4.8e-31 Score=289.41 Aligned_cols=225 Identities=25% Similarity=0.343 Sum_probs=168.9
Q ss_pred cccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHH
Q psy12447 242 KVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 321 (551)
Q Consensus 242 ~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~ 321 (551)
....|+++|+++++.++++.-|+|..|+|.+|.+++..+...-+. ..|.-+.++.+..-
T Consensus 654 ~~~~Lt~lsiElha~sr~dl~PDP~~D~V~~l~~~vq~dtp~pd~-----------~si~~~gv~Vv~~~---------- 712 (1488)
T KOG0968|consen 654 QTQLLTILSIELHATSRGDLEPDPVFDSVASLFLCVQEDTPMPDA-----------DSIVSVGVIVVDKV---------- 712 (1488)
T ss_pred ccceeeeeeeeccccccCCCCCCcccccchhhhhhhccCCCCCcc-----------cceeeeeEEEEecc----------
Confidence 446789999999999999999999999999999987654221100 00111112212100
Q ss_pred HHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCc
Q psy12447 322 IRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKN 401 (551)
Q Consensus 322 ~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~ 401 (551)
+ |-. .+....-..+.|+.|..+.+|.+|+..++.++.++||||++||.+.+++||||++|++.||++.
T Consensus 713 --------~--~ds--~~~t~~~~~~~~~~V~~~~sE~elf~ev~~~i~q~DPDIl~GyEi~~~SWGyl~eR~~~l~~di 780 (1488)
T KOG0968|consen 713 --------C--PDS--HVQTTTLGGIYGCRVVVMESELELFEEVAKLIVQYDPDILLGYEIHNLSWGYLIERAKLLGIDI 780 (1488)
T ss_pred --------C--ccc--cccccccCCcCCceEEEehhHHHHHHHHHHHHHhcCcceeeeeeecccchHHHHHHHHHhcchH
Confidence 0 000 0111111446789999999999999999999999999999999999999999999999999998
Q ss_pred ccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceee
Q psy12447 402 FTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTI 481 (551)
Q Consensus 402 ~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~ 481 (551)
...++|++...... .. -.-++||..+.+.+
T Consensus 781 ~~~lsRv~~~~~~n------------------~~--------------------------------d~~~ewg~tt~S~i 810 (1488)
T KOG0968|consen 781 SRDLSRVKCYEKTN------------------ES--------------------------------DDEREWGYTTISGI 810 (1488)
T ss_pred HHHHhcCCChhhhh------------------hh--------------------------------hhhhhccceeeccc
Confidence 77889987542100 00 00125777778889
Q ss_pred eeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc-------cccccccccC
Q psy12447 482 NFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP-------KSNAAPLRYS 549 (551)
Q Consensus 482 ~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~-------~D~~l~~rl~ 549 (551)
.+.||+++++||.+|.+.+|.+|+|++|+.++|+++.|-++++.+++||.+....-+- +.|-+.+.||
T Consensus 811 ~i~GR~~lNiWRilR~eV~L~nYtlEsv~~nVL~kk~P~~~~~~Lt~~~~s~~~~~r~~~l~y~l~Ra~~NlelL 885 (1488)
T KOG0968|consen 811 NIVGRHVLNIWRILRSEVALTNYTLESVVFNVLRKKIPMFDFAVLTRWWKSKRSAERNDVLNYLLSRARLNLELL 885 (1488)
T ss_pred cccchhhhhHHHHHhhhhhhhhccHHHHHHHHHHhhcCCCcHHHHHHHHhcccHHHHHHHHHHHHHHhhhhHHHH
Confidence 9999999999999999999999999999999999999999999999999987433211 5555555554
No 18
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=99.97 E-value=5.2e-30 Score=247.56 Aligned_cols=195 Identities=38% Similarity=0.531 Sum_probs=147.2
Q ss_pred eEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhCC
Q psy12447 248 ILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQ 327 (551)
Q Consensus 248 ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~ 327 (551)
+|||||||.+..+ ||+|..|+|++||++....|... ++.... .
T Consensus 1 v~~~DIEt~~~~~-~p~~~~d~Ii~I~~~~~~~g~~~------~~~~~~-~----------------------------- 43 (199)
T cd05160 1 VLSFDIETTPPVG-GPEPDRDPIICITYADSFDGVKV------VFLLKT-S----------------------------- 43 (199)
T ss_pred CccEEEeecCCCC-CcCCCCCCEEEEEEEEeeCCcee------eEEEee-c-----------------------------
Confidence 5899999999776 89999999999999865344322 000000 0
Q ss_pred CCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCccccccc
Q psy12447 328 GASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGR 407 (551)
Q Consensus 328 ~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R 407 (551)
+ .......+.+..|..|++|++||.+|+++++.+|||+++|||+.+||||||.+||+.+|++.+...+|
T Consensus 44 -----~------~~~~~~~i~~~~v~~~~~E~~lL~~f~~~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r 112 (199)
T cd05160 44 -----T------VGDDIEFIDGIEVEYFADEKELLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYR 112 (199)
T ss_pred -----c------cCCcCCCCCCceEEEeCCHHHHHHHHHHHHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCccccccc
Confidence 0 00001135678899999999999999999999999999999999999999999999999976522333
Q ss_pred ccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeeeecee
Q psy12447 408 VKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRV 487 (551)
Q Consensus 408 ~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~ 487 (551)
..... .. .+......+.||+
T Consensus 113 ~~~~~------------------------------------------------------~~------~~~~~~~~~~gr~ 132 (199)
T cd05160 113 RSGGE------------------------------------------------------KS------SGSTERIAVKGRV 132 (199)
T ss_pred ccCCC------------------------------------------------------cc------CCcccceeeeccE
Confidence 21100 00 0112357899999
Q ss_pred eeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHh-cCCCCCcc---cccccccccCC
Q psy12447 488 CFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQI-ALLQPSDP---KSNAAPLRYSP 550 (551)
Q Consensus 488 ~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~-~~~~~~~~---~D~~l~~rl~~ 550 (551)
++|+|.++|+..+++||+|++||+++||.+|+++++..+.+|+. ++....++ +||.++++||.
T Consensus 133 ~~D~~~~~r~~~~l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~~ 199 (199)
T cd05160 133 VFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQILE 199 (199)
T ss_pred eeehHHHHHHhcCcccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999998632 22222222 99999999984
No 19
>PHA02528 43 DNA polymerase; Provisional
Probab=99.96 E-value=9.4e-30 Score=289.43 Aligned_cols=213 Identities=26% Similarity=0.354 Sum_probs=152.8
Q ss_pred ccCceeEEEEEEeccCCCCCCCCC--CCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHH
Q psy12447 243 VAPLRILSFDIECAGRKGIFPDPN--HDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 320 (551)
Q Consensus 243 ~p~l~ils~DIE~~~~~~~fP~~~--~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~ 320 (551)
.|+|+++||||||++..| ||+|+ .|||++||+. ..+ ... ..++.+.+..+ |.
T Consensus 103 ~p~lrv~s~DIE~~~~~g-fP~p~~~~d~IisIsl~--~~~-~~~---~~v~~~~~~~~------------------~~- 156 (881)
T PHA02528 103 RSKIRIANLDIEVTAEDG-FPDPEEAKYEIDAITHY--DSI-DDR---FYVFDLGSVEE------------------WD- 156 (881)
T ss_pred CCCccEEEEEEEECCCCC-CCCcccCCCcEEEEEEe--cCC-CCE---EEEEEecCccc------------------cc-
Confidence 489999999999988766 99998 7899999974 111 110 01222211110 00
Q ss_pred HHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHH-cCC
Q psy12447 321 FIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKH-LGV 399 (551)
Q Consensus 321 ~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~-l~i 399 (551)
. .| +. .......+..+..|++|++||.+|+++|+++|||||+|||+.+||||||++||+. +|+
T Consensus 157 ----~-~~----~~-------~~~~~~~~v~~~~~~sE~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~ 220 (881)
T PHA02528 157 ----A-KG----DE-------VPQEILDKVVYMPFDTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGE 220 (881)
T ss_pred ----c-cC----Cc-------ccccccCCeeEEEcCCHHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCc
Confidence 0 00 00 0001224567788999999999999999999999999999999999999999996 576
Q ss_pred CcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccce
Q psy12447 400 KNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENK 479 (551)
Q Consensus 400 ~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~ 479 (551)
.....+++...... ..+ +..+|.+. .
T Consensus 221 ~~~~~l~~~~~~~~----------------------------------------------------~~~-~~~~g~~~-~ 246 (881)
T PHA02528 221 KTAKRLSPWGKVKE----------------------------------------------------RTI-ENMYGREE-I 246 (881)
T ss_pred cccccccccccccc----------------------------------------------------ccc-cccccccc-e
Confidence 53222222211000 000 12345332 3
Q ss_pred eeeeeceeeeeHHHHHHHH-c-cCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---cccccccccCCC
Q psy12447 480 TINFEGRVCFDLLFVLLRE-Y-KLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPLRYSPK 551 (551)
Q Consensus 480 ~~~i~GR~~lDl~~~~~~~-~-kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~rl~~~ 551 (551)
.+.++||+++|+|.++|+. + +++||+|++||+++||++|+++++++|.+||.++....++ +||.|+++|+.|
T Consensus 247 ~~~i~GRv~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 247 AYDISGISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred eEEEcceEEEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999983 4 7999999999999999999999999999999987755555 999999999864
No 20
>KOG1798|consensus
Probab=99.96 E-value=8e-29 Score=276.43 Aligned_cols=329 Identities=22% Similarity=0.280 Sum_probs=245.8
Q ss_pred CccEEEEEeecCCCcEEEEEEeceeeEEEEeCCCCCChhHHHHHHHHHHHHHHHHhccCcccccceEEEEEEEEeeeeee
Q psy12447 50 PVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNSTHCRAFKEALNRAIIADMRGNKDEIQEAVLMVEIVQKQTVFG 129 (551)
Q Consensus 50 ~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~ie~V~k~~lyg 129 (551)
..-.+-+|..+.+|.+..+.+ .|+||||+.+.++... .+.+.|.+. ..-.+..++.|.|.+|.-
T Consensus 68 ~~S~VD~yFi~~dG~~Fk~~~-py~PYFyiAt~d~~e~----~Ve~yL~Kk-----------y~g~i~~ie~v~kEDL~l 131 (2173)
T KOG1798|consen 68 GISAVDLYFIDDDGSSFKVKY-PYRPYFYIATRDGMEL----EVEEYLRKK-----------YEGQIADIEIVHKEDLDL 131 (2173)
T ss_pred ceeEEEEEEEccCCCeEEEee-cccceEEEeeccccHH----HHHHHHHHH-----------HhhhhhheeEecHhhcCc
Confidence 456799999999999999999 5999999998755321 112222222 112467888899988753
Q ss_pred e--cCCCcccEEEEEccc--------------------------------CCC--------cCCCcccccccCcchhhhh
Q psy12447 130 F--WGEELENFLKITESV--------------------------------FPT--------FPTHTYKAFESNIDFDIRF 167 (551)
Q Consensus 130 y--~~~~~~~flKI~~~~--------------------------------~~~--------l~~~~~~vyEa~I~~~~rF 167 (551)
+ -.+-.+.|+|+.+.. .+. ..+...++-|.||||+.|+
T Consensus 132 kNHLsGlqk~yiKlsF~t~~~L~~vrK~l~~iV~~N~~q~~a~daY~~~ls~~~~~~~q~D~ld~IvDiREYDVPyHvR~ 211 (2173)
T KOG1798|consen 132 KNHLSGLQKTYIKLSFDTVNQLVEVRKDLRPIVKRNKAQFDALDAYTNILSGNLNGRDQGDALDSIVDIREYDVPYHVRV 211 (2173)
T ss_pred hhhhhcccccEEEEEEecHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhccCCcccchHhhhhhHhhcCCceEEEE
Confidence 2 234468999999310 000 1123468999999999999
Q ss_pred hhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCCCcccccCCCCCcccccCce
Q psy12447 168 MVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDIVSHAPEGEWSKVAPLR 247 (551)
Q Consensus 168 liD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~~~~~~~~~~~~~p~l~ 247 (551)
.+|.+|..+-|+.+.-. ...+|+. -.+ +.-..|.++
T Consensus 212 sID~~IrvG~WY~V~~~-------------------~~~v~i~--~r~-----------------------~~i~radp~ 247 (2173)
T KOG1798|consen 212 SIDLDIRVGQWYNVSYN-------------------SGPVEIE--RRT-----------------------DLIERADPR 247 (2173)
T ss_pred eecCCeeeeeeeeeeee-------------------ccceEEE--ecc-----------------------cccccCCce
Confidence 99999999999988521 1123321 111 011357899
Q ss_pred eEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhCC
Q psy12447 248 ILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQ 327 (551)
Q Consensus 248 ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~ 327 (551)
||||||||....-+||+++.|+|+|||+.+..+|... +++.|++.+| .+|.+++.
T Consensus 248 VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLI-----------tNREiVs~DI-------------edfEYTPK- 302 (2173)
T KOG1798|consen 248 VLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLI-----------TNREIVSEDI-------------EDFEYTPK- 302 (2173)
T ss_pred EEEEeeecccCCCCCCCcccceEEEEEEEecCceEEE-----------echhhhccch-------------hhcccCCc-
Confidence 9999999999999999999999999999986555433 5677766554 22333322
Q ss_pred CCccCceeeeeeecCCCCCccC-cEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccc
Q psy12447 328 GASENIFVKNVFTLNTCAPIVG-SQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLG 406 (551)
Q Consensus 328 ~~~~~p~~~~~f~~~~~~~~~g-~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~ 406 (551)
|. ..| -.|+.-++|.+||.+|++.+++..|-||++||++-|||||+..||+.+|+++...+|
T Consensus 303 -----pE------------~eG~F~v~Ne~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiG 365 (2173)
T KOG1798|consen 303 -----PE------------YEGPFCVFNEPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIG 365 (2173)
T ss_pred -----cc------------cccceEEecCCcHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcC
Confidence 21 122 257888999999999999999999999999999999999999999999999877777
Q ss_pred cccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceeeeeece
Q psy12447 407 RVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGR 486 (551)
Q Consensus 407 R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR 486 (551)
..++.. | ...-+-.
T Consensus 366 F~~D~~-------------------------------------------------------------g-----Eyks~~c 379 (2173)
T KOG1798|consen 366 FRRDSQ-------------------------------------------------------------G-----EYKSPFC 379 (2173)
T ss_pred ceeccc-------------------------------------------------------------c-----cccccce
Confidence 654311 1 1222336
Q ss_pred eeeeHHHHHHHHccC--CCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---ccccccc
Q psy12447 487 VCFDLLFVLLREYKL--RSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPL 546 (551)
Q Consensus 487 ~~lDl~~~~~~~~kl--~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~ 546 (551)
+|+|.++++|++--| -|-.|..|++.-||.....++++.|..+..+.|+.++. .||+.+.
T Consensus 380 ~HmDcfrWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATY 444 (2173)
T KOG1798|consen 380 IHMDCFRWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATY 444 (2173)
T ss_pred eehhhhhhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHH
Confidence 899999999998655 69999999999999999999999999999999999998 8887654
No 21
>PHA03036 DNA polymerase; Provisional
Probab=99.96 E-value=2.2e-29 Score=284.07 Aligned_cols=222 Identities=23% Similarity=0.227 Sum_probs=164.4
Q ss_pred ccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEe-eccCCCccccccccccc-CCcccccCceeeeecchhhHHHHHHH
Q psy12447 243 VAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMC-ISQGASENIFVKNVFTL-NTCAPIVGSQVICCKTETELLDKWSA 320 (551)
Q Consensus 243 ~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~-~~~~~~~~~~~~~~~~l-~~~~~i~~~~v~~~~~e~~~~~~~~~ 320 (551)
.-|++.|||||||.. +|.||.|..|||++||+++ ...|... .|+| +.+....
T Consensus 157 ~~~~~~lsfDIEC~~-~g~FPs~~~~pvshIs~~~~~~~~~~~------~~~l~n~~~~~~------------------- 210 (1004)
T PHA03036 157 DIPRSYLFLDIECHF-DKKFPSVFINPVSHISCCYIDLSGKEK------RFTLINEDMLSE------------------- 210 (1004)
T ss_pred cCcceeEEEEEEecc-CCCCCCcccCcceEEEEEEEecCCCee------EEEEeccccccc-------------------
Confidence 358999999999996 6779999999999999743 3444322 3444 2211110
Q ss_pred HHHHhCCCCccCceeeeeeecCCCCCc---cCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHc
Q psy12447 321 FIRTMGQGASENIFVKNVFTLNTCAPI---VGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397 (551)
Q Consensus 321 ~~~~~~~~~~~~p~~~~~f~~~~~~~~---~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l 397 (551)
..|..+.+|.++.|+.+ .+..++.|.+|++|| +|++.+++.|||+|+|||+++||||||.+||+.|
T Consensus 211 ----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~~R~~~L 279 (1004)
T PHA03036 211 ----------DEIEEAVKRGYYEIESLLDMDYSKELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYISNRLELL 279 (1004)
T ss_pred ----------cccccceeeeeeccccccccCCceeeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHHHHHHHh
Confidence 01344567788788876 788999999999977 7799999999999999999999999999999998
Q ss_pred CCCc--ccccccccccccccchhhhhhhcccccccccccccCCCcccccccccccccccccccccccccccccccccc--
Q psy12447 398 GVKN--FTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQM-- 473 (551)
Q Consensus 398 ~i~~--~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~-- 473 (551)
.... +..+++...... ++-+..++|.+.
T Consensus 280 ~~~~~~~~~~~~~~~~~~------------------------------------------------~v~~r~~~s~~~~g 311 (1004)
T PHA03036 280 TGEKIIFRSPDGKETVHL------------------------------------------------CIYERNLSSHKGVG 311 (1004)
T ss_pred ccCceeeccCCCcccccc------------------------------------------------eeeccccccccccC
Confidence 5421 222333322211 111122333322
Q ss_pred C-cccceeee-eeceeeeeHHHHHHHHccCCCCCHHHHHHHhh-----------------c-------------------
Q psy12447 474 G-KRENKTIN-FEGRVCFDLLFVLLREYKLRSYTLNSVSYHFL-----------------Q------------------- 515 (551)
Q Consensus 474 g-~~~~~~~~-i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~L-----------------g------------------- 515 (551)
| .+....+. ++||+++|||.++|+.++|+||+|++||+++| |
T Consensus 312 g~~~~t~~i~~~~G~i~fDLy~~i~k~~~L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl~t 391 (1004)
T PHA03036 312 GVANTTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVLST 391 (1004)
T ss_pred ccccceEEecccCCeEEEEhHHHHhhhcCcccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhhcc
Confidence 2 23344555 79999999999999999999999999999977 5
Q ss_pred -------c------------------------------------CCCCCChhhHHHHHhcCCCCCcc------ccccccc
Q psy12447 516 -------E------------------------------------QKEDVQHSIISDLQIALLQPSDP------KSNAAPL 546 (551)
Q Consensus 516 -------~------------------------------------~k~~~~~~~i~~~~~~~~~~~~~------~D~~l~~ 546 (551)
+ +|.|++..+|.+.|+. ++|++ +||+||+
T Consensus 392 ~ny~~i~~~~~~k~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~KdDV~~~~i~~~~~~--~~r~rla~YClkDa~L~l 469 (1004)
T PHA03036 392 GNYVTINDDDICKILDKDIIENSFTVKVICKNNYIPGDTYTLSFGKDDVDLSDMYKNYNL--EIALEMARYCIHDACLCK 469 (1004)
T ss_pred cceeeecccchhhhcccccccccceeeeecccccccccceeecccccCCCHHHHHHHhCh--hHHHHHHHHHHHHHHHHH
Confidence 5 8999999999999974 45555 9999999
Q ss_pred ccCCC
Q psy12447 547 RYSPK 551 (551)
Q Consensus 547 rl~~~ 551 (551)
|||.|
T Consensus 470 ~L~~~ 474 (1004)
T PHA03036 470 YLWEY 474 (1004)
T ss_pred HHHHH
Confidence 99864
No 22
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=99.96 E-value=4.8e-29 Score=240.86 Aligned_cols=188 Identities=28% Similarity=0.375 Sum_probs=138.0
Q ss_pred cccCceeEEEEEEeccCC-CCCCCCCC--CcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHH
Q psy12447 242 KVAPLRILSFDIECAGRK-GIFPDPNH--DPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKW 318 (551)
Q Consensus 242 ~~p~l~ils~DIE~~~~~-~~fP~~~~--d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~ 318 (551)
++|+|++|||||||.+.. +.||+|+. |+|++||+. ..++.. .++.++.+..
T Consensus 1 ~~P~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~-~~~~~~------~v~~~~~~~~------------------- 54 (204)
T cd05783 1 PIPKLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA-GSDGLK------RVLVLKREGV------------------- 54 (204)
T ss_pred CCCCceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc-CCCCCc------EEEEEecCCc-------------------
Confidence 379999999999999865 67999986 899999975 112211 1111110000
Q ss_pred HHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcC
Q psy12447 319 SAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLG 398 (551)
Q Consensus 319 ~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~ 398 (551)
.........+..|..|.+|++||.+|+++++++ |+|+|||+.+||||||.+||+.+|
T Consensus 55 ---------------------~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~--~~iig~N~~~FDlpyl~~R~~~~g 111 (204)
T cd05783 55 ---------------------EGLEGLLPEGAEVEFFDSEKELIREAFKIISEY--PIVLTFNGDNFDLPYLYNRALKLG 111 (204)
T ss_pred ---------------------ccccccCCCCCeEEecCCHHHHHHHHHHHHhcC--CEEEEeCCCCcCHHHHHHHHHHhC
Confidence 000001124668999999999999999999987 588999999999999999999999
Q ss_pred CCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccc
Q psy12447 399 VKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKREN 478 (551)
Q Consensus 399 i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~ 478 (551)
++.- ..+ + .+|.
T Consensus 112 i~~~----~~~----------------------------------------------------------~---~~~~--- 123 (204)
T cd05783 112 IPKE----EIP----------------------------------------------------------I---YLKR--- 123 (204)
T ss_pred CChh----hCc----------------------------------------------------------e---eecC---
Confidence 8631 000 0 0121
Q ss_pred eeeeeeceeeeeHHHHHHHH--------ccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---cccccccc
Q psy12447 479 KTINFEGRVCFDLLFVLLRE--------YKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPLR 547 (551)
Q Consensus 479 ~~~~i~GR~~lDl~~~~~~~--------~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~r 547 (551)
....+.||+++|+|++++.. .++.+|+|++||+++||++|.+++ .+|.++ +.+..+. +||.|+++
T Consensus 124 ~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~~L~~Va~~~lg~~K~~~~-~~i~~~---~~~~l~~Y~~~D~~lt~~ 199 (204)
T cd05783 124 DYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREYTLDAVAKALLGEGKVELE-KNISEL---NLYELAEYNYRDAELTLE 199 (204)
T ss_pred CceeccCcEEeECHHHhhccchhhhhhccccccCcHHHHHHHhcCCCcccCC-chhhhh---cHHHHHHhhHHHHHHHHH
Confidence 13678999999999998762 278999999999999999999997 567776 4444444 99999999
Q ss_pred cCC
Q psy12447 548 YSP 550 (551)
Q Consensus 548 l~~ 550 (551)
|++
T Consensus 200 L~~ 202 (204)
T cd05783 200 LTT 202 (204)
T ss_pred Hhc
Confidence 974
No 23
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=99.95 E-value=7.6e-28 Score=256.20 Aligned_cols=208 Identities=22% Similarity=0.317 Sum_probs=150.7
Q ss_pred cCceeEEEEEEeccCCCCCCCCC--CCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHH
Q psy12447 244 APLRILSFDIECAGRKGIFPDPN--HDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 321 (551)
Q Consensus 244 p~l~ils~DIE~~~~~~~fP~~~--~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~ 321 (551)
-.++|+.+|||+.+. .||+|. .-||-+|+..-..++... .-+|+|-+. + ..|.
T Consensus 104 ~~i~~~~~DIEv~~~--~fp~~~~a~~~i~~i~~~d~~~~~~~----~~~~~~~~~-------~----------~~~~-- 158 (498)
T PHA02524 104 DDVVIDVVDIEVTAP--EFPEPKYAKYEIDMISHVRLHNGKKT----YYIFDLVKD-------V----------GHWD-- 158 (498)
T ss_pred hhceEEEEEEEecCC--CCCChhhcCCceEEEEeeecccCCcc----EEEEecccc-------c----------cCCC--
Confidence 468999999999874 499996 579999996421111111 112332100 0 0111
Q ss_pred HHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHH-cCCC
Q psy12447 322 IRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKH-LGVK 400 (551)
Q Consensus 322 ~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~-l~i~ 400 (551)
|... .-.+..+.|+.|+.|++|++||.+|+++|+++|||||+|||+.+||||||.+||+. ||+.
T Consensus 159 -----------~~~~----~~~~~~~~~v~v~~f~sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~ 223 (498)
T PHA02524 159 -----------PKKS----VLEKYILDNVVYMPFEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEK 223 (498)
T ss_pred -----------cccc----cccccccCCeEEEEeCCHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCc
Confidence 1000 00123367899999999999999999999999999999999999999999999975 8885
Q ss_pred c---ccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCccc
Q psy12447 401 N---FTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRE 477 (551)
Q Consensus 401 ~---~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~ 477 (551)
. +..+||.... .+++++|.+
T Consensus 224 ~~~~~~~~Gr~~~~--------------------------------------------------------~s~~~~G~~- 246 (498)
T PHA02524 224 AANQLSPYGKITSK--------------------------------------------------------TITNLYGEK- 246 (498)
T ss_pred cccccccccccccc--------------------------------------------------------cceeecCce-
Confidence 3 3344543211 112345643
Q ss_pred ceeeeeeceeeeeHHHHHHHH--ccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc---cccccccccCC
Q psy12447 478 NKTINFEGRVCFDLLFVLLRE--YKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP---KSNAAPLRYSP 550 (551)
Q Consensus 478 ~~~~~i~GR~~lDl~~~~~~~--~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~---~D~~l~~rl~~ 550 (551)
..+.++||+++|++.++++. ++|+||+|++||+++||++|.++.. .|.++|.++....++ +||.||++|..
T Consensus 247 -~~~~I~GRv~iDl~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K~d~~~-~I~~l~~~d~~rla~YclkDa~L~~~L~~ 322 (498)
T PHA02524 247 -IIYKIHGIALMDYMDVFKKFSFTPMPDYKLGNVGYREVKADKLDYEG-PINKFRKADHQRYVDYCVRDTDIILLIDG 322 (498)
T ss_pred -eEEEEeeEEEeEHHHHHHHhhhccCCCCCHHHHHHHhcCCccccchh-hHHHHhcCchHHHHHHHHHHHHHHHHHHH
Confidence 35799999999999999996 7999999999999999999998863 589999876644444 99999987753
No 24
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=99.94 E-value=1.7e-26 Score=250.49 Aligned_cols=211 Identities=36% Similarity=0.543 Sum_probs=168.6
Q ss_pred cCceeEEEEEEeccCCCCCCCCC--CCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHH
Q psy12447 244 APLRILSFDIECAGRKGIFPDPN--HDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 321 (551)
Q Consensus 244 p~l~ils~DIE~~~~~~~fP~~~--~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~ 321 (551)
|+++++||||||.+..+.||++. .|+|++|++.+...+...
T Consensus 1 ~~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~------------------------------------- 43 (471)
T smart00486 1 PPLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKG------------------------------------- 43 (471)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCC-------------------------------------
Confidence 57899999999999888899998 799999999875432211
Q ss_pred HHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCc
Q psy12447 322 IRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKN 401 (551)
Q Consensus 322 ~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~ 401 (551)
+..+.+|+++.+..+.+..+..|++|++||.+|++++++.|||+++|||+.+||++||.+|+..+++..
T Consensus 44 -----------~~~~~~~~~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~ 112 (471)
T smart00486 44 -----------PEERICFTLGTCKEIDGVEVYEFNNEKELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKP 112 (471)
T ss_pred -----------CceeEEEEecCcCCCCCCeEEecCCHHHHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCC
Confidence 223457777777888888999999999999999999999999999999999999999999999999987
Q ss_pred ccccccccccccccchhhhhhhcccccccccccccCCCccccccccccccccccccccccccccccccccccCcccceee
Q psy12447 402 FTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTI 481 (551)
Q Consensus 402 ~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~ 481 (551)
+..+||...... ... . ..+.....+ ......
T Consensus 113 ~~~i~r~~~~~~-~~~-------------~----------------------------------~~~~~~~~~-~~~~~~ 143 (471)
T smart00486 113 LSFIGRLKNIID-IKR-------------K----------------------------------KPLFGSKSF-GKTIKV 143 (471)
T ss_pred HHHcCcCCCCCC-ccc-------------c----------------------------------cCccccccc-ccccee
Confidence 666788654210 000 0 000000001 123468
Q ss_pred eeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHHHhcCCCCCcc------cccccccccCCC
Q psy12447 482 NFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDLQIALLQPSDP------KSNAAPLRYSPK 551 (551)
Q Consensus 482 ~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~~~~~~~~~~~------~D~~l~~rl~~~ 551 (551)
.+.||+++|+|..+++.+++.+|+|++||+++||++|.++++.+|.++|..+...+.+ +||.|+++|+.+
T Consensus 144 ~~~g~~~~Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~ 219 (471)
T smart00486 144 KIKGRLVIDLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNK 219 (471)
T ss_pred EeccEEEEEhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999986333333 999999998753
No 25
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.92 E-value=2.5e-26 Score=271.33 Aligned_cols=245 Identities=24% Similarity=0.244 Sum_probs=187.7
Q ss_pred CcccccccCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCccccceeEEEEEcCcccCCCCcccccCCCcc
Q psy12447 152 HTYKAFESNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQLEIDVSTDDIVSHAPEEIDVSTDDI 231 (551)
Q Consensus 152 ~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~iEi~v~~~~I~n~~~~~~~~~~~~~ 231 (551)
...+.+|++||+..|+|+|+.+.++.| + .+... + ..
T Consensus 154 ~~~~~~e~di~~~~r~~~d~~~~p~~~---~--~~~~~-------------~----------~~---------------- 189 (1172)
T TIGR00592 154 AVVDIVKKAIPVSTRYLLEKILIPVPL---K--RAEFA-------------G----------GD---------------- 189 (1172)
T ss_pred cccccccCCCCccccccccccccCCCC---C--ccccc-------------c----------cc----------------
Confidence 346799999999999999999999754 1 11100 0 00
Q ss_pred cccCCCCCcccccCceeEEEEEEeccCCC--CCC--CCCCCcEEEEEEE----eeccCCCcccccccccccCCcccccCc
Q psy12447 232 VSHAPEGEWSKVAPLRILSFDIECAGRKG--IFP--DPNHDPIIQIANM----CISQGASENIFVKNVFTLNTCAPIVGS 303 (551)
Q Consensus 232 ~~~~~~~~~~~~p~l~ils~DIE~~~~~~--~fP--~~~~d~I~~Is~~----~~~~~~~~~~~~~~~~~l~~~~~i~~~ 303 (551)
.....+|+++++||||||.+..| .|| ++..|+|+||++. +...+..+
T Consensus 190 ------~~~~~~p~~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~~~~~~~~~~------------------- 244 (1172)
T TIGR00592 190 ------VQMEGDPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWDYESE------------------- 244 (1172)
T ss_pred ------ccccCCCcccccccccccccccccccCcccccccccccccccccccccccccCCC-------------------
Confidence 01124699999999999998754 455 4557999999864 11122211
Q ss_pred eeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeeccc
Q psy12447 304 QVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQ 383 (551)
Q Consensus 304 ~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~ 383 (551)
|..+.+|+++.|+++.|+.|..|.+|.+||.+|.+++++.||||++|||+.
T Consensus 245 -----------------------------~~~~~~~~~~~~~~~~~~~v~~~~~E~~~L~~f~~~i~~~dpdii~gYNi~ 295 (1172)
T TIGR00592 245 -----------------------------PEARVVTWKKPDKPTTGSYVESVSEEISMIKRFWDVIDQEDTDVEITVNGD 295 (1172)
T ss_pred -----------------------------ccchhhhccCccccCCCccceeccchHHHHhhHHHHHhhcCcchhcccccc
Confidence 445668899999999999999999999999999999999999999999999
Q ss_pred CCChHHHHH-------------HHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCccccccccccc
Q psy12447 384 NFDFPYLIN-------------RAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSDRRETLGVKNF 450 (551)
Q Consensus 384 ~fdl~yL~~-------------R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~~~~~l~~~~~ 450 (551)
+||||||.+ |++.+|. +..+||....
T Consensus 296 ~FD~pyl~~~~~~~~~~da~~dr~~~~G~--~~lfGr~~~~--------------------------------------- 334 (1172)
T TIGR00592 296 NFDLVYLADRQVFQFYWDAYEDPAEKLGV--VLLFGRDVDH--------------------------------------- 334 (1172)
T ss_pred cCccceecCCceEEeeHHhhhHHhhCCCe--EEEecccCCc---------------------------------------
Confidence 999999998 5555554 2244551100
Q ss_pred cccccccccccccccccccccccC-cccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhccCCCCCChhhHHHH
Q psy12447 451 TFLGRVKDIRSVIKDSFIQSKQMG-KRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQEQKEDVQHSIISDL 529 (551)
Q Consensus 451 ~~lg~~k~~~~~i~~~~~~s~~~g-~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~~k~~~~~~~i~~~ 529 (551)
....+...| .|....+.+.||+.+|++..+++.++|.+|+|+.|++++||.+|.++++..|.+.
T Consensus 335 ---------------~s~~~~v~g~~R~~~~l~~~Grv~~D~~~~~~~~~~l~~y~le~vs~~~lg~~k~dv~~k~I~~~ 399 (1172)
T TIGR00592 335 ---------------VSPCVQVKGINRDLFFLPREGKIDFDLGKVTRRTINLPDYYLEFVSELALGYKKEKFRAKPIAKK 399 (1172)
T ss_pred ---------------eeEEEEECCeeeeeEEeeccccccccccchhcccccHHHHHHHHHHHHHhhcCcCceeeEEehhh
Confidence 012223455 4456678899999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcc----cccccccccCC
Q psy12447 530 QIALLQPSDP----KSNAAPLRYSP 550 (551)
Q Consensus 530 ~~~~~~~~~~----~D~~l~~rl~~ 550 (551)
|..+..++-. +|+.++++|+.
T Consensus 400 ~~~~~~~~~v~y~~~~lkv~y~l~~ 424 (1172)
T TIGR00592 400 YEFEAPDIDAPYSSEYLEVTYELGK 424 (1172)
T ss_pred ccCCCCccCCcCCcceEEEEEccCc
Confidence 9987653222 99999999754
No 26
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=99.79 E-value=6.4e-19 Score=171.07 Aligned_cols=131 Identities=19% Similarity=0.147 Sum_probs=104.1
Q ss_pred EcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccc
Q psy12447 354 CCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTI 433 (551)
Q Consensus 354 ~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~ 433 (551)
.+.+|++||.+|+++|++++| +++|||+.+||+|||..||..+|++.-..+++...
T Consensus 74 ~~~~E~elL~~F~~~i~~~~p-~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~----------------------- 129 (208)
T cd05782 74 DGADEKELLEDFFQLIEKKNP-RLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNK----------------------- 129 (208)
T ss_pred CCCCHHHHHHHHHHHHHHhCC-EEEecCCCcCCHHHHHHHHHHhCCCCccccCcccc-----------------------
Confidence 357999999999999999998 88999999999999999999999854222211100
Q ss_pred cccCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHh
Q psy12447 434 NFEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHF 513 (551)
Q Consensus 434 ~~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~ 513 (551)
+ ..++. .+.|| |+|+|.+++...++.+|+|++||+.+
T Consensus 130 ----------------------------------~--~~y~~------r~~~~-h~DL~~~~~~~~~~~~~~L~~va~~l 166 (208)
T cd05782 130 ----------------------------------D--WNYRN------RYSER-HLDLMDLLAFYGARARASLDLLAKLL 166 (208)
T ss_pred ----------------------------------h--hhccC------cCCCC-cccHHHHHhccCccCCCCHHHHHHHh
Confidence 0 01222 23578 99999999987788999999999866
Q ss_pred hccCCCCCChhhHHHHHhcCCCCCcc----cccccccccCCC
Q psy12447 514 LQEQKEDVQHSIISDLQIALLQPSDP----KSNAAPLRYSPK 551 (551)
Q Consensus 514 Lg~~k~~~~~~~i~~~~~~~~~~~~~----~D~~l~~rl~~~ 551 (551)
...+|.+++..++.++|..+...+.+ +|+..+..|+.|
T Consensus 167 G~~~K~d~~G~~v~~~y~~g~~~~I~~Yc~~Dv~~t~~l~lr 208 (208)
T cd05782 167 GIPGKMDVDGSQVWELYAEGKLDEIAEYCETDVLNTYLLYLR 208 (208)
T ss_pred CCCCCcCCCHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHhC
Confidence 66799999999999999987644333 999999988764
No 27
>KOG0969|consensus
Probab=99.48 E-value=6e-15 Score=158.77 Aligned_cols=140 Identities=40% Similarity=0.627 Sum_probs=112.6
Q ss_pred cccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHH
Q psy12447 290 NVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFI 369 (551)
Q Consensus 290 ~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i 369 (551)
++|+|++|+||+|++|+++.+|++||+.|..|++.++ | +.|.|+||..|+--+ ||.+...+
T Consensus 317 nvf~l~~capI~G~~V~~~~~e~elL~~W~~firevD------P-----------DvI~GYNi~nFDiPY-ll~RA~~L- 377 (1066)
T KOG0969|consen 317 NVFTLKTCAPIVGSNVHSYETEKELLESWRKFIREVD------P-----------DVIIGYNICNFDIPY-LLNRAKTL- 377 (1066)
T ss_pred hhhcccCcCCCCCceeEEeccHHHHHHHHHHHHHhcC------C-----------CeEecccccccccce-ecChHhhc-
Confidence 5889999999999999999999999999999999987 4 567899999999988 77777522
Q ss_pred HhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCc---------
Q psy12447 370 RELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSD--------- 440 (551)
Q Consensus 370 ~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~--------- 440 (551)
-++ ++||| .|.+..+. ++++.. .+|+++|.++++.++++||++
T Consensus 378 -----------~Ie--~Fp~L-GRikn~~s-------~irDtt-------fSSkq~GtRetK~v~I~GRlqfDllqvi~R 429 (1066)
T KOG0969|consen 378 -----------GIE--NFPYL-GRIKNSRS-------VIRDST-------FSSKQYGTRETKEVNIDGRLQFDLLQVILR 429 (1066)
T ss_pred -----------Ccc--ccccc-ceecccce-------eeeccc-------cchhhcCcccceEEeecceeeehHHHHHHH
Confidence 234 56666 67665432 333332 378999999999999999974
Q ss_pred ----ccccccccccccccccccc--ccccccccccccccCcc
Q psy12447 441 ----RRETLGVKNFTFLGRVKDI--RSVIKDSFIQSKQMGKR 476 (551)
Q Consensus 441 ----~~~~l~~~~~~~lg~~k~~--~~~i~~~~~~s~~~g~~ 476 (551)
|+|+||+||.||||+||++ |++|+|......+..+|
T Consensus 430 d~KLrSytLNaVs~hFL~EQKEDV~~siItdLQng~~~TRRR 471 (1066)
T KOG0969|consen 430 DYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQTRRR 471 (1066)
T ss_pred hhhhhhcchhhhHHHhhhhhcccccccchhhhhcCcHHHHHH
Confidence 9999999999999999985 89998876554444433
No 28
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=99.43 E-value=1e-13 Score=158.16 Aligned_cols=191 Identities=17% Similarity=0.175 Sum_probs=119.0
Q ss_pred ccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcc-cccccccccccccchhhhhhhcc
Q psy12447 347 IVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNF-TFLGRVKDIRSVIKDSFIQSKQM 425 (551)
Q Consensus 347 ~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~-~~l~R~~~~~~~~~~~f~~s~~~ 425 (551)
++...+..|++|.+||.+|+..+++. .||+--||.+ ||+..|..|.....-.-- ..+++--... -+.|.+ ..
T Consensus 320 ~t~~~~~~c~~e~~~l~~fl~~~~~~-v~vlyv~n~~-fdv~vi~~rl~~y~~~~~~~~~~~~l~~~---~~~~~s--~~ 392 (1545)
T PHA03334 320 VTRIEFVACADELEMLLAFLNRLRKS-VNVLYVYNAE-FDVQVIQSRLNYYAFKQRPHPLTKALMEA---WEAFLS--KD 392 (1545)
T ss_pred eeeeEEEEeccHHHHHHHHHHHHHhh-ccEEEEeccc-ccHHHHHHHHHHhhccCCCCcHHHHHHHH---HHHHhc--cC
Confidence 45678899999999999999999973 5699999986 899999999986532100 0111100000 000100 00
Q ss_pred cccccccccccCCC-c---------------------cc-cccccccccccccccccccccccccccccccCcccceeee
Q psy12447 426 GKRENKTINFEGNS-D---------------------RR-ETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTIN 482 (551)
Q Consensus 426 g~~~~~~~~~~~~~-~---------------------~~-~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~ 482 (551)
++.-.-++.|.... . |+ -.-.....+|+...+.+ .+=+..++. .-.+.+.
T Consensus 393 ~~~~~~~~~f~~~~~~s~y~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~v----~~f~~n~~~---~~~~kv~ 465 (1545)
T PHA03334 393 PQLVPAQLLFGSDILNSNYLELLDVIESHKAQFKATCRKAAARKEEIGSYMKTRDTV----QDFNDNDKK---YLNSTSH 465 (1545)
T ss_pred CccCCceeEehhhHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHH----Hhhcccccc---cccceee
Confidence 00000001110000 0 00 00000001111111100 000011111 1234689
Q ss_pred eeceeeeeHHHHHHH---HccCCCCCHHHHHHHhhccCC-----------CCCChhhHHHHHhcCCCCCcc------ccc
Q psy12447 483 FEGRVCFDLLFVLLR---EYKLRSYTLNSVSYHFLQEQK-----------EDVQHSIISDLQIALLQPSDP------KSN 542 (551)
Q Consensus 483 i~GR~~lDl~~~~~~---~~kl~sYsL~~V~~~~Lg~~k-----------~~~~~~~i~~~~~~~~~~~~~------~D~ 542 (551)
+.||+++|||.++++ +++|.||+||+||+++||++| +|++|.+|+++|.+++.+|+| +||
T Consensus 466 ~~GrviiDMy~Vc~~K~~~~kL~sYkLNTVA~~~LgeqKp~k~~~k~~K~eDV~YkeI~~lf~~g~e~RaRla~YCLkDA 545 (1545)
T PHA03334 466 GFGAHIIDLMRVCNTKSIKAKCSSRKLDTVARLIISKSKPHKNPPKIGKMDDVKYTEMDGMFTAGGAALARYLIYNLVDS 545 (1545)
T ss_pred eccEEEEehHHHHhhcccccCccCCcHHHHHHHHHhcccccccccccCcccCCCHHHHHHHHhcChhhHHHHHHHHHHHH
Confidence 999999999999999 599999999999999999999 899999999999999999999 999
Q ss_pred ccccccCCC
Q psy12447 543 AAPLRYSPK 551 (551)
Q Consensus 543 ~l~~rl~~~ 551 (551)
+||+||+.|
T Consensus 546 ~LvlrLlkk 554 (1545)
T PHA03334 546 ELLIRIAKN 554 (1545)
T ss_pred HHHHHHHHH
Confidence 999999864
No 29
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=99.12 E-value=3.5e-10 Score=108.61 Aligned_cols=126 Identities=21% Similarity=0.253 Sum_probs=94.2
Q ss_pred CCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccc
Q psy12447 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINF 435 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~ 435 (551)
.+|++||.+|.+.|.+..|- +||||+.+||+|||..||-.+|++.-..+.+..
T Consensus 35 ~~E~~lL~~F~~~~~~~~p~-LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~-------------------------- 87 (209)
T PF10108_consen 35 DDEKELLQDFFDLVEKYNPQ-LVSFNGRGFDLPVLCRRALIHGISAPRYLDIGN-------------------------- 87 (209)
T ss_pred CCHHHHHHHHHHHHHhCCCe-EEecCCccCCHHHHHHHHHHhCCCCchhhhcCC--------------------------
Confidence 36999999999999999985 699999999999999999999996422111100
Q ss_pred cCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhc
Q psy12447 436 EGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQ 515 (551)
Q Consensus 436 ~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg 515 (551)
++|.+ |..| .. -+ |+|++..+...-.-.+.+|+.+|. +||
T Consensus 88 ------------------------------k~Wen--Y~~R----y~--~~-H~DLmd~l~~~g~~~~~sLd~la~-~lg 127 (209)
T PF10108_consen 88 ------------------------------KPWEN--YRNR----YS--ER-HLDLMDLLSFYGAKARTSLDELAA-LLG 127 (209)
T ss_pred ------------------------------CCccc--cccc----cC--cc-cccHHHHHhccCccccCCHHHHHH-HcC
Confidence 01210 1111 11 14 999999987655667889999998 677
Q ss_pred -cCCCCCChhhHHHHHhcCCCCCcc----ccccccccc
Q psy12447 516 -EQKEDVQHSIISDLQIALLQPSDP----KSNAAPLRY 548 (551)
Q Consensus 516 -~~k~~~~~~~i~~~~~~~~~~~~~----~D~~l~~rl 548 (551)
.+|.+++-+++.++|.++...+++ +|+.-+..|
T Consensus 128 iPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~l 165 (209)
T PF10108_consen 128 IPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLL 165 (209)
T ss_pred CCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 569999999999999988877777 777655444
No 30
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.26 E-value=1.4e-06 Score=81.15 Aligned_cols=90 Identities=29% Similarity=0.439 Sum_probs=54.3
Q ss_pred CHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhccccccccccccc
Q psy12447 357 TETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFE 436 (551)
Q Consensus 357 ~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~ 436 (551)
+|.+++.++++.+.+. +.++|||+..||+|+|..|+..++++.
T Consensus 42 ~ee~~~~~~~~~l~~~--~~iv~yng~~FD~p~L~~~~~~~~~~~----------------------------------- 84 (164)
T PF13482_consen 42 DEEEIILEFFELLDEA--DNIVTYNGKNFDIPFLKRRAKRYGLPP----------------------------------- 84 (164)
T ss_dssp HHHHHHHH--HHHHTT----EEESSTTTTHHHHHHHHH-HHHH-------------------------------------
T ss_pred HHHHHHHHHHHHHhcC--CeEEEEeCcccCHHHHHHHHHHcCCCc-----------------------------------
Confidence 4555666655666655 689999999999999999986554321
Q ss_pred CCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHHHccCCCCCHHHHHHHhhcc
Q psy12447 437 GNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREYKLRSYTLNSVSYHFLQE 516 (551)
Q Consensus 437 ~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~kl~sYsL~~V~~~~Lg~ 516 (551)
..-++|++..+++... ++|+|.+|+..+..+
T Consensus 85 ------------------------------------------------~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~ 115 (164)
T PF13482_consen 85 ------------------------------------------------PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIE 115 (164)
T ss_dssp ------------------------------------------------GGGEEEHHHHHT-TTS-CCTT--SHHH-----
T ss_pred ------------------------------------------------ccchhhHHHHHHhccC-CCCCHHHHhhhcccc
Confidence 1227899999976544 999999999985445
Q ss_pred CC-CCCChhhHHHHHhc
Q psy12447 517 QK-EDVQHSIISDLQIA 532 (551)
Q Consensus 517 ~k-~~~~~~~i~~~~~~ 532 (551)
.+ .+++..++..+|..
T Consensus 116 ~~~~~~~G~~~~~~~~~ 132 (164)
T PF13482_consen 116 RRDDDISGSESVKLYKE 132 (164)
T ss_dssp ------HHHHHHHHHH-
T ss_pred cccCCCCHHHHHHHHHH
Confidence 55 57888888888876
No 31
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.82 E-value=1.1e-05 Score=95.50 Aligned_cols=129 Identities=36% Similarity=0.589 Sum_probs=94.6
Q ss_pred cccccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHH
Q psy12447 290 NVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFI 369 (551)
Q Consensus 290 ~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i 369 (551)
.+|++++|+++.|++|..+++|.+||.+|..+++..+ | +.+.|+|+..|+-.+ |+.|...+
T Consensus 309 ~vftl~~c~~i~g~~V~~f~sE~eLL~~f~~~I~~~D------P-----------DII~GYNi~~FDlpY-L~~Ra~~l- 369 (1054)
T PTZ00166 309 FIFTLKECASIAGANVLSFETEKELLLAWAEFVIAVD------P-----------DFLTGYNIINFDLPY-LLNRAKAL- 369 (1054)
T ss_pred EEEecCccccCCCceEEEeCCHHHHHHHHHHHHHhcC------C-----------CEEEecCCcCCcHHH-HHHHHHHh-
Confidence 3678889999999999999999999999999999876 4 557899999999999 99998643
Q ss_pred HhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCc---------
Q psy12447 370 RELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSD--------- 440 (551)
Q Consensus 370 ~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~--------- 440 (551)
++.. |.+| .|..... ++.+... .+++++|.++.+.+++.||+.
T Consensus 370 -----------~i~~--~~~l-gR~~~~~-------~~~~~~~-------~~~~~~g~~~~~~~~i~GR~~iDl~~~~~~ 421 (1054)
T PTZ00166 370 -----------KLND--FKYL-GRIKSTR-------SVIKDSK-------FSSKQMGTRESKEINIEGRIQFDVMDLIRR 421 (1054)
T ss_pred -----------CCCc--hhhc-CcccCCC-------ccccccc-------cccccccccccceeEeeeEEEEEHHHHHHH
Confidence 2322 2222 3432211 1111111 135678888888899999863
Q ss_pred ----ccccccccccccccccccc--cccccc
Q psy12447 441 ----RRETLGVKNFTFLGRVKDI--RSVIKD 465 (551)
Q Consensus 441 ----~~~~l~~~~~~~lg~~k~~--~~~i~~ 465 (551)
++|+|++++.||||++|.+ +..|.+
T Consensus 422 ~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~ 452 (1054)
T PTZ00166 422 DYKLKSYSLNYVSFEFLKEQKEDVHYSIISD 452 (1054)
T ss_pred hcCcCcCCHHHHHHHHhCCCCCCCCHHHHHH
Confidence 8899999999999999963 344443
No 32
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.69 E-value=0.00027 Score=68.64 Aligned_cols=92 Identities=20% Similarity=0.226 Sum_probs=66.4
Q ss_pred CCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccc
Q psy12447 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINF 435 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~ 435 (551)
..|..+|..|...+ |-.+++.||+..||+|||. |+.+..++..
T Consensus 141 ~~E~avle~fl~~~---~~~~lvsfNGkaFD~Pfik-R~v~~~~el~--------------------------------- 183 (278)
T COG3359 141 EEEVAVLENFLHDP---DFNMLVSFNGKAFDIPFIK-RMVRDRLELS--------------------------------- 183 (278)
T ss_pred chhhHHHHHHhcCC---CcceEEEecCcccCcHHHH-HHHhcccccC---------------------------------
Confidence 37888999997655 6679999999999999997 8655433220
Q ss_pred cCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHHH--ccCCCCCHHHHHHHh
Q psy12447 436 EGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLRE--YKLRSYTLNSVSYHF 513 (551)
Q Consensus 436 ~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~--~kl~sYsL~~V~~~~ 513 (551)
+ -+-|+|||.-+|+. +.|.+-+|.+|-+ .
T Consensus 184 --------------------------------l----------------~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~ 214 (278)
T COG3359 184 --------------------------------L----------------EFGHFDLYHPSRRLWKHLLPRCGLKTVER-I 214 (278)
T ss_pred --------------------------------c----------------cccchhhhhhhhhhhhccCCCCChhhHHH-H
Confidence 0 03389999999985 4689999999988 9
Q ss_pred hccCCCC-CCh---hhHHHHHhcC
Q psy12447 514 LQEQKED-VQH---SIISDLQIAL 533 (551)
Q Consensus 514 Lg~~k~~-~~~---~~i~~~~~~~ 533 (551)
||.++.+ .+. -++-..|...
T Consensus 215 LGi~R~edtdG~~~p~lyr~~~~~ 238 (278)
T COG3359 215 LGIRREEDTDGYDGPELYRLYRRY 238 (278)
T ss_pred hCccccccCCCcchHHHHHHHHHc
Confidence 9966653 443 3455555543
No 33
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=97.45 E-value=0.00011 Score=72.71 Aligned_cols=120 Identities=39% Similarity=0.622 Sum_probs=80.0
Q ss_pred cccCCcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHh
Q psy12447 292 FTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRE 371 (551)
Q Consensus 292 ~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~ 371 (551)
|+|++|.++.++.|..+++|.+|+.+|..+++..+ | +.+.|+|+..|+-.+ |+.|...+
T Consensus 52 ~~l~~~~~~~~~~v~~~~~E~eLL~~f~~~i~~~D------P-----------Dii~GyN~~~FDl~y-L~~R~~~l--- 110 (230)
T cd05777 52 FTLKTCAPIVGAQVFSFETEEELLLAWRDFVQEVD------P-----------DIITGYNICNFDLPY-LLERAKAL--- 110 (230)
T ss_pred EEeCCCCCCCCCEEEEECCHHHHHHHHHHHHHhcC------C-----------CEEEEecCCCCCHHH-HHHHHHHh---
Confidence 34456777888999999999999999999998766 4 457899999999999 88887542
Q ss_pred cCCceEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCc-----------
Q psy12447 372 LDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSD----------- 440 (551)
Q Consensus 372 ~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~----------- 440 (551)
++..|+ ...|...-... .+.... +++++|.+....+.+.|++.
T Consensus 111 ---------~i~~~~---~lgR~~~~~~~-------~~~~~~-------~~~~~g~~~~~~~~i~GR~~iD~~~~~~~~~ 164 (230)
T cd05777 111 ---------KLNTFP---FLGRIKNIKST-------IKDTTF-------SSKQMGTRETKEINIEGRIQFDLLQVIQRDY 164 (230)
T ss_pred ---------CCcccc---ccccccCCcee-------EeCCcc-------cccccccccceEEEEcCEEeeeHHHHHHHhc
Confidence 222222 12333221110 000000 12345555555567777752
Q ss_pred --cccccccccccccccccc
Q psy12447 441 --RRETLGVKNFTFLGRVKD 458 (551)
Q Consensus 441 --~~~~l~~~~~~~lg~~k~ 458 (551)
.+|+|++++.|+||++|.
T Consensus 165 kl~sy~L~~Va~~~Lg~~k~ 184 (230)
T cd05777 165 KLRSYSLNSVSAHFLGEQKE 184 (230)
T ss_pred CcccCcHHHHHHHHhCCCCC
Confidence 789999999999998874
No 34
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=97.40 E-value=0.00017 Score=71.36 Aligned_cols=114 Identities=16% Similarity=0.212 Sum_probs=79.0
Q ss_pred ccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceE
Q psy12447 298 APIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIF 377 (551)
Q Consensus 298 ~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii 377 (551)
.++.+..|..+++|.+|+.+|..+++..+ | +.+.|+++..|+-.+ |+.|...+
T Consensus 68 ~~~~~~~v~~~~~E~~LL~~f~~~i~~~D------P-----------Dii~GyNi~~fd~~Y-L~~Ra~~l--------- 120 (231)
T cd05778 68 SGLSGIPVEVVESELELFEELIDLVRRFD------P-----------DILSGYEIQRSSWGY-LIERAAAL--------- 120 (231)
T ss_pred cCCCCCeEEEeCCHHHHHHHHHHHHHHhC------C-----------CEEEEeccccCcHHH-HHHHHHHh---------
Confidence 35677889999999999999999999876 4 567899999999999 88888644
Q ss_pred EeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhcccccccccccccCCCc-------------cccc
Q psy12447 378 TGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGNSD-------------RRET 444 (551)
Q Consensus 378 ~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~~~~~~~-------------~~~~ 444 (551)
++. ++ ..+.-+++...... .... ++++|.++.+.+.+.||+. ++|+
T Consensus 121 ---~~~--~~---~~~lgR~~~~~~~~---~~~~----------~~~~g~~~~~~~~i~GRi~lD~~~~~r~~~kl~sYs 179 (231)
T cd05778 121 ---GID--DL---LDEISRVPSDSNGK---FGDR----------DDEWGYTHTSGIKIVGRHILNVWRLMRSELALTNYT 179 (231)
T ss_pred ---CCc--ch---hhhccCCCCCCccc---cccc----------ccccccccCCceEEeeEEEeEhHHHHHHHcCcccCC
Confidence 111 11 11212222211111 1110 1346666667788899862 8899
Q ss_pred ccccccccccccccc
Q psy12447 445 LGVKNFTFLGRVKDI 459 (551)
Q Consensus 445 l~~~~~~~lg~~k~~ 459 (551)
|++++.|+||++|..
T Consensus 180 L~~V~~~~L~~~k~~ 194 (231)
T cd05778 180 LENVVYHVLHQRIPL 194 (231)
T ss_pred HHHHHHHHhCCCCCC
Confidence 999999999999864
No 35
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.24 E-value=0.0024 Score=63.27 Aligned_cols=47 Identities=26% Similarity=0.407 Sum_probs=36.9
Q ss_pred EEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 351 QVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 351 ~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
.|...+...+.+..|.+++. +.++++|||+..||+++|.+-+.+.|+
T Consensus 59 ~v~~~p~f~ev~~~~~~fi~--~~~~lVaHN~~~FD~~~L~~e~~r~g~ 105 (232)
T PRK06309 59 EVADAPKFPEAYQKFIEFCG--TDNILVAHNNDAFDFPLLRKECRRHGL 105 (232)
T ss_pred HHhCCCCHHHHHHHHHHHHc--CCCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence 45556677888999998874 346999999999999999766666665
No 36
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=97.18 E-value=0.0019 Score=54.77 Aligned_cols=35 Identities=37% Similarity=0.645 Sum_probs=31.1
Q ss_pred HHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 365 WSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 365 f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
|..+++...|.+++|||. .||++||.+++++++++
T Consensus 35 f~~~l~~~~~~v~V~hn~-~fD~~fL~~~~~~~~~~ 69 (96)
T cd06125 35 LKDILRDKPLAILVGHNG-SFDLPFLNNRCAELGLK 69 (96)
T ss_pred HHHHHhhCCCCEEEEeCc-HHhHHHHHHHHHHcCCC
Confidence 777888888899999999 89999999999988764
No 37
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.10 E-value=0.0036 Score=62.94 Aligned_cols=44 Identities=20% Similarity=0.553 Sum_probs=33.7
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+..-+...+.+..|..++. -.+++|||. .||+.+|..-+.+.|.
T Consensus 128 l~~ap~~~evl~~f~~fl~---~~v~VaHNa-~FD~~fL~~~l~r~g~ 171 (257)
T PRK08517 128 LENAPSLKEVLEEFRLFLG---DSVFVAHNV-NFDYNFISRSLEEIGL 171 (257)
T ss_pred HcCCCCHHHHHHHHHHHHC---CCeEEEECH-HHHHHHHHHHHHHcCC
Confidence 3445678889999998875 368999999 8999999665555544
No 38
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=97.06 E-value=0.0059 Score=63.76 Aligned_cols=41 Identities=15% Similarity=0.148 Sum_probs=30.4
Q ss_pred EcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcC
Q psy12447 354 CCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLG 398 (551)
Q Consensus 354 ~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~ 398 (551)
.-++-.+++..|..++.. .++++||.. ||++||..-+++.+
T Consensus 108 ~AP~f~eVl~el~~fL~g---~vLVaHNA~-FD~~FL~~e~~r~~ 148 (377)
T PRK05601 108 QGKRFSQILKPLDRLIDG---RTLILHNAP-RTWGFIVSEAKRAM 148 (377)
T ss_pred cCCCHHHHHHHHHHHhCC---CEEEEECcH-HHHHHHHHHHHHhh
Confidence 334556788888888763 379999976 99999987666543
No 39
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.04 E-value=0.0047 Score=61.91 Aligned_cols=46 Identities=20% Similarity=0.367 Sum_probs=34.6
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
|...++..+++..|.+++.. .++++|||+ .||+++|..-+.+.|++
T Consensus 68 v~~~p~~~ev~~~~~~fl~~--~~~lvghn~-~FD~~~L~~~~~r~g~~ 113 (250)
T PRK06310 68 LRDKPKIAEVFPQIKGFFKE--GDYIVGHSV-GFDLQVLSQESERIGET 113 (250)
T ss_pred HhCCCCHHHHHHHHHHHhCC--CCEEEEECH-HHHHHHHHHHHHHcCCC
Confidence 44446777888888888742 479999987 59999997777666653
No 40
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=97.02 E-value=0.0062 Score=58.01 Aligned_cols=43 Identities=21% Similarity=0.171 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
.++.++|..|..++.+ ...+++|||...||+.+|..=+.+.+.
T Consensus 67 ~~~~~~l~~~~~~~~~-~~~~lVahn~~~FD~~fL~~~~~r~~~ 109 (183)
T cd06138 67 LSEYEFIAKIHRLFNT-PGTCIVGYNNIRFDDEFLRFAFYRNLY 109 (183)
T ss_pred CCHHHHHHHHHHHHcc-CCCcEEeeCchhhHHHHHHHHHHHCCC
Confidence 4677899999999874 345899999889999999644445444
No 41
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=97.02 E-value=0.013 Score=55.50 Aligned_cols=39 Identities=28% Similarity=0.431 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhcC-CceEEeecccCCChHHHHHHHHHcCC
Q psy12447 361 LLDKWSAFIRELD-PDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 361 LL~~f~~~i~~~d-PDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+...+..++...+ +.+++|||...||+++|..-++++|+
T Consensus 84 ~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~ 123 (177)
T cd06136 84 TANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGT 123 (177)
T ss_pred HHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCC
Confidence 4455555555544 56899999999999999777666665
No 42
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.92 E-value=0.0025 Score=76.40 Aligned_cols=44 Identities=23% Similarity=0.459 Sum_probs=35.8
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+..-.+..+.|..|.+++. ..+++||| ..||+++|...+.++|+
T Consensus 251 L~~ap~~~evl~~f~~fl~---~~iLVaHN-a~FD~~fL~~~~~r~g~ 294 (1213)
T TIGR01405 251 LENAPEIEEVLEKFKEFFK---DSILVAHN-ASFDIGFLNTNFEKVGL 294 (1213)
T ss_pred HhCCCCHHHHHHHHHHHhC---CCeEEEEC-hHHHHHHHHHHHHHcCC
Confidence 3344578899999999986 47999999 79999999887777665
No 43
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.91 E-value=0.0099 Score=61.56 Aligned_cols=44 Identities=16% Similarity=0.335 Sum_probs=31.8
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+..-+.-.+.+..|.+++. -++++|||. .||+.+|..-+.+.|+
T Consensus 75 l~~ap~f~ev~~~l~~~l~---~~~lVaHNa-~FD~~fL~~~~~r~g~ 118 (313)
T PRK06063 75 LEGQPQFADIAGEVAELLR---GRTLVAHNV-AFDYSFLAAEAERAGA 118 (313)
T ss_pred HhCCCCHHHHHHHHHHHcC---CCEEEEeCH-HHHHHHHHHHHHHcCC
Confidence 3334555678888887764 579999997 7999999755555543
No 44
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.86 E-value=0.0023 Score=66.24 Aligned_cols=44 Identities=27% Similarity=0.456 Sum_probs=35.2
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+.......+.+..|.+++. -++++|||+ .||+++|..-+.++|+
T Consensus 69 l~~~~~~~evl~~f~~fl~---~~~lVaHNa-~FD~~fL~~~~~~~gl 112 (313)
T PRK06807 69 VSDAPTIEEVLPLFLAFLH---TNVIVAHNA-SFDMRFLKSNVNMLGL 112 (313)
T ss_pred HhCCCCHHHHHHHHHHHHc---CCeEEEEcH-HHHHHHHHHHHHHcCC
Confidence 3445677889999999875 467899998 9999999877777765
No 45
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.82 E-value=0.015 Score=57.83 Aligned_cols=41 Identities=27% Similarity=0.268 Sum_probs=31.1
Q ss_pred EcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcC
Q psy12447 354 CCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLG 398 (551)
Q Consensus 354 ~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~ 398 (551)
.-+...+.+..|.+++.. ..++|||. .||+++|..-+.++|
T Consensus 69 ~~p~f~ev~~~f~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g 109 (240)
T PRK05711 69 DKPTFAEVADEFLDFIRG---AELIIHNA-PFDIGFMDYEFALLG 109 (240)
T ss_pred CCCCHHHHHHHHHHHhCC---CEEEEEcc-HHhHHHHHHHHHHhC
Confidence 345667899999988764 45799998 699999975555555
No 46
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.78 E-value=0.017 Score=56.98 Aligned_cols=39 Identities=26% Similarity=0.341 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcC
Q psy12447 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLG 398 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~ 398 (551)
+...+.+..|.+++.. ..++|||. .||+++|..-+.++|
T Consensus 67 p~f~ev~~~f~~fi~~---~~lVaHNa-~FD~~fL~~el~r~g 105 (225)
T TIGR01406 67 PKFKEIADEFLDFIGG---SELVIHNA-AFDVGFLNYELERLG 105 (225)
T ss_pred CCHHHHHHHHHHHhCC---CEEEEEec-HHHHHHHHHHHHHhC
Confidence 4667789999998764 46899998 699999976665555
No 47
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=96.65 E-value=0.022 Score=52.15 Aligned_cols=40 Identities=20% Similarity=0.265 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
....+.+.+|.+++.. ++++|||. .||+.+|..-+...|+
T Consensus 62 ~~~~~v~~~l~~~l~~---~~lv~hn~-~fD~~~l~~~~~~~g~ 101 (156)
T cd06130 62 PTFPEVWPEIKPFLGG---SLVVAHNA-SFDRSVLRAALEAYGL 101 (156)
T ss_pred CCHHHHHHHHHHHhCC---CEEEEeCh-HHhHHHHHHHHHHcCC
Confidence 4556788888888765 79999998 8999999766666554
No 48
>PRK07883 hypothetical protein; Validated
Probab=96.55 E-value=0.017 Score=64.58 Aligned_cols=45 Identities=24% Similarity=0.335 Sum_probs=35.9
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
+.....+.+.+..|.+++. ..+++|||. .||+++|..-++..|++
T Consensus 76 l~~ap~~~evl~~f~~fl~---~~~lVaHNa-~FD~~fL~~~~~r~g~~ 120 (557)
T PRK07883 76 VAGAPPIEEVLPAFLEFAR---GAVLVAHNA-PFDIGFLRAAAARCGYP 120 (557)
T ss_pred HhCCCCHHHHHHHHHHHhc---CCEEEEeCc-HHHHHHHHHHHHHcCCC
Confidence 4445678889999988876 479999998 79999998777776653
No 49
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.53 E-value=0.038 Score=54.71 Aligned_cols=41 Identities=20% Similarity=0.281 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHhc--CCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 358 ETELLDKWSAFIREL--DPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 358 E~~LL~~f~~~i~~~--dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+.+.|..|...+..+ .-.+++|||. .||+.+|..=+++.|+
T Consensus 75 ~~~vl~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~~~~r~~~ 117 (232)
T PRK07942 75 AAEVLAEIADALREAWARGVPVVVFNA-PYDLTVLDRELRRHGL 117 (232)
T ss_pred HHHHHHHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHHHHHHcCC
Confidence 456888888888753 4578999999 6999999655555554
No 50
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=96.46 E-value=0.037 Score=51.49 Aligned_cols=42 Identities=26% Similarity=0.316 Sum_probs=31.5
Q ss_pred EcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 354 CCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 354 ~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
......+.+..|.+++.. ..++|||+ .||+.+|..-+.+.|+
T Consensus 64 ~~~~~~~v~~~l~~~l~~---~~lv~hn~-~fD~~~l~~~~~~~~~ 105 (167)
T cd06131 64 DKPKFAEIADEFLDFIRG---AELVIHNA-SFDVGFLNAELSLLGL 105 (167)
T ss_pred cCCCHHHHHHHHHHHHCC---CeEEEeCh-HHhHHHHHHHHHHhCC
Confidence 335667889999888754 56899998 6999999766666554
No 51
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.41 E-value=0.027 Score=58.23 Aligned_cols=44 Identities=14% Similarity=0.177 Sum_probs=32.2
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
|..-+...+.+..|.+++. -++++|||. .||+.+|..-+.+.++
T Consensus 61 v~~ap~f~ev~~~~~~fl~---~~~lVaHNa-~FD~~fL~~~~~r~~~ 104 (309)
T PRK06195 61 VEDELEFDKIWEKIKHYFN---NNLVIAHNA-SFDISVLRKTLELYNI 104 (309)
T ss_pred HhCCCCHHHHHHHHHHHhC---CCEEEEECc-HHHHHHHHHHHHHhCC
Confidence 4444566778888888874 479999998 6999999655555443
No 52
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=96.36 E-value=0.031 Score=50.60 Aligned_cols=39 Identities=23% Similarity=0.466 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcC
Q psy12447 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLG 398 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~ 398 (551)
....+.+.++.+++.. ++++|||+ .||+.+|...+..++
T Consensus 64 ~~~~~~~~~~~~~l~~---~~~v~~n~-~fD~~~l~~~~~~~~ 102 (159)
T cd06127 64 PPFEEVLPEFLEFLGG---RVLVAHNA-SFDLRFLNRELRRLG 102 (159)
T ss_pred CCHHHHHHHHHHHHCC---CEEEEeCc-HhhHHHHHHHHHHhC
Confidence 3556788888887765 89999999 899999987777765
No 53
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=96.30 E-value=0.016 Score=67.53 Aligned_cols=110 Identities=26% Similarity=0.392 Sum_probs=67.7
Q ss_pred cccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHH
Q psy12447 242 KVAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 321 (551)
Q Consensus 242 ~~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~ 321 (551)
++-.-+-+-|||||..- .|..|.|+.|+.+-...|...+ +--+-+++..|+..
T Consensus 417 ~l~datyVVfDiETTGL-----s~~~d~iIE~aAvKikng~iId---~f~~Fi~P~~pl~~------------------- 469 (1444)
T COG2176 417 KLDDATYVVFDIETTGL-----SPVYDEIIEIAAVKIKNGRIID---KFQFFIKPGRPLSA------------------- 469 (1444)
T ss_pred ccccccEEEEEeecCCc-----CcccchhhhheeeeeeCCcchH---HHHHhcCCCCcCch-------------------
Confidence 34566788999999863 3567999999977544443321 11122233333321
Q ss_pred HHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 322 IRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 322 ~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
++.. -..|+.--+..-....+.|..|.+++. =.|+|-|| ..||++||..+.+.+++.
T Consensus 470 -----------------~~te-lTgITdeml~~a~~i~~vL~kf~~~~~---d~IlVAHN-asFD~gFl~~~~~k~~~~ 526 (1444)
T COG2176 470 -----------------TITE-LTGITDEMLENAPEIEEVLEKFREFIG---DSILVAHN-ASFDMGFLNTNYEKYGLE 526 (1444)
T ss_pred -----------------hhhh-ccccCHHHHcCCccHHHHHHHHHHHhc---CcEEEecc-CccchhHHHHHHHHhCCc
Confidence 1100 011222234444566778888877765 57999999 899999999888887764
No 54
>PRK07740 hypothetical protein; Provisional
Probab=96.29 E-value=0.038 Score=55.14 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=29.2
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHH
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLIN 392 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~ 392 (551)
+.......+.+.+|.+++. -++++|||. .||+.+|..
T Consensus 122 l~~ap~~~evl~~f~~fi~---~~~lVahna-~fD~~fL~~ 158 (244)
T PRK07740 122 VAFAPPLAEVLHRFYAFIG---AGVLVAHHA-GHDKAFLRH 158 (244)
T ss_pred HhCCCCHHHHHHHHHHHhC---CCEEEEeCH-HHHHHHHHH
Confidence 4455678889999988865 468999996 899998853
No 55
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.16 E-value=0.011 Score=69.67 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=33.4
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+..-+...+.+.+|.+++. -.+++|||+ .||+++|..-+...|+
T Consensus 61 l~~ap~~~ev~~~l~~~l~---~~~~VahN~-~fD~~fL~~~~~~~g~ 104 (850)
T TIGR01407 61 LQQAPYFSQVAQEIYDLLE---DGIFVAHNV-HFDLNFLAKALKDCGY 104 (850)
T ss_pred HhCCCCHHHHHHHHHHHhC---CCEEEEeCc-HHHHHHHHHHHHHcCC
Confidence 3345677788888888874 578999997 6999999766666554
No 56
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.04 E-value=0.13 Score=47.45 Aligned_cols=42 Identities=29% Similarity=0.468 Sum_probs=32.7
Q ss_pred cCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 355 CKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 355 ~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
-..+.+.+.+|..++.. ..+++||...||+.+|..-+.+.|+
T Consensus 64 ~~~~~~~~~~~~~~l~~---~~~v~~n~~~fD~~~L~~~~~~~~~ 105 (169)
T smart00479 64 APTFEEVLEELLEFLKG---KILVAGNALNFDLRFLKLEHPRLGI 105 (169)
T ss_pred CCCHHHHHHHHHHHhcC---CEEEEeCCHHHhHHHHHHHHHHhCC
Confidence 35677888888888754 4689999999999999766666554
No 57
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.04 E-value=0.013 Score=69.45 Aligned_cols=44 Identities=16% Similarity=0.273 Sum_probs=32.8
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+..-+...+.+..|..++. ..+++|||+ .||+++|..-+...|+
T Consensus 65 l~~ap~f~ev~~~l~~~l~---~~~~VaHN~-~FD~~fL~~~~~~~g~ 108 (928)
T PRK08074 65 VKQAPLFEDVAPEIVELLE---GAYFVAHNV-HFDLNFLNEELERAGY 108 (928)
T ss_pred HhcCCCHHHHHHHHHHHhC---CCeEEEECh-HHHHHHHHHHHHHcCC
Confidence 4444567788888888874 568999997 5999999665555554
No 58
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.91 E-value=0.071 Score=53.08 Aligned_cols=39 Identities=8% Similarity=0.048 Sum_probs=28.7
Q ss_pred EcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHH
Q psy12447 354 CCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKH 396 (551)
Q Consensus 354 ~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~ 396 (551)
.-.+..+.+..|..++ ..++++|||. .||+++|..-+..
T Consensus 112 ~ap~~~evl~~l~~~~---~~~~lVaHna-~FD~~fL~~~l~~ 150 (239)
T PRK09146 112 DAPDLERILDELLEAL---AGKVVVVHYR-RIERDFLDQALRN 150 (239)
T ss_pred CCCCHHHHHHHHHHHh---CCCEEEEECH-HHHHHHHHHHHHH
Confidence 3346677888888776 4579999996 5999999655544
No 59
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.90 E-value=0.059 Score=52.76 Aligned_cols=41 Identities=20% Similarity=0.218 Sum_probs=31.0
Q ss_pred eEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHc
Q psy12447 353 ICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHL 397 (551)
Q Consensus 353 ~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l 397 (551)
..-+...+++..|.+++. .++++|||. .||+++|..-+.++
T Consensus 69 ~~~p~~~ev~~~~~~~~~---~~~lVaHNa-~FD~~fL~~~~~r~ 109 (217)
T TIGR00573 69 KDKPDFKEIAEDFADYIR---GAELVIHNA-SFDVGFLNYEFSKL 109 (217)
T ss_pred cCCCCHHHHHHHHHHHhC---CCEEEEecc-HHHHHHHHHHHHHh
Confidence 334567788999988875 478999998 79999996555443
No 60
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=95.79 E-value=0.01 Score=64.67 Aligned_cols=50 Identities=8% Similarity=0.073 Sum_probs=44.0
Q ss_pred ccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 300 IVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 300 i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
+.|+.+++|.+|.+||.+|..+++..+ | +.+.|+|+..|+-.+ |+.|.-.
T Consensus 169 ~~~v~v~~f~sE~eLL~~F~~~i~~~D------P-----------DIItGYNi~nFDlPY-L~~Ra~~ 218 (498)
T PHA02524 169 LDNVVYMPFEDEVDLLLNYIQLWKANT------P-----------DLVFGWNSEGFDIPY-IITRITN 218 (498)
T ss_pred cCCeEEEEeCCHHHHHHHHHHHHHHhC------C-----------CEEEeCCCcccCHHH-HHHHHHH
Confidence 678899999999999999999999876 4 557899999999999 9988853
No 61
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=95.63 E-value=0.14 Score=49.77 Aligned_cols=47 Identities=19% Similarity=0.223 Sum_probs=32.9
Q ss_pred EEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 351 QVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 351 ~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
.|..-.+..+.+.+|.+++... +.++++| . .||+.+|..-++..|++
T Consensus 72 ~l~~ap~~~evl~~f~~~~~~~-~~~iv~~-~-~fD~~fL~~~~~~~~~~ 118 (207)
T PRK07748 72 DVDKGISFEELVEKLAEYDKRC-KPTIVTW-G-NMDMKVLKHNCEKAGVP 118 (207)
T ss_pred HHccCCCHHHHHHHHHHHhCcC-CeEEEEE-C-HHHHHHHHHHHHHcCCC
Confidence 3445567788999999988643 2366665 3 79999997777666653
No 62
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.58 E-value=0.028 Score=54.12 Aligned_cols=37 Identities=27% Similarity=0.452 Sum_probs=29.3
Q ss_pred EEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHH
Q psy12447 351 QVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYL 390 (551)
Q Consensus 351 ~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL 390 (551)
.|..-+.-.+.|.+|.+++. ..+++|||...||+.+|
T Consensus 64 ~v~~ap~~~evl~~f~~f~~---~~~lVaHNa~~fD~~fL 100 (195)
T PRK07247 64 KIADAPKVEEVLAAFKEFVG---ELPLIGYNAQKSDLPIL 100 (195)
T ss_pred HHhCCCCHHHHHHHHHHHHC---CCeEEEEeCcHhHHHHH
Confidence 34444567789999998885 44689999999999887
No 63
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.40 E-value=0.028 Score=65.71 Aligned_cols=39 Identities=18% Similarity=0.215 Sum_probs=29.6
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHH
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRA 394 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~ 394 (551)
+..-+...+.+..|.+++. -.+++|||. .||+++|..-+
T Consensus 67 l~~ap~~~ev~~~~~~~l~---~~~lVaHN~-~FD~~fL~~~~ 105 (820)
T PRK07246 67 LAQAPDFSQVARHIYDLIE---DCIFVAHNV-KFDANLLAEAL 105 (820)
T ss_pred HhcCCCHHHHHHHHHHHhC---CCEEEEECc-HHHHHHHHHHH
Confidence 4445677788889988875 378999998 59999995433
No 64
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=95.04 E-value=0.33 Score=46.41 Aligned_cols=41 Identities=27% Similarity=0.322 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhcC------CceEEeecccCCChHHHHHHHHHcCC
Q psy12447 358 ETELLDKWSAFIRELD------PDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 358 E~~LL~~f~~~i~~~d------PDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+.+-+..|...+.++- =.+++|||. .||+.+|..=++++|+
T Consensus 80 ~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~ 126 (189)
T cd06134 80 EKEALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKI 126 (189)
T ss_pred hHHHHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCC
Confidence 3445666666665431 258999998 6999999655556655
No 65
>PRK11779 sbcB exonuclease I; Provisional
Probab=94.93 E-value=0.13 Score=56.11 Aligned_cols=37 Identities=22% Similarity=0.146 Sum_probs=29.4
Q ss_pred CHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHH
Q psy12447 357 TETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRA 394 (551)
Q Consensus 357 ~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~ 394 (551)
+|.+.+..+..++.. ...+++|||...||+.+|..-+
T Consensus 77 ~e~e~~~~i~~~l~~-~~~~lVGhNni~FD~eflr~~~ 113 (476)
T PRK11779 77 PEAEFAARIHAEFSQ-PGTCILGYNNIRFDDEVTRYIF 113 (476)
T ss_pred CHHHHHHHHHHHHhc-CCCEEEEeCchhhcHHHHHHHH
Confidence 678888888888863 2368999999999999995444
No 66
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=94.65 E-value=0.11 Score=47.82 Aligned_cols=36 Identities=17% Similarity=0.231 Sum_probs=28.6
Q ss_pred EEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHH
Q psy12447 351 QVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYL 390 (551)
Q Consensus 351 ~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL 390 (551)
.+..-++..+.+.+|..++. ..+++|||. .||+.+|
T Consensus 57 ~v~~a~~~~~~~~~l~~~l~---~~vlVgHn~-~fD~~~L 92 (152)
T cd06144 57 HLKDAPDFEEVQKKVAELLK---GRILVGHAL-KNDLKVL 92 (152)
T ss_pred HHcCCCCHHHHHHHHHHHhC---CCEEEEcCc-HHHHHHh
Confidence 45556677888888888875 479999999 5999877
No 67
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=94.45 E-value=0.23 Score=46.14 Aligned_cols=31 Identities=19% Similarity=0.272 Sum_probs=21.6
Q ss_pred eeeHHHHHHHHcc-C---CCCCHHHHHHHhhccCC
Q psy12447 488 CFDLLFVLLREYK-L---RSYTLNSVSYHFLQEQK 518 (551)
Q Consensus 488 ~lDl~~~~~~~~k-l---~sYsL~~V~~~~Lg~~k 518 (551)
++|+..++++... + .+|+|++++++++|...
T Consensus 106 ~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~ 140 (161)
T cd06137 106 VVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKI 140 (161)
T ss_pred eeEehhhhhhccCCCcCCCCccHHHHHHHHCCchh
Confidence 4566666655432 2 68999999999998543
No 68
>PRK05168 ribonuclease T; Provisional
Probab=94.41 E-value=0.23 Score=48.44 Aligned_cols=42 Identities=26% Similarity=0.478 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHHHHhc------CCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 357 TETELLDKWSAFIREL------DPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 357 ~E~~LL~~f~~~i~~~------dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
.+.+.+..|..++..+ +=.+++|||. .||+.+|..-+++.|+
T Consensus 91 ~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~ 138 (211)
T PRK05168 91 SEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGL 138 (211)
T ss_pred ChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCC
Confidence 4555677777776642 1258999998 7999999777777765
No 69
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=94.23 E-value=0.75 Score=44.42 Aligned_cols=42 Identities=24% Similarity=0.384 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHHhc------CCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 357 TETELLDKWSAFIREL------DPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 357 ~E~~LL~~f~~~i~~~------dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
.+.+.+..+...+..+ +-.+++|||.. ||+.+|..=++++|.
T Consensus 82 ~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~-FD~~fL~~~~~r~~~ 129 (200)
T TIGR01298 82 SEYEALHEIFKVVRKAMKASGCQRAILVGHNAN-FDLGFLNAAVERTSL 129 (200)
T ss_pred chHHHHHHHHHHHHHHHHhcccCCCEEEEECch-hhHHHHHHHHHHhCC
Confidence 4445566666665422 33589999985 999999655555543
No 70
>PRK05359 oligoribonuclease; Provisional
Probab=94.03 E-value=0.43 Score=45.36 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHHHHhcC---CceEEeecccCCChHHHHHHHHHcCC
Q psy12447 355 CKTETELLDKWSAFIRELD---PDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 355 ~~~E~~LL~~f~~~i~~~d---PDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
-.++.+.+..|.+++...- -.+++|+|+ .||+.+|..-+..++.
T Consensus 76 ~~~~~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~~~~~~~~ 122 (181)
T PRK05359 76 TVSEAEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLARYMPELEA 122 (181)
T ss_pred CCCHHHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHhcc
Confidence 3477889999999997531 235788775 7999999877776654
No 71
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=93.72 E-value=0.5 Score=51.69 Aligned_cols=96 Identities=17% Similarity=0.213 Sum_probs=69.2
Q ss_pred CCHHHHHHHHHHHHHhcCCc-eEEeecccCCChHHHHHHHHHcCCCcccccccccccccccchhhhhhhccccccccccc
Q psy12447 356 KTETELLDKWSAFIRELDPD-IFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTIN 434 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPD-ii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~~~~~~~~f~~s~~~g~~~~~~~~ 434 (551)
.+|++++.+|++++..+ |+ -|..|| +|..++|.+.|..+|... ..+
T Consensus 326 ~~E~~~~~~f~~~l~~~-~~~~i~hY~--~~e~~~l~rla~~~~~~~-~~~----------------------------- 372 (457)
T TIGR03491 326 NTEELAWQQFLQLLQSY-PDAPIYHYG--ETEKDSLRRLAKRYGTPE-AEI----------------------------- 372 (457)
T ss_pred hHHHHHHHHHHHHHHHC-CCCeEEeeC--HHHHHHHHHHHHHcCCCH-HHH-----------------------------
Confidence 58999999999999987 77 589999 566888887777776531 000
Q ss_pred ccCCCccccccccccccccccccccccccccccccccccCcccceeeeeeceeeeeHHHHHHHHc--cCCCCCHHHHHHH
Q psy12447 435 FEGNSDRRETLGVKNFTFLGRVKDIRSVIKDSFIQSKQMGKRENKTINFEGRVCFDLLFVLLREY--KLRSYTLNSVSYH 512 (551)
Q Consensus 435 ~~~~~~~~~~l~~~~~~~lg~~k~~~~~i~~~~~~s~~~g~~~~~~~~i~GR~~lDl~~~~~~~~--kl~sYsL~~V~~~ 512 (551)
..+. +-.+|+|.++++.+ ...||+|.+|+.
T Consensus 373 -------------------------------~~l~----------------~~~vDL~~~vr~~~~~p~~sysLK~v~~- 404 (457)
T TIGR03491 373 -------------------------------EELL----------------KRFVDIHTIVRRSWILPIESYSLKSIAR- 404 (457)
T ss_pred -------------------------------HHHH----------------HHheehHHHHHhhEECCCCCCCHHHHHH-
Confidence 0000 13899999999875 568999999988
Q ss_pred hhccCCC--CCChhhHHHHHhc
Q psy12447 513 FLQEQKE--DVQHSIISDLQIA 532 (551)
Q Consensus 513 ~Lg~~k~--~~~~~~i~~~~~~ 532 (551)
+||-... ..+..+...||..
T Consensus 405 ~lg~~~~~~~~~G~~ai~~y~~ 426 (457)
T TIGR03491 405 WLGFEWRQKEASGAKSLLWYRQ 426 (457)
T ss_pred HhCcccCCCCCCHHHHHHHHHH
Confidence 5575332 4777777777753
No 72
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=93.28 E-value=0.41 Score=44.56 Aligned_cols=46 Identities=13% Similarity=0.251 Sum_probs=33.3
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCC
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGV 399 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i 399 (551)
+.......+.+.+|.+++....+.++++|+ .||+..|...+...+.
T Consensus 69 l~~~~~~~~vl~~~~~~l~~~~~~~~v~~~--~~d~~~l~~~~~~~~~ 114 (176)
T cd06133 69 VDNAPSFPEVLKEFLEWLGKNGKYAFVTWG--DWDLKDLLQNQCKYKI 114 (176)
T ss_pred HhcCCCHHHHHHHHHHHHHhCCCeEEEeec--HhhHHHHHHHHHHhcC
Confidence 344567888999999999875445777775 6898888766655443
No 73
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=92.78 E-value=0.73 Score=45.61 Aligned_cols=39 Identities=28% Similarity=0.547 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 359 TELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 359 ~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
.+.+..|.+++... .++++|| ..||+++|..++..++.+
T Consensus 82 ~~v~~~~~~~i~~~--~~~Vahn-a~fD~~fl~~~~~~~~~~ 120 (243)
T COG0847 82 AEVLPEFLDFIGGL--RLLVAHN-AAFDVGFLRVESERLGIE 120 (243)
T ss_pred HHHHHHHHHHHCCC--CeEEEEc-hhhcHHHHHHHHHHcCCC
Confidence 55666666665543 8999999 899999998888776653
No 74
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=92.37 E-value=0.13 Score=50.90 Aligned_cols=49 Identities=18% Similarity=0.268 Sum_probs=42.0
Q ss_pred CceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHH
Q psy12447 302 GSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 368 (551)
Q Consensus 302 ~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~ 368 (551)
+..|..+++|.+||.+|..+++..| | +.+.|+++..|+-++ |+.|...+
T Consensus 73 ~~~v~~~~~E~~LL~~f~~~i~~~D------P-----------DiivG~Ni~~fdl~~-L~~R~~~l 121 (234)
T cd05776 73 KTKVRIFENERALLNFFLAKLQKID------P-----------DVLVGHDLEGFDLDV-LLSRIQEL 121 (234)
T ss_pred CCcEEEeCCHHHHHHHHHHHHhhcC------C-----------CEEEeeccCCCCHHH-HHHHHHHh
Confidence 4568889999999999999998876 4 567899999999999 88888744
No 75
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=91.88 E-value=0.68 Score=42.52 Aligned_cols=31 Identities=23% Similarity=0.321 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHHHhcCCceEEeecccCCChHHH
Q psy12447 357 TETELLDKWSAFIRELDPDIFTGYNIQNFDFPYL 390 (551)
Q Consensus 357 ~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL 390 (551)
++.+.+.+|.+++.. =.+++|||.. ||+.+|
T Consensus 61 ~~~~v~~~~~~fl~~--~~vlVgHn~~-fD~~fL 91 (150)
T cd06145 61 TLEDVQKKLLSLISP--DTILVGHSLE-NDLKAL 91 (150)
T ss_pred CHHHHHHHHHHHhCC--CCEEEEcChH-HHHHHh
Confidence 788899999988851 1599999995 999887
No 76
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=91.86 E-value=0.16 Score=62.23 Aligned_cols=43 Identities=23% Similarity=0.413 Sum_probs=34.4
Q ss_pred EcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 354 CCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 354 ~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
.-.+..+.|..|.+++. -.++++||. .||+++|...++++|++
T Consensus 482 ~aps~~EaL~~f~~fig---g~vLVAHNa-~FD~~fL~~~l~rlgl~ 524 (1437)
T PRK00448 482 DAPSIEEVLPKFKEFCG---DSILVAHNA-SFDVGFINTNYEKLGLE 524 (1437)
T ss_pred CCCCHHHHHHHHHHHhC---CCEEEEeCc-cccHHHHHHHHHHcCCc
Confidence 34567788888888764 468999999 79999998888887764
No 77
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=91.85 E-value=0.72 Score=44.50 Aligned_cols=41 Identities=27% Similarity=0.344 Sum_probs=31.8
Q ss_pred EeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHH
Q psy12447 352 VICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKH 396 (551)
Q Consensus 352 V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~ 396 (551)
+..-..+.+.+.+|.+++. -.+++|||. .||+.+|..-++.
T Consensus 92 l~~~~~~~~vl~~~~~~i~---~~~lv~hn~-~fD~~fL~~~~~~ 132 (202)
T PRK09145 92 LEDGLSEEEALRQLLAFIG---NRPLVGYYL-EFDVAMLNRYVRP 132 (202)
T ss_pred HhcCCCHHHHHHHHHHHHc---CCeEEEeCH-HHHHHHHHHHHHH
Confidence 3344578889999999986 367999996 6999999766654
No 78
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=90.85 E-value=0.34 Score=46.99 Aligned_cols=54 Identities=17% Similarity=0.044 Sum_probs=41.6
Q ss_pred CcccccC-ceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 296 TCAPIVG-SQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 296 ~~~~i~~-~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
+|.++.+ ..++.+.+|.+||.+|..+++..+ | +.+.|+|+..|+-.+ |+.|...
T Consensus 57 ~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~~------P-----------d~i~gyN~~~FD~py-l~~R~~~ 111 (204)
T cd05779 57 PKPEYEGPFKVFNEPDEKALLQRFFEHIREVK------P-----------HIIVTYNGDFFDWPF-VEARAAI 111 (204)
T ss_pred CCCCCCCceEEecCCCHHHHHHHHHHHHHHhC------C-----------CEEEecCccccCHHH-HHHHHHH
Confidence 3444444 356778999999999999998765 3 346799999999988 8888753
No 79
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=90.60 E-value=0.33 Score=49.84 Aligned_cols=32 Identities=28% Similarity=0.335 Sum_probs=25.3
Q ss_pred ccCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeec
Q psy12447 243 VAPLRILSFDIECAGRKGIFPDPNHDPIIQIANMCIS 279 (551)
Q Consensus 243 ~p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~ 279 (551)
.++-+++.+|+||..- +|..|+|+.|+++...
T Consensus 34 ~~~~~~vvlD~ETTGL-----d~~~d~IIEIg~V~v~ 65 (294)
T PRK09182 34 EFVRLGVILDTETTGL-----DPRKDEIIEIGMVAFE 65 (294)
T ss_pred CCCCeEEEEEeeCCCC-----CCCCCeEEEEEEEEEE
Confidence 4566889999999863 4577999999988644
No 80
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=89.72 E-value=2.4 Score=39.86 Aligned_cols=44 Identities=16% Similarity=0.148 Sum_probs=33.0
Q ss_pred EcCCHHHHHHHHHHHHHhc---CCceEEeecccCCChHHHHHHHHHcC
Q psy12447 354 CCKTETELLDKWSAFIREL---DPDIFTGYNIQNFDFPYLINRAKHLG 398 (551)
Q Consensus 354 ~~~~E~~LL~~f~~~i~~~---dPDii~GyNi~~fdl~yL~~R~~~l~ 398 (551)
.-.++.+.+..|.+++... +-.+++|+| ..||+.+|..=+.++|
T Consensus 71 ~~~~~~~vl~~~~~f~~~~~~~~~~~lvgh~-~~FD~~fL~~~~~~~~ 117 (173)
T cd06135 71 STVTLAQAEAELLEFIKKYVPKGKSPLAGNS-VHQDRRFLDKYMPELE 117 (173)
T ss_pred CCCCHHHHHHHHHHHHHHhcCCCCCceeecc-hhhCHHHHHHHHHHHh
Confidence 3457888999999999853 445777766 5899999976666665
No 81
>PHA02528 43 DNA polymerase; Provisional
Probab=87.69 E-value=0.4 Score=56.32 Aligned_cols=49 Identities=14% Similarity=0.125 Sum_probs=40.9
Q ss_pred CceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHH
Q psy12447 302 GSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAF 368 (551)
Q Consensus 302 ~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~ 368 (551)
+..+..+.+|.+||.+|..+++..+ | +.+.|+|+..|+-.+ |+.|.-.+
T Consensus 169 ~v~~~~~~sE~eLL~~F~~~i~~~D------P-----------DII~GyNi~~FDlpY-L~~Ra~~~ 217 (881)
T PHA02528 169 KVVYMPFDTEREMLLEYINFWEENT------P-----------VIFTGWNVELFDVPY-IINRIKNI 217 (881)
T ss_pred CeeEEEcCCHHHHHHHHHHHHHHhC------C-----------cEEEecCCccCCHHH-HHHHHHHH
Confidence 4556778999999999999988766 4 557899999999999 99887653
No 82
>PRK06722 exonuclease; Provisional
Probab=84.87 E-value=0.75 Score=46.85 Aligned_cols=46 Identities=20% Similarity=0.254 Sum_probs=32.8
Q ss_pred EEeEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCC
Q psy12447 351 QVICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVK 400 (551)
Q Consensus 351 ~V~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~ 400 (551)
.|..-+.-.+.+..|.+++.. +.++++|. .||+.+|..=+...|++
T Consensus 70 mV~~AP~f~eVl~ef~~fig~---~~lvahna-~FD~~FL~~~l~~~gi~ 115 (281)
T PRK06722 70 DLIGVEKFPQIIEKFIQFIGE---DSIFVTWG-KEDYRFLSHDCTLHSVE 115 (281)
T ss_pred HHcCCCCHHHHHHHHHHHHCC---CcEEEEEe-HHHHHHHHHHHHHcCCC
Confidence 344555667899999999863 34455554 79999998777777764
No 83
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=84.12 E-value=1.3 Score=42.56 Aligned_cols=89 Identities=20% Similarity=0.209 Sum_probs=71.8
Q ss_pred cCceeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHH
Q psy12447 244 APLRILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIR 323 (551)
Q Consensus 244 p~l~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~ 323 (551)
|+|++|||||||.+.+ +|.+|++.- .+. +.++++..+.+..|..+..+++|.+||.+|..+++
T Consensus 1 p~l~~~~fDIE~~~~~---------~i~~i~~~~--~~~------~~i~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~ 63 (193)
T cd05784 1 PKLKVVSLDIETSMDG---------ELYSIGLYG--EGQ------ERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFA 63 (193)
T ss_pred CCccEEEEEeecCCCC---------CEEEEEeec--CCC------CEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHH
Confidence 7999999999997632 788888642 222 24677777778888899999999999999999998
Q ss_pred HhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 324 TMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 324 ~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
..+ | +.+.|+|+..|+-.+ |+.|...
T Consensus 64 ~~d------P-----------Dvi~g~N~~~FD~~y-l~~R~~~ 89 (193)
T cd05784 64 QYD------P-----------DIIIGWNVINFDLRL-LQRRAEA 89 (193)
T ss_pred hhC------C-----------CEEEECCCcCcCHHH-HHHHHHH
Confidence 765 3 446899999999999 9998864
No 84
>PHA03036 DNA polymerase; Provisional
Probab=83.85 E-value=0.54 Score=55.37 Aligned_cols=63 Identities=8% Similarity=-0.070 Sum_probs=50.7
Q ss_pred ccccccccCCcccc---cCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHH
Q psy12447 287 FVKNVFTLNTCAPI---VGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLD 363 (551)
Q Consensus 287 ~~~~~~~l~~~~~i---~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~ 363 (551)
..+.++++..|+++ .++.++++.+|.+|+ .|..++++.+ | +.+.|+|...||-.+ ++.
T Consensus 214 ~~~~~~~~~~~~~~~~~~~~~~~~~~sE~~ml-~~~~~i~~~d------~-----------D~i~~yNg~nFD~~Y-i~~ 274 (1004)
T PHA03036 214 EEAVKRGYYEIESLLDMDYSKELILCSEIVLL-RIAKKLLELE------F-----------DYVVTFNGHNFDLRY-ISN 274 (1004)
T ss_pred ccceeeeeeccccccccCCceeeecCCHHHHH-HHHHHHHhcC------C-----------CEEEeccCCCcchHH-HHH
Confidence 45678888889988 778999999999988 5677777665 3 557899999999998 888
Q ss_pred HHHHH
Q psy12447 364 KWSAF 368 (551)
Q Consensus 364 ~f~~~ 368 (551)
|.-.+
T Consensus 275 R~~~L 279 (1004)
T PHA03036 275 RLELL 279 (1004)
T ss_pred HHHHh
Confidence 87644
No 85
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=82.04 E-value=0.87 Score=46.85 Aligned_cols=59 Identities=27% Similarity=0.410 Sum_probs=47.7
Q ss_pred ccccCCccccc-CceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 291 VFTLNTCAPIV-GSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 291 ~~~l~~~~~i~-~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
+++++.|.... +..|..+++|.+||.+|..+++..+ | +.+.|+++..|+-.+ |+.|...
T Consensus 201 ~~~~~~~~~~~~~~~v~~~~~E~~lL~~f~~~i~~~d------P-----------Dii~GyN~~~fD~~y-l~~R~~~ 260 (325)
T PF03104_consen 201 VFTLGSCDSIEDNVEVIYFDSEKELLEAFLDIIQEYD------P-----------DIITGYNIDGFDLPY-LIERAKK 260 (325)
T ss_dssp EEECSCSCCTTCTTEEEEESSHHHHHHHHHHHHHHHS------------------SEEEESSTTTTHHHH-HHHHHHH
T ss_pred EEEecCCCCCCCCcEEEEECCHHHHHHHHHHHHHhcC------C-----------cEEEEecccCCCHHH-HHHHHHH
Confidence 34555666666 8889999999999999999999876 4 557899999999888 8888863
No 86
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=80.63 E-value=0.72 Score=42.63 Aligned_cols=30 Identities=33% Similarity=0.671 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhcCCce-EEeecccCCChHHHHHH
Q psy12447 361 LLDKWSAFIRELDPDI-FTGYNIQNFDFPYLINR 393 (551)
Q Consensus 361 LL~~f~~~i~~~dPDi-i~GyNi~~fdl~yL~~R 393 (551)
++..+..++. ||++ .+|||+. ||+..|...
T Consensus 65 ~~~~l~~ll~--~~~i~kv~~n~~-~D~~~L~~~ 95 (176)
T PF01612_consen 65 ILDALKELLE--DPNIIKVGHNAK-FDLKWLYRS 95 (176)
T ss_dssp HHHHHHHHHT--TTTSEEEESSHH-HHHHHHHHH
T ss_pred hHHHHHHHHh--CCCccEEEEEEe-chHHHHHHH
Confidence 3444444444 6664 8999995 799888543
No 87
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=73.22 E-value=3.9 Score=36.61 Aligned_cols=35 Identities=31% Similarity=0.589 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHHHhcCCceEEeecccCCChHHHHHH
Q psy12447 356 KTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYLINR 393 (551)
Q Consensus 356 ~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R 393 (551)
....+.+..|.+++... .+++||| ..||.+.+..=
T Consensus 67 ~~~~~~~~~~~~~~~~~--~~~v~~n-~~fd~~~l~~~ 101 (164)
T PF00929_consen 67 PSFEEALDEFEEFLKKN--DILVGHN-ASFDIGFLRRE 101 (164)
T ss_dssp CEHHHHHHHHHHHHHHH--TEEEETT-CCHEEESSHHH
T ss_pred CcHHHHHHhhhhhhhcc--ccccccc-ccchhhHHHHh
Confidence 34556788888888744 6899999 88998877433
No 88
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=65.35 E-value=40 Score=38.13 Aligned_cols=158 Identities=19% Similarity=0.269 Sum_probs=94.6
Q ss_pred cCcchhhhhhhhCCCCcceEEEeCCCeeEecCCCCCCCCCCCcccccee--EEEEEcCcccCCCCcccccCCCcccccCC
Q psy12447 159 SNIDFDIRFMVDNDIVGCNWIEIPPGKWQLRGQHKFSNTNRPCVSRCQL--EIDVSTDDIVSHAPEEIDVSTDDIVSHAP 236 (551)
Q Consensus 159 a~I~~~~rFliD~~I~g~~Wi~i~~~~~~~~~~~~~~~~~~~r~S~c~i--Ei~v~~~~I~n~~~~~~~~~~~~~~~~~~ 236 (551)
..+.-+-++|+++||.--..+..+..+. ... +...+-+ |+. ...|-+|. ++...
T Consensus 128 ~siseiN~WL~~~GL~~YRfvny~d~r~--~~~---------~~~~~TlID~M~--I~~iG~hy-----------IWVKd 183 (651)
T PF03337_consen 128 VSISEINYWLCRNGLERYRFVNYKDERR--LKL---------PNGSYTLIDDMV--ICYIGYHY-----------IWVKD 183 (651)
T ss_pred ccHHHHHHHHHhcChhheeeeechhhhh--hcc---------ccccceeeeeee--ecccceeE-----------EEEcC
Confidence 5778888999999999888877765321 100 1111211 222 12232221 22222
Q ss_pred CCCcccccCceeEEEEEEeccCCC----CCC-CCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecch
Q psy12447 237 EGEWSKVAPLRILSFDIECAGRKG----IFP-DPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTE 311 (551)
Q Consensus 237 ~~~~~~~p~l~ils~DIE~~~~~~----~fP-~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e 311 (551)
...+ .-|.+-|+.+||+..+... .+| +|....|++|++.-. .... +|.
T Consensus 184 ~~~Y-~RPE~DIl~~di~~ia~~~~W~~~~~~~~~~~~v~ai~v~a~--it~~-------------gp~----------- 236 (651)
T PF03337_consen 184 KENY-TRPEIDILPYDIKAIAQKSNWSKLRPYNPRALKVFAISVNAI--ITPN-------------GPS----------- 236 (651)
T ss_pred hhhc-cCccceeecccHHhhhchhcccccccCCcccceEEEEEEEEE--ecCC-------------Cce-----------
Confidence 1123 3588999999999998643 234 444567777765421 1111 111
Q ss_pred hhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHHHHHh-cC----CceEEeecccCCC
Q psy12447 312 TELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRE-LD----PDIFTGYNIQNFD 386 (551)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~~i~~-~d----PDii~GyNi~~fd 386 (551)
|+ ++.+. +|-..+.|++-+.|+..|+.+|++ +. -=+++||=..-||
T Consensus 237 ---------------------iy--mIsty------PG~~F~nf~s~~~li~~FL~Wl~e~~~~n~~ti~LvGy~ss~FD 287 (651)
T PF03337_consen 237 ---------------------IY--MISTY------PGKCFINFDSNKALISDFLKWLRECIMKNIRTIILVGYFSSFFD 287 (651)
T ss_pred ---------------------eE--EEEec------CCceEEeCCCchHHHHHHHHHHHHHHhccCceEEEeehhhhhhc
Confidence 11 12211 344456888888899999999998 44 5589999999999
Q ss_pred hHHHHHHHHH
Q psy12447 387 FPYLINRAKH 396 (551)
Q Consensus 387 l~yL~~R~~~ 396 (551)
+|.|..+...
T Consensus 288 ~pLLra~wp~ 297 (651)
T PF03337_consen 288 FPLLRAYWPK 297 (651)
T ss_pred cHHHHhhccc
Confidence 9999766543
No 89
>KOG0968|consensus
Probab=61.27 E-value=23 Score=42.26 Aligned_cols=134 Identities=28% Similarity=0.531 Sum_probs=108.8
Q ss_pred CCccEEEEEeecCCCcEEEEEEeceeeEEEEeCCCCCCh------hHHHHHHHHHHHHHHHHhccCcccccc---eEEEE
Q psy12447 49 KPVPIVRMFGVTMEGNSVCCHVHGFSPYLYVSAPKEFNS------THCRAFKEALNRAIIADMRGNKDEIQE---AVLMV 119 (551)
Q Consensus 49 ~~~pvI~lfG~te~G~svcv~V~gf~PYFYv~~~~~~~~------~~~~~~~~~l~~~l~~~~~~~~~~~~~---~i~~i 119 (551)
...+++++||..++|+.+|+++||..||.|+......++ ..++++...++.++....+++++.... .+-++
T Consensus 47 q~tqv~~v~~a~~~g~~~~~~s~g~l~~i~~k~d~~~t~t~l~~~d~~aqi~k~le~a~~~~~~a~~esq~~~~~~v~sv 126 (1488)
T KOG0968|consen 47 QPTQVIRVFGANEEGETVCCFSHGVLPYIYVKYDSFATTTDLEVPDFLAQIQKSLEYALALAARANPESQKPNLNAVQSV 126 (1488)
T ss_pred CCCccceecccccccceeeeeecccchhhhhhhhhhccccccccccHHHHHHHHHHHHHHHHhhcChhhhcchHHHHHHH
Confidence 356789999999999999999999999999987764332 346778888888877776665443333 56778
Q ss_pred EEEEeeeeeeecCCCcccEEEEEccc------------CCCcCCCcccccccCcchhhhhhhhCCCCcceEEEeCC
Q psy12447 120 EIVQKQTVFGFWGEELENFLKITESV------------FPTFPTHTYKAFESNIDFDIRFMVDNDIVGCNWIEIPP 183 (551)
Q Consensus 120 e~V~k~~lygy~~~~~~~flKI~~~~------------~~~l~~~~~~vyEa~I~~~~rFliD~~I~g~~Wi~i~~ 183 (551)
++|+..++|||+. ....|+||+... .+++.++.+.+||+|+||.++++.|.+++||+|+++..
T Consensus 127 ~~vk~~p~~~~~~-~~s~~~k~~l~~~sck~rl~el~rdg~ipnk~is~~esh~~y~~~r~~d~n~~~~~~ikvds 201 (1488)
T KOG0968|consen 127 QLVKGIPFYGYSF-CFSKFLKICLFSPSCKDRLVELFRDGAIPNKVISVYESHLPYLLQRMVDHNLYGCAPIKVDS 201 (1488)
T ss_pred HhcCCCCcccccc-chhhHHHHHhcCchhHHHHHHHHhcccCCCcccccchhccchhhhhhhhcccccceeeecch
Confidence 9999999999997 488999998321 24566788999999999999999999999999999864
No 90
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=56.04 E-value=25 Score=32.40 Aligned_cols=34 Identities=15% Similarity=0.189 Sum_probs=25.6
Q ss_pred eEcCCHHHHHHHHHHHHHhcCCceEEeecccCCChHHH
Q psy12447 353 ICCKTETELLDKWSAFIRELDPDIFTGYNIQNFDFPYL 390 (551)
Q Consensus 353 ~~~~~E~~LL~~f~~~i~~~dPDii~GyNi~~fdl~yL 390 (551)
..-.+-.+.+.+|.+++. -.+++|||. .||+.+|
T Consensus 59 ~~a~~~~~v~~~l~~~l~---~~vlV~Hn~-~~D~~~l 92 (157)
T cd06149 59 VNATPFAVAQKEILKILK---GKVVVGHAI-HNDFKAL 92 (157)
T ss_pred hcCCCHHHHHHHHHHHcC---CCEEEEeCc-HHHHHHh
Confidence 334566778888888875 469999996 6788777
No 91
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=42.81 E-value=30 Score=32.85 Aligned_cols=50 Identities=26% Similarity=0.269 Sum_probs=40.9
Q ss_pred ccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 300 IVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 300 i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
+.+..|..+++|.+++.+|..++...+ | +.+.|+|+..|+-.+ |+.|...
T Consensus 52 i~~~~v~~~~~E~~lL~~f~~~i~~~d------p-----------diivg~N~~~FD~~~-L~~R~~~ 101 (199)
T cd05160 52 IDGIEVEYFADEKELLKRFFDIIREYD------P-----------DILTGYNIDDFDLPY-LLKRAEA 101 (199)
T ss_pred CCCceEEEeCCHHHHHHHHHHHHHhcC------C-----------CEEEEeccCCCcHHH-HHHHHHH
Confidence 456778899999999999999988654 3 346789999999888 8888864
No 92
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=42.78 E-value=14 Score=36.12 Aligned_cols=17 Identities=24% Similarity=0.364 Sum_probs=14.6
Q ss_pred CCceEEeecccCCChHHH
Q psy12447 373 DPDIFTGYNIQNFDFPYL 390 (551)
Q Consensus 373 dPDii~GyNi~~fdl~yL 390 (551)
.-++++|||.. ||+.+|
T Consensus 73 ~~~~lVaHNa~-FD~~~L 89 (219)
T PRK07983 73 GSEWYVAHNAS-FDRRVL 89 (219)
T ss_pred CCCEEEEeCcH-hhHHHH
Confidence 56799999985 999888
No 93
>PTZ00315 2'-phosphotransferase; Provisional
Probab=41.54 E-value=37 Score=38.11 Aligned_cols=44 Identities=11% Similarity=0.018 Sum_probs=30.7
Q ss_pred EEeEcCCHHHHHHHHHHHHHhcCC-------ceEEeecccCCChH-HHHHHHH
Q psy12447 351 QVICCKTETELLDKWSAFIRELDP-------DIFTGYNIQNFDFP-YLINRAK 395 (551)
Q Consensus 351 ~V~~~~~E~~LL~~f~~~i~~~dP-------Dii~GyNi~~fdl~-yL~~R~~ 395 (551)
.|..-.+-.+.+..|.+++..... .+++++|+ .||+. +|..-++
T Consensus 123 ~V~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~ 174 (582)
T PTZ00315 123 MVSRADPFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMR 174 (582)
T ss_pred HHhcCCCHHHHHHHHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHH
Confidence 355555667899999999987641 36788886 68985 6655444
No 94
>PHA03334 putative DNA polymerase catalytic subunit; Provisional
Probab=37.63 E-value=2.9 Score=50.46 Aligned_cols=180 Identities=16% Similarity=0.197 Sum_probs=92.6
Q ss_pred ceeeeecchhhHHHHHHHHHHH-hCCCCccCceeeeeeecCCC-C-C-c-cCcEEeEcC-----CHHHHHHHHHHHHHh-
Q psy12447 303 SQVICCKTETELLDKWSAFIRT-MGQGASENIFVKNVFTLNTC-A-P-I-VGSQVICCK-----TETELLDKWSAFIRE- 371 (551)
Q Consensus 303 ~~v~~~~~e~~~~~~~~~~~~~-~~~~~~~~p~~~~~f~~~~~-~-~-~-~g~~V~~~~-----~E~~LL~~f~~~i~~- 371 (551)
..+..|.+|-+||-+|-.-+++ .+ .+|..+-. + . + ...+.+.+. --++|..+|-.++..
T Consensus 323 ~~~~~c~~e~~~l~~fl~~~~~~v~----------vlyv~n~~fdv~vi~~rl~~y~~~~~~~~~~~~l~~~~~~~~s~~ 392 (1545)
T PHA03334 323 IEFVACADELEMLLAFLNRLRKSVN----------VLYVYNAEFDVQVIQSRLNYYAFKQRPHPLTKALMEAWEAFLSKD 392 (1545)
T ss_pred eEEEEeccHHHHHHHHHHHHHhhcc----------EEEEecccccHHHHHHHHHHhhccCCCCcHHHHHHHHHHHHhccC
Confidence 4678899999999998877765 22 22322210 0 0 0 011111121 225688888888864
Q ss_pred ---cCCceEEeecccCCChHHHHHHHHHcCCCccccccccccc-----------ccccchhh-hhhhccccccccccccc
Q psy12447 372 ---LDPDIFTGYNIQNFDFPYLINRAKHLGVKNFTFLGRVKDI-----------RSVIKDSF-IQSKQMGKRENKTINFE 436 (551)
Q Consensus 372 ---~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~~l~R~~~~-----------~~~~~~~f-~~s~~~g~~~~~~~~~~ 436 (551)
+.|+++.+=|+.+-.-.=|++-+..+.-..|+ ..|-... .... ..| .+++. --+.++.+.
T Consensus 393 ~~~~~~~~~f~~~~~~s~y~~ll~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~r~~v-~~f~~n~~~---~~~~kv~~~ 467 (1545)
T PHA03334 393 PQLVPAQLLFGSDILNSNYLELLDVIESHKAQFKA-TCRKAAARKEEIGSYMKTRDTV-QDFNDNDKK---YLNSTSHGF 467 (1545)
T ss_pred CccCCceeEehhhHHHHHHHHHHHHHHHHHHHhhh-HHHHHHHHHHHhhhHHHHHHHH-Hhhcccccc---cccceeeec
Confidence 67888887776654333333333222111111 1110000 0000 011 01111 113456677
Q ss_pred CCCc----------------ccccccccccccccccc-----------c-c-ccccccccccccccCcccceeeeeecee
Q psy12447 437 GNSD----------------RRETLGVKNFTFLGRVK-----------D-I-RSVIKDSFIQSKQMGKRENKTINFEGRV 487 (551)
Q Consensus 437 ~~~~----------------~~~~l~~~~~~~lg~~k-----------~-~-~~~i~~~~~~s~~~g~~~~~~~~i~GR~ 487 (551)
|++. ++||||+|++||||+|| + + ++.|++....+++...+-..+......+
T Consensus 468 GrviiDMy~Vc~~K~~~~kL~sYkLNTVA~~~LgeqKp~k~~~k~~K~eDV~YkeI~~lf~~g~e~RaRla~YCLkDA~L 547 (1545)
T PHA03334 468 GAHIIDLMRVCNTKSIKAKCSSRKLDTVARLIISKSKPHKNPPKIGKMDDVKYTEMDGMFTAGGAALARYLIYNLVDSEL 547 (1545)
T ss_pred cEEEEehHHHHhhcccccCccCCcHHHHHHHHHhcccccccccccCcccCCCHHHHHHHHhcChhhHHHHHHHHHHHHHH
Confidence 7642 67999999999999999 4 3 5666655333222112223345566677
Q ss_pred eeeHHHHHHH
Q psy12447 488 CFDLLFVLLR 497 (551)
Q Consensus 488 ~lDl~~~~~~ 497 (551)
+++|++.++-
T Consensus 548 vlrLlkkl~~ 557 (1545)
T PHA03334 548 LIRIAKNLDP 557 (1545)
T ss_pred HHHHHHHHHH
Confidence 7777776654
No 95
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=30.28 E-value=55 Score=35.19 Aligned_cols=54 Identities=24% Similarity=0.373 Sum_probs=41.1
Q ss_pred CcccccCceeeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 296 TCAPIVGSQVICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 296 ~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
.+..+.+..+..+++|.+|+.+|..++...+ | +.+.|+|+..|+-.. |+.+...
T Consensus 54 ~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~d------p-----------dii~g~N~~~FD~~~-i~~R~~~ 107 (471)
T smart00486 54 TCKEIDGVEVYEFNNEKELLKAFLEFIKKYD------P-----------DIIYGHNISNFDLPY-IISRLEK 107 (471)
T ss_pred CcCCCCCCeEEecCCHHHHHHHHHHHHHHhC------C-----------CEEEeecCCCCCHHH-HHHHHHH
Confidence 3444556678888999999999999988765 3 345688888899887 7777764
No 96
>PRK05755 DNA polymerase I; Provisional
Probab=29.24 E-value=4e+02 Score=31.85 Aligned_cols=29 Identities=31% Similarity=0.591 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHhcCCce-EEeecccCCChHHHH
Q psy12447 360 ELLDKWSAFIRELDPDI-FTGYNIQNFDFPYLI 391 (551)
Q Consensus 360 ~LL~~f~~~i~~~dPDi-i~GyNi~~fdl~yL~ 391 (551)
+.+..|..++. |+++ +++||. .||+..|.
T Consensus 357 ~~l~~l~~~L~--d~~v~kV~HNa-kfDl~~L~ 386 (880)
T PRK05755 357 EVLAALKPLLE--DPAIKKVGQNL-KYDLHVLA 386 (880)
T ss_pred HHHHHHHHHHh--CCCCcEEEecc-HhHHHHHH
Confidence 45666666666 4554 699999 78998885
No 97
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=25.42 E-value=72 Score=30.38 Aligned_cols=45 Identities=16% Similarity=0.099 Sum_probs=36.6
Q ss_pred eeeecchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 305 VICCKTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 305 v~~~~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
+..+.+|.+|+.+|..+++..+ | +.+.|+|+..|+-.+ |+.|...
T Consensus 50 v~~~~~E~~lL~~F~~~i~~~d------p-----------diivgyN~~~FD~py-L~~R~~~ 94 (195)
T cd05780 50 VEVVKTEKEMIKRFIEIVKEKD------P-----------DVIYTYNGDNFDFPY-LKKRAEK 94 (195)
T ss_pred EEEeCCHHHHHHHHHHHHHHcC------C-----------CEEEecCCCCCcHHH-HHHHHHH
Confidence 4457899999999999988754 3 446799999999999 8888754
No 98
>TIGR00215 lpxB lipid-A-disaccharide synthase. Lipid-A precursor biosynthesis producing lipid A disaccharide in a condensation reaction. transcribed as part of an operon including lpxA
Probab=24.62 E-value=1.2e+02 Score=32.11 Aligned_cols=42 Identities=17% Similarity=0.366 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhcCCceEEeecccCCChHHHHHHHHHcCCCccc
Q psy12447 361 LLDKWSAFIRELDPDIFTGYNIQNFDFPYLINRAKHLGVKNFT 403 (551)
Q Consensus 361 LL~~f~~~i~~~dPDii~GyNi~~fdl~yL~~R~~~l~i~~~~ 403 (551)
++.....++++..||+++|.....|.+... ..|+.+|++..-
T Consensus 77 ~~~~~~~~l~~~kPd~vi~~g~~~~~~~~a-~aa~~~gip~v~ 118 (385)
T TIGR00215 77 IRKEVVQLAKQAKPDLLVGIDAPDFNLTKE-LKKKDPGIKIIY 118 (385)
T ss_pred HHHHHHHHHHhcCCCEEEEeCCCCccHHHH-HHHhhCCCCEEE
Confidence 555667888999999999999877666433 567778887643
No 99
>PHA02952 EEV maturation protein; Provisional
Probab=23.89 E-value=1.9e+02 Score=32.94 Aligned_cols=45 Identities=27% Similarity=0.423 Sum_probs=37.8
Q ss_pred CcEEeEcCCHHHHHHHHHHHHHh----cCCceEEeecccCCChHHHHHHH
Q psy12447 349 GSQVICCKTETELLDKWSAFIRE----LDPDIFTGYNIQNFDFPYLINRA 394 (551)
Q Consensus 349 g~~V~~~~~E~~LL~~f~~~i~~----~dPDii~GyNi~~fdl~yL~~R~ 394 (551)
|--.+.|++ +.|+..|+.++++ .+-=+++||=..-||++.|..+.
T Consensus 245 G~~f~~~~s-k~li~~FL~Wl~e~~~n~~ti~LvGy~Ss~FD~pLL~~~w 293 (648)
T PHA02952 245 GKCFINFDS-KKLILDFLKWLKEVMTNTSTIILVGYLSSFFDFPLLKAYW 293 (648)
T ss_pred CceEecCCH-HHHHHHHHHHHHHHhcCCceEEEEEhhhhhcchHHHHhhc
Confidence 334567778 7799999999998 77779999999999999997665
No 100
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=21.21 E-value=1.1e+02 Score=28.76 Aligned_cols=113 Identities=18% Similarity=0.295 Sum_probs=67.7
Q ss_pred eeEEEEEEeccCCCCCCCCCCCcEEEEEEEeeccCCCcccccccccccCCcccccCceeeeecchhhHHHHHHHHHHHhC
Q psy12447 247 RILSFDIECAGRKGIFPDPNHDPIIQIANMCISQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSAFIRTMG 326 (551)
Q Consensus 247 ~ils~DIE~~~~~~~fP~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~l~~~~~i~~~~v~~~~~e~~~~~~~~~~~~~~~ 326 (551)
..|.+|+|.....|..| +...+|+-|.+.+... -+.+.++.|+.|+|-.
T Consensus 5 ~lLIID~EaT~~eG~~~-~~e~eiiei~a~lv~~-----------------------------id~~vvd~F~syVRP~- 53 (210)
T COG5018 5 SLLIIDFEATMPEGKYS-PQEFEIIEIEAGLVKS-----------------------------IDDEVVDTFSSYVRPK- 53 (210)
T ss_pred eEEEEEeeeeccCCCCC-chhceeeeehhhHHHH-----------------------------hhHHHHHHHHHhcCcc-
Confidence 45788999999887665 3456777777653110 1334678888887621
Q ss_pred CCCccCceeeeeeecCCCCCccCcEEeEcCCHH----HHHHHHHHHHHhcCCceEEeeccc-CCChHHHHHHHHHcCCC
Q psy12447 327 QGASENIFVKNVFTLNTCAPIVGSQVICCKTET----ELLDKWSAFIRELDPDIFTGYNIQ-NFDFPYLINRAKHLGVK 400 (551)
Q Consensus 327 ~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~----~LL~~f~~~i~~~dPDii~GyNi~-~fdl~yL~~R~~~l~i~ 400 (551)
..|.. .+.|....+..=..+ +|. ..+..|+.++++++|----.|-.. ..|...|..-+...++.
T Consensus 54 ----~~P~L-----t~~Ckslt~I~Q~~V-D~apifs~v~E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~ 122 (210)
T COG5018 54 ----KFPKL-----TKRCKSLTKITQKQV-DEAPIFSMVFEDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIP 122 (210)
T ss_pred ----cCchH-----HHHHHHhhhhhhhhc-cccchHHHHHHHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCC
Confidence 11210 012332222111111 233 578899999999999875445544 36788888888877775
No 101
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=20.28 E-value=89 Score=30.23 Aligned_cols=41 Identities=24% Similarity=0.269 Sum_probs=33.4
Q ss_pred cchhhHHHHHHHHHHHhCCCCccCceeeeeeecCCCCCccCcEEeEcCCHHHHHHHHHH
Q psy12447 309 KTETELLDKWSAFIRTMGQGASENIFVKNVFTLNTCAPIVGSQVICCKTETELLDKWSA 367 (551)
Q Consensus 309 ~~e~~~~~~~~~~~~~~~~~~~~~p~~~~~f~~~~~~~~~g~~V~~~~~E~~LL~~f~~ 367 (551)
.+|.+||.+|..++...+ | +.+.|+|+..|+-.+ |+.+...
T Consensus 56 ~~E~~lL~~f~~~i~~~d------P-----------dii~g~N~~~FD~py-l~~R~~~ 96 (207)
T cd05785 56 AAEKELLEELVAIIRERD------P-----------DVIEGHNIFRFDLPY-LRRRCRR 96 (207)
T ss_pred CCHHHHHHHHHHHHHHhC------C-----------CEEeccCCcccCHHH-HHHHHHH
Confidence 468899999999998765 4 446799999999888 8877764
Done!