Query 019538
Match_columns 339
No_of_seqs 225 out of 1374
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 02:33:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019538hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08517 DNA polymerase III su 100.0 2E-33 4.3E-38 261.5 22.8 208 98-325 36-253 (257)
2 PRK09146 DNA polymerase III su 100.0 2.7E-31 5.9E-36 244.9 21.3 184 117-314 38-238 (239)
3 PRK05711 DNA polymerase III su 100.0 2.3E-31 4.9E-36 245.3 20.6 163 127-305 4-175 (240)
4 TIGR01406 dnaQ_proteo DNA poly 100.0 3E-31 6.5E-36 242.7 20.3 163 128-306 1-172 (225)
5 PRK06310 DNA polymerase III su 100.0 6.3E-31 1.4E-35 244.2 22.1 177 127-320 7-187 (250)
6 PRK07740 hypothetical protein; 100.0 1.8E-30 4E-35 240.3 22.1 180 119-316 52-240 (244)
7 PRK07748 sporulation inhibitor 100.0 5.6E-31 1.2E-35 238.1 17.5 178 127-318 4-199 (207)
8 PRK07942 DNA polymerase III su 100.0 3.1E-30 6.8E-35 237.1 21.3 182 127-317 6-195 (232)
9 PRK06309 DNA polymerase III su 100.0 3.4E-30 7.3E-35 236.9 21.3 177 128-321 3-182 (232)
10 cd06131 DNA_pol_III_epsilon_Ec 100.0 2.4E-30 5.3E-35 225.4 19.3 158 129-302 1-166 (167)
11 PRK06807 DNA polymerase III su 100.0 7.5E-30 1.6E-34 243.7 21.7 163 126-306 7-172 (313)
12 PRK06063 DNA polymerase III su 100.0 6.6E-30 1.4E-34 244.4 21.1 164 127-307 15-180 (313)
13 TIGR00573 dnaq exonuclease, DN 100.0 9.7E-30 2.1E-34 231.6 20.9 168 127-308 7-179 (217)
14 smart00479 EXOIII exonuclease 100.0 2.4E-29 5.2E-34 218.1 20.6 164 128-306 1-167 (169)
15 PRK07883 hypothetical protein; 100.0 1.6E-29 3.4E-34 258.4 22.6 182 121-318 10-198 (557)
16 PRK06195 DNA polymerase III su 100.0 5.2E-29 1.1E-33 238.2 23.5 169 127-315 1-174 (309)
17 cd06130 DNA_pol_III_epsilon_li 100.0 4.8E-29 1E-33 214.3 19.3 152 129-300 1-155 (156)
18 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 2E-29 4.4E-34 222.6 17.3 157 129-301 1-176 (177)
19 PRK09145 DNA polymerase III su 100.0 1.2E-28 2.7E-33 221.9 20.7 164 127-304 29-199 (202)
20 PRK05601 DNA polymerase III su 100.0 4.9E-28 1.1E-32 232.0 24.7 170 120-305 40-248 (377)
21 PRK05168 ribonuclease T; Provi 100.0 1.6E-28 3.4E-33 222.8 20.2 174 122-307 13-202 (211)
22 COG2176 PolC DNA polymerase II 100.0 9.6E-30 2.1E-34 265.6 12.3 170 120-307 415-587 (1444)
23 cd06134 RNaseT DEDDh 3'-5' exo 100.0 3E-28 6.5E-33 217.3 19.7 168 128-305 6-188 (189)
24 PRK07247 DNA polymerase III su 100.0 5.6E-28 1.2E-32 216.3 21.3 162 127-307 5-170 (195)
25 PRK06722 exonuclease; Provisio 100.0 1E-28 2.2E-33 231.6 17.2 166 127-305 5-180 (281)
26 TIGR01298 RNaseT ribonuclease 100.0 3.4E-28 7.5E-33 218.8 19.0 170 127-307 8-193 (200)
27 PRK07246 bifunctional ATP-depe 100.0 7.5E-28 1.6E-32 255.8 22.2 173 127-318 7-186 (820)
28 PRK07983 exodeoxyribonuclease 100.0 1.8E-27 3.9E-32 216.7 20.9 165 129-325 2-173 (219)
29 PRK08074 bifunctional ATP-depe 100.0 1.2E-27 2.5E-32 257.8 22.5 174 127-317 3-184 (928)
30 TIGR01407 dinG_rel DnaQ family 100.0 2.3E-27 4.9E-32 254.1 22.3 173 128-317 1-180 (850)
31 TIGR01405 polC_Gram_pos DNA po 100.0 5.7E-27 1.2E-31 254.8 22.2 171 127-314 190-367 (1213)
32 cd06133 ERI-1_3'hExo_like DEDD 100.0 7.8E-27 1.7E-31 204.2 18.5 161 129-302 1-175 (176)
33 cd06138 ExoI_N N-terminal DEDD 99.9 7.9E-27 1.7E-31 207.1 16.5 160 130-299 1-182 (183)
34 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 3.1E-27 6.6E-32 205.6 11.3 149 130-300 1-161 (161)
35 cd06127 DEDDh DEDDh 3'-5' exon 99.9 5.5E-26 1.2E-30 193.2 17.2 154 130-300 1-159 (159)
36 cd06149 ISG20 DEDDh 3'-5' exon 99.9 5.9E-26 1.3E-30 196.8 13.3 146 130-300 1-157 (157)
37 PRK09182 DNA polymerase III su 99.9 1.9E-25 4.1E-30 211.6 17.3 176 127-326 37-222 (294)
38 cd06145 REX1_like DEDDh 3'-5' 99.9 1.4E-25 3.1E-30 193.0 14.0 144 130-300 1-150 (150)
39 COG0847 DnaQ DNA polymerase II 99.9 8.3E-25 1.8E-29 201.9 19.2 164 127-305 13-181 (243)
40 PTZ00315 2'-phosphotransferase 99.9 1.7E-24 3.6E-29 218.2 21.5 175 127-306 56-255 (582)
41 cd06144 REX4_like DEDDh 3'-5' 99.9 3.1E-25 6.7E-30 191.2 12.8 146 130-300 1-152 (152)
42 PRK05359 oligoribonuclease; Pr 99.9 3.5E-24 7.6E-29 189.9 16.4 161 127-307 3-176 (181)
43 cd06135 Orn DEDDh 3'-5' exonuc 99.9 2.6E-24 5.5E-29 189.4 15.0 156 129-305 1-171 (173)
44 PRK00448 polC DNA polymerase I 99.9 5.1E-24 1.1E-28 234.4 18.9 174 127-317 419-599 (1437)
45 PRK11779 sbcB exonuclease I; P 99.9 1.5E-23 3.4E-28 209.5 20.0 184 127-318 6-222 (476)
46 PF00929 RNase_T: Exonuclease; 99.9 2E-26 4.3E-31 196.3 -1.0 156 130-299 1-164 (164)
47 KOG0542 Predicted exonuclease 99.8 7.2E-20 1.6E-24 165.2 11.5 171 128-307 57-243 (280)
48 KOG4793 Three prime repair exo 99.7 7.9E-20 1.7E-24 166.1 -1.7 310 6-332 2-317 (318)
49 COG5018 KapD Inhibitor of the 99.7 5.3E-18 1.2E-22 144.6 7.7 168 128-305 5-184 (210)
50 KOG2249 3'-5' exonuclease [Rep 99.7 6.7E-16 1.5E-20 140.7 14.5 157 126-307 104-267 (280)
51 COG2925 SbcB Exonuclease I [DN 99.6 1.3E-14 2.9E-19 137.9 12.1 171 127-305 9-200 (475)
52 cd06143 PAN2_exo DEDDh 3'-5' e 99.6 3.6E-14 7.8E-19 124.0 12.0 148 128-300 6-174 (174)
53 cd05160 DEDDy_DNA_polB_exo DED 99.5 3E-13 6.6E-18 121.1 16.7 136 129-280 1-161 (199)
54 COG1949 Orn Oligoribonuclease 99.5 2.1E-13 4.5E-18 116.1 9.5 156 127-304 6-176 (184)
55 KOG3242 Oligoribonuclease (3'- 99.4 3E-13 6.6E-18 116.1 8.7 157 127-304 26-197 (208)
56 PF13482 RNase_H_2: RNase_H su 99.2 4E-11 8.7E-16 103.8 7.8 136 130-305 1-136 (164)
57 cd05780 DNA_polB_Kod1_like_exo 99.2 7.3E-10 1.6E-14 99.3 13.9 128 128-282 4-157 (195)
58 cd05781 DNA_polB_B3_exo DEDDy 99.1 1.6E-09 3.5E-14 96.6 14.2 118 128-280 4-144 (188)
59 cd06139 DNA_polA_I_Ecoli_like_ 99.1 2.4E-09 5.1E-14 94.6 13.4 158 127-320 5-186 (193)
60 cd06125 DnaQ_like_exo DnaQ-lik 99.1 2.7E-09 5.8E-14 84.9 11.6 82 130-252 1-83 (96)
61 KOG2248 3'-5' exonuclease [Rep 99.0 3E-09 6.4E-14 103.8 11.2 154 127-305 216-374 (380)
62 COG3359 Predicted exonuclease 98.9 3.2E-08 7E-13 89.9 13.6 120 128-281 99-219 (278)
63 cd05785 DNA_polB_like2_exo Unc 98.9 8.9E-08 1.9E-12 86.7 15.4 125 127-282 9-170 (207)
64 PRK05755 DNA polymerase I; Pro 98.9 2.3E-08 5E-13 108.3 13.6 150 127-320 315-485 (880)
65 cd05782 DNA_polB_like1_exo Unc 98.9 6.9E-08 1.5E-12 87.5 14.3 113 135-282 42-171 (208)
66 cd05779 DNA_polB_epsilon_exo D 98.8 2.8E-07 6E-12 83.3 16.7 142 128-281 3-169 (204)
67 PF10108 DNA_pol_B_exo2: Predi 98.8 2.5E-07 5.3E-12 83.5 15.3 130 143-304 8-171 (209)
68 cd05777 DNA_polB_delta_exo DED 98.7 2.6E-06 5.7E-11 78.3 18.3 133 127-279 7-181 (230)
69 KOG4793 Three prime repair exo 98.6 6.9E-08 1.5E-12 88.7 7.5 175 127-306 13-218 (318)
70 cd05784 DNA_polB_II_exo DEDDy 98.4 3.9E-06 8.4E-11 75.2 12.7 124 128-279 4-152 (193)
71 PF01612 DNA_pol_A_exo1: 3'-5' 98.4 1.7E-05 3.7E-10 68.5 14.6 137 127-307 20-176 (176)
72 PHA02570 dexA exonuclease; Pro 98.3 1.2E-05 2.6E-10 72.6 12.1 125 129-255 3-156 (220)
73 cd05783 DNA_polB_B1_exo DEDDy 98.3 5.5E-05 1.2E-09 68.4 16.1 137 127-279 5-169 (204)
74 PF04857 CAF1: CAF1 family rib 98.2 5.6E-06 1.2E-10 77.6 9.5 164 127-301 22-262 (262)
75 cd05778 DNA_polB_zeta_exo inac 98.1 0.00011 2.5E-09 67.6 15.9 168 127-306 4-223 (231)
76 KOG0304 mRNA deadenylase subun 98.1 3.3E-05 7.2E-10 69.3 10.8 182 113-304 10-237 (239)
77 PTZ00166 DNA polymerase delta 98.1 7.7E-05 1.7E-09 82.3 15.7 159 127-303 264-483 (1054)
78 cd06140 DNA_polA_I_Bacillus_li 97.9 0.00019 4.2E-09 62.6 12.9 148 128-320 4-171 (178)
79 PF03104 DNA_pol_B_exo1: DNA p 97.9 0.00018 3.8E-09 68.7 13.5 127 127-273 157-325 (325)
80 PRK05762 DNA polymerase II; Re 97.9 0.00016 3.5E-09 77.7 14.6 149 127-302 155-348 (786)
81 cd00007 35EXOc 3'-5' exonuclea 97.9 0.00042 9.2E-09 58.1 14.0 133 129-305 2-154 (155)
82 smart00486 POLBc DNA polymeras 97.8 0.0013 2.8E-08 65.7 17.8 156 127-302 3-220 (471)
83 PHA02528 43 DNA polymerase; Pr 97.8 0.00098 2.1E-08 72.3 17.0 159 127-301 106-323 (881)
84 cd06146 mut-7_like_exo DEDDy 3 97.7 0.00065 1.4E-08 60.8 12.8 145 127-303 22-192 (193)
85 COG0749 PolA DNA polymerase I 97.6 0.00064 1.4E-08 70.0 12.4 150 129-321 24-197 (593)
86 cd06141 WRN_exo DEDDy 3'-5' ex 97.6 0.00067 1.5E-08 58.9 10.6 130 127-303 18-169 (170)
87 KOG1275 PAB-dependent poly(A) 97.6 4.1E-05 9E-10 80.5 3.0 170 127-318 910-1109(1118)
88 COG0349 Rnd Ribonuclease D [Tr 97.6 0.00073 1.6E-08 65.6 11.3 135 127-307 17-167 (361)
89 cd05776 DNA_polB_alpha_exo ina 97.5 0.0011 2.4E-08 61.1 11.5 141 128-280 4-186 (234)
90 cd06142 RNaseD_exo DEDDy 3'-5' 97.5 0.0026 5.6E-08 55.2 13.2 142 128-316 13-171 (178)
91 PRK10829 ribonuclease D; Provi 97.5 0.0041 8.9E-08 61.3 15.4 132 127-307 22-171 (373)
92 TIGR03491 RecB family nuclease 97.4 0.0026 5.7E-08 64.3 13.8 122 128-282 285-411 (457)
93 smart00474 35EXOc 3'-5' exonuc 97.4 0.0075 1.6E-07 51.4 14.4 134 128-306 22-171 (172)
94 TIGR01388 rnd ribonuclease D. 97.4 0.0059 1.3E-07 60.1 15.0 132 127-307 18-167 (367)
95 cd06129 RNaseD_like DEDDy 3'-5 97.3 0.0023 4.9E-08 55.4 10.5 130 127-303 13-160 (161)
96 KOG1798 DNA polymerase epsilon 97.1 0.011 2.4E-07 65.6 14.3 161 128-305 247-453 (2173)
97 cd06148 Egl_like_exo DEDDy 3'- 97.0 0.016 3.4E-07 51.9 12.8 97 198-307 55-178 (197)
98 TIGR00593 pola DNA polymerase 96.8 0.0026 5.5E-08 69.3 6.9 108 193-318 363-490 (887)
99 PHA02524 43A DNA polymerase su 96.7 0.02 4.3E-07 58.3 12.2 135 127-276 106-282 (498)
100 TIGR00592 pol2 DNA polymerase 96.6 0.08 1.7E-06 59.6 16.9 140 128-279 507-681 (1172)
101 COG0417 PolB DNA polymerase el 96.4 0.057 1.2E-06 58.4 14.0 127 127-277 154-304 (792)
102 PHA03036 DNA polymerase; Provi 96.0 0.18 3.8E-06 55.4 15.0 202 94-307 126-393 (1004)
103 KOG0969 DNA polymerase delta, 95.8 0.0049 1.1E-07 64.5 2.3 161 127-304 274-492 (1066)
104 cd06147 Rrp6p_like_exo DEDDy 3 95.8 0.072 1.6E-06 47.2 9.3 133 128-307 25-173 (192)
105 COG5228 POP2 mRNA deadenylase 94.4 0.24 5.2E-06 45.0 8.4 183 113-305 28-252 (299)
106 PRK05761 DNA polymerase I; Rev 93.7 0.34 7.4E-06 52.4 9.6 101 192-299 209-334 (787)
107 PHA02563 DNA polymerase; Provi 93.3 0.5 1.1E-05 49.7 9.7 79 127-238 12-90 (630)
108 cd09018 DEDDy_polA_RNaseD_like 93.2 0.66 1.4E-05 38.6 8.8 64 200-280 45-109 (150)
109 PF13017 Maelstrom: piRNA path 89.6 3 6.6E-05 37.9 9.6 110 145-258 9-131 (213)
110 cd06128 DNA_polA_exo DEDDy 3'- 88.7 1.1 2.3E-05 37.7 5.7 64 200-280 45-109 (151)
111 PF11074 DUF2779: Domain of un 82.8 11 0.00025 31.5 8.9 46 183-234 47-92 (130)
112 KOG3657 Mitochondrial DNA poly 69.4 4.4 9.4E-05 43.6 3.3 37 213-254 241-277 (1075)
113 KOG0970 DNA polymerase alpha, 58.6 47 0.001 37.4 8.6 159 127-302 529-751 (1429)
114 PF09281 Taq-exonuc: Taq polym 56.1 90 0.0019 26.3 8.0 69 226-306 70-138 (138)
115 TIGR00592 pol2 DNA polymerase 43.6 14 0.0003 42.1 2.0 91 127-231 198-304 (1172)
116 KOG0968 DNA polymerase zeta, c 43.0 62 0.0013 36.5 6.5 58 178-241 724-781 (1488)
117 KOG2206 Exosome 3'-5' exoribon 33.2 63 0.0014 33.9 4.6 96 193-307 250-361 (687)
118 KOG3506 40S ribosomal protein 30.8 17 0.00037 25.7 0.1 14 26-39 24-37 (56)
119 PF06471 NSP11: NSP11; InterP 30.7 17 0.00036 37.1 0.0 105 128-237 89-206 (593)
120 PRK14975 bifunctional 3'-5' ex 24.6 3.1E+02 0.0066 28.6 8.0 68 234-307 63-145 (553)
No 1
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=2e-33 Score=261.48 Aligned_cols=208 Identities=25% Similarity=0.349 Sum_probs=179.1
Q ss_pred chhhhhhhhccchhh-hhhhh---hhccCccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCC
Q 019538 98 NKTEISKIQRIQHYD-IEQII---AENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQV 172 (339)
Q Consensus 98 ~~~~l~~~~~~~~~~-~~~~~---~~~~~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i 172 (339)
...|+.+.+|++.+. .+..+ +..+++.+ ..||+||+||||+++..++|||||||.+++|.+ ++|+.+|+|. ++
T Consensus 36 ~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~-~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~i 113 (257)
T PRK08517 36 IDLELLKALGLPLVENKENLITLKTRFTPIKD-QVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EV 113 (257)
T ss_pred HHHHHHHHCCCceEEcCCCeEEeccCCCCCCC-CCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CC
Confidence 447889999999944 33333 33456666 699999999999999889999999999998876 8999999996 67
Q ss_pred CC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHH
Q 019538 173 PN--AHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTL 250 (339)
Q Consensus 173 ~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl 250 (339)
++ +++|||+++++. ++|++.+|+.+|.+|+++ .++||||+ .||+.||.+++.++|+.... ..++||+
T Consensus 114 p~~~~~itGIt~e~l~--~ap~~~evl~~f~~fl~~-------~v~VaHNa-~FD~~fL~~~l~r~g~~~~~-~~~ldtl 182 (257)
T PRK08517 114 PEYITELTGITYEDLE--NAPSLKEVLEEFRLFLGD-------SVFVAHNV-NFDYNFISRSLEEIGLGPLL-NRKLCTI 182 (257)
T ss_pred ChhhhhhcCcCHHHHc--CCCCHHHHHHHHHHHHCC-------CeEEEECH-HHHHHHHHHHHHHcCCCCCC-CCcEehH
Confidence 66 899999999999 899999999999999974 48999999 99999999999999987553 3689999
Q ss_pred HHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhc---cCHHHHHHhcCCCCCCCC
Q 019538 251 TLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLK---LSLCDLIERGFTPSDLIN 325 (339)
Q Consensus 251 ~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~---~tl~~L~~~s~~~~~~~~ 325 (339)
.+++.+++.. +++|++|++++|++.+ .+|+|++||.+|++||..+..+++ .++.+|+.++..+..+..
T Consensus 183 ~la~~~~~~~------~~~L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~~~~~t~~~L~~~~k~~~~~~~ 253 (257)
T PRK08517 183 DLAKRTIESP------RYGLSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLPSYIKTTEDLIDFSKTAKTLKK 253 (257)
T ss_pred HHHHHHccCC------CCCHHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhHHhhcCHHHHHHHhhhcccccC
Confidence 9999887653 8899999999999987 799999999999999999998775 588999999987666543
No 2
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=2.7e-31 Score=244.92 Aligned_cols=184 Identities=23% Similarity=0.355 Sum_probs=155.1
Q ss_pred hhhccCccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee---eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCC
Q 019538 117 IAENKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN---STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVP 191 (339)
Q Consensus 117 ~~~~~~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i---~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap 191 (339)
+..++++.+ ..|++||+||||++|..++|||||+|.++++.+ +.|+++|+|..++++ ..|||||++++. ++|
T Consensus 38 ~~~~~~~~~-~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~--~ap 114 (239)
T PRK09146 38 VSPDTPLSE-VPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQ--DAP 114 (239)
T ss_pred CCCCCCccc-CCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHh--CCC
Confidence 344566777 699999999999999999999999999998865 689999999999987 899999999999 899
Q ss_pred CHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcC---------CC
Q 019538 192 RMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSG---------GS 262 (339)
Q Consensus 192 ~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~---------~~ 262 (339)
++.+++.+|.+++.+ .++||||+ .||+.||.+++.+++...+ ...++||+.+++.+++.. ..
T Consensus 115 ~~~evl~~l~~~~~~-------~~lVaHna-~FD~~fL~~~l~~~~~~~~-~~~~iDTl~Lar~l~~~~~~~~~~~~~~~ 185 (239)
T PRK09146 115 DLERILDELLEALAG-------KVVVVHYR-RIERDFLDQALRNRIGEGI-EFPVIDTMEIEARIQRKQAGGLWNRLKGK 185 (239)
T ss_pred CHHHHHHHHHHHhCC-------CEEEEECH-HHHHHHHHHHHHHhcCCCC-CCceechHHHHHHHcccccccccchhccC
Confidence 999999999999974 48999999 9999999999987543222 346899999999987642 11
Q ss_pred CCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhc---cCHHHHH
Q 019538 263 NLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLK---LSLCDLI 314 (339)
Q Consensus 263 ~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~---~tl~~L~ 314 (339)
..+ +++|++++++|||+.. .+|+|++||.+|++||.++..... .++.+|+
T Consensus 186 ~~~-~~~L~~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~~~~~~~~~~l~ 238 (239)
T PRK09146 186 KPE-SIRLADSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHHFSPDTPISKLW 238 (239)
T ss_pred CCC-CCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHcCCCCCHHHHh
Confidence 113 7899999999999976 699999999999999999987653 4566654
No 3
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=2.3e-31 Score=245.27 Aligned_cols=163 Identities=31% Similarity=0.517 Sum_probs=145.7
Q ss_pred CcEEEEEEecCCCCCC-CCcEEEEEEEEEcCCee--eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRE-NERIIEIAFQDLLGGEN--STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILL 201 (339)
Q Consensus 127 ~~~vviDiETTGl~p~-~~~IIEIgav~v~~g~i--~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~ 201 (339)
+++|+||+||||++|. .++|||||+|.+.++.+ ..|+.||+|.+++++ .+|||||.+++. ++|.|.+++.+|.
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~--~~p~f~ev~~~f~ 81 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLA--DKPTFAEVADEFL 81 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHc--CCCCHHHHHHHHH
Confidence 6899999999999997 79999999999988765 689999999999988 899999999999 8999999999999
Q ss_pred HHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC---CCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhC
Q 019538 202 HYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN---NWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYG 278 (339)
Q Consensus 202 ~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~---~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~g 278 (339)
+|+.+ .++|+||+ .||+.||.+++.++|..+|. ...++||+.+++.++|.. +++|++|+++||
T Consensus 82 ~fi~~-------~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~------~~~L~aL~~~~g 147 (240)
T PRK05711 82 DFIRG-------AELIIHNA-PFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGK------RNSLDALCKRYG 147 (240)
T ss_pred HHhCC-------CEEEEEcc-HHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCC------CCCHHHHHHHCC
Confidence 99974 47999999 99999999999999865542 135899999999998864 779999999999
Q ss_pred CCCCC-CCCChHHHHHHHHHHHHHHHHh
Q 019538 279 IPLVG-SAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 279 I~~~~-~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
|+..+ .+|+|+.||+++++||..|...
T Consensus 148 i~~~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 148 IDNSHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 98764 4699999999999999999875
No 4
>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=99.98 E-value=3e-31 Score=242.75 Aligned_cols=163 Identities=33% Similarity=0.503 Sum_probs=143.6
Q ss_pred cEEEEEEecCCCCCCC-CcEEEEEEEEEcCCee--eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 128 TAIVFDIETTGFSREN-ERIIEIAFQDLLGGEN--STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 128 ~~vviDiETTGl~p~~-~~IIEIgav~v~~g~i--~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
++|++|+||||++|.. ++|||||+|.+.++.+ +.|+.||+|..++++ .+|||||.++++ ++|+|.+++.+|.+
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~--~~p~f~ev~~~f~~ 78 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLA--DKPKFKEIADEFLD 78 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHh--CCCCHHHHHHHHHH
Confidence 4799999999999875 8999999998887643 789999999999987 899999999999 88999999999999
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC---CCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP---NNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGI 279 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p---~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI 279 (339)
|+++ .++|+||+ .||+.||.+++.++|...+ ....++||+.+++.++|.. +++|++|+++|||
T Consensus 79 fi~~-------~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~------~~~L~~L~~~~gi 144 (225)
T TIGR01406 79 FIGG-------SELVIHNA-AFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQ------RNSLDALCKRFKV 144 (225)
T ss_pred HhCC-------CEEEEEec-HHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCC------CCCHHHHHHhcCC
Confidence 9974 47999999 9999999999999984322 1247999999999998764 7899999999999
Q ss_pred CCCC-CCCChHHHHHHHHHHHHHHHHhh
Q 019538 280 PLVG-SAHRAMADVNCLSLILQRLTFDL 306 (339)
Q Consensus 280 ~~~~-~aH~Al~DA~~ta~L~~~l~~~l 306 (339)
+..+ .+|+|+.||.++++||..|....
T Consensus 145 ~~~~r~~H~Al~DA~~~a~v~~~l~~~~ 172 (225)
T TIGR01406 145 DNSHRTLHGALLDAHLLAEVYLALTGGQ 172 (225)
T ss_pred CCCCCCCcCHHHHHHHHHHHHHHHHcCC
Confidence 9764 47999999999999999998754
No 5
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=6.3e-31 Score=244.18 Aligned_cols=177 Identities=29% Similarity=0.443 Sum_probs=157.7
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
+++|+||+||||+++..++|||||+|.++++.+ +.|+.+|+|..+|++ +.+||||+++++ ++|++.+++.+|.+|
T Consensus 7 ~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~--~~p~~~ev~~~~~~f 84 (250)
T PRK06310 7 TEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLR--DKPKIAEVFPQIKGF 84 (250)
T ss_pred CcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHh--CCCCHHHHHHHHHHH
Confidence 689999999999999899999999999987765 889999999999988 899999999999 899999999999999
Q ss_pred HHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC-CCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 204 VKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN-NWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~-~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
+.+ ..++||||+ .||+.||.+++.++|++++. .+.++||+.+++.+ +. .+ +++|++|+++||++..
T Consensus 85 l~~------~~~lvghn~-~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~-~~----~~-~~~L~~l~~~~g~~~~ 151 (250)
T PRK06310 85 FKE------GDYIVGHSV-GFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEY-GD----SP-NNSLEALAVHFNVPYD 151 (250)
T ss_pred hCC------CCEEEEECH-HHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhc-cc----CC-CCCHHHHHHHCCCCCC
Confidence 974 358999999 99999999999999988764 36799999999864 32 23 7899999999999987
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhhccCHHHHHHhcCCC
Q 019538 283 GSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFTP 320 (339)
Q Consensus 283 ~~aH~Al~DA~~ta~L~~~l~~~l~~tl~~L~~~s~~~ 320 (339)
.+|+|++||.+|++||..+..... ++++|++.+..|
T Consensus 152 -~aH~Al~Da~at~~vl~~l~~~~~-~~~~l~~~~~~~ 187 (250)
T PRK06310 152 -GNHRAMKDVEINIKVFKHLCKRFR-TLEQLKQILSKP 187 (250)
T ss_pred -CCcChHHHHHHHHHHHHHHHHhcc-cHHHHHHHhhcC
Confidence 699999999999999999987764 578898888766
No 6
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=1.8e-30 Score=240.29 Aligned_cols=180 Identities=30% Similarity=0.477 Sum_probs=155.2
Q ss_pred hccCccCCCcEEEEEEecCCCCCCC-CcEEEEEEEEEcCCee--eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCH
Q 019538 119 ENKDLAKLVTAIVFDIETTGFSREN-ERIIEIAFQDLLGGEN--STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRM 193 (339)
Q Consensus 119 ~~~~l~~~~~~vviDiETTGl~p~~-~~IIEIgav~v~~g~i--~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~ 193 (339)
...++.+ .++|+||+||||++|.. ++|||||+|.++++.+ +.|+++|+|..++++ .++||||+++++ ++|++
T Consensus 52 ~~~~~~~-~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~--~ap~~ 128 (244)
T PRK07740 52 LDIPLTD-LPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVA--FAPPL 128 (244)
T ss_pred cCCCccC-CCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHh--CCCCH
Confidence 3445555 58999999999999876 8999999999998865 889999999999888 799999999999 78999
Q ss_pred HHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHH
Q 019538 194 EDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQAL 273 (339)
Q Consensus 194 ~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L 273 (339)
.+++.+|.+|+.+ .++||||+ .||..||.+++.+... .+....++||+.+++.+.+.. + +++|+++
T Consensus 129 ~evl~~f~~fi~~-------~~lVahna-~fD~~fL~~~~~~~~~-~~~~~~~iDt~~l~r~l~~~~----~-~~sL~~l 194 (244)
T PRK07740 129 AEVLHRFYAFIGA-------GVLVAHHA-GHDKAFLRHALWRTYR-QPFTHRLIDTMFLTKLLAHER----D-FPTLDDA 194 (244)
T ss_pred HHHHHHHHHHhCC-------CEEEEeCH-HHHHHHHHHHHHHhcC-CCcCCCeechHHHHHHHcCCC----C-CCCHHHH
Confidence 9999999999974 48999999 9999999998876532 334457999999999887653 2 8899999
Q ss_pred HHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhc----cCHHHHHHh
Q 019538 274 REYYGIPLVGSAHRAMADVNCLSLILQRLTFDLK----LSLCDLIER 316 (339)
Q Consensus 274 ~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~~~ 316 (339)
+++||++.. .+|+|++||++|++||.+++.++. .++.+|++.
T Consensus 195 ~~~~gi~~~-~~H~Al~Da~ata~l~~~ll~~~~~~~~~~~~dl~~~ 240 (244)
T PRK07740 195 LAYYGIPIP-RRHHALGDALMTAKLWAILLVEAQQRGITTLHDLYAA 240 (244)
T ss_pred HHHCCcCCC-CCCCcHHHHHHHHHHHHHHHHHHHHcCCcCHHHHHHH
Confidence 999999998 589999999999999999987654 678888765
No 7
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.97 E-value=5.6e-31 Score=238.09 Aligned_cols=178 Identities=20% Similarity=0.213 Sum_probs=150.6
Q ss_pred CcEEEEEEecCCCCCC------CCcEEEEEEEEEcCCee-eeEEEEEcCCC--CCCC--ccccCCcHHhhcCCCCCCHHH
Q 019538 127 VTAIVFDIETTGFSRE------NERIIEIAFQDLLGGEN-STFQTLVNPKR--QVPN--AHVHGITTDMVCKPDVPRMED 195 (339)
Q Consensus 127 ~~~vviDiETTGl~p~------~~~IIEIgav~v~~g~i-~~f~~lV~P~~--~i~~--~~itGIt~e~l~~~~ap~~~e 195 (339)
++||+||+||||+++. .++|||||||.+++|.+ +.|++||+|.. ++++ +++||||+++++ ++|++.+
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~--~ap~~~e 81 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVD--KGISFEE 81 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHc--cCCCHHH
Confidence 5899999999997642 37999999999998876 89999999987 5776 899999999999 8999999
Q ss_pred HHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHH
Q 019538 196 LIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALRE 275 (339)
Q Consensus 196 vl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~ 275 (339)
|+.+|.+|++++ . .+|+||+ .||+.||.+++.++|+..|....++|+..+++.+++... .++|.++++
T Consensus 82 vl~~f~~~~~~~-----~-~~iv~~~-~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~-----~~~L~~~~~ 149 (207)
T PRK07748 82 LVEKLAEYDKRC-----K-PTIVTWG-NMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERN-----QTGLWKAIE 149 (207)
T ss_pred HHHHHHHHhCcC-----C-eEEEEEC-HHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCC-----CCCHHHHHH
Confidence 999999999741 2 3444567 899999999999999887754568999988887776432 789999999
Q ss_pred HhCCCCCCCCCChHHHHHHHHHHHHHHHHhh-------ccCHHHHHHhcC
Q 019538 276 YYGIPLVGSAHRAMADVNCLSLILQRLTFDL-------KLSLCDLIERGF 318 (339)
Q Consensus 276 ~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l-------~~tl~~L~~~s~ 318 (339)
+|||+..+.+|+|++||.+|++||.+|..+. ..++.+|+..++
T Consensus 150 ~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~~~~~~~~~~~~~~~~ 199 (207)
T PRK07748 150 EYGKEGTGKHHCALDDAMTTYNIFKLVEKDKEYLVKPEPPTIGERVDFSK 199 (207)
T ss_pred HcCCCCCCCCcChHHHHHHHHHHHHHHHhCcceeecCCCCccccceeHHH
Confidence 9999987678999999999999999999874 257777776653
No 8
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=3.1e-30 Score=237.12 Aligned_cols=182 Identities=26% Similarity=0.308 Sum_probs=151.4
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcC-Cee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLG-GEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~-g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
.+|++||+||||++|..++|||||+|.+++ |.+ +.|+++|+|..++++ +.|||||++++.+. .+++.+++.+|.+
T Consensus 6 ~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~-g~~~~~vl~e~~~ 84 (232)
T PRK07942 6 GPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAH-GRPAAEVLAEIAD 84 (232)
T ss_pred CcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhh-CCCHHHHHHHHHH
Confidence 589999999999999999999999999983 554 889999999999988 89999999999843 4457889998888
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
++.+... +..++||||+ .||+.||.+++.++|+..+....++||+.+++.+.+... . +++|++|+++||++..
T Consensus 85 ~l~~~~~--~~~~lVahNa-~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~---~-~~~L~~l~~~~gi~~~ 157 (232)
T PRK07942 85 ALREAWA--RGVPVVVFNA-PYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRK---G-KRTLTALCEHYGVRLD 157 (232)
T ss_pred HHHHHhh--cCCEEEEeCc-HhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccC---C-CCCHHHHHHHcCCCCC
Confidence 8753110 2358999999 999999999999999875544568999999988766421 2 7899999999999987
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhhc----cCHHHHHHhc
Q 019538 283 GSAHRAMADVNCLSLILQRLTFDLK----LSLCDLIERG 317 (339)
Q Consensus 283 ~~aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~~~s 317 (339)
.+|+|++||.+|++||.++....+ .++.+|+++.
T Consensus 158 -~aH~Al~Da~ata~l~~~l~~~~~~l~~~~~~~l~~~q 195 (232)
T PRK07942 158 -NAHEATADALAAARVAWALARRFPELAALSPAELHELQ 195 (232)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHH
Confidence 699999999999999999987543 6677777654
No 9
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.4e-30 Score=236.94 Aligned_cols=177 Identities=38% Similarity=0.592 Sum_probs=152.7
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHHH
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYVK 205 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l~ 205 (339)
++|+||+||||+++..++|||||++. ++....|+.+|+|..+|++ ++|||||+++++ ++|++.+++.+|.+|+.
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIeig~v~--~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~--~~p~f~ev~~~~~~fi~ 78 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAAYN--GVTSESFQTLVNPEIPIPAEASKIHGITTDEVA--DAPKFPEAYQKFIEFCG 78 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEEEc--CccccEEEEEeCCCCCCChhHHhhcCCCHHHHh--CCCCHHHHHHHHHHHHc
Confidence 69999999999999899999999963 3334789999999999988 899999999999 89999999999999997
Q ss_pred hcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCC
Q 019538 206 SRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSA 285 (339)
Q Consensus 206 ~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~a 285 (339)
+ ..++||||+..||++||.+++.++|++.+. +.++||+.+++.+++. ++ .++|.+++++||++.. .+
T Consensus 79 ~------~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~-~~~iDt~~l~~~~~~~----~~-~~~L~~l~~~~~~~~~-~a 145 (232)
T PRK06309 79 T------DNILVAHNNDAFDFPLLRKECRRHGLEPPT-LRTIDSLKWAQKYRPD----LP-KHNLQYLRQVYGFEEN-QA 145 (232)
T ss_pred C------CCEEEEeCCHHHHHHHHHHHHHHcCCCCCC-CcEEeHHHHHHHHcCC----CC-CCCHHHHHHHcCCCCC-CC
Confidence 3 458999994279999999999999998765 6899999999987764 33 8899999999999876 69
Q ss_pred CChHHHHHHHHHHHHHHHHhhc-cCHHHHHHhcCCCC
Q 019538 286 HRAMADVNCLSLILQRLTFDLK-LSLCDLIERGFTPS 321 (339)
Q Consensus 286 H~Al~DA~~ta~L~~~l~~~l~-~tl~~L~~~s~~~~ 321 (339)
|+|++||.+|++||.++..++. ..+.+|.+++..+.
T Consensus 146 H~Al~Da~~t~~vl~~l~~~~~~~~l~~l~~~~~~~~ 182 (232)
T PRK06309 146 HRALDDVITLHRVFSALVGDLSPQQVYDLLNESCHPR 182 (232)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhccCc
Confidence 9999999999999999998775 34566666655554
No 10
>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=99.97 E-value=2.4e-30 Score=225.39 Aligned_cols=158 Identities=36% Similarity=0.556 Sum_probs=139.7
Q ss_pred EEEEEEecCCCCC-CCCcEEEEEEEEEcCCee--eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 129 AIVFDIETTGFSR-ENERIIEIAFQDLLGGEN--STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 129 ~vviDiETTGl~p-~~~~IIEIgav~v~~g~i--~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
+|+||+||||+++ ..++|||||++.++++.+ +.|+.+|+|..++++ +++|||++++++ ++|++.+++.+|.+|
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~--~~~~~~~v~~~l~~~ 78 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLA--DKPKFAEIADEFLDF 78 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHh--cCCCHHHHHHHHHHH
Confidence 5899999999998 678999999999987764 689999999998887 899999999999 788899999999999
Q ss_pred HHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC--CCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCC
Q 019538 204 VKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP--NNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPL 281 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p--~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~ 281 (339)
+.+ .++|+||+ .||+.||.+++.++|+..+ .+..++||+.+++.+++.. .++|++++++||++.
T Consensus 79 l~~-------~~lv~hn~-~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~------~~~L~~l~~~~~i~~ 144 (167)
T cd06131 79 IRG-------AELVIHNA-SFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGK------PNSLDALCKRFGIDN 144 (167)
T ss_pred HCC-------CeEEEeCh-HHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCC------CCCHHHHHHHCCCCC
Confidence 974 37899999 9999999999999877543 3457899999999887643 789999999999998
Q ss_pred CC-CCCChHHHHHHHHHHHHHH
Q 019538 282 VG-SAHRAMADVNCLSLILQRL 302 (339)
Q Consensus 282 ~~-~aH~Al~DA~~ta~L~~~l 302 (339)
++ .+|+|++||++|++||.+|
T Consensus 145 ~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 145 SHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCChHHHHHHHHHHHHHh
Confidence 64 5899999999999999876
No 11
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=7.5e-30 Score=243.69 Aligned_cols=163 Identities=34% Similarity=0.549 Sum_probs=148.9
Q ss_pred CCcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 126 LVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 126 ~~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
+.++|+||+||||++|..++|||||||.+++|++ +.|+.+|+|..++++ +.+||||+++++ ++|++.+|+.+|.+
T Consensus 7 ~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~--~~~~~~evl~~f~~ 84 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVS--DAPTIEEVLPLFLA 84 (313)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHh--CCCCHHHHHHHHHH
Confidence 4689999999999999889999999999998877 899999999999888 899999999999 78999999999999
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
|+++ .++||||+ .||+.||.+++.++|++.+. ..++||+.+++.+++.. + +++|++|+++||++.
T Consensus 85 fl~~-------~~lVaHNa-~FD~~fL~~~~~~~gl~~~~-~~~iDtl~la~~~~~~~----~-~~kL~~L~~~lgi~~- 149 (313)
T PRK06807 85 FLHT-------NVIVAHNA-SFDMRFLKSNVNMLGLPEPK-NKVIDTVFLAKKYMKHA----P-NHKLETLKRMLGIRL- 149 (313)
T ss_pred HHcC-------CeEEEEcH-HHHHHHHHHHHHHcCCCCCC-CCEeeHHHHHHHHhCCC----C-CCCHHHHHHHcCCCC-
Confidence 9974 37899999 99999999999999997664 46999999999988753 3 889999999999998
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhh
Q 019538 283 GSAHRAMADVNCLSLILQRLTFDL 306 (339)
Q Consensus 283 ~~aH~Al~DA~~ta~L~~~l~~~l 306 (339)
.+|+|++||.+|+.||.++....
T Consensus 150 -~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 150 -SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred -CCcChHHHHHHHHHHHHHHHHhh
Confidence 59999999999999999998865
No 12
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=6.6e-30 Score=244.38 Aligned_cols=164 Identities=32% Similarity=0.468 Sum_probs=146.8
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEc-CCee-eeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLL-GGEN-STFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~-~g~i-~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
.+||+||+||||+++..++|||||+|.++ +|.+ +.|+++|+|..+.....||||++++++ ++|.|.+++.+|.+|+
T Consensus 15 ~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~--~ap~f~ev~~~l~~~l 92 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLE--GQPQFADIAGEVAELL 92 (313)
T ss_pred CCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHh--CCCCHHHHHHHHHHHc
Confidence 58999999999999988999999999996 5666 899999999875545899999999999 8999999999999999
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGS 284 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~ 284 (339)
.+ .++||||+ .||+.||.++|.++|...|.+ .++||+.+++.+++.. + +++|++|+++|||+.. .
T Consensus 93 ~~-------~~lVaHNa-~FD~~fL~~~~~r~g~~~~~~-~~ldTl~lar~~~~~~----~-~~kL~~l~~~~gi~~~-~ 157 (313)
T PRK06063 93 RG-------RTLVAHNV-AFDYSFLAAEAERAGAELPVD-QVMCTVELARRLGLGL----P-NLRLETLAAHWGVPQQ-R 157 (313)
T ss_pred CC-------CEEEEeCH-HHHHHHHHHHHHHcCCCCCCC-CEEehHHHHHHhccCC----C-CCCHHHHHHHcCCCCC-C
Confidence 74 38999999 999999999999999887654 5899999999876543 3 8999999999999976 7
Q ss_pred CCChHHHHHHHHHHHHHHHHhhc
Q 019538 285 AHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 285 aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
+|+|++||.+|++||.+++....
T Consensus 158 ~H~Al~DA~ata~l~~~ll~~~~ 180 (313)
T PRK06063 158 PHDALDDARVLAGILRPSLERAR 180 (313)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999988764
No 13
>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=99.97 E-value=9.7e-30 Score=231.63 Aligned_cols=168 Identities=30% Similarity=0.370 Sum_probs=145.9
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCC-ee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGG-EN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g-~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
..||+||+||||++|..+ |||||+|.+.++ .+ +.|+++|+|..++++ ..+||||++++. ++|++.+++.+|.+
T Consensus 7 ~~fvv~D~ETTGl~~~~~-IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~--~~p~~~ev~~~~~~ 83 (217)
T TIGR00573 7 DTETTGDNETTGLYAGHD-IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLK--DKPDFKEIAEDFAD 83 (217)
T ss_pred cCEEEEEecCCCCCCCCC-EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHc--CCCCHHHHHHHHHH
Confidence 589999999999999777 999999996654 44 899999999998887 899999999999 78999999999999
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
|+.+ .++||||+ .||+.||.++|.+.+...+..+.++|++.+++.+++.... . +++|.+++++||++..
T Consensus 84 ~~~~-------~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~--~-~~~L~~l~~~~gl~~~ 152 (217)
T TIGR00573 84 YIRG-------AELVIHNA-SFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPG--K-RNTLDALCKRYEITNS 152 (217)
T ss_pred HhCC-------CEEEEecc-HHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCC--C-CCCHHHHHHHcCCCCC
Confidence 9974 48999999 9999999999998876555556789999999888875321 2 7799999999999865
Q ss_pred C-CCCChHHHHHHHHHHHHHHHHhhcc
Q 019538 283 G-SAHRAMADVNCLSLILQRLTFDLKL 308 (339)
Q Consensus 283 ~-~aH~Al~DA~~ta~L~~~l~~~l~~ 308 (339)
+ .+|+|++||.+|++||.++..+...
T Consensus 153 ~~~~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 153 HRALHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred CcccCCHHHHHHHHHHHHHHHHhcchh
Confidence 3 5899999999999999999987653
No 14
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.97 E-value=2.4e-29 Score=218.09 Aligned_cols=164 Identities=38% Similarity=0.595 Sum_probs=146.1
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
.+|+||+||||+++..++|+|||+|.++++.+ +.|+.+|+|..++++ +++|||++++++ +++++.+++.+|.+|+
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~--~~~~~~~~~~~~~~~l 78 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLD--DAPTFEEVLEELLEFL 78 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHh--CCCCHHHHHHHHHHHh
Confidence 38999999999999889999999999998765 899999999888887 899999999999 7888999999999999
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGS 284 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~ 284 (339)
.+ .++|+||+..||+.+|.+++.+.|+..|....++|++.+++.+++.. +++|++++++||++..+.
T Consensus 79 ~~-------~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~------~~~L~~l~~~~~~~~~~~ 145 (169)
T smart00479 79 KG-------KILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR------KYSLKKLAERLGLEVIGR 145 (169)
T ss_pred cC-------CEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC------CCCHHHHHHHCCCCCCCC
Confidence 74 25677777589999999999999988776556899999999887642 789999999999999865
Q ss_pred CCChHHHHHHHHHHHHHHHHhh
Q 019538 285 AHRAMADVNCLSLILQRLTFDL 306 (339)
Q Consensus 285 aH~Al~DA~~ta~L~~~l~~~l 306 (339)
+|+|++||++|++||.++...+
T Consensus 146 ~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 146 AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CcCcHHHHHHHHHHHHHHHHHh
Confidence 6999999999999999998764
No 15
>PRK07883 hypothetical protein; Validated
Probab=99.97 E-value=1.6e-29 Score=258.41 Aligned_cols=182 Identities=36% Similarity=0.554 Sum_probs=162.5
Q ss_pred cCccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHH
Q 019538 121 KDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLI 197 (339)
Q Consensus 121 ~~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl 197 (339)
.++.+ +.||+||+||||++|..++|||||+|.+++|.+ +.|+.+|+|..++++ +.+||||+++++ ++|++.+++
T Consensus 10 ~~~~~-~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~--~ap~~~evl 86 (557)
T PRK07883 10 TPLRD-VTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVA--GAPPIEEVL 86 (557)
T ss_pred CCCcC-CCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHh--CCCCHHHHH
Confidence 45666 699999999999999889999999999998876 899999999999988 899999999999 889999999
Q ss_pred HHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh
Q 019538 198 PILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY 277 (339)
Q Consensus 198 ~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~ 277 (339)
..|.+|+.+ .++||||+ .||+.||..++.++|++++. +.++||+.+++.+++.. ..+ +++|++|++++
T Consensus 87 ~~f~~fl~~-------~~lVaHNa-~FD~~fL~~~~~r~g~~~~~-~~~iDTl~lar~l~~~~--~~~-~~~L~~L~~~~ 154 (557)
T PRK07883 87 PAFLEFARG-------AVLVAHNA-PFDIGFLRAAAARCGYPWPG-PPVLCTVRLARRVLPRD--EAP-NVRLSTLARLF 154 (557)
T ss_pred HHHHHHhcC-------CEEEEeCc-HHHHHHHHHHHHHcCCCCCC-CCcEecHHHHHHhcccC--CCC-CCCHHHHHHHC
Confidence 999999974 48999999 99999999999999998764 47899999999988732 234 89999999999
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHhhc----cCHHHHHHhcC
Q 019538 278 GIPLVGSAHRAMADVNCLSLILQRLTFDLK----LSLCDLIERGF 318 (339)
Q Consensus 278 gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~~~s~ 318 (339)
|++.. .+|+|++||.+|++||.+++.++. .++.+|+.+..
T Consensus 155 gi~~~-~~H~Al~DA~ata~l~~~l~~~~~~~~~~~~~~l~~~~~ 198 (557)
T PRK07883 155 GATTT-PTHRALDDARATVDVLHGLIERLGNLGVHTLEELLTYLP 198 (557)
T ss_pred CcccC-CCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHhhh
Confidence 99987 689999999999999999988874 57889988764
No 16
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=5.2e-29 Score=238.16 Aligned_cols=169 Identities=24% Similarity=0.392 Sum_probs=148.1
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCC-CCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQ-VPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~-i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
++||+||+||||. ..++|||||+|.+++|.+ +.|++||+|... +++ ..|||||+++++ ++|+|.+++.+|.+
T Consensus 1 ~~~vviD~ETTg~--~~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~--~ap~f~ev~~~~~~ 76 (309)
T PRK06195 1 MNFVAIDFETANE--KRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVE--DELEFDKIWEKIKH 76 (309)
T ss_pred CcEEEEEEeCCCC--CCCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHh--CCCCHHHHHHHHHH
Confidence 4699999999985 468999999999998876 899999999853 444 899999999999 89999999999999
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
|+.+ .++||||+ .||+.||.+++.++++.+|. ..++||+.+++.+++.. + +++|..|+++||++.
T Consensus 77 fl~~-------~~lVaHNa-~FD~~fL~~~~~r~~~~~~~-~~~idT~~lar~l~~~~----~-~~~L~~L~~~~gi~~- 141 (309)
T PRK06195 77 YFNN-------NLVIAHNA-SFDISVLRKTLELYNIPMPS-FEYICTMKLAKNFYSNI----D-NARLNTVNNFLGYEF- 141 (309)
T ss_pred HhCC-------CEEEEECc-HHHHHHHHHHHHHhCCCCCC-CCEEEHHHHHHHHcCCC----C-cCCHHHHHHHcCCCC-
Confidence 9974 48999999 99999999999999988764 47899999999998753 3 899999999999985
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhhc-cCHHHHHH
Q 019538 283 GSAHRAMADVNCLSLILQRLTFDLK-LSLCDLIE 315 (339)
Q Consensus 283 ~~aH~Al~DA~~ta~L~~~l~~~l~-~tl~~L~~ 315 (339)
.+|+|++||++|++||.++..++. .++.+|.+
T Consensus 142 -~~H~Al~DA~ata~l~~~l~~~~~~~~~~~l~~ 174 (309)
T PRK06195 142 -KHHDALADAMACSNILLNISKELNSKDINEISK 174 (309)
T ss_pred -cccCCHHHHHHHHHHHHHHHHHhccCCHHHHHH
Confidence 489999999999999999999876 45555544
No 17
>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=99.97 E-value=4.8e-29 Score=214.26 Aligned_cols=152 Identities=29% Similarity=0.439 Sum_probs=137.6
Q ss_pred EEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHHH
Q 019538 129 AIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYVK 205 (339)
Q Consensus 129 ~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l~ 205 (339)
||++|+||||.. .++|||||+|.+++|++ ++|+.+|+|..++++ .++|||++++++ +++++.+++.+|.+|+.
T Consensus 1 ~v~~D~Ettg~~--~~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~--~~~~~~~v~~~l~~~l~ 76 (156)
T cd06130 1 FVAIDFETANAD--RASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVA--DAPTFPEVWPEIKPFLG 76 (156)
T ss_pred CEEEEEeCCCCC--CCceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHh--cCCCHHHHHHHHHHHhC
Confidence 689999999966 57899999999998877 899999999988877 899999999999 78889999999999997
Q ss_pred hcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCC
Q 019538 206 SRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSA 285 (339)
Q Consensus 206 ~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~a 285 (339)
+ .++||||+ .||+.||.+++.++|+..+ +..++||+.+++.+++.. + +++|++|+++||++.. +
T Consensus 77 ~-------~~lv~hn~-~fD~~~l~~~~~~~g~~~~-~~~~idt~~~~~~~~~~~----~-~~~L~~l~~~~g~~~~--~ 140 (156)
T cd06130 77 G-------SLVVAHNA-SFDRSVLRAALEAYGLPPP-PYQYLCTVRLARRVWPLL----P-NHKLNTVAEHLGIELN--H 140 (156)
T ss_pred C-------CEEEEeCh-HHhHHHHHHHHHHcCCCCC-CCCEEEHHHHHHHHhccC----C-CCCHHHHHHHcCCCcc--C
Confidence 4 48999999 9999999999999998876 457999999999987653 3 8999999999999987 9
Q ss_pred CChHHHHHHHHHHHH
Q 019538 286 HRAMADVNCLSLILQ 300 (339)
Q Consensus 286 H~Al~DA~~ta~L~~ 300 (339)
|+|++||++|++||.
T Consensus 141 H~Al~Da~~ta~l~~ 155 (156)
T cd06130 141 HDALEDARACAEILL 155 (156)
T ss_pred cCchHHHHHHHHHHh
Confidence 999999999999985
No 18
>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=99.97 E-value=2e-29 Score=222.61 Aligned_cols=157 Identities=25% Similarity=0.412 Sum_probs=131.9
Q ss_pred EEEEEEecCCCC-CCCCcEEEEEEEEEcCCe--------------eeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCC
Q 019538 129 AIVFDIETTGFS-RENERIIEIAFQDLLGGE--------------NSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVP 191 (339)
Q Consensus 129 ~vviDiETTGl~-p~~~~IIEIgav~v~~g~--------------i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap 191 (339)
|++||+||||++ +..++|||||+|.++++. +++|+++|+|..+|++ +.|||||.+++. ++|
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~--~~~ 78 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLE--HKA 78 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHh--cCC
Confidence 689999999999 578999999999998653 2579999999999988 899999999999 677
Q ss_pred CHHH-HHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCH
Q 019538 192 RMED-LIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSL 270 (339)
Q Consensus 192 ~~~e-vl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L 270 (339)
++.+ +++.+.+|+... .++.++||||+..||++||.+++.++|+.++.+..++||+.+++.+. . +|
T Consensus 79 ~~~~~~~~~l~~f~~~~---~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~---------~-~L 145 (177)
T cd06136 79 PFDSDTANLIKLFLRRQ---PKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD---------Q-SL 145 (177)
T ss_pred CccHHHHHHHHHHHHhc---CCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH---------h-hH
Confidence 6653 666677777632 13458999997359999999999999998775557899999999765 2 79
Q ss_pred HHHHHH-hCCCCCCCCCChHHHHHHHHHHHHH
Q 019538 271 QALREY-YGIPLVGSAHRAMADVNCLSLILQR 301 (339)
Q Consensus 271 ~~L~~~-~gI~~~~~aH~Al~DA~~ta~L~~~ 301 (339)
++|+++ ||++.. .+|+|++||.+|+++|.+
T Consensus 146 ~~l~~~~~~~~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 146 GSLYKRLFGQEPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHHHHhCCCcc-cccchHHHHHHHHHHHhh
Confidence 999885 899987 699999999999999864
No 19
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.2e-28 Score=221.92 Aligned_cols=164 Identities=20% Similarity=0.279 Sum_probs=139.3
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee---eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN---STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILL 201 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i---~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~ 201 (339)
.++|+||+||||++|..++|||||+|.++++.+ +.|+.+|+|..++++ +++|||++++++ ++|++.+|+.+|.
T Consensus 29 ~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~--~~~~~~~vl~~~~ 106 (202)
T PRK09145 29 DEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLE--DGLSEEEALRQLL 106 (202)
T ss_pred CCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHh--cCCCHHHHHHHHH
Confidence 489999999999999889999999999998765 579999999988877 899999999999 8899999999999
Q ss_pred HHHHhcCCCCCceEEEEECCcchhHHHHHHHHHh-cCCCCCCCCceeeHHHHHHHHHhc-CCCCCCCCCCHHHHHHHhCC
Q 019538 202 HYVKSRQKPGGYILFVAHNARSFDVPFLINEFSR-CSYEVPNNWLFMDTLTLARELMKS-GGSNLPSKVSLQALREYYGI 279 (339)
Q Consensus 202 ~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r-~gl~~p~~~~~iDtl~lar~l~~~-~~~~l~~~~~L~~L~~~~gI 279 (339)
+|+.+ .++||||+ .||+.||.+++.+ .+..++ ..++|+..++...... ..+..+ +++|++++++||+
T Consensus 107 ~~i~~-------~~lv~hn~-~fD~~fL~~~~~~~~~~~~~--~~~id~~~l~~~~~~~~~~~~~~-~~~L~~l~~~~gi 175 (202)
T PRK09145 107 AFIGN-------RPLVGYYL-EFDVAMLNRYVRPLLGIPLP--NPLIEVSALYYDKKERHLPDAYI-DLRFDAILKHLDL 175 (202)
T ss_pred HHHcC-------CeEEEeCH-HHHHHHHHHHHHHhcCCCCC--CCeeeHHHHHHHHhhccCCCccc-CCCHHHHHHHcCC
Confidence 99974 37999999 9999999999986 455544 3579998776543221 111223 6899999999999
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHH
Q 019538 280 PLVGSAHRAMADVNCLSLILQRLTF 304 (339)
Q Consensus 280 ~~~~~aH~Al~DA~~ta~L~~~l~~ 304 (339)
+.. .+|+|++||.+|++||.+|++
T Consensus 176 ~~~-~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 176 PVL-GRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCC-CCCCcHHHHHHHHHHHHHHHh
Confidence 987 589999999999999999875
No 20
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4.9e-28 Score=232.02 Aligned_cols=170 Identities=19% Similarity=0.339 Sum_probs=144.4
Q ss_pred ccCccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEc-CCee-eeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHH
Q 019538 120 NKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLL-GGEN-STFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLI 197 (339)
Q Consensus 120 ~~~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~-~g~i-~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl 197 (339)
..++.+ ..||+||+||||++|..++|||||||.+. +|.+ +.|+++|+|..++.+..||||++++++ ++|.|.+++
T Consensus 40 ~~~~~~-~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La--~AP~f~eVl 116 (377)
T PRK05601 40 QEAIEA-APFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFA--QGKRFSQIL 116 (377)
T ss_pred CCCCCC-CCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHh--cCCCHHHHH
Confidence 345555 58999999999999999999999999887 6776 999999999987666789999999999 899999999
Q ss_pred HHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCC--------------------------CCCCCCceeeHHH
Q 019538 198 PILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSY--------------------------EVPNNWLFMDTLT 251 (339)
Q Consensus 198 ~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl--------------------------~~p~~~~~iDtl~ 251 (339)
.+|.+|+.+ .++|+||+ .||+.||.+++.+++. ..|.+..++||+.
T Consensus 117 ~el~~fL~g-------~vLVaHNA-~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~ 188 (377)
T PRK05601 117 KPLDRLIDG-------RTLILHNA-PRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLA 188 (377)
T ss_pred HHHHHHhCC-------CEEEEECc-HHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHH
Confidence 999999985 38999999 9999999999876421 1233346899999
Q ss_pred HHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC---------CCCCChH--HHHHHHHHHHHHHHHh
Q 019538 252 LARELMKSGGSNLPSKVSLQALREYYGIPLV---------GSAHRAM--ADVNCLSLILQRLTFD 305 (339)
Q Consensus 252 lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~---------~~aH~Al--~DA~~ta~L~~~l~~~ 305 (339)
+++++++.. + +++|..|+++|||+.+ ...|+|+ +||+.+++||.++.+.
T Consensus 189 LARrl~p~l----~-~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 189 TARRQGVAL----D-DIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred HHHHHcCCC----C-CCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 999999754 3 9999999999999882 1567888 5999999999987443
No 21
>PRK05168 ribonuclease T; Provisional
Probab=99.96 E-value=1.6e-28 Score=222.78 Aligned_cols=174 Identities=24% Similarity=0.340 Sum_probs=142.8
Q ss_pred CccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEc---CCee---eeEEEEEcC--CCCCCC--ccccCCcHHh-hcCCCC
Q 019538 122 DLAKLVTAIVFDIETTGFSRENERIIEIAFQDLL---GGEN---STFQTLVNP--KRQVPN--AHVHGITTDM-VCKPDV 190 (339)
Q Consensus 122 ~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~---~g~i---~~f~~lV~P--~~~i~~--~~itGIt~e~-l~~~~a 190 (339)
++.+ ..+|+||+||||+++..++|||||+|.+. +|.+ ++|+++|+| ..++++ +++|||++++ ++ ++
T Consensus 13 ~~~~-~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~--~~ 89 (211)
T PRK05168 13 RFRG-FLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLR--GA 89 (211)
T ss_pred HhcC-CceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhh--cC
Confidence 3445 58999999999999989999999999986 3532 799999999 456777 8999999986 66 67
Q ss_pred CCHHHHHHHHHHHHHhcCCC--CCceEEEEECCcchhHHHHHHHHHhcCCCC-C-CCCceeeHHHHHHHHHhcCCCCCCC
Q 019538 191 PRMEDLIPILLHYVKSRQKP--GGYILFVAHNARSFDVPFLINEFSRCSYEV-P-NNWLFMDTLTLARELMKSGGSNLPS 266 (339)
Q Consensus 191 p~~~evl~~~~~~l~~~~~~--~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~-p-~~~~~iDtl~lar~l~~~~~~~l~~ 266 (339)
+++.+++.++.+|+.+.... .++.++||||+ .||+.||.+++.++|+.. + .++.++||+.+++.+++
T Consensus 90 ~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~-------- 160 (211)
T PRK05168 90 VSEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG-------- 160 (211)
T ss_pred CChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC--------
Confidence 77899999999888632110 02368999999 999999999999998742 2 23568999999998764
Q ss_pred CCCHHHHHHHhCCCCCC-CCCChHHHHHHHHHHHHHHHHhhc
Q 019538 267 KVSLQALREYYGIPLVG-SAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 267 ~~~L~~L~~~~gI~~~~-~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
..+|+.+++++|++..+ .+|+|++||.+|++||.+|..++.
T Consensus 161 ~~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 161 QTVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred CCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 56899999999998653 699999999999999999998764
No 22
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.96 E-value=9.6e-30 Score=265.60 Aligned_cols=170 Identities=33% Similarity=0.486 Sum_probs=156.8
Q ss_pred ccCccCCCcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHH
Q 019538 120 NKDLAKLVTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDL 196 (339)
Q Consensus 120 ~~~l~~~~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~ev 196 (339)
+..+.+ ++||+||+|||||++..++||||||+.+.+|.+ +.|+.+++|+++++. +++||||+++|. ++++.++|
T Consensus 415 d~~l~d-atyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~--~a~~i~~v 491 (1444)
T COG2176 415 DQKLDD-ATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLE--NAPEIEEV 491 (1444)
T ss_pred cccccc-ccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHc--CCccHHHH
Confidence 334555 799999999999999999999999999998876 999999999999999 899999999999 89999999
Q ss_pred HHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH
Q 019538 197 IPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY 276 (339)
Q Consensus 197 l~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~ 276 (339)
+.+|.+|+++ .++||||+ +||++||+..+.++++... ..++|||+.++|.++|... +++|..||+.
T Consensus 492 L~kf~~~~~d-------~IlVAHNa-sFD~gFl~~~~~k~~~~~~-~~pvIDTL~lar~L~P~~k-----sh~Lg~l~kk 557 (1444)
T COG2176 492 LEKFREFIGD-------SILVAHNA-SFDMGFLNTNYEKYGLEPL-TNPVIDTLELARALNPEFK-----SHRLGTLCKK 557 (1444)
T ss_pred HHHHHHHhcC-------cEEEeccC-ccchhHHHHHHHHhCCccc-cCchhhHHHHHHHhChhhh-----hcchHHHHHH
Confidence 9999999974 59999999 9999999999999998854 4579999999999998753 9999999999
Q ss_pred hCCCCCCCCCChHHHHHHHHHHHHHHHHhhc
Q 019538 277 YGIPLVGSAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 277 ~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
||+..+ .+|||..||.+|+.||..++++++
T Consensus 558 ~~v~le-~hHRA~yDaeat~~vf~~f~~~~k 587 (1444)
T COG2176 558 LGVELE-RHHRADYDAEATAKVFFVFLKDLK 587 (1444)
T ss_pred hCccHH-HhhhhhhhHHHHHHHHHHHHHHHH
Confidence 999997 899999999999999999998876
No 23
>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=99.96 E-value=3e-28 Score=217.34 Aligned_cols=168 Identities=24% Similarity=0.315 Sum_probs=133.9
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcC---Cee---eeEEEEEcC--CCCCCC--ccccCCcHHhhcCCCCCCHHHHH
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLG---GEN---STFQTLVNP--KRQVPN--AHVHGITTDMVCKPDVPRMEDLI 197 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~---g~i---~~f~~lV~P--~~~i~~--~~itGIt~e~l~~~~ap~~~evl 197 (339)
.+|+||+||||++|..++|||||+|.+.+ |.+ +.|+++|+| ..++++ ..||||+++++.. ..+...+++
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~-~~~~~~~~~ 84 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFR-FAVDEKEAL 84 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhc-cccchHHHH
Confidence 58999999999999899999999999963 332 799999999 467877 8999999987332 455566666
Q ss_pred HHHHHHHHhcCCC--CCceEEEEECCcchhHHHHHHHHHhcCCC-CCC-CCceeeHHHHHHHHHhcCCCCCCCCCCHHHH
Q 019538 198 PILLHYVKSRQKP--GGYILFVAHNARSFDVPFLINEFSRCSYE-VPN-NWLFMDTLTLARELMKSGGSNLPSKVSLQAL 273 (339)
Q Consensus 198 ~~~~~~l~~~~~~--~~~~~lV~hN~~~FD~~fL~~~~~r~gl~-~p~-~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L 273 (339)
.+|.+++.+.... .++.++||||+ .||+.||.+++.++|+. .+. ++.++||+.+++.+++ .++|+++
T Consensus 85 ~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~--------~~~L~~l 155 (189)
T cd06134 85 KEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG--------QTVLAKA 155 (189)
T ss_pred HHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC--------CCcHHHH
Confidence 6666666421100 02358999999 99999999999999983 332 3468999999998764 5689999
Q ss_pred HHHhCCCCC-CCCCChHHHHHHHHHHHHHHHHh
Q 019538 274 REYYGIPLV-GSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 274 ~~~~gI~~~-~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
+++|||+.. ..+|+|++||.+|++||.+|+++
T Consensus 156 ~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 156 CQAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred HHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 999999864 36899999999999999999865
No 24
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=5.6e-28 Score=216.35 Aligned_cols=162 Identities=20% Similarity=0.331 Sum_probs=133.9
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
.+||++|+||||+++ .++|||||+|.+++|.+ +.|+.||+|..+++. +++|||++++++ ++|++.+++.+|.+|
T Consensus 5 ~~~vvlD~EtTGl~~-~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~--~ap~~~evl~~f~~f 81 (195)
T PRK07247 5 ETYIAFDLEFNTVNG-VSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIA--DAPKVEEVLAAFKEF 81 (195)
T ss_pred CeEEEEEeeCCCCCC-CCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHh--CCCCHHHHHHHHHHH
Confidence 589999999999985 68899999999998866 899999999999887 899999999999 899999999999999
Q ss_pred HHhcCCCCCceEEEEECCcc-hhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 204 VKSRQKPGGYILFVAHNARS-FDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~-FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
+++ .++||||+ . ||+.||.. .|...+. ...+|++..+........+.++ +++|.+|+++||++.
T Consensus 82 ~~~-------~~lVaHNa-~~fD~~fL~~----~g~~~~~-~~~idt~~~~~~~~~~~~~~~~-~~~L~~La~~~gi~~- 146 (195)
T PRK07247 82 VGE-------LPLIGYNA-QKSDLPILAE----NGLDLSD-QYQVDLYDEAFERRSSDLNGIA-NLKLQTVADFLGIKG- 146 (195)
T ss_pred HCC-------CeEEEEeC-cHhHHHHHHH----cCCCcCC-CceeehHHHHHHhhccccCCCC-CCCHHHHHHhcCCCC-
Confidence 974 37999999 7 89999854 5665432 2457887554222111112345 899999999999985
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhhc
Q 019538 283 GSAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 283 ~~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
.+|+|++||++|+.||.+++...+
T Consensus 147 -~~HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 147 -RGHNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred -CCcCCHHHHHHHHHHHHHHHhhcc
Confidence 489999999999999999988654
No 25
>PRK06722 exonuclease; Provisional
Probab=99.96 E-value=1e-28 Score=231.57 Aligned_cols=166 Identities=22% Similarity=0.261 Sum_probs=139.9
Q ss_pred CcEEEEEEecCCCCC---CCCcEEEEEEEEEcCC--ee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHH
Q 019538 127 VTAIVFDIETTGFSR---ENERIIEIAFQDLLGG--EN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIP 198 (339)
Q Consensus 127 ~~~vviDiETTGl~p---~~~~IIEIgav~v~~g--~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~ 198 (339)
..|+|||+||||... ..++|||||||.+++| ++ +.|+.||+|..++++ +.+||||++|+. ++|++.+|+.
T Consensus 5 ~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~--~AP~f~eVl~ 82 (281)
T PRK06722 5 THFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLI--GVEKFPQIIE 82 (281)
T ss_pred CEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHc--CCCCHHHHHH
Confidence 579999999996432 2389999999999987 55 899999999999988 899999999999 8999999999
Q ss_pred HHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCC--CceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH
Q 019538 199 ILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNN--WLFMDTLTLARELMKSGGSNLPSKVSLQALREY 276 (339)
Q Consensus 199 ~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~--~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~ 276 (339)
+|.+|+++ .++|+||+ .||+.||.+++.++|+..|.. ..++|+..++...++...+ . .++|..++++
T Consensus 83 ef~~fig~-------~~lvahna-~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~--~-~~sL~~l~~~ 151 (281)
T PRK06722 83 KFIQFIGE-------DSIFVTWG-KEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFE--H-TPSLQSAVEQ 151 (281)
T ss_pred HHHHHHCC-------CcEEEEEe-HHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhcc--C-CCCHHHHHHH
Confidence 99999974 25677778 899999999999999876532 2358888877766654211 1 5789999999
Q ss_pred hCCCCCCCCCChHHHHHHHHHHHHHHHHh
Q 019538 277 YGIPLVGSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 277 ~gI~~~~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
+||+..+.+|+|++||.+|+.||.+|..+
T Consensus 152 lgL~~~g~~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 152 LGLIWEGKQHRALADAENTANILLKAYSE 180 (281)
T ss_pred CCCCCCCCCcCcHHHHHHHHHHHHHHhcc
Confidence 99998878999999999999999999853
No 26
>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=99.96 E-value=3.4e-28 Score=218.81 Aligned_cols=170 Identities=25% Similarity=0.301 Sum_probs=138.3
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEc---CCee---eeEEEEEcCC--CCCCC--ccccCCcHH-hhcCCCCCCHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLL---GGEN---STFQTLVNPK--RQVPN--AHVHGITTD-MVCKPDVPRMED 195 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~---~g~i---~~f~~lV~P~--~~i~~--~~itGIt~e-~l~~~~ap~~~e 195 (339)
..+++||+||||++|..++|||||+|.+. +|.+ ++|+++|+|. .+|++ ..|||||++ ++. ++++..+
T Consensus 8 ~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~--~~~~~~~ 85 (200)
T TIGR01298 8 YLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLR--GAVSEYE 85 (200)
T ss_pred CeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhh--cCcchHH
Confidence 47999999999999988999999999986 3444 5699999974 67887 799999976 577 7788888
Q ss_pred HHHHHHHHHHhcCCC--CCceEEEEECCcchhHHHHHHHHHhcCCCC-C-CCCceeeHHHHHHHHHhcCCCCCCCCCCHH
Q 019538 196 LIPILLHYVKSRQKP--GGYILFVAHNARSFDVPFLINEFSRCSYEV-P-NNWLFMDTLTLARELMKSGGSNLPSKVSLQ 271 (339)
Q Consensus 196 vl~~~~~~l~~~~~~--~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~-p-~~~~~iDtl~lar~l~~~~~~~l~~~~~L~ 271 (339)
++.++.+++.+.... .++.++||||+ .||+.||.+++.++|... + .+..++||+.+++.+++ .++|+
T Consensus 86 ~~~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~--------~~~L~ 156 (200)
T TIGR01298 86 ALHEIFKVVRKAMKASGCQRAILVGHNA-NFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG--------QTVLA 156 (200)
T ss_pred HHHHHHHHHHHHHHhcccCCCEEEEECc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC--------cccHH
Confidence 888888877421110 12458999999 999999999999988753 2 13358999999987753 56899
Q ss_pred HHHHHhCCCCC-CCCCChHHHHHHHHHHHHHHHHhhc
Q 019538 272 ALREYYGIPLV-GSAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 272 ~L~~~~gI~~~-~~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
.++++||++.. ..+|+|++||.+|++||.+|+.++.
T Consensus 157 ~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 157 KACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred HHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 99999999864 2689999999999999999988753
No 27
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=7.5e-28 Score=255.80 Aligned_cols=173 Identities=28% Similarity=0.405 Sum_probs=155.3
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
.+||+||+||||+++ .++|||||+|.+++|++ +.|+++|+|..++++ +.+|||++++++ ++|++++++.+|.+|
T Consensus 7 ~~~vvvD~ETTGl~~-~d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~--~ap~~~ev~~~~~~~ 83 (820)
T PRK07246 7 RKYAVVDLEATGAGP-NASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLA--QAPDFSQVARHIYDL 83 (820)
T ss_pred CCEEEEEEecCCcCC-CCeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHh--cCCCHHHHHHHHHHH
Confidence 589999999999987 58999999999999877 999999999999988 899999999999 899999999999999
Q ss_pred HHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCC
Q 019538 204 VKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVG 283 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~ 283 (339)
+.+ .++||||+ .||+.||.+++.+.|.+.+ .+++||+.+++.++|.. + +++|.+|+++||++..
T Consensus 84 l~~-------~~lVaHN~-~FD~~fL~~~~~~~g~~~~--~~~iDT~~la~~~~p~~----~-~~~L~~L~~~lgl~~~- 147 (820)
T PRK07246 84 IED-------CIFVAHNV-KFDANLLAEALFLEGYELR--TPRVDTVELAQVFFPTL----E-KYSLSHLSRELNIDLA- 147 (820)
T ss_pred hCC-------CEEEEECc-HHHHHHHHHHHHHcCCCCC--CCceeHHHHHHHHhCCC----C-CCCHHHHHHHcCCCCC-
Confidence 974 48999999 9999999999988887765 35799999999998754 3 8999999999999987
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhc----cCHHHHHHhcC
Q 019538 284 SAHRAMADVNCLSLILQRLTFDLK----LSLCDLIERGF 318 (339)
Q Consensus 284 ~aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~~~s~ 318 (339)
.+|+|++||.+|++||.++..++. .++.+|.+++.
T Consensus 148 ~~H~Al~DA~ata~L~~~l~~~l~~l~~~~l~~l~~~~~ 186 (820)
T PRK07246 148 DAHTAIADARATAELFLKLLQKIESLPKECLERLLEYAD 186 (820)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhcCchhHHHHHHHHh
Confidence 699999999999999999998764 46777777763
No 28
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.96 E-value=1.8e-27 Score=216.73 Aligned_cols=165 Identities=32% Similarity=0.366 Sum_probs=142.2
Q ss_pred EEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHHH
Q 019538 129 AIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYVK 205 (339)
Q Consensus 129 ~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l~ 205 (339)
+++||+||||+++ .|||||+|.+.+|.+ +.|+++|+|+.+|++ +.|||||+++++ ++|++.+++..| ++
T Consensus 2 ~~vlD~ETTGl~~---~IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~--~ap~~~ev~~~~---~~ 73 (219)
T PRK07983 2 LRVIDTETCGLQG---GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVA--DKPWIEDVIPHY---YG 73 (219)
T ss_pred eEEEEEECCCCCC---CCEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHc--CCCCHHHHHHHH---cC
Confidence 7899999999975 399999999988877 899999999999987 899999999999 899999998873 33
Q ss_pred hcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC---
Q 019538 206 SRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV--- 282 (339)
Q Consensus 206 ~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~--- 282 (339)
..++||||+ .||+.||.. . ...++||+.+++.++|.. .++|..|++++|++..
T Consensus 74 -------~~~lVaHNa-~FD~~~L~~--------~--~~~~idTl~lar~l~p~~------~~~l~~L~~~~~l~~~~~~ 129 (219)
T PRK07983 74 -------SEWYVAHNA-SFDRRVLPE--------M--PGEWICTMKLARRLWPGI------KYSNMALYKSRKLNVQTPP 129 (219)
T ss_pred -------CCEEEEeCc-HhhHHHHhC--------c--CCCcEeHHHHHHHHccCC------CCCHHHHHHHcCCCCCCCC
Confidence 359999999 999999942 1 235899999999999864 6899999999998642
Q ss_pred -CCCCChHHHHHHHHHHHHHHHHhhccCHHHHHHhcCCCCCCCC
Q 019538 283 -GSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFTPSDLIN 325 (339)
Q Consensus 283 -~~aH~Al~DA~~ta~L~~~l~~~l~~tl~~L~~~s~~~~~~~~ 325 (339)
..+|+|++||++|+.||.++++....+.++|++.++.|.-+..
T Consensus 130 ~~~aHrAl~Da~ata~ll~~l~~~~~~~~~~l~~~~~~~~~~~~ 173 (219)
T PRK07983 130 GLHHHRALYDCYITAALLIDIMNTSGWTAEEMADITGRPSLLTT 173 (219)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcCCccCCC
Confidence 3699999999999999999998777778999999988765543
No 29
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.2e-27 Score=257.83 Aligned_cols=174 Identities=33% Similarity=0.507 Sum_probs=155.9
Q ss_pred CcEEEEEEecCCCCCCC-CcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSREN-ERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~-~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
.+||+||+||||++|.. ++|||||+|.+++|++ ++|+.+|+|..++++ +.+|||++++++ ++|.|.+++.+|.+
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~--~ap~f~ev~~~l~~ 80 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVK--QAPLFEDVAPEIVE 80 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHh--cCCCHHHHHHHHHH
Confidence 47999999999998764 8999999999999887 899999999999988 899999999999 89999999999999
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
|+.+ .++||||+ .||++||.++|.++|++.+. ..++||+.+++.++|.. + +++|++|++++|++..
T Consensus 81 ~l~~-------~~~VaHN~-~FD~~fL~~~~~~~g~~~~~-~~~iDt~~la~~~~p~~----~-~~~L~~l~~~l~i~~~ 146 (928)
T PRK08074 81 LLEG-------AYFVAHNV-HFDLNFLNEELERAGYTEIH-CPKLDTVELARILLPTA----E-SYKLRDLSEELGLEHD 146 (928)
T ss_pred HhCC-------CeEEEECh-HHHHHHHHHHHHHcCCCCCC-CCeeeHHHHHHHhcCCC----C-CCCHHHHHHhCCCCCC
Confidence 9974 48999999 99999999999999987553 47899999999998753 3 8999999999999987
Q ss_pred CCCCChHHHHHHHHHHHHHHHHhhc----cCHHHHHHhc
Q 019538 283 GSAHRAMADVNCLSLILQRLTFDLK----LSLCDLIERG 317 (339)
Q Consensus 283 ~~aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~~~s 317 (339)
.+|+|++||.+|++||.+|+.++. .++.+|+.++
T Consensus 147 -~~H~Al~DA~ata~l~~~l~~~~~~l~~~~l~~l~~~~ 184 (928)
T PRK08074 147 -QPHRADSDAEVTAELFLQLLNKLERLPLVTLQQLRRLS 184 (928)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHH
Confidence 799999999999999999988764 4667666665
No 30
>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=99.95 E-value=2.3e-27 Score=254.08 Aligned_cols=173 Identities=29% Similarity=0.437 Sum_probs=154.2
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
+||+||+||||++|..++|||||+|.+++|++ +.|+++|+|..++++ +.+||||+++++ ++|.|.+++.+|.+|+
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~--~ap~~~ev~~~l~~~l 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQ--QAPYFSQVAQEIYDLL 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHh--CCCCHHHHHHHHHHHh
Confidence 48999999999999899999999999998876 899999999999988 899999999999 8999999999999999
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGS 284 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~ 284 (339)
++ .++||||+ .||+.||.++|.++|++.. +..++||+.+++.++|.. + +++|.+|++++|++.. .
T Consensus 79 ~~-------~~~VahN~-~fD~~fL~~~~~~~g~~~~-~~~~iDt~~l~~~~~p~~----~-~~~L~~l~~~~gi~~~-~ 143 (850)
T TIGR01407 79 ED-------GIFVAHNV-HFDLNFLAKALKDCGYEPL-PKPRIDTVELAQIFFPTE----E-SYQLSELSEALGLTHE-N 143 (850)
T ss_pred CC-------CEEEEeCc-HHHHHHHHHHHHHcCCCCC-CCCeEeHHHHHHHhcCCC----C-CCCHHHHHHHCCCCCC-C
Confidence 74 48999999 9999999999999998743 346899999999988754 3 8999999999999987 6
Q ss_pred CCChHHHHHHHHHHHHHHHHhhc----cCHHHHHHhc
Q 019538 285 AHRAMADVNCLSLILQRLTFDLK----LSLCDLIERG 317 (339)
Q Consensus 285 aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~~~s 317 (339)
+|+|++||.+|++||.++..++. .++.+|+..+
T Consensus 144 ~H~Al~DA~ata~l~~~l~~~~~~l~~~~l~~l~~~~ 180 (850)
T TIGR01407 144 PHRADSDAQATAELLLLLFEKMEKLPLDTLEQLLELS 180 (850)
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhcCCccHHHHHHHH
Confidence 99999999999999999988654 4566665555
No 31
>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=99.95 E-value=5.7e-27 Score=254.78 Aligned_cols=171 Identities=32% Similarity=0.481 Sum_probs=154.4
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
.+||+||+||||+++..++|||||||.+++|.+ ++|+++|+|..++++ +++||||+++++ ++|++.+++.+|.+|
T Consensus 190 ~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~--~ap~~~evl~~f~~f 267 (1213)
T TIGR01405 190 ATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLE--NAPEIEEVLEKFKEF 267 (1213)
T ss_pred CcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHh--CCCCHHHHHHHHHHH
Confidence 689999999999999999999999999998876 899999999999988 899999999999 899999999999999
Q ss_pred HHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCC
Q 019538 204 VKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVG 283 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~ 283 (339)
+.+ .++||||+ .||+.||.+.+.++|+.. ....++||+.+++.++|.. + +++|++|++++|++..
T Consensus 268 l~~-------~iLVaHNa-~FD~~fL~~~~~r~g~~~-~~~~~IDTl~lar~l~p~~----k-~~kL~~Lak~lgi~~~- 332 (1213)
T TIGR01405 268 FKD-------SILVAHNA-SFDIGFLNTNFEKVGLEP-LENPVIDTLELARALNPEY----K-SHRLGNICKKLGVDLD- 332 (1213)
T ss_pred hCC-------CeEEEECh-HHHHHHHHHHHHHcCCCc-cCCCEeEHHHHHHHHhccC----C-CCCHHHHHHHcCCCCC-
Confidence 974 48999999 999999999999999863 3347999999999988653 3 8999999999999998
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhc----cCHHHHH
Q 019538 284 SAHRAMADVNCLSLILQRLTFDLK----LSLCDLI 314 (339)
Q Consensus 284 ~aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~ 314 (339)
.+|+|++||.+|++||..++.++. .++.+|.
T Consensus 333 ~~HrAl~DA~aTa~I~~~ll~~l~~~~i~~~~~l~ 367 (1213)
T TIGR01405 333 DHHRADYDAEATAKVFKVMVEQLKEKGITNLEELN 367 (1213)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHcCCccHHHHH
Confidence 599999999999999999998775 4566665
No 32
>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=99.95 E-value=7.8e-27 Score=204.20 Aligned_cols=161 Identities=21% Similarity=0.310 Sum_probs=137.9
Q ss_pred EEEEEEecCCCCCCC-----CcEEEEEEEEEcCC---eeeeEEEEEcCCC--CCCC--ccccCCcHHhhcCCCCCCHHHH
Q 019538 129 AIVFDIETTGFSREN-----ERIIEIAFQDLLGG---ENSTFQTLVNPKR--QVPN--AHVHGITTDMVCKPDVPRMEDL 196 (339)
Q Consensus 129 ~vviDiETTGl~p~~-----~~IIEIgav~v~~g---~i~~f~~lV~P~~--~i~~--~~itGIt~e~l~~~~ap~~~ev 196 (339)
||+||+||||+++.. ++|||||+|.++++ .++.|+++|+|.. .+++ .++||||.++++ ++|++.+|
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~--~~~~~~~v 78 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVD--NAPSFPEV 78 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHh--cCCCHHHH
Confidence 689999999999764 89999999999854 3489999999998 6766 799999999999 78999999
Q ss_pred HHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCC--CCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHH
Q 019538 197 IPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYE--VPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALR 274 (339)
Q Consensus 197 l~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~--~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~ 274 (339)
+.+|.+|+++.. ..+++|++ .||..++..++.+.+.. .+..+.++|+..+++.+++.. + .++|++++
T Consensus 79 l~~~~~~l~~~~-----~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~----~-~~~L~~l~ 147 (176)
T cd06133 79 LKEFLEWLGKNG-----KYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLK----K-RTGLSKAL 147 (176)
T ss_pred HHHHHHHHHhCC-----CeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCC----C-CCCHHHHH
Confidence 999999998520 14556667 79999988888887764 344568999999999988753 2 89999999
Q ss_pred HHhCCCCCCCCCChHHHHHHHHHHHHHH
Q 019538 275 EYYGIPLVGSAHRAMADVNCLSLILQRL 302 (339)
Q Consensus 275 ~~~gI~~~~~aH~Al~DA~~ta~L~~~l 302 (339)
++||++..+.+|+|++||++|++||.+|
T Consensus 148 ~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 148 EYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred HHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 9999999878999999999999999987
No 33
>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=99.95 E-value=7.9e-27 Score=207.08 Aligned_cols=160 Identities=21% Similarity=0.233 Sum_probs=131.2
Q ss_pred EEEEEecCCCCCCCCcEEEEEEEEEcCC-ee-eeEEEEEcCCCC--CCC--ccccCCcHHhhcCCC-CCCHHHHHHHHHH
Q 019538 130 IVFDIETTGFSRENERIIEIAFQDLLGG-EN-STFQTLVNPKRQ--VPN--AHVHGITTDMVCKPD-VPRMEDLIPILLH 202 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIgav~v~~g-~i-~~f~~lV~P~~~--i~~--~~itGIt~e~l~~~~-ap~~~evl~~~~~ 202 (339)
++||+||||+++..++|||||+|.++++ .+ +.|+++|+|... +++ ..+|||+++++. . +|++.+++.+|.+
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~--~~~~~~~~~l~~~~~ 78 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLL--KEGLSEYEFIAKIHR 78 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHH--hcCCCHHHHHHHHHH
Confidence 5899999999998999999999999865 33 889999998753 444 789999999999 6 7889999999999
Q ss_pred HHHhcCCCCCceEEEEEC-CcchhHHHHHHHHHhcCCCCCC-----CCceeeHHHHHHHHH---hc--CCC----CCCCC
Q 019538 203 YVKSRQKPGGYILFVAHN-ARSFDVPFLINEFSRCSYEVPN-----NWLFMDTLTLARELM---KS--GGS----NLPSK 267 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN-~~~FD~~fL~~~~~r~gl~~p~-----~~~~iDtl~lar~l~---~~--~~~----~l~~~ 267 (339)
|+.+ ++.++|||| + .||+.||.+++.+++...+. ....+||+.+++..+ +. ..+ +++ +
T Consensus 79 ~~~~-----~~~~lVahn~~-~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~-~ 151 (183)
T cd06138 79 LFNT-----PGTCIVGYNNI-RFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKP-S 151 (183)
T ss_pred HHcc-----CCCcEEeeCch-hhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCc-c
Confidence 9963 235799997 6 89999999999999875431 224589998888654 21 011 234 7
Q ss_pred CCHHHHHHHhCCCCCCCCCChHHHHHHHHHHH
Q 019538 268 VSLQALREYYGIPLVGSAHRAMADVNCLSLIL 299 (339)
Q Consensus 268 ~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~ 299 (339)
++|++|+++||++.. .+|+|++||.+|++|+
T Consensus 152 ~~L~~l~~~~gi~~~-~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 152 FKLEDLAQANGIEHS-NAHDALSDVEATIALA 182 (183)
T ss_pred hhHHHHHHHCCCCcc-ccccHHHHHHHHHHHh
Confidence 899999999999986 7999999999999886
No 34
>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=99.94 E-value=3.1e-27 Score=205.61 Aligned_cols=149 Identities=22% Similarity=0.340 Sum_probs=124.4
Q ss_pred EEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCC-------HHHHHHHH
Q 019538 130 IVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPR-------MEDLIPIL 200 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~-------~~evl~~~ 200 (339)
|+||+||||+++..++|+|||+|.+.+|.+. |+.||+|..++++ +.+||||+++++ ++|+ +++++++|
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~-~~~~v~P~~~i~~~~~~i~GIt~~~l~--~a~~~~~~~~~~~~~~~~~ 77 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVL-IDSLVRPSVRVTDWRTRFSGVTPADLE--EAAKAGKTIFGWEAARAAL 77 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEE-EeccccCCCCCCccceeccCCCHHHHh--hhhhcCCccccHHHHHHHH
Confidence 5899999999998999999999999877764 9999999999887 899999999998 6654 45899999
Q ss_pred HHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hCC
Q 019538 201 LHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY-YGI 279 (339)
Q Consensus 201 ~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~gI 279 (339)
.+|+++ ..++||||+ .||+.||... ...++||+.+++.+.+.... .+ +++|.+|+++ +|+
T Consensus 78 ~~~i~~------~~vlVgHn~-~fD~~fL~~~----------~~~~iDT~~l~~~~~~~~~~-~~-~~~L~~L~~~~~~~ 138 (161)
T cd06137 78 WKFIDP------DTILVGHSL-QNDLDALRMI----------HTRVVDTAILTREAVKGPLA-KR-QWSLRTLCRDFLGL 138 (161)
T ss_pred HHhcCC------CcEEEeccH-HHHHHHHhCc----------CCCeeEehhhhhhccCCCcC-CC-CccHHHHHHHHCCc
Confidence 999973 259999999 9999999641 12589999999988765310 02 8999999986 687
Q ss_pred CCC--CCCCChHHHHHHHHHHHH
Q 019538 280 PLV--GSAHRAMADVNCLSLILQ 300 (339)
Q Consensus 280 ~~~--~~aH~Al~DA~~ta~L~~ 300 (339)
+.. ..+|+|++||.+|++||+
T Consensus 139 ~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 139 KIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred hhcCCCCCCCcHHHHHHHHHHhC
Confidence 763 258999999999999983
No 35
>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=99.94 E-value=5.5e-26 Score=193.20 Aligned_cols=154 Identities=44% Similarity=0.689 Sum_probs=136.2
Q ss_pred EEEEEecCCCCCCCCcEEEEEEEEEcCC-e-eeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHHH
Q 019538 130 IVFDIETTGFSRENERIIEIAFQDLLGG-E-NSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYVK 205 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIgav~v~~g-~-i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l~ 205 (339)
|++|+||||+++..++|+|||++.++++ + +..|+.+|+|...+++ +.+|||+++++. +++++.+++.+|.+|+.
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~--~~~~~~~~~~~~~~~l~ 78 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLA--DAPPFEEVLPEFLEFLG 78 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHh--cCCCHHHHHHHHHHHHC
Confidence 5899999999998999999999999876 3 4899999999988776 789999999999 78889999999999997
Q ss_pred hcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHH-HHHhCCCCCCC
Q 019538 206 SRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQAL-REYYGIPLVGS 284 (339)
Q Consensus 206 ~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L-~~~~gI~~~~~ 284 (339)
+ .++||||+ .||+.+|.+.|.+++.. +.++.++||+.+++.+++... .+++..+ ++.+|++.. .
T Consensus 79 ~-------~~~v~~n~-~fD~~~l~~~~~~~~~~-~~~~~~iDt~~~~~~~~~~~~-----~~~l~~~~~~~~~~~~~-~ 143 (159)
T cd06127 79 G-------RVLVAHNA-SFDLRFLNRELRRLGGP-PLPNPWIDTLRLARRLLPGLR-----SHRLGLLLAERYGIPLE-G 143 (159)
T ss_pred C-------CEEEEeCc-HhhHHHHHHHHHHhCCC-CCCCCeeEHHHHHHHHcCCCC-----cCchHHHHHHHcCCCCC-C
Confidence 4 48999999 99999999999998833 345689999999999887642 7889998 889999876 7
Q ss_pred CCChHHHHHHHHHHHH
Q 019538 285 AHRAMADVNCLSLILQ 300 (339)
Q Consensus 285 aH~Al~DA~~ta~L~~ 300 (339)
+|+|++||.+|++||.
T Consensus 144 ~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 144 AHRALADALATAELLL 159 (159)
T ss_pred CCCcHHHHHHHHHHhC
Confidence 9999999999999973
No 36
>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=99.93 E-value=5.9e-26 Score=196.82 Aligned_cols=146 Identities=17% Similarity=0.232 Sum_probs=120.1
Q ss_pred EEEEEecCCCCCC--CCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHHH
Q 019538 130 IVFDIETTGFSRE--NERIIEIAFQDLLGGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYVK 205 (339)
Q Consensus 130 vviDiETTGl~p~--~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l~ 205 (339)
|+||+||||++|. .++|++|+++.+++..+ |+++|+|..++++ +.+|||++++++ ++|++++++.+|.+|+.
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~--~~~lv~P~~~i~~~~~~i~GIt~~~l~--~a~~~~~v~~~l~~~l~ 76 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVL--YDKYIRPEGPVTDYRTRWSGIRRQHLV--NATPFAVAQKEILKILK 76 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEE--EEEeECCCCccCccceECCCCCHHHHh--cCCCHHHHHHHHHHHcC
Confidence 5899999999986 47899999998865544 9999999999987 899999999999 89999999999999997
Q ss_pred hcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHH--HHHH--HhcCCCCCCCCCCHHHHHHHh---C
Q 019538 206 SRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTL--AREL--MKSGGSNLPSKVSLQALREYY---G 278 (339)
Q Consensus 206 ~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~l--ar~l--~~~~~~~l~~~~~L~~L~~~~---g 278 (339)
+ .++||||+ .||+.||... .+ ...++||..+ +++. +|. .+ +++|..|+++| +
T Consensus 77 ~-------~vlV~Hn~-~~D~~~l~~~-------~~-~~~~~Dt~~l~~~~~~~~~p~----~~-~~~L~~L~~~~~~~~ 135 (157)
T cd06149 77 G-------KVVVGHAI-HNDFKALKYF-------HP-KHMTRDTSTIPLLNRKAGFPE----NC-RVSLKVLAKRLLHRD 135 (157)
T ss_pred C-------CEEEEeCc-HHHHHHhccc-------CC-CcCEEECcccccchhhcCCcc----cC-ChhHHHHHHHHcChh
Confidence 4 48999999 9999999632 22 1246787654 4333 333 23 79999999999 6
Q ss_pred CCCCCCCCChHHHHHHHHHHHH
Q 019538 279 IPLVGSAHRAMADVNCLSLILQ 300 (339)
Q Consensus 279 I~~~~~aH~Al~DA~~ta~L~~ 300 (339)
++..+.+|+|++||++|++||+
T Consensus 136 i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 136 IQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred hcCCCCCcCcHHHHHHHHHHhC
Confidence 7764568999999999999984
No 37
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1.9e-25 Score=211.61 Aligned_cols=176 Identities=26% Similarity=0.310 Sum_probs=139.5
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEc---CCe---e-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLL---GGE---N-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLI 197 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~---~g~---i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl 197 (339)
.++|+||+||||+++..++|||||+|.++ +|. + +.|+.+++|..+|++ +.|||||+++++ +++...+.
T Consensus 37 ~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~--~~~~~~~~- 113 (294)
T PRK09182 37 RLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVA--GQTIDPAA- 113 (294)
T ss_pred CeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHh--cCCCcHHH-
Confidence 47999999999999999999999999987 342 3 789999999999988 899999999999 76654443
Q ss_pred HHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh
Q 019538 198 PILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY 277 (339)
Q Consensus 198 ~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~ 277 (339)
+.+|+.. ..++||||+ .||+.||.+.+.... ...+.|++.......+ .++ +++|++|+.+|
T Consensus 114 --l~~fl~~------~~vlVAHNA-~FD~~fL~~~~~~~~-----~~~~~ct~~~i~~~~~----~~~-~~kL~~La~~~ 174 (294)
T PRK09182 114 --VDALIAP------ADLIIAHNA-GFDRPFLERFSPVFA-----TKPWACSVSEIDWSAR----GFE-GTKLGYLAGQA 174 (294)
T ss_pred --HHHHhcC------CCEEEEeCH-HHHHHHHHHHHHhcc-----CCcccccHHHHhhccc----cCC-CCCHHHHHHHc
Confidence 4556653 258999999 999999988765432 1246788876543222 234 89999999999
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHhhc-cCHHHHHHhcCCCCCCCCc
Q 019538 278 GIPLVGSAHRAMADVNCLSLILQRLTFDLK-LSLCDLIERGFTPSDLINP 326 (339)
Q Consensus 278 gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~-~tl~~L~~~s~~~~~~~~~ 326 (339)
| ... .+|+|++||.+|++|+..++.... ..+.+|+..+..|.-++..
T Consensus 175 g-~~~-~aHrAl~Da~Ata~ll~~~l~~~~~~~l~~Ll~~~~~~~~~~~a 222 (294)
T PRK09182 175 G-FFH-EGHRAVDDCQALLELLARPLPETGQPPLAELLEASRRSRVRIWA 222 (294)
T ss_pred C-CCC-CCcChHHHHHHHHHHHHHHHhhcCCcCHHHHHHHhccCeeEEEc
Confidence 9 443 699999999999999998776655 7899999998777665543
No 38
>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=99.93 E-value=1.4e-25 Score=193.01 Aligned_cols=144 Identities=22% Similarity=0.271 Sum_probs=120.7
Q ss_pred EEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCC-CHHHHHHHHHHHHHh
Q 019538 130 IVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVP-RMEDLIPILLHYVKS 206 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap-~~~evl~~~~~~l~~ 206 (339)
|++||||||++.. ++|++|+++.+++.. .|++||+|..++++ +++||||+++++ ++| ++++++.+|.+|+.+
T Consensus 1 ~~iD~E~~g~~~g-~ei~~i~~v~~~~~~--~f~~lv~P~~~i~~~~t~itGIt~~~l~--~a~~~~~~v~~~~~~fl~~ 75 (150)
T cd06145 1 FALDCEMCYTTDG-LELTRVTVVDENGKV--VLDELVKPDGEIVDYNTRFSGITEEMLE--NVTTTLEDVQKKLLSLISP 75 (150)
T ss_pred CEEeeeeeeecCC-CEEEEEEEEeCCCCE--EEEEeECCCCccchhccCcCCCCHHHhc--cCCCCHHHHHHHHHHHhCC
Confidence 5899999999875 999999999886644 59999999999988 899999999999 784 899999999999962
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCC--C
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLV--G 283 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~--~ 283 (339)
+.++||||+ .||+.||... ...++||+.+++.+++.. . +++|++|+++| ++... +
T Consensus 76 ------~~vlVgHn~-~fD~~fL~~~----------~~~~iDT~~l~r~~~~~~----~-~~~L~~L~~~~~~~~i~~~~ 133 (150)
T cd06145 76 ------DTILVGHSL-ENDLKALKLI----------HPRVIDTAILFPHPRGPP----Y-KPSLKNLAKKYLGRDIQQGE 133 (150)
T ss_pred ------CCEEEEcCh-HHHHHHhhcc----------CCCEEEcHHhccccCCCC----C-ChhHHHHHHHHCCcceeCCC
Confidence 359999999 9999999641 124899999988766543 2 78999999876 54322 3
Q ss_pred CCCChHHHHHHHHHHHH
Q 019538 284 SAHRAMADVNCLSLILQ 300 (339)
Q Consensus 284 ~aH~Al~DA~~ta~L~~ 300 (339)
.+|+|++||++|++||.
T Consensus 134 ~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 134 GGHDSVEDARAALELVK 150 (150)
T ss_pred CCCCcHHHHHHHHHHhC
Confidence 68999999999999983
No 39
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.93 E-value=8.3e-25 Score=201.86 Aligned_cols=164 Identities=39% Similarity=0.584 Sum_probs=147.7
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee--eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN--STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i--~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
.++++||+||||+++..++|||||+|.+.++.+ ..|+.+|+|..++++ .++|||+.+++. ++|.|.+++.+|.+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~--~~p~~~~v~~~~~~ 90 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLA--DAPKFAEVLPEFLD 90 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHh--cCCCHHHHHHHHHH
Confidence 479999999999999899999999999998876 459999999888887 899999999999 88999999999999
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
|+.+ ..++|+||+ .||+.||..++.+++...+ ...++||+.+++..++.. + .++|+.|++++||+..
T Consensus 91 ~i~~------~~~~Vahna-~fD~~fl~~~~~~~~~~~~-~~~~~~t~~~~r~~~~~~----~-~~~L~~l~~~~gi~~~ 157 (243)
T COG0847 91 FIGG------LRLLVAHNA-AFDVGFLRVESERLGIEIP-GDPVLDTLALARRHFPGF----D-RSSLDALAERLGIDRN 157 (243)
T ss_pred HHCC------CCeEEEEch-hhcHHHHHHHHHHcCCCcc-cCceehHHHHHHHHcCCC----c-cchHHHHHHHcCCCcC
Confidence 9984 259999999 9999999999999998876 346899999999999872 3 8999999999999943
Q ss_pred -CCCCChHHHHHHHHHHHHHHHHh
Q 019538 283 -GSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 283 -~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
...|+|+.||.+++.+|..+...
T Consensus 158 ~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 158 PFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CcCCcchHHHHHHHHHHHHHHHhc
Confidence 26799999999999999999985
No 40
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.93 E-value=1.7e-24 Score=218.18 Aligned_cols=175 Identities=17% Similarity=0.235 Sum_probs=141.0
Q ss_pred CcEEEEEEecCCCCCC---CCcEEEEEEEEEc--CCee-eeEEEEEcCCC--CCCC--ccccCCcHHhhcCCCCCCHHHH
Q 019538 127 VTAIVFDIETTGFSRE---NERIIEIAFQDLL--GGEN-STFQTLVNPKR--QVPN--AHVHGITTDMVCKPDVPRMEDL 196 (339)
Q Consensus 127 ~~~vviDiETTGl~p~---~~~IIEIgav~v~--~g~i-~~f~~lV~P~~--~i~~--~~itGIt~e~l~~~~ap~~~ev 196 (339)
..||+||+||||+++. .++|||||+|.++ ++++ +.|+.||+|.. .+++ +++|||++++++ ++|+|.+|
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~--~Ap~F~eV 133 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVS--RADPFPVV 133 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHh--cCCCHHHH
Confidence 5799999999999863 4899999999996 6766 99999999986 4777 899999999999 89999999
Q ss_pred HHHHHHHHHhcCC---CCCceEEEEECCcchhH-HHHHHHHHh---cCCCCCCCCceeeHH-HHHHHHHhcC-------C
Q 019538 197 IPILLHYVKSRQK---PGGYILFVAHNARSFDV-PFLINEFSR---CSYEVPNNWLFMDTL-TLARELMKSG-------G 261 (339)
Q Consensus 197 l~~~~~~l~~~~~---~~~~~~lV~hN~~~FD~-~fL~~~~~r---~gl~~p~~~~~iDtl-~lar~l~~~~-------~ 261 (339)
+.+|.+|+.+... +.....+|+||+ .||+ .||..++.. .+++.... .++|+. .+++.+++.. .
T Consensus 134 l~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~~~~~~g~p~~f~-~widLk~~lar~l~p~~~~~~~~~~ 211 (582)
T PTZ00315 134 YCEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMRVSGQQGTPLSFQ-RWCNLKKYMSQLGFGNGSGCGGGAT 211 (582)
T ss_pred HHHHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHHHhhhcCCCcccc-eEEEhHHHHHHHhCccccccccccc
Confidence 9999999986421 011236899999 9999 499888873 45554332 455643 4666666531 1
Q ss_pred CCCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhh
Q 019538 262 SNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDL 306 (339)
Q Consensus 262 ~~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l 306 (339)
+.+. .++|.+|++.+|+++.|.+|+|++||++|++||.+|+.++
T Consensus 212 ~~~~-~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g 255 (582)
T PTZ00315 212 PPLG-PSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRG 255 (582)
T ss_pred cccC-CcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcC
Confidence 2334 7899999999999999999999999999999999999875
No 41
>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=99.93 E-value=3.1e-25 Score=191.19 Aligned_cols=146 Identities=21% Similarity=0.309 Sum_probs=114.3
Q ss_pred EEEEEecCCCCCCCCcEEEEE---EEEEcCCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 130 IVFDIETTGFSRENERIIEIA---FQDLLGGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIg---av~v~~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
|++|+||||++|. ++++||+ ++..+++. .|+.||+|..++++ +.+||||+++++ ++|++.+++.+|.+|+
T Consensus 1 v~lD~EttGl~~~-~~~~~i~~v~~v~~~~~~--~~~~~v~P~~~i~~~~~~ihGIt~~~v~--~a~~~~~~~~~l~~~l 75 (152)
T cd06144 1 VALDCEMVGVGPD-GSESALARVSIVNEDGNV--VYDTYVKPQEPVTDYRTAVSGIRPEHLK--DAPDFEEVQKKVAELL 75 (152)
T ss_pred CEEEEEeecccCC-CCEEEEEEEEEEeCCCCE--EEEEEECCCCCCCcccccCCCCCHHHHc--CCCCHHHHHHHHHHHh
Confidence 5899999999985 3455554 44443333 49999999988887 899999999999 8999999999999999
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hCCCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY-YGIPLVG 283 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~gI~~~~ 283 (339)
.+ .++||||+ .||+.||. ...+. ..++||..+.....+.. .+ +++|++|+++ +|++...
T Consensus 76 ~~-------~vlVgHn~-~fD~~~L~-------~~~~~-~~~~dt~~l~~~~~~~~---~~-~~sL~~l~~~~lgi~~~~ 135 (152)
T cd06144 76 KG-------RILVGHAL-KNDLKVLK-------LDHPK-KLIRDTSKYKPLRKTAK---GK-SPSLKKLAKQLLGLDIQE 135 (152)
T ss_pred CC-------CEEEEcCc-HHHHHHhc-------CcCCC-ccEEEeEEeeccccccC---CC-ChhHHHHHHHHcCcccCC
Confidence 74 48999999 99999995 22222 35788877543332211 23 8999999997 6998754
Q ss_pred CCCChHHHHHHHHHHHH
Q 019538 284 SAHRAMADVNCLSLILQ 300 (339)
Q Consensus 284 ~aH~Al~DA~~ta~L~~ 300 (339)
.+|+|++||++|++||+
T Consensus 136 ~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 136 GEHSSVEDARAAMRLYR 152 (152)
T ss_pred CCcCcHHHHHHHHHHhC
Confidence 68999999999999984
No 42
>PRK05359 oligoribonuclease; Provisional
Probab=99.92 E-value=3.5e-24 Score=189.86 Aligned_cols=161 Identities=20% Similarity=0.158 Sum_probs=129.2
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCe--e-eeEEEEEcCCCCC----CC--ccc---cCCcHHhhcCCCCCCHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGE--N-STFQTLVNPKRQV----PN--AHV---HGITTDMVCKPDVPRME 194 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~--i-~~f~~lV~P~~~i----~~--~~i---tGIt~e~l~~~~ap~~~ 194 (339)
.+|||+|+||||++|..++|||||||.++++. + +.|+.+|+|...+ ++ ..+ |||++++++ +++++.
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~--~~~~~~ 80 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRA--STVSEA 80 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHh--cCCCHH
Confidence 47999999999999999999999999998764 2 6699999998653 33 344 599999999 889999
Q ss_pred HHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHH-HHHHHHHhcCCCCCCCCCCHHHH
Q 019538 195 DLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTL-TLARELMKSGGSNLPSKVSLQAL 273 (339)
Q Consensus 195 evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl-~lar~l~~~~~~~l~~~~~L~~L 273 (339)
+++.+|.+|+.+... .+..++||||+ .||+.||.+.+.+.+..+..++..+|++ .+++.++|..
T Consensus 81 e~~~~~l~fl~~~~~-~~~~~l~g~~v-~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P~~------------- 145 (181)
T PRK05359 81 EAEAQTLEFLKQWVP-AGKSPLCGNSI-GQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKPEI------------- 145 (181)
T ss_pred HHHHHHHHHHHHhcC-CCCCceeecch-hhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhChhh-------------
Confidence 999999999986432 23457899999 9999999999988776654432223477 6888887641
Q ss_pred HHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhc
Q 019538 274 REYYGIPLVGSAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 274 ~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
+++++.. ..|||++||+.+...+..+...+.
T Consensus 146 --~~~~~~~-~~HRal~D~~~s~~~~~~~~~~~~ 176 (181)
T PRK05359 146 --LNGFKKQ-GTHRALADIRESIAELKYYREHFF 176 (181)
T ss_pred --hhCCCCc-CCcccHHHHHHHHHHHHHHHHHhc
Confidence 3577776 589999999999999998877543
No 43
>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=99.92 E-value=2.6e-24 Score=189.41 Aligned_cols=156 Identities=20% Similarity=0.217 Sum_probs=125.4
Q ss_pred EEEEEEecCCCCCCCCcEEEEEEEEEcCC--ee-eeEEEEEcCCCCCCC------c---cccCCcHHhhcCCCCCCHHHH
Q 019538 129 AIVFDIETTGFSRENERIIEIAFQDLLGG--EN-STFQTLVNPKRQVPN------A---HVHGITTDMVCKPDVPRMEDL 196 (339)
Q Consensus 129 ~vviDiETTGl~p~~~~IIEIgav~v~~g--~i-~~f~~lV~P~~~i~~------~---~itGIt~e~l~~~~ap~~~ev 196 (339)
+++||+||||++|..++|||||+|.++++ ++ +.|+.+|+|..++++ . .+|||++++++ ++|++.++
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~--~~~~~~~v 78 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRA--STVTLAQA 78 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHh--CCCCHHHH
Confidence 58999999999998999999999999875 44 889999999876542 2 44699999998 89999999
Q ss_pred HHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeH---HHHHHHHHhcCCCCCCCCCCHHHH
Q 019538 197 IPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDT---LTLARELMKSGGSNLPSKVSLQAL 273 (339)
Q Consensus 197 l~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDt---l~lar~l~~~~~~~l~~~~~L~~L 273 (339)
+.+|.+|+.+.. ..+..++||||+ .||+.||.+++.+.|..+ .+..+|+ +.+++.++|.. +
T Consensus 79 l~~~~~f~~~~~-~~~~~~lvgh~~-~FD~~fL~~~~~~~~~~~--~~~~~D~~~l~~l~~~l~p~~-------~----- 142 (173)
T cd06135 79 EAELLEFIKKYV-PKGKSPLAGNSV-HQDRRFLDKYMPELEEYL--HYRILDVSSIKELARRWYPEI-------Y----- 142 (173)
T ss_pred HHHHHHHHHHhc-CCCCCceeecch-hhCHHHHHHHHHHHhccC--CcchhhHHHHHHHHHHhCcHh-------h-----
Confidence 999999998521 112458999999 999999999999987433 3456887 56788777642 1
Q ss_pred HHHhCCCCCCCCCChHHHHHHHHHHHHHHHHh
Q 019538 274 REYYGIPLVGSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 274 ~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
.++++.. .+|||++||.+++.+|.++++.
T Consensus 143 --~~~~~~~-~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 143 --RKAPKKK-GTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred --hcCCCCC-CCcchHHHHHHHHHHHHHHHHH
Confidence 1566555 6899999999999999988764
No 44
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.92 E-value=5.1e-24 Score=234.40 Aligned_cols=174 Identities=33% Similarity=0.507 Sum_probs=156.1
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
.++|++|+||||+++..++|||||++.+++|.+ +.|+.||+|..++++ +++|||+++++. +++++.+|+..|.+|
T Consensus 419 ~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~--~aps~~EaL~~f~~f 496 (1437)
T PRK00448 419 ATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVK--DAPSIEEVLPKFKEF 496 (1437)
T ss_pred CcEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHc--CCCCHHHHHHHHHHH
Confidence 489999999999999999999999999998876 899999999999988 899999999999 889999999999999
Q ss_pred HHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCC
Q 019538 204 VKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVG 283 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~ 283 (339)
+++ .++||||+ .||+.||...+.++|++.+. ..++||+.+++.+++.. . +++|+.|+++||++..
T Consensus 497 igg-------~vLVAHNa-~FD~~fL~~~l~rlgl~~l~-~~~IDTLelar~l~p~~----k-~~kL~~LAk~lGL~~~- 561 (1437)
T PRK00448 497 CGD-------SILVAHNA-SFDVGFINTNYEKLGLEKIK-NPVIDTLELSRFLYPEL----K-SHRLNTLAKKFGVELE- 561 (1437)
T ss_pred hCC-------CEEEEeCc-cccHHHHHHHHHHcCCcccc-ccceeHHHHHHHHcCcc----c-cccHHHHHHHcCCCCC-
Confidence 964 58999999 99999999999999986543 46899999999888643 3 8999999999999998
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhc----cCHHHHHHhc
Q 019538 284 SAHRAMADVNCLSLILQRLTFDLK----LSLCDLIERG 317 (339)
Q Consensus 284 ~aH~Al~DA~~ta~L~~~l~~~l~----~tl~~L~~~s 317 (339)
.+|+|++||.+|++||.+++.++. .++.+|....
T Consensus 562 ~~HrAl~DA~aTa~lf~~ll~~l~~~gi~~~~~L~~~~ 599 (1437)
T PRK00448 562 HHHRADYDAEATAYLLIKFLKDLKEKGITNLDELNKKL 599 (1437)
T ss_pred CCcChHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHh
Confidence 589999999999999999998775 5677777553
No 45
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.91 E-value=1.5e-23 Score=209.52 Aligned_cols=184 Identities=21% Similarity=0.201 Sum_probs=139.9
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCC--ee-eeEEEEEcCCCCC--CC--ccccCCcHHhhcCCCCCCHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGG--EN-STFQTLVNPKRQV--PN--AHVHGITTDMVCKPDVPRMEDLIPI 199 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g--~i-~~f~~lV~P~~~i--~~--~~itGIt~e~l~~~~ap~~~evl~~ 199 (339)
.+|||+|+||||++|..|+|||||+|.++++ .+ ..|..+++|.... ++ ..|||||++++.+.+. +..+++.+
T Consensus 6 ~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~-~e~e~~~~ 84 (476)
T PRK11779 6 PTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGL-PEAEFAAR 84 (476)
T ss_pred CcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCC-CHHHHHHH
Confidence 4799999999999999999999999999865 34 6799999998642 22 7999999999974233 57899999
Q ss_pred HHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCC-----CC---CCceeeHHHHHHHHHhcC--CC----CCC
Q 019538 200 LLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEV-----PN---NWLFMDTLTLARELMKSG--GS----NLP 265 (339)
Q Consensus 200 ~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~-----p~---~~~~iDtl~lar~l~~~~--~~----~l~ 265 (339)
|.+++.. ++.++||||...||..||++.|.+..+.. .. .|..+|++.+++.+.+.. .| +.+
T Consensus 85 i~~~l~~-----~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~ 159 (476)
T PRK11779 85 IHAEFSQ-----PGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLP 159 (476)
T ss_pred HHHHHhc-----CCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCC
Confidence 9999962 23579999833899999999997765431 11 233444444444433221 11 234
Q ss_pred CCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHh---h---------ccCHHHHHHhcC
Q 019538 266 SKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFD---L---------KLSLCDLIERGF 318 (339)
Q Consensus 266 ~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~---l---------~~tl~~L~~~s~ 318 (339)
+++|++|++++||+.. .+|+|++||.+|++|+..+... + +..+.+|+..+.
T Consensus 160 -s~rLe~L~~~~gI~~~-~AHdALsDa~aT~~la~~l~~~qP~l~~~~~~~~~k~~v~~l~~~~~ 222 (476)
T PRK11779 160 -SFKLEHLTKANGIEHE-NAHDAMSDVYATIAMAKLIKQKQPKLFDYLFQLRNKRKVAALIDVPA 222 (476)
T ss_pred -CCcHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHhChHHHHHHHHhcchHHHHHHhhhhc
Confidence 8999999999999987 7999999999999999999876 3 134677777765
No 46
>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=99.91 E-value=2e-26 Score=196.34 Aligned_cols=156 Identities=37% Similarity=0.614 Sum_probs=134.4
Q ss_pred EEEEEecCCCCCCCCcEEEEEEEEEcCCe--e-eeEEEEEcCCCC--CCC--ccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 130 IVFDIETTGFSRENERIIEIAFQDLLGGE--N-STFQTLVNPKRQ--VPN--AHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIgav~v~~g~--i-~~f~~lV~P~~~--i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
|+||+||||+++..++|+|||+|.++++. . ..|+++|+|..+ +++ +.+|||+.+++. +++++.+++.+|.+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~--~~~~~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLE--DAPSFEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHH--CHCEHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccc--cCCcHHHHHHhhhh
Confidence 79999999999988999999999998764 3 889999999987 777 899999999999 88889999999999
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcC-CCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCS-YEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPL 281 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~g-l~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~ 281 (339)
|+.+ ..++||||+ .||..++...+.+.+ ...|....++|++.+.+..++... .++|++|+++||++.
T Consensus 79 ~~~~------~~~~v~~n~-~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~l~~l~~~~~~~~ 146 (164)
T PF00929_consen 79 FLKK------NDILVGHNA-SFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRK-----KYSLDDLAEYFGIPF 146 (164)
T ss_dssp HHHH------HTEEEETTC-CHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHH-----HHSHHHHHHHTTSSS
T ss_pred hhhc------ccccccccc-cchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccc-----cCCHHHHHHHcCCCC
Confidence 9984 259999998 999999988888863 333312357888888888777542 679999999999999
Q ss_pred CCCCCChHHHHHHHHHHH
Q 019538 282 VGSAHRAMADVNCLSLIL 299 (339)
Q Consensus 282 ~~~aH~Al~DA~~ta~L~ 299 (339)
.+.+|+|++||++|++||
T Consensus 147 ~~~~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 147 DGTAHDALDDARATAELF 164 (164)
T ss_dssp TSTTTSHHHHHHHHHHHH
T ss_pred CCCCcChHHHHHHHhCcC
Confidence 866899999999999987
No 47
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.82 E-value=7.2e-20 Score=165.22 Aligned_cols=171 Identities=18% Similarity=0.314 Sum_probs=145.8
Q ss_pred cEEEEEEecCCCCCC----CCcEEEEEEEEEc---CCee-eeEEEEEcCCCC--CCC--ccccCCcHHhhcCCCCCCHHH
Q 019538 128 TAIVFDIETTGFSRE----NERIIEIAFQDLL---GGEN-STFQTLVNPKRQ--VPN--AHVHGITTDMVCKPDVPRMED 195 (339)
Q Consensus 128 ~~vviDiETTGl~p~----~~~IIEIgav~v~---~g~i-~~f~~lV~P~~~--i~~--~~itGIt~e~l~~~~ap~~~e 195 (339)
.++++|+|+|+.+.. .+||||+.+|.++ .++| ++|+.||+|... +++ +.+|||.+++++ .+|.|.+
T Consensus 57 YLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD--~a~~f~~ 134 (280)
T KOG0542|consen 57 YLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVD--EAPTFPQ 134 (280)
T ss_pred eEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhc--cCCCHHH
Confidence 589999999977532 3789999999665 3456 599999999764 555 899999999999 8999999
Q ss_pred HHHHHHHHHHhcCC-CC-CceEEEEECCcchhH-HHHHHHHHhcCCCCCC-CCceeeHHHHHHHHHhcCCCCCCCCCCHH
Q 019538 196 LIPILLHYVKSRQK-PG-GYILFVAHNARSFDV-PFLINEFSRCSYEVPN-NWLFMDTLTLARELMKSGGSNLPSKVSLQ 271 (339)
Q Consensus 196 vl~~~~~~l~~~~~-~~-~~~~lV~hN~~~FD~-~fL~~~~~r~gl~~p~-~~~~iDtl~lar~l~~~~~~~l~~~~~L~ 271 (339)
|+.+|..|+....- ++ ++..+|++. ++|+ .||..+|...++..|. ...|||....++.++.... ..++.
T Consensus 135 vl~~f~~Wlr~~~~~~k~~~~Afvtdg--~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~-----~t~it 207 (280)
T KOG0542|consen 135 VLSEFDSWLRKDSLGDKNGKFAFVTDG--DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPA-----PTNIT 207 (280)
T ss_pred HHHHHHHHHHHhhcccccCceEEEeCc--hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCcc-----ccCHH
Confidence 99999999987542 23 678889887 5898 6799999999999884 3479999999999887632 77999
Q ss_pred HHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhc
Q 019538 272 ALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 272 ~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
.|.+++|+++.|++|++++||..+++|..+|.+++.
T Consensus 208 ~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~ 243 (280)
T KOG0542|consen 208 GMLEHYGLQFEGRAHSGIDDARNIARIAQKMIRDGA 243 (280)
T ss_pred HHHHHhCCcccCCcccCchhHHHHHHHHHHHHhCCc
Confidence 999999999999999999999999999999999875
No 48
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=99.75 E-value=7.9e-20 Score=166.10 Aligned_cols=310 Identities=33% Similarity=0.391 Sum_probs=234.2
Q ss_pred eeeEeeeecceehhhhhhHhhhhhhhhhhhcCCCCccccccccccccccCccchhhhhcccCccCccccccccccccccc
Q 019538 6 MCFSILEVPKGRINSLANFCRESFHSFSRRYGHSPSFKLLCSKTYGLEDQDSYTERWSRRRITTGTEGSKKTIQSHKLKN 85 (339)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (339)
||-+|.|+||.|++++.+.||++.|++.+ +.++|.||..+...+++ .+||+++..+++..|++ .+
T Consensus 2 ~~i~~se~pr~~tf~fldleat~lp~~~~---~iteLcLlav~assle~----k~~e~dq~~~~tlp~~R--------vl 66 (318)
T KOG4793|consen 2 GCISISEVPRLRTFSFLDLEATGLPGWIP---NITELCLLAVHASSLEG----KAREIDQNVSTTLPGSR--------VL 66 (318)
T ss_pred CccccCcCCceeEEEeeeeccccCCcccc---cchhhhHHHHHHHhhcC----CccccccCCCccCCccc--------hh
Confidence 79999999999999999999999999998 78999999999999998 46899999999998886 24
Q ss_pred ccccccccccccchhhhhhhhccch--hhhhhhhhhccCccCCCcEEEEEEecCC---CCCCCCcEEEEEEEEEcCCeee
Q 019538 86 IKFEATSTTINVNKTEISKIQRIQH--YDIEQIIAENKDLAKLVTAIVFDIETTG---FSRENERIIEIAFQDLLGGENS 160 (339)
Q Consensus 86 ~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~~l~~~~~~vviDiETTG---l~p~~~~IIEIgav~v~~g~i~ 160 (339)
.|.+-.--+..+...+-+++-|+.. +.++.+...++++..+-..+.=|.+++| .....+.+++|.+..+.++.+.
T Consensus 67 ~Klsvl~~p~~v~~p~aeeitgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~ 146 (318)
T KOG4793|consen 67 DKLSVLGGPVPVTRPIAEEITGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYS 146 (318)
T ss_pred hhhhhccCCcCCcChhhhhhcccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCcc
Confidence 4443222222223333333444433 4466666666666654344555778887 4555677888888777766667
Q ss_pred eEEEEEcCCCCCCC-ccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCC
Q 019538 161 TFQTLVNPKRQVPN-AHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYE 239 (339)
Q Consensus 161 ~f~~lV~P~~~i~~-~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~ 239 (339)
.++.+++++. ++. ..+-. ..++..+...+........|..+.++++++++-...+.||+..|+..|..++|-|.+.+
T Consensus 147 lpq~lvcvds-lpa~~ald~-a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~de 224 (318)
T KOG4793|consen 147 LPQDLVCVDS-LPALNALDR-ANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSDE 224 (318)
T ss_pred chhhhcCcch-hHHHHHHhh-hcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHhh
Confidence 7888888763 222 11111 33333332334455666778889998888888888999999999999999999999988
Q ss_pred CCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHhhccCHHHHHHhcCC
Q 019538 240 VPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFDLKLSLCDLIERGFT 319 (339)
Q Consensus 240 ~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~l~~tl~~L~~~s~~ 319 (339)
.+.+|..++.|..++.-.....|+..+.+++++|+.++....++.+|+|+.|+..+.++++++..++...+.+|.=....
T Consensus 225 qa~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~~~k~~q~~~idlla~l~~lai~~~~ 304 (318)
T KOG4793|consen 225 QARPWLLIRPLYLARENAKSVEPTPKLVSSLEALATYYSLTPELDAHRALSDVLLLSKVFQKLTIDLLASLSDLAIRCHT 304 (318)
T ss_pred cCCCcccccchhhhhhhccccCCCCccchhHHHHHHHhhcCcccchhhhccccchhhhHHHHhhhhhhhhhhhhhhhhhc
Confidence 88889999999988877666555444588999999999988888999999999999999999999999888888888888
Q ss_pred CCCCCCccccccC
Q 019538 320 PSDLINPKKKKKS 332 (339)
Q Consensus 320 ~~~~~~~~~~~~~ 332 (339)
.+++....-|+|+
T Consensus 305 v~~l~~~~~~~k~ 317 (318)
T KOG4793|consen 305 VSDLSAAMAKNKK 317 (318)
T ss_pred cccchhhhhcCCC
Confidence 8888776655554
No 49
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.73 E-value=5.3e-18 Score=144.62 Aligned_cols=168 Identities=18% Similarity=0.228 Sum_probs=138.4
Q ss_pred cEEEEEEecCCCC----CCCCcEEEEEEEEEc--CC-eeeeEEEEEcCCCC--CCC--ccccCCcHHhhcCCCCCCHHHH
Q 019538 128 TAIVFDIETTGFS----RENERIIEIAFQDLL--GG-ENSTFQTLVNPKRQ--VPN--AHVHGITTDMVCKPDVPRMEDL 196 (339)
Q Consensus 128 ~~vviDiETTGl~----p~~~~IIEIgav~v~--~g-~i~~f~~lV~P~~~--i~~--~~itGIt~e~l~~~~ap~~~ev 196 (339)
.+++||+|+|..+ +..-+||||+|-.++ +. +++.|++||+|... ++. ..++||++..++ ++|-|..+
T Consensus 5 ~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD--~apifs~v 82 (210)
T COG5018 5 SLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVD--EAPIFSMV 82 (210)
T ss_pred eEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhcc--ccchHHHH
Confidence 4789999998553 445789999997665 34 44999999999864 344 789999999999 89999999
Q ss_pred HHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCC-CCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHH
Q 019538 197 IPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYE-VPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALRE 275 (339)
Q Consensus 197 l~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~-~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~ 275 (339)
+++|..|+.++. |.....+++++ ++|+..|.+.+..+++. .+...+.+|....+...+.... -.+|..+++
T Consensus 83 ~E~f~r~L~~h~-Pr~~~~wa~wG--~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr-----~tgln~ale 154 (210)
T COG5018 83 FEDFIRKLNEHD-PRKNSTWATWG--NMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPR-----LTGLNKALE 154 (210)
T ss_pred HHHHHHHHHhcC-cccCCcccccc--chhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCc-----cccHHHHHH
Confidence 999999999864 44445566666 69999999998888887 5556678999888888776431 478999999
Q ss_pred HhCCCCCCCCCChHHHHHHHHHHHHHHHHh
Q 019538 276 YYGIPLVGSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 276 ~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
.+|..+.|..|+|++||+.+++|+..+..+
T Consensus 155 ~~G~sf~G~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 155 EYGDSFTGTHHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred HhccccCCchhhhHHHHHHHHHHHHHHcch
Confidence 999999999999999999999999988764
No 50
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.68 E-value=6.7e-16 Score=140.72 Aligned_cols=157 Identities=20% Similarity=0.330 Sum_probs=123.7
Q ss_pred CCcEEEEEEecCCCCCCC--CcEEEEEEEEEcCCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHH
Q 019538 126 LVTAIVFDIETTGFSREN--ERIIEIAFQDLLGGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILL 201 (339)
Q Consensus 126 ~~~~vviDiETTGl~p~~--~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~ 201 (339)
++++|++|||+.|..|+. +-+.-|++|...|.. .|+.||+|..+|.+ +.++||.++.+. ++.+|+.|..++.
T Consensus 104 ~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~V--vyDkyVkP~~~VtDyRT~vSGIrpehm~--~A~pf~~aQ~ev~ 179 (280)
T KOG2249|consen 104 LTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHV--VYDKYVKPTEPVTDYRTRVSGIRPEHMR--DAMPFKVAQKEVL 179 (280)
T ss_pred cceEEEEeeeEeccCCCccceeeeEEEEeeccCcE--eeeeecCCCcccccceeeecccCHHHhc--cCccHHHHHHHHH
Confidence 357999999999999853 456667777666665 49999999999999 999999999999 8888999999999
Q ss_pred HHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHH--HHHHHhcCCCCCCCCCCHHHHHH-HhC
Q 019538 202 HYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTL--ARELMKSGGSNLPSKVSLQALRE-YYG 278 (339)
Q Consensus 202 ~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~l--ar~l~~~~~~~l~~~~~L~~L~~-~~g 278 (339)
++|.++ ++|||.. ..|+..|.- ..|.. .+-||... ...+..... ..+|..|++ .+|
T Consensus 180 klL~gR-------IlVGHaL-hnDl~~L~l-------~hp~s-~iRDTs~~~pl~k~~~~~~-----tpSLK~Lt~~~Lg 238 (280)
T KOG2249|consen 180 KLLKGR-------ILVGHAL-HNDLQALKL-------EHPRS-MIRDTSKYPPLMKLLSKKA-----TPSLKKLTEALLG 238 (280)
T ss_pred HHHhCC-------EEecccc-ccHHHHHhh-------hCchh-hhcccccCchHHHHhhccC-----CccHHHHHHHHhc
Confidence 999965 9999999 899988854 33322 34566542 222223222 889999986 467
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHhhc
Q 019538 279 IPLVGSAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 279 I~~~~~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
++..-..|+..+||.+|++||..+..+++
T Consensus 239 ~~IQ~GeHsSvEDA~AtM~LY~~vk~qwe 267 (280)
T KOG2249|consen 239 KDIQVGEHSSVEDARATMELYKRVKVQWE 267 (280)
T ss_pred hhhhccccCcHHHHHHHHHHHHHHHHHHH
Confidence 66654579999999999999999988765
No 51
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.58 E-value=1.3e-14 Score=137.91 Aligned_cols=171 Identities=19% Similarity=0.206 Sum_probs=139.9
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCC--ee-eeEEEEEcCCCC-CCC---ccccCCcHHhhcCCCCCCHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGG--EN-STFQTLVNPKRQ-VPN---AHVHGITTDMVCKPDVPRMEDLIPI 199 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g--~i-~~f~~lV~P~~~-i~~---~~itGIt~e~l~~~~ap~~~evl~~ 199 (339)
.+|++.|.||.|.+|..+++.++++|+.+.. .| +....|.+|... +|. .-|||||++...+.|.+ ..++...
T Consensus 9 ~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~-E~~F~~~ 87 (475)
T COG2925 9 PTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGIN-EAAFAAR 87 (475)
T ss_pred CcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCC-hHHHHHH
Confidence 4799999999999999999999999988743 44 678889999765 443 78999999998876766 5677777
Q ss_pred HHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC--------CCCceeeHHHHHHHHHhc------CCCCCC
Q 019538 200 LLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP--------NNWLFMDTLTLARELMKS------GGSNLP 265 (339)
Q Consensus 200 ~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p--------~~~~~iDtl~lar~l~~~------~~~~l~ 265 (339)
+..-+.. .+.+++|+|...||-.+.+..|.|.-+++- +.|..+|.+...+.+-|. ...+++
T Consensus 88 I~~~ls~-----P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~p 162 (475)
T COG2925 88 IHAELTQ-----PNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLP 162 (475)
T ss_pred HHHHhCC-----CCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCc
Confidence 7776664 457899999989999999999988766531 356778888888888653 334677
Q ss_pred CCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHh
Q 019538 266 SKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 266 ~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
+++|++|...-||++. .+|+||+|+++|..+.+.+...
T Consensus 163 -SFkLEhLt~ANgieH~-nAHdAmsDVyATIamAklvk~~ 200 (475)
T COG2925 163 -SFKLEHLTKANGIEHS-NAHDAMSDVYATIAMAKLVKTA 200 (475)
T ss_pred -chhhHHHhhccccccc-hhhHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999998 8999999999999998877653
No 52
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. 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. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with 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.
Probab=99.56 E-value=3.6e-14 Score=123.98 Aligned_cols=148 Identities=16% Similarity=0.198 Sum_probs=106.4
Q ss_pred cEEEEEEecCCCCCCC-C--------cEEEEEEEEEc---CCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCC---
Q 019538 128 TAIVFDIETTGFSREN-E--------RIIEIAFQDLL---GGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDV--- 190 (339)
Q Consensus 128 ~~vviDiETTGl~p~~-~--------~IIEIgav~v~---~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~a--- 190 (339)
+||.+|.|++++.++. . ++.-|++|..+ .|+ .-++.||+|..+|.+ |.++||++++++ ++
T Consensus 6 e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~-vllD~~VkP~~~V~DYrT~~SGIt~~~L~--~a~~~ 82 (174)
T cd06143 6 EFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGV-PFIDDYISTTEPVVDYLTRFSGIKPGDLD--PKTSS 82 (174)
T ss_pred eEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCC-EEEeeeECCCCCccCcCccccccCHHHcC--ccccc
Confidence 4555555554444332 2 35556666531 222 468999999999988 999999999998 44
Q ss_pred ---CCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCC
Q 019538 191 ---PRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSK 267 (339)
Q Consensus 191 ---p~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~ 267 (339)
.+++++..++.+++.. +.++|||.. ..|+..| ++..|. ..++||..++.. +.. . .
T Consensus 83 ~~~~t~~~v~~~l~~li~~------~tILVGHsL-~nDL~aL-------~l~hp~-~~viDTa~l~~~--~~~----r-~ 140 (174)
T cd06143 83 KNLTTLKSAYLKLRLLVDL------GCIFVGHGL-AKDFRVI-------NIQVPK-EQVIDTVELFHL--PGQ----R-K 140 (174)
T ss_pred cccCCHHHHHHHHHHHcCC------CCEEEeccc-hhHHHHh-------cCcCCC-cceEEcHHhccC--CCC----C-C
Confidence 3588999999998863 369999999 9999877 455443 258999866532 221 2 6
Q ss_pred CCHHHHHH-HhCCCCCCCCCChHHHHHHHHHHHH
Q 019538 268 VSLQALRE-YYGIPLVGSAHRAMADVNCLSLILQ 300 (339)
Q Consensus 268 ~~L~~L~~-~~gI~~~~~aH~Al~DA~~ta~L~~ 300 (339)
++|..|++ ++|.......|+.++||+++++||+
T Consensus 141 ~sLk~La~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 141 LSLRFLAWYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred hhHHHHHHHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 89999976 5676665568999999999999983
No 53
>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=99.54 E-value=3e-13 Score=121.05 Aligned_cols=136 Identities=20% Similarity=0.250 Sum_probs=103.2
Q ss_pred EEEEEEecCCC----CCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 129 AIVFDIETTGF----SRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 129 ~vviDiETTGl----~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
+++||+||||. ++..++|++||++...+|....+.....+.... +.||+..++. ..++..+++..|.+++
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~----~~~i~~~~v~--~~~~E~~lL~~f~~~i 74 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDD----IEFIDGIEVE--YFADEKELLKRFFDII 74 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCc----CCCCCCceEE--EeCCHHHHHHHHHHHH
Confidence 36899999998 777899999999987555443333333222111 1166767777 6788999999999999
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC---------------------CCCceeeHHHHHHHHHhcCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP---------------------NNWLFMDTLTLARELMKSGGSN 263 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p---------------------~~~~~iDtl~lar~l~~~~~~~ 263 (339)
... ++.++||||+..||++||...+.++|++.. .....+|++.+++...+
T Consensus 75 ~~~----dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~----- 145 (199)
T cd05160 75 REY----DPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK----- 145 (199)
T ss_pred Hhc----CCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC-----
Confidence 975 456999999988999999999999888761 01247999999988776
Q ss_pred CCCCCCHHHHHHHhCCC
Q 019538 264 LPSKVSLQALREYYGIP 280 (339)
Q Consensus 264 l~~~~~L~~L~~~~gI~ 280 (339)
++ +++|+++++.++..
T Consensus 146 l~-sy~L~~v~~~~l~~ 161 (199)
T cd05160 146 LK-SYTLDAVAEELLGE 161 (199)
T ss_pred cc-cCCHHHHHHHHhCC
Confidence 23 99999999977644
No 54
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.47 E-value=2.1e-13 Score=116.09 Aligned_cols=156 Identities=21% Similarity=0.205 Sum_probs=112.0
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee---eeEEEEEcCCCC-CC---C-----ccccCCcHHhhcCCCCCCHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN---STFQTLVNPKRQ-VP---N-----AHVHGITTDMVCKPDVPRME 194 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i---~~f~~lV~P~~~-i~---~-----~~itGIt~e~l~~~~ap~~~ 194 (339)
.++|++|+|+|||+|..++||||+++..+.... +.+...|..... +. + ..-+|++....+ +.-+..
T Consensus 6 ~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~--S~~t~~ 83 (184)
T COG1949 6 NNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKA--STVTEA 83 (184)
T ss_pred CceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHH--hhccHH
Confidence 589999999999999999999999999886532 445555554322 11 1 355788888777 677789
Q ss_pred HHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeH---HHHHHHHHhcCCCCCCCCCCHH
Q 019538 195 DLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDT---LTLARELMKSGGSNLPSKVSLQ 271 (339)
Q Consensus 195 evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDt---l~lar~l~~~~~~~l~~~~~L~ 271 (339)
+|..+.++|+++..+. +..++.|..+ .-|+.||.++|.+.---+. ++.+|+ ..++++|.|.-
T Consensus 84 ~aE~~~l~flkkwvp~-~~spicGNSI-~qDRrFl~r~MP~Le~yfH--YR~lDVSTlKELa~RW~P~i----------- 148 (184)
T COG1949 84 EAEAQTLDFLKKWVPK-GVSPICGNSI-AQDRRFLFRYMPKLEAYFH--YRYLDVSTLKELARRWNPEI----------- 148 (184)
T ss_pred HHHHHHHHHHHHhCCC-CCCCCccchh-hHHHHHHHHHhhhHHHHhh--hHhhhHHHHHHHHHhhCcHh-----------
Confidence 9999999999987655 6678888888 9999999999887443333 345553 33677777642
Q ss_pred HHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 019538 272 ALREYYGIPLVGSAHRAMADVNCLSLILQRLTF 304 (339)
Q Consensus 272 ~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~ 304 (339)
..| +..+..|+|++|++-...=++...+
T Consensus 149 ----~~~-~~K~~~H~Al~DI~ESI~EL~~YR~ 176 (184)
T COG1949 149 ----LAG-FKKGGTHRALDDIRESIAELRYYRE 176 (184)
T ss_pred ----hhc-cccccchhHHHHHHHHHHHHHHHHH
Confidence 223 2233789999999776555544443
No 55
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.45 E-value=3e-13 Score=116.08 Aligned_cols=157 Identities=22% Similarity=0.245 Sum_probs=117.4
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCee---eeEEEEEcCCCCC----CC-----ccccCCcHHhhcCCCCCCHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGEN---STFQTLVNPKRQV----PN-----AHVHGITTDMVCKPDVPRME 194 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i---~~f~~lV~P~~~i----~~-----~~itGIt~e~l~~~~ap~~~ 194 (339)
+++||+|+|+|||+...++|+||+++..+++.. .-+...|+...++ .+ ..-+|++...++ +.-+++
T Consensus 26 q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~--S~~tl~ 103 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLA--SKITLA 103 (208)
T ss_pred CceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHH--hhccHH
Confidence 479999999999999999999999999887632 5577777754332 12 466799999988 788899
Q ss_pred HHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeH---HHHHHHHHhcCCCCCCCCCCHH
Q 019538 195 DLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDT---LTLARELMKSGGSNLPSKVSLQ 271 (339)
Q Consensus 195 evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDt---l~lar~l~~~~~~~l~~~~~L~ 271 (339)
+|-+++++|++.+.+ .+.+++.|..+ ..|+.||..+|...--..+ ++++|+ ..++++|+|....
T Consensus 104 ~aEnevl~yikk~ip-~~~~~laGNSV-~~DrlFl~k~mPk~~~~lh--yrivDVStIkeL~~Rw~P~~~~--------- 170 (208)
T KOG3242|consen 104 DAENEVLEYIKKHIP-KGKCPLAGNSV-YMDRLFLKKYMPKLIKHLH--YRIVDVSTIKELARRWYPDIKA--------- 170 (208)
T ss_pred HHHHHHHHHHHHhCC-CCCCCccCcch-hhHHHHHHHHhHHHHHhcc--eeeeeHHHHHHHHHHhCchhhc---------
Confidence 999999999998765 56677888888 8999999999987543433 457774 4479999886421
Q ss_pred HHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 019538 272 ALREYYGIPLVGSAHRAMADVNCLSLILQRLTF 304 (339)
Q Consensus 272 ~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~ 304 (339)
+ -|.....|||++|..-...=++....
T Consensus 171 -----~-aPkK~~~HrAldDI~ESI~ELq~Yr~ 197 (208)
T KOG3242|consen 171 -----R-APKKKATHRALDDIRESIKELQYYRE 197 (208)
T ss_pred -----c-CcccccccchHHHHHHHHHHHHHHHH
Confidence 1 11122589999999876665555444
No 56
>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=99.20 E-value=4e-11 Score=103.81 Aligned_cols=136 Identities=24% Similarity=0.318 Sum_probs=72.7
Q ss_pred EEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCC
Q 019538 130 IVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQK 209 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~ 209 (339)
++||+||||+.|..+.|.-||++.++++....|..+... .+..++.+.++.+++.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~---------------------~~~ee~~~~~~~~~l~~--- 56 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAE---------------------DPDEEEIILEFFELLDE--- 56 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GG---------------------GHHHHHHHHH--HHHHT---
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhcc---------------------CcHHHHHHHHHHHHHhc---
Confidence 589999999999888899999998877654333333321 11123444444467774
Q ss_pred CCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCCCChH
Q 019538 210 PGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAM 289 (339)
Q Consensus 210 ~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~aH~Al 289 (339)
...+|+||+..||+++|.+.+.+++++. ....+|++..++.... + +++|..++..+|+.... .-
T Consensus 57 ---~~~iv~yng~~FD~p~L~~~~~~~~~~~--~~~~iDl~~~~~~~~~------~-~~~Lk~ve~~lg~~~~~----~~ 120 (164)
T PF13482_consen 57 ---ADNIVTYNGKNFDIPFLKRRAKRYGLPP--PFNHIDLLKIIKKHFL------E-SYSLKNVEKFLGIERRD----DD 120 (164)
T ss_dssp ---T--EEESSTTTTHHHHHHHHH-HHHH----GGGEEEHHHHHT-TTS------C-CTT--SHHH--------------
T ss_pred ---CCeEEEEeCcccCHHHHHHHHHHcCCCc--ccchhhHHHHHHhccC------C-CCCHHHHhhhccccccc----CC
Confidence 3589999988999999999998877665 3468999998865433 2 88999999999987541 12
Q ss_pred HHHHHHHHHHHHHHHh
Q 019538 290 ADVNCLSLILQRLTFD 305 (339)
Q Consensus 290 ~DA~~ta~L~~~l~~~ 305 (339)
.+......+|......
T Consensus 121 ~~G~~~~~~~~~~~~~ 136 (164)
T PF13482_consen 121 ISGSESVKLYKEYLET 136 (164)
T ss_dssp -HHHHHHHHHH---TT
T ss_pred CCHHHHHHHHHHHHhc
Confidence 3444455556654443
No 57
>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=99.16 E-value=7.3e-10 Score=99.32 Aligned_cols=128 Identities=25% Similarity=0.370 Sum_probs=91.2
Q ss_pred cEEEEEEecC---CC-CCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 128 TAIVFDIETT---GF-SRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 128 ~~vviDiETT---Gl-~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
++++||+||+ |+ ++..++|+.||++...++.+-.+ .+. ....+. ...+..+.+..|.++
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~----~~~-----------~~~~v~--~~~~E~~lL~~F~~~ 66 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW----KKF-----------DLPFVE--VVKTEKEMIKRFIEI 66 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe----cCC-----------CCCeEE--EeCCHHHHHHHHHHH
Confidence 7899999998 54 56779999999976433322111 110 000122 234467899999999
Q ss_pred HHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC---------------------CCceeeHHHHHHHHHhcCCC
Q 019538 204 VKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN---------------------NWLFMDTLTLARELMKSGGS 262 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~---------------------~~~~iDtl~lar~l~~~~~~ 262 (339)
+... ++.++||||+..||+++|...+.++|+..+. ....+|++.+++....
T Consensus 67 i~~~----dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~---- 138 (195)
T cd05780 67 VKEK----DPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN---- 138 (195)
T ss_pred HHHc----CCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC----
Confidence 9975 4568999999889999999999999987542 1247899999887543
Q ss_pred CCCCCCCHHHHHH-HhCCCCC
Q 019538 263 NLPSKVSLQALRE-YYGIPLV 282 (339)
Q Consensus 263 ~l~~~~~L~~L~~-~~gI~~~ 282 (339)
++ +++|+++++ .+|.+..
T Consensus 139 -l~-sy~L~~v~~~~Lg~~k~ 157 (195)
T cd05780 139 -LT-RYTLERVYEELFGIEKE 157 (195)
T ss_pred -CC-cCcHHHHHHHHhCCCCC
Confidence 45 999999976 6776543
No 58
>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=99.11 E-value=1.6e-09 Score=96.63 Aligned_cols=118 Identities=23% Similarity=0.363 Sum_probs=90.2
Q ss_pred cEEEEEEecC---CC-CCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHH
Q 019538 128 TAIVFDIETT---GF-SRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHY 203 (339)
Q Consensus 128 ~~vviDiETT---Gl-~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~ 203 (339)
+.++||+||+ |+ ++..++|+.||+...++.. +.+. . ...+..+.+..|.++
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~----~~~~-------------------~--~~~~E~~lL~~F~~~ 58 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDV----EFIL-------------------A--EGLDDRKIIREFVKY 58 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCE----EEEE-------------------e--cCCCHHHHHHHHHHH
Confidence 7899999999 54 5677999999998755431 1111 1 123468899999999
Q ss_pred HHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCC-------------------CceeeHHHHHHHHHhcCCCCC
Q 019538 204 VKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNN-------------------WLFMDTLTLARELMKSGGSNL 264 (339)
Q Consensus 204 l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~-------------------~~~iDtl~lar~l~~~~~~~l 264 (339)
+... ++.+++|||+..||+++|...+.++|+..+.. ...+|.+.+.+.... +
T Consensus 59 i~~~----dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~-----l 129 (188)
T cd05781 59 VKEY----DPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE-----V 129 (188)
T ss_pred HHHc----CCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC-----C
Confidence 9986 45689999998999999999999998765310 127899998887643 4
Q ss_pred CCCCCHHHHHHHhCCC
Q 019538 265 PSKVSLQALREYYGIP 280 (339)
Q Consensus 265 ~~~~~L~~L~~~~gI~ 280 (339)
+ +++|+++++++|+.
T Consensus 130 ~-~y~L~~Va~~Lg~~ 144 (188)
T cd05781 130 K-VKTLENVAEYLGVM 144 (188)
T ss_pred C-CCCHHHHHHHHCCC
Confidence 5 99999999999975
No 59
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved 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 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.07 E-value=2.4e-09 Score=94.60 Aligned_cols=158 Identities=22% Similarity=0.229 Sum_probs=111.3
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHh
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKS 206 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~ 206 (339)
..++++|+||+|+.+..++|+.+++..-. + ..|...+.+. . .. +.+...+++..|.+++.+
T Consensus 5 ~~~~a~d~e~~~~~~~~~~i~~l~~~~~~-~--~~~~~~~~~~------~--------~~--~~~~~~~~~~~l~~~l~~ 65 (193)
T cd06139 5 AKVFAFDTETTSLDPMQAELVGISFAVEP-G--EAYYIPLGHD------Y--------GG--EQLPREEVLAALKPLLED 65 (193)
T ss_pred CCeEEEEeecCCCCcCCCeEEEEEEEcCC-C--CEEEEecCCC------c--------cc--cCCCHHHHHHHHHHHHhC
Confidence 46899999999999878889888876322 2 1222212211 0 01 233477888889999975
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCC----
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPL---- 281 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~---- 281 (339)
....+|+||+ +||+.+|. ++|+..+. .++||+.+++.+.|... +++|+++++.| +...
T Consensus 66 -----~~~~~v~hn~-k~d~~~l~----~~gi~~~~--~~~Dt~l~a~ll~p~~~-----~~~l~~l~~~~l~~~~~~~~ 128 (193)
T cd06139 66 -----PSIKKVGQNL-KFDLHVLA----NHGIELRG--PAFDTMLASYLLNPGRR-----RHGLDDLAERYLGHKTISFE 128 (193)
T ss_pred -----CCCcEEeecc-HHHHHHHH----HCCCCCCC--CcccHHHHHHHhCCCCC-----CCCHHHHHHHHhCCCCccHH
Confidence 2347999999 89999985 46777543 47999999999887541 56899998765 4320
Q ss_pred ------------CC-----CCCChHHHHHHHHHHHHHHHHhhc--cCHHHHHHhcCCC
Q 019538 282 ------------VG-----SAHRAMADVNCLSLILQRLTFDLK--LSLCDLIERGFTP 320 (339)
Q Consensus 282 ------------~~-----~aH~Al~DA~~ta~L~~~l~~~l~--~tl~~L~~~s~~~ 320 (339)
+. ..|.|..||.++.+++..+..++. ..+.+|+...+.|
T Consensus 129 ~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~~iE~P 186 (193)
T cd06139 129 DLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKEEPGLLELYEEIEMP 186 (193)
T ss_pred HHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhcc
Confidence 00 123588899999999999999885 4688888887776
No 60
>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=99.06 E-value=2.7e-09 Score=84.95 Aligned_cols=82 Identities=35% Similarity=0.542 Sum_probs=63.0
Q ss_pred EEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCC
Q 019538 130 IVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQK 209 (339)
Q Consensus 130 vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~ 209 (339)
+++|+||||+++..++|++|++...+++. .| +. + |.+|+++.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~--~~----------------------~~--~----------f~~~l~~~-- 42 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPED--TA----------------------VI--D----------LKDILRDK-- 42 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCC--EE----------------------Ee--h----------HHHHHhhC--
Confidence 48999999999999999999998753221 00 01 1 66788753
Q ss_pred CCCceEEEEECCcchhHHHHHHHHHhcCCCCCC-CCceeeHHHH
Q 019538 210 PGGYILFVAHNARSFDVPFLINEFSRCSYEVPN-NWLFMDTLTL 252 (339)
Q Consensus 210 ~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~-~~~~iDtl~l 252 (339)
...++|+||+ .||++||.+++.++++..|. ...++||+.+
T Consensus 43 --~~~v~V~hn~-~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 43 --PLAILVGHNG-SFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred --CCCEEEEeCc-HHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 1258999999 89999999999999988763 4578999966
No 61
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.99 E-value=3e-09 Score=103.83 Aligned_cols=154 Identities=21% Similarity=0.244 Sum_probs=117.3
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCC--ccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPN--AHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~--~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
.+++++|||+...... -++..+++|+.++.. .++.+|+|..+|.+ +.++|||.++++. ..-+++++..++..|+
T Consensus 216 ~~i~AlDCEm~~te~g-~el~RVt~VD~~~~v--i~D~fVkP~~~VvDy~T~~SGIT~~~~e~-~t~tl~dvq~~l~~~~ 291 (380)
T KOG2248|consen 216 PNIFALDCEMVVTENG-LELTRVTAVDRDGKV--ILDTFVKPNKPVVDYNTRYSGITEEDLEN-STITLEDVQKELLELI 291 (380)
T ss_pred CCeEEEEeeeeeeccc-eeeEEeeeeeccCcE--EeEEeecCCCcccccccccccccHHHHhc-CccCHHHHHHHHHhhc
Confidence 5899999999876654 789999999988765 59999999999988 8999999999983 4456899999999998
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hC--CCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY-YG--IPL 281 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~g--I~~ 281 (339)
.. +.++|||.. .-|+..|+- ..+ .++||..++..-.+ + ++...+|..|++. +| |+.
T Consensus 292 ~~------~TILVGHSL-enDL~aLKl-------~H~---~ViDTa~lf~~~~g---~-~~~k~sLk~L~~~~L~~~Iq~ 350 (380)
T KOG2248|consen 292 SK------NTILVGHSL-ENDLKALKL-------DHP---SVIDTAVLFKHPTG---P-YPFKSSLKNLAKSYLGKLIQE 350 (380)
T ss_pred Cc------CcEEEeech-hhHHHHHhh-------hCC---ceeeeeEEEecCCC---C-ccchHHHHHHHHHHHHHHHhc
Confidence 84 579999999 999988853 222 47899854432111 1 1215678888764 44 441
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHh
Q 019538 282 VGSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 282 ~~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
....|++..||.++.+|+......
T Consensus 351 ~~~~HdS~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 351 GVGGHDSVEDALACMKLVKLKIKN 374 (380)
T ss_pred cCCCCccHHHHHHHHHHHHHHHhc
Confidence 124699999999999999776654
No 62
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.90 E-value=3.2e-08 Score=89.91 Aligned_cols=120 Identities=24% Similarity=0.410 Sum_probs=86.1
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHH-HHHHHHHHHHHh
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRME-DLIPILLHYVKS 206 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~-evl~~~~~~l~~ 206 (339)
++++||+||||+++..+.|+-+|...+.++.. +|+ +.. . .+|..+ .+++. |+..
T Consensus 99 ~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~-----~Vr--------------q~~-l--p~p~~E~avle~---fl~~ 153 (278)
T COG3359 99 DVAFFDIETTGLDRAGNTITLVGGARGVDDTM-----HVR--------------QHF-L--PAPEEEVAVLEN---FLHD 153 (278)
T ss_pred ceEEEeeeccccCCCCCeEEEEEEEEccCceE-----EEE--------------eec-C--CCcchhhHHHHH---HhcC
Confidence 69999999999999777888888887766543 222 111 1 233222 22333 3332
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCC
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPL 281 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~ 281 (339)
. .-..+|++|++.||++|++ .|.+..++.......+|.+..+|++++.. ++ +.+|..+-+.+||.-
T Consensus 154 ~----~~~~lvsfNGkaFD~Pfik-R~v~~~~el~l~~~H~DL~h~~RRlwk~~---l~-~c~Lk~VEr~LGi~R 219 (278)
T COG3359 154 P----DFNMLVSFNGKAFDIPFIK-RMVRDRLELSLEFGHFDLYHPSRRLWKHL---LP-RCGLKTVERILGIRR 219 (278)
T ss_pred C----CcceEEEecCcccCcHHHH-HHHhcccccCccccchhhhhhhhhhhhcc---CC-CCChhhHHHHhCccc
Confidence 1 2248999999999999999 47777777666667899999999999764 56 889999999998753
No 63
>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=98.86 E-value=8.9e-08 Score=86.74 Aligned_cols=125 Identities=25% Similarity=0.390 Sum_probs=89.2
Q ss_pred CcEEEEEEecCCC--------CCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHH
Q 019538 127 VTAIVFDIETTGF--------SRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIP 198 (339)
Q Consensus 127 ~~~vviDiETTGl--------~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~ 198 (339)
-+++.||+|+++. ++..++|+.||...-.+.. ..+ . . ..++..+++.
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~-----~~~--------------~----~--~~~~E~~lL~ 63 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWE-----EVL--------------H----A--EDAAEKELLE 63 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCce-----eee--------------c----c--CCCCHHHHHH
Confidence 3899999999653 2345889999986432211 000 0 1 2345788999
Q ss_pred HHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC-----------------------------CCceeeH
Q 019538 199 ILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN-----------------------------NWLFMDT 249 (339)
Q Consensus 199 ~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~-----------------------------~~~~iDt 249 (339)
.|.+++.+. ++.++||||+..||+++|...+.++|+..+. ....+|+
T Consensus 64 ~f~~~i~~~----dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl 139 (207)
T cd05785 64 ELVAIIRER----DPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDT 139 (207)
T ss_pred HHHHHHHHh----CCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEc
Confidence 999999986 4579999999999999999999999887631 0123899
Q ss_pred HHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 250 LTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 250 l~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
+.+.+++.... ..++ +++|+++++.+|+...
T Consensus 140 ~~~~~~~~~~~-~~l~-sysL~~Va~~~g~~~~ 170 (207)
T cd05785 140 YFLVQLFDVSS-RDLP-SYGLKAVAKHFGLASP 170 (207)
T ss_pred HHHHHhhcccc-cCCC-CCCHHHHHHHhcccCC
Confidence 99888753321 1345 8999999999987543
No 64
>PRK05755 DNA polymerase I; Provisional
Probab=98.86 E-value=2.3e-08 Score=108.30 Aligned_cols=150 Identities=21% Similarity=0.278 Sum_probs=108.4
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHh
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKS 206 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~ 206 (339)
..++++|+||+|+++..++|+.|++. ..+|. ..+|.+. ++ + .+++..|.+++.+
T Consensus 315 ~~~~a~DtEt~~l~~~~~~i~~i~ls-~~~g~----~~~ip~~---------~i----------~--~~~l~~l~~~L~d 368 (880)
T PRK05755 315 AGLFAFDTETTSLDPMQAELVGLSFA-VEPGE----AAYIPLD---------QL----------D--REVLAALKPLLED 368 (880)
T ss_pred cCeEEEEeccCCCCcccccEEEEEEE-eCCCc----EEEEecc---------cc----------c--HHHHHHHHHHHhC
Confidence 46899999999999988999999874 33332 1223211 11 1 1567778888885
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCC---
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLV--- 282 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~--- 282 (339)
...++|+||+ +||+.+|.+ +|+..+. .++||+.+++.+.+.. .++|++|++.| |+...
T Consensus 369 -----~~v~kV~HNa-kfDl~~L~~----~gi~~~~--~~~DT~iAa~Ll~~~~------~~~L~~L~~~ylg~~~~~~~ 430 (880)
T PRK05755 369 -----PAIKKVGQNL-KYDLHVLAR----YGIELRG--IAFDTMLASYLLDPGR------RHGLDSLAERYLGHKTISFE 430 (880)
T ss_pred -----CCCcEEEecc-HhHHHHHHh----CCCCcCC--CcccHHHHHHHcCCCC------CCCHHHHHHHHhCCCccchH
Confidence 3456899999 999999964 5776543 5899999999887753 47999998876 55410
Q ss_pred ---------------CCCCChHHHHHHHHHHHHHHHHhhcc--CHHHHHHhcCCC
Q 019538 283 ---------------GSAHRAMADVNCLSLILQRLTFDLKL--SLCDLIERGFTP 320 (339)
Q Consensus 283 ---------------~~aH~Al~DA~~ta~L~~~l~~~l~~--tl~~L~~~s~~~ 320 (339)
...|.|..|+.++++||..+...+.. .+.+++...+.|
T Consensus 431 ~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l~~l~~eiE~p 485 (880)
T PRK05755 431 EVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYEEIELP 485 (880)
T ss_pred HhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhhch
Confidence 12367999999999999999998752 566776655444
No 65
>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=98.85 E-value=6.9e-08 Score=87.51 Aligned_cols=113 Identities=19% Similarity=0.212 Sum_probs=82.6
Q ss_pred ecCCCCCCCCcEEEEEEEEEc--CCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCC
Q 019538 135 ETTGFSRENERIIEIAFQDLL--GGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGG 212 (339)
Q Consensus 135 ETTGl~p~~~~IIEIgav~v~--~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~ 212 (339)
+++|+.+..++||.||++..+ ++.+. +. + . ...+..+.+..|.+++.+.
T Consensus 42 ~~~~l~~~~~~Iv~Is~~~~~~~~~~~~----~~------------~------~--~~~~E~elL~~F~~~i~~~----- 92 (208)
T cd05782 42 GSDFLPLPFHKVVSISALYRDDDGGFLK----VR------------T------L--DGADEKELLEDFFQLIEKK----- 92 (208)
T ss_pred CCCCCccccCceEEEEEEEEecCCCeEE----Ee------------e------c--CCCCHHHHHHHHHHHHHHh-----
Confidence 366788778999999999873 33210 00 0 0 1223578999999999974
Q ss_pred ceEEEEECCcchhHHHHHHHHHhcCCCCCCCC---------------ceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh
Q 019538 213 YILFVAHNARSFDVPFLINEFSRCSYEVPNNW---------------LFMDTLTLARELMKSGGSNLPSKVSLQALREYY 277 (339)
Q Consensus 213 ~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~---------------~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~ 277 (339)
++++|+||+..||+++|...+..+|+..|..+ ..+|++.+.+.... +. +++|+.+++.+
T Consensus 93 ~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~-----~~-~~~L~~va~~l 166 (208)
T cd05782 93 NPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGA-----RA-RASLDLLAKLL 166 (208)
T ss_pred CCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCc-----cC-CCCHHHHHHHh
Confidence 35899999999999999999999999755321 27899988764322 23 89999999999
Q ss_pred CCCCC
Q 019538 278 GIPLV 282 (339)
Q Consensus 278 gI~~~ 282 (339)
|++..
T Consensus 167 G~~~K 171 (208)
T cd05782 167 GIPGK 171 (208)
T ss_pred CCCCC
Confidence 99543
No 66
>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=98.81 E-value=2.8e-07 Score=83.33 Aligned_cols=142 Identities=19% Similarity=0.224 Sum_probs=90.4
Q ss_pred cEEEEEEecCCC-----CCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCC-C---CCccccCCcHHhhcCCCCCCHHHHHH
Q 019538 128 TAIVFDIETTGF-----SRENERIIEIAFQDLLGGENSTFQTLVNPKRQ-V---PNAHVHGITTDMVCKPDVPRMEDLIP 198 (339)
Q Consensus 128 ~~vviDiETTGl-----~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~-i---~~~~itGIt~e~l~~~~ap~~~evl~ 198 (339)
++++||+||.+. +|..+.||+|+++.-.+|.......++.+... + +...+.|. -.+. ..++..+.+.
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~v~--~~~~E~~lL~ 78 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGP--FKVF--NEPDEKALLQ 78 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCc--eEEe--cCCCHHHHHH
Confidence 689999999853 46679999999886554532100001100000 0 00011110 0011 1345788999
Q ss_pred HHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC--CC-------------CceeeHHHHHHHHHhcCCCC
Q 019538 199 ILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP--NN-------------WLFMDTLTLARELMKSGGSN 263 (339)
Q Consensus 199 ~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p--~~-------------~~~iDtl~lar~l~~~~~~~ 263 (339)
+|.+++.+. ++.+++|||+..||+++|...+.++|+... .. ...+|.+.+.+..... .
T Consensus 79 ~f~~~i~~~----~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l---~ 151 (204)
T cd05779 79 RFFEHIREV----KPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYL---P 151 (204)
T ss_pred HHHHHHHHh----CCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcC---C
Confidence 999999986 556899999999999999999998887643 10 1268999888764321 1
Q ss_pred CCCCCCHHHHHHH-hCCCC
Q 019538 264 LPSKVSLQALREY-YGIPL 281 (339)
Q Consensus 264 l~~~~~L~~L~~~-~gI~~ 281 (339)
.+ +++|+++++. +|...
T Consensus 152 ~~-sysLd~Va~~~Lg~~K 169 (204)
T cd05779 152 QG-SQGLKAVTKAKLGYDP 169 (204)
T ss_pred CC-CccHHHHHHHHhCCCc
Confidence 12 8999999984 77643
No 67
>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=98.78 E-value=2.5e-07 Score=83.51 Aligned_cols=130 Identities=21% Similarity=0.271 Sum_probs=92.9
Q ss_pred CCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCc
Q 019538 143 NERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNAR 222 (339)
Q Consensus 143 ~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~ 222 (339)
.++||.|+++..+++.. | ++..+ .. ...+.++.++.|.+++.+. .+.+|+||++
T Consensus 8 f~kIV~Is~~~~~~~~~--~-------------~v~s~-----~~-~~~~E~~lL~~F~~~~~~~-----~p~LVs~NG~ 61 (209)
T PF10108_consen 8 FHKIVCISVVYADDDGQ--F-------------KVKSL-----GG-PDDDEKELLQDFFDLVEKY-----NPQLVSFNGR 61 (209)
T ss_pred CCCeEEEEEEEEecCCc--E-------------EEEec-----cC-CCCCHHHHHHHHHHHHHhC-----CCeEEecCCc
Confidence 57899999996654321 1 01111 10 1123688999999999864 4689999999
Q ss_pred chhHHHHHHHHHhcCCCCCC-------CC---------ceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCC--
Q 019538 223 SFDVPFLINEFSRCSYEVPN-------NW---------LFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGS-- 284 (339)
Q Consensus 223 ~FD~~fL~~~~~r~gl~~p~-------~~---------~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~-- 284 (339)
.||+++|....-.+|+..|. +| ..+|+|.+...+.... ..+|+.||..+|||....
T Consensus 62 ~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~------~~sLd~la~~lgiPgK~~id 135 (209)
T PF10108_consen 62 GFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKA------RTSLDELAALLGIPGKDDID 135 (209)
T ss_pred cCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccc------cCCHHHHHHHcCCCCCCCCC
Confidence 99999999999999998763 12 2588888755432221 889999999999986421
Q ss_pred ----------------CCChHHHHHHHHHHHHHHHH
Q 019538 285 ----------------AHRAMADVNCLSLILQRLTF 304 (339)
Q Consensus 285 ----------------aH~Al~DA~~ta~L~~~l~~ 304 (339)
+.-...|+.+|+.||.++..
T Consensus 136 Gs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 136 GSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12237899999999999865
No 68
>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=98.65 E-value=2.6e-06 Score=78.29 Aligned_cols=133 Identities=21% Similarity=0.253 Sum_probs=89.3
Q ss_pred CcEEEEEEecCCC-----CCCCCcEEEEEEEEEcCCe--e-eeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHH
Q 019538 127 VTAIVFDIETTGF-----SRENERIIEIAFQDLLGGE--N-STFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIP 198 (339)
Q Consensus 127 ~~~vviDiETTGl-----~p~~~~IIEIgav~v~~g~--i-~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~ 198 (339)
.+.++||+||... +|..++|+.||++.-.+|. . ...-..+.+..+++... +. ..++..+.+.
T Consensus 7 l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------v~--~~~~E~eLL~ 76 (230)
T cd05777 7 LRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQ--------VF--SFETEEELLL 76 (230)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCCCCE--------EE--EECCHHHHHH
Confidence 4789999999842 5667999999999654442 1 11111122222222111 11 1345788999
Q ss_pred HHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC---------------------------------CCc
Q 019538 199 ILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN---------------------------------NWL 245 (339)
Q Consensus 199 ~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~---------------------------------~~~ 245 (339)
.|.+++... ++.+++|||+..||+++|.+.+.++|+.... ...
T Consensus 77 ~f~~~i~~~----DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~ 152 (230)
T cd05777 77 AWRDFVQEV----DPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRI 152 (230)
T ss_pred HHHHHHHhc----CCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEE
Confidence 999999976 5679999999899999999999888765210 013
Q ss_pred eeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hCC
Q 019538 246 FMDTLTLARELMKSGGSNLPSKVSLQALREY-YGI 279 (339)
Q Consensus 246 ~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~gI 279 (339)
.+|++...+.... ++ +++|++++++ +|.
T Consensus 153 ~iD~~~~~~~~~k-----l~-sy~L~~Va~~~Lg~ 181 (230)
T cd05777 153 QFDLLQVIQRDYK-----LR-SYSLNSVSAHFLGE 181 (230)
T ss_pred eeeHHHHHHHhcC-----cc-cCcHHHHHHHHhCC
Confidence 5688888876542 45 9999999874 453
No 69
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=98.64 E-value=6.9e-08 Score=88.73 Aligned_cols=175 Identities=21% Similarity=0.267 Sum_probs=121.3
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEc-----CC--ee--------------eeEEEEEcCCCCCCC--ccccCCcHH
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLL-----GG--EN--------------STFQTLVNPKRQVPN--AHVHGITTD 183 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~-----~g--~i--------------~~f~~lV~P~~~i~~--~~itGIt~e 183 (339)
..++|+|+|+||+......|.|+....+. +. ++ +..+.++.|.....+ .+|||++++
T Consensus 13 ~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeitgls~~ 92 (318)
T KOG4793|consen 13 RTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEITGLSQP 92 (318)
T ss_pred eEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhcccccH
Confidence 57999999999998777788888766443 21 11 233445555544433 799999996
Q ss_pred hhcCCCCCCHHHHH-HHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCC-
Q 019538 184 MVCKPDVPRMEDLI-PILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGG- 261 (339)
Q Consensus 184 ~l~~~~ap~~~evl-~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~- 261 (339)
.++.+....|+..+ +-+..|+..- ....++|+||+..||.++|.++++..|+..|-....+|++.+...+.....
T Consensus 93 ~~~l~rr~~~D~dla~LL~afls~l---p~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~s~ 169 (318)
T KOG4793|consen 93 FLALQRRLAFDKDLAKLLTAFLSRL---PTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRANSM 169 (318)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHhcC---CCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhcCc
Confidence 66532333355444 4455566643 245689999999999999999999999998866678999998887765321
Q ss_pred ----CCCCCCCCHHHHHHH-hCC-CCCCCCCChHHHHHHHHHHHHHHHHhh
Q 019538 262 ----SNLPSKVSLQALREY-YGI-PLVGSAHRAMADVNCLSLILQRLTFDL 306 (339)
Q Consensus 262 ----~~l~~~~~L~~L~~~-~gI-~~~~~aH~Al~DA~~ta~L~~~l~~~l 306 (339)
...+ .+.|.-+-.. ++- +.+ ..|.|..|.....-+|+....++
T Consensus 170 ~tr~~~~~-~~~l~~If~ry~~q~epp-a~~~~e~d~~~l~~~fqf~~~el 218 (318)
T KOG4793|consen 170 VTRPEVRR-MYSLGSIFLRYVEQREPP-AGHVAEGDVNGLLFIFQFRINEL 218 (318)
T ss_pred ccCCCCCc-ccccchHHHhhhcccCCC-cceeeecccchhHHHHHHHHHHH
Confidence 1223 6777777554 443 333 58999999988888888776664
No 70
>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=98.43 E-value=3.9e-06 Score=75.25 Aligned_cols=124 Identities=13% Similarity=0.133 Sum_probs=83.1
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhc
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSR 207 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~ 207 (339)
++++||+||+|.. +|+.||........+ -.+-.+.. . .|. .+. -.++..+.+..|.+++...
T Consensus 4 ~~~~fDIE~~~~~----~i~~i~~~~~~~~~i---~~~~~~~~-~-----~~~---~v~--~~~~E~~lL~~f~~~i~~~ 65 (193)
T cd05784 4 KVVSLDIETSMDG----ELYSIGLYGEGQERV---LMVGDPED-D-----APD---NIE--WFADEKSLLLALIAWFAQY 65 (193)
T ss_pred cEEEEEeecCCCC----CEEEEEeecCCCCEE---EEECCCCC-C-----CCC---EEE--EECCHHHHHHHHHHHHHhh
Confidence 7899999998754 788998865332221 11111110 0 011 111 1245678999999999976
Q ss_pred CCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC-----------------------CCceeeHHHHHHH-HHhcCCCC
Q 019538 208 QKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN-----------------------NWLFMDTLTLARE-LMKSGGSN 263 (339)
Q Consensus 208 ~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~-----------------------~~~~iDtl~lar~-l~~~~~~~ 263 (339)
++.+++|||+..||+++|.+.+..+|+.... ....+|++.+.+. .+ .
T Consensus 66 ----dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~-----k 136 (193)
T cd05784 66 ----DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATY-----H 136 (193)
T ss_pred ----CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccC-----C
Confidence 5569999999999999999999998887420 0126898887765 22 2
Q ss_pred CCCCCCHHHHHHH-hCC
Q 019538 264 LPSKVSLQALREY-YGI 279 (339)
Q Consensus 264 l~~~~~L~~L~~~-~gI 279 (339)
+. +|+|++++++ +|.
T Consensus 137 l~-sy~L~~Va~~~Lg~ 152 (193)
T cd05784 137 FE-SFSLENVAQELLGE 152 (193)
T ss_pred CC-cCCHHHHHHHHhCC
Confidence 44 9999999985 453
No 71
>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=98.35 E-value=1.7e-05 Score=68.53 Aligned_cols=137 Identities=26% Similarity=0.303 Sum_probs=85.6
Q ss_pred CcEEEEEEecCCCCCC--CCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRE--NERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 127 ~~~vviDiETTGl~p~--~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
.++++||+||+|+.+. ...+..|.+.. + ....++.|. .. +... ++..+.+++
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~~~~~iq~~~---~---~~~~i~~~~----------------~~-~~~~---~~~~l~~ll 73 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNPKIALIQLAT---G---EGCYIIDPI----------------DL-GDNW---ILDALKELL 73 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSEEEEEEEEEE---S---CEEEEECGT----------------TS-TTTT---HHHHHHHHH
T ss_pred CCeEEEEEEECCCCccccCCeEEEEEEec---C---CCceeeeec----------------cc-cccc---hHHHHHHHH
Confidence 4699999999999873 33333333332 1 112222221 10 1111 556666777
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hC-CCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY-YG-IPLV 282 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~g-I~~~ 282 (339)
.. .+...|+||+ +||..+|.+. .|+... .++||+..++.+.+.. +++|++|+.. +| ++.+
T Consensus 74 ~~-----~~i~kv~~n~-~~D~~~L~~~---~~i~~~---~~~D~~l~~~~l~~~~------~~~L~~L~~~~l~~~~~~ 135 (176)
T PF01612_consen 74 ED-----PNIIKVGHNA-KFDLKWLYRS---FGIDLK---NVFDTMLAAYLLDPTR------SYSLKDLAEEYLGNIDLD 135 (176)
T ss_dssp TT-----TTSEEEESSH-HHHHHHHHHH---HTS--S---SEEEHHHHHHHTTTST------TSSHHHHHHHHHSEEE-G
T ss_pred hC-----CCccEEEEEE-echHHHHHHH---hccccC---Cccchhhhhhcccccc------cccHHHHHHHHhhhccCc
Confidence 75 4578999999 8999999765 566543 4799966666655443 4899999764 46 2221
Q ss_pred -----CCC-----------CChHHHHHHHHHHHHHHHHhhc
Q 019538 283 -----GSA-----------HRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 283 -----~~a-----------H~Al~DA~~ta~L~~~l~~~l~ 307 (339)
+.. .-|..||..+.+||..|..+++
T Consensus 136 ~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 136 KKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 111 1267899999999999988763
No 72
>PHA02570 dexA exonuclease; Provisional
Probab=98.28 E-value=1.2e-05 Score=72.65 Aligned_cols=125 Identities=18% Similarity=0.214 Sum_probs=77.4
Q ss_pred EEEEEEecCCCCCCCCcEEEEEEEEEc--CCeeeeEEEEEcCCCCCC--CccccC--C------------cHH---hhc-
Q 019538 129 AIVFDIETTGFSRENERIIEIAFQDLL--GGENSTFQTLVNPKRQVP--NAHVHG--I------------TTD---MVC- 186 (339)
Q Consensus 129 ~vviDiETTGl~p~~~~IIEIgav~v~--~g~i~~f~~lV~P~~~i~--~~~itG--I------------t~e---~l~- 186 (339)
=++||+||.|..| .+.|++||||.++ .+....|+.+|.....+- ...-.| . +.| .+.
T Consensus 3 dlMIDlETmG~~p-~AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~ 81 (220)
T PHA02570 3 DFIIDFETFGNTP-DGAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKP 81 (220)
T ss_pred eEEEEeeccCCCC-CceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccC
Confidence 3689999999987 6889999999887 444477877775322110 000001 1 001 111
Q ss_pred CCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhc----C--CCCCC-CCceeeHHHHHHH
Q 019538 187 KPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRC----S--YEVPN-NWLFMDTLTLARE 255 (339)
Q Consensus 187 ~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~----g--l~~p~-~~~~iDtl~lar~ 255 (339)
.....++.+++.+|.+|+...........+.|-+. .||..+|...+++. + .+.|. .|..-|+..+...
T Consensus 82 s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~-sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~ 156 (220)
T PHA02570 82 SDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGN-SFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEA 156 (220)
T ss_pred CCccccHHHHHHHHHHHHHHcCCCccceeEecCCC-ccCHHHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhh
Confidence 11234589999999999997532222345666666 99999999999887 6 34442 2334565554443
No 73
>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=98.26 E-value=5.5e-05 Score=68.41 Aligned_cols=137 Identities=17% Similarity=0.228 Sum_probs=82.4
Q ss_pred CcEEEEEEecCCC----CC--CC--CcEEEEEEEEEcCCeeeeEEEEEc-CCCCCCC-ccccCCcHHhhcCCCCCCHHHH
Q 019538 127 VTAIVFDIETTGF----SR--EN--ERIIEIAFQDLLGGENSTFQTLVN-PKRQVPN-AHVHGITTDMVCKPDVPRMEDL 196 (339)
Q Consensus 127 ~~~vviDiETTGl----~p--~~--~~IIEIgav~v~~g~i~~f~~lV~-P~~~i~~-~~itGIt~e~l~~~~ap~~~ev 196 (339)
-++++||+||++. .| .. +.||+|+...- ++ ...+ .++. +.....+ ...-+. .+. ...+..+.
T Consensus 5 lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~-~~-~~~v-~~~~~~~~~~~~~~~~~~~---~v~--~~~~E~~l 76 (204)
T cd05783 5 LKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGS-DG-LKRV-LVLKREGVEGLEGLLPEGA---EVE--FFDSEKEL 76 (204)
T ss_pred ceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCC-CC-CcEE-EEEecCCcccccccCCCCC---eEE--ecCCHHHH
Confidence 3899999999742 12 22 68999998632 12 1111 1121 1111000 000010 111 22457889
Q ss_pred HHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCC---CCC----------CCceeeHHHHHHH-HH---hc
Q 019538 197 IPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYE---VPN----------NWLFMDTLTLARE-LM---KS 259 (339)
Q Consensus 197 l~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~---~p~----------~~~~iDtl~lar~-l~---~~ 259 (339)
+.+|.+++.+. .++|+||+..||+++|...+.++|+. .|. ....+|.+..... .. ..
T Consensus 77 L~~F~~~i~~~------~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~ 150 (204)
T cd05783 77 IREAFKIISEY------PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAF 150 (204)
T ss_pred HHHHHHHHhcC------CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhh
Confidence 99999999863 48999999999999999999999987 211 1246888876543 11 00
Q ss_pred CCCCCCCCCCHHHHHHHh-CC
Q 019538 260 GGSNLPSKVSLQALREYY-GI 279 (339)
Q Consensus 260 ~~~~l~~~~~L~~L~~~~-gI 279 (339)
+..++ +++|+++++.+ |.
T Consensus 151 -~~~~~-~~~L~~Va~~~lg~ 169 (204)
T cd05783 151 -GNKYR-EYTLDAVAKALLGE 169 (204)
T ss_pred -ccccc-cCcHHHHHHHhcCC
Confidence 01234 99999999866 54
No 74
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=98.23 E-value=5.6e-06 Score=77.60 Aligned_cols=164 Identities=22% Similarity=0.248 Sum_probs=94.2
Q ss_pred CcEEEEEEecCCCCCC---------------------CCcEEEEEEEEE-c-CCee-e-----eEEEEEcCCCC-CCC--
Q 019538 127 VTAIVFDIETTGFSRE---------------------NERIIEIAFQDL-L-GGEN-S-----TFQTLVNPKRQ-VPN-- 174 (339)
Q Consensus 127 ~~~vviDiETTGl~p~---------------------~~~IIEIgav~v-~-~g~i-~-----~f~~lV~P~~~-i~~-- 174 (339)
..||+||+|.||+... .-.|+|+|+..+ + ++.. . .|..++-|... ...
T Consensus 22 ~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~~ 101 (262)
T PF04857_consen 22 ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQAS 101 (262)
T ss_dssp SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEHH
T ss_pred CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecch
Confidence 5899999999998532 125999999988 3 3332 2 23333233222 111
Q ss_pred ----ccccCCcHHhhcCCCCCCHHHHH-HHHHHHHHhcC----CCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCC--
Q 019538 175 ----AHVHGITTDMVCKPDVPRMEDLI-PILLHYVKSRQ----KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNN-- 243 (339)
Q Consensus 175 ----~~itGIt~e~l~~~~ap~~~evl-~~~~~~l~~~~----~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~-- 243 (339)
-.-+|+.-+.....|.|-..... .++.+.+.-+. ....+.++||||+ -+|+.+|-+.|.. +.|..
T Consensus 102 sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~-~~Dl~~l~~~f~~---~LP~t~~ 177 (262)
T PF04857_consen 102 SLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNG-LYDLMYLYKKFIG---PLPETLE 177 (262)
T ss_dssp HHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESST-HHHHHHHHHHHTT---S--SSHH
T ss_pred hHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeCh-HhHHHHHHHHhcC---CCCCCHH
Confidence 23466666555444555322221 11112222111 0123478999999 8999999877654 33311
Q ss_pred ----------CceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCC-----------------------CCC-CCChH
Q 019538 244 ----------WLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPL-----------------------VGS-AHRAM 289 (339)
Q Consensus 244 ----------~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~-----------------------~~~-aH~Al 289 (339)
..++||..++..... . ..+|+.|++.+++.. .+. .|.|-
T Consensus 178 eF~~~~~~~FP~i~DtK~la~~~~~------~-~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAG 250 (262)
T PF04857_consen 178 EFKELLRELFPRIYDTKYLAEECPG------K-STSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAG 250 (262)
T ss_dssp HHHHHHHHHSSSEEEHHHHHTSTTT------S--SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHH
T ss_pred HHHHHHHHHCcccccHHHHHHhccc------c-ccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcc
Confidence 137899888865431 1 779999999998765 344 99999
Q ss_pred HHHHHHHHHHHH
Q 019538 290 ADVNCLSLILQR 301 (339)
Q Consensus 290 ~DA~~ta~L~~~ 301 (339)
.||++|+.+|.+
T Consensus 251 yDA~mTg~~F~~ 262 (262)
T PF04857_consen 251 YDAYMTGCVFIK 262 (262)
T ss_dssp HHHHHHHHHHHH
T ss_pred hHHHHHHHHHcC
Confidence 999999999853
No 75
>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=98.14 E-value=0.00011 Score=67.56 Aligned_cols=168 Identities=12% Similarity=0.073 Sum_probs=103.6
Q ss_pred CcEEEEEEecCC-----CCCCCCcEEEEEEEEEcCCeeee------EEEEEcCCCC-CCC-ccccCCcHHhhcCCCCCCH
Q 019538 127 VTAIVFDIETTG-----FSRENERIIEIAFQDLLGGENST------FQTLVNPKRQ-VPN-AHVHGITTDMVCKPDVPRM 193 (339)
Q Consensus 127 ~~~vviDiETTG-----l~p~~~~IIEIgav~v~~g~i~~------f~~lV~P~~~-i~~-~~itGIt~e~l~~~~ap~~ 193 (339)
.+++.+|+|+.+ .+|..|+|+.|+.+.-++..... .-.++.+... ... .....+....+. -.++.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~--~~~~E 81 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVE--VVESE 81 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEE--EeCCH
Confidence 368899999874 24678999999998554443211 1222332221 000 001111112223 34567
Q ss_pred HHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC----CC---------------C----------
Q 019538 194 EDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP----NN---------------W---------- 244 (339)
Q Consensus 194 ~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p----~~---------------~---------- 244 (339)
.+.+.+|.+++... ++.+++|||+..||+++|...+...++... .+ |
T Consensus 82 ~~LL~~f~~~i~~~----DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i 157 (231)
T cd05778 82 LELFEELIDLVRRF----DPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKI 157 (231)
T ss_pred HHHHHHHHHHHHHh----CCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEE
Confidence 88999999999976 677999999999999999888877655321 00 1
Q ss_pred ---ceeeHHHHHHHHHhcCCCCCCCCCCHHHHHH-HhCCCCCCCCCChHHHHH------HHHHHHHHHHHhh
Q 019538 245 ---LFMDTLTLARELMKSGGSNLPSKVSLQALRE-YYGIPLVGSAHRAMADVN------CLSLILQRLTFDL 306 (339)
Q Consensus 245 ---~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~-~~gI~~~~~aH~Al~DA~------~ta~L~~~l~~~l 306 (339)
..+|++.+.+... .+. +|+|++++. .+|-..+.-.+..+.+.. ...++....+.+.
T Consensus 158 ~GRi~lD~~~~~r~~~-----kl~-sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~ 223 (231)
T cd05778 158 VGRHILNVWRLMRSEL-----ALT-NYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRV 223 (231)
T ss_pred eeEEEeEhHHHHHHHc-----Ccc-cCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHH
Confidence 2468888887644 345 999999987 567655534455555542 3455555555543
No 76
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=98.09 E-value=3.3e-05 Score=69.30 Aligned_cols=182 Identities=19% Similarity=0.195 Sum_probs=114.8
Q ss_pred hhhhhhhccCccCCCcEEEEEEecCCCC--CC-------------------CCcEEEEEEEEEcC-Cee-----eeEEEE
Q 019538 113 IEQIIAENKDLAKLVTAIVFDIETTGFS--RE-------------------NERIIEIAFQDLLG-GEN-----STFQTL 165 (339)
Q Consensus 113 ~~~~~~~~~~l~~~~~~vviDiETTGl~--p~-------------------~~~IIEIgav~v~~-g~i-----~~f~~l 165 (339)
+++++..-..+-+..++|++|+|.-|.= |. .-.+||+|.-..+. |.+ +.++.-
T Consensus 10 l~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWqfN 89 (239)
T KOG0304|consen 10 LEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQFN 89 (239)
T ss_pred HHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCCCCCceeEEe
Confidence 3444443333332258999999987751 10 12599999987772 322 233332
Q ss_pred E---cCCCCCCC------ccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhc
Q 019538 166 V---NPKRQVPN------AHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRC 236 (339)
Q Consensus 166 V---~P~~~i~~------~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~ 236 (339)
. ++...+-. -.-+||.-+...+.|.. ..+..+.+..-.. ...++..+|.+.+ .+|..+|.+-+...
T Consensus 90 F~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~-~~~F~ellm~sg~---v~~~~V~WvTFhs-~YDfgYLlK~Lt~~ 164 (239)
T KOG0304|consen 90 FSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGID-IEEFAELLMTSGL---VLDENVTWVTFHS-GYDFGYLLKILTGK 164 (239)
T ss_pred cccCCchhhccchhhHHHHHHcCcCHHHHHHcCCC-HHHHHHHHHHhhh---hccCceEEEEeec-cchHHHHHHHHcCC
Confidence 2 23333222 35588888877765665 3333333332111 1225789999999 89999998877664
Q ss_pred CCCCCC----------CCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 019538 237 SYEVPN----------NWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTF 304 (339)
Q Consensus 237 gl~~p~----------~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~ 304 (339)
.++... ...++|+..+++.-.... . ..+|+.+|+.++++-.|.+|.|-+|++.|+.+|.+|.+
T Consensus 165 ~LP~~~~eF~~~v~~~fp~vYDiK~l~~~c~~~~----l-~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 165 PLPETEEEFFEIVRQLFPFVYDVKYLMKFCEGLS----L-KGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred CCcchHHHHHHHHHHHcchhhhHHHHHHhhhhhh----h-hcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 444210 013566666665432211 1 78999999999999999999999999999999999875
No 77
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=98.08 E-value=7.7e-05 Score=82.32 Aligned_cols=159 Identities=19% Similarity=0.231 Sum_probs=102.4
Q ss_pred CcEEEEEEecCCC------CCCCCcEEEEEEEEEcCCee-eeEEE-EEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHH
Q 019538 127 VTAIVFDIETTGF------SRENERIIEIAFQDLLGGEN-STFQT-LVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIP 198 (339)
Q Consensus 127 ~~~vviDiETTGl------~p~~~~IIEIgav~v~~g~i-~~f~~-lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~ 198 (339)
.+++.|||||.+. ++..++||+||.+....|.. ..+.. ++-+.. ...+.|. .+. ..++..+.+.
T Consensus 264 lrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~---c~~i~g~---~V~--~f~sE~eLL~ 335 (1054)
T PTZ00166 264 LRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE---CASIAGA---NVL--SFETEKELLL 335 (1054)
T ss_pred cEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc---cccCCCc---eEE--EeCCHHHHHH
Confidence 4899999999863 23569999999986554421 11111 111110 0112221 122 2345788999
Q ss_pred HHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCC-C--------C------------------------CCc
Q 019538 199 ILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEV-P--------N------------------------NWL 245 (339)
Q Consensus 199 ~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~-p--------~------------------------~~~ 245 (339)
.|.+++... ++.+++|||+..||+++|...+...|+.. + . ...
T Consensus 336 ~f~~~I~~~----DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~ 411 (1054)
T PTZ00166 336 AWAEFVIAV----DPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRI 411 (1054)
T ss_pred HHHHHHHhc----CCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEE
Confidence 999999976 56799999998899999999888766541 0 0 013
Q ss_pred eeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hCCCCCCC-------------------CCChHHHHHHHHHHHHHHH
Q 019538 246 FMDTLTLARELMKSGGSNLPSKVSLQALREY-YGIPLVGS-------------------AHRAMADVNCLSLILQRLT 303 (339)
Q Consensus 246 ~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~gI~~~~~-------------------aH~Al~DA~~ta~L~~~l~ 303 (339)
.+|++.+.+... .++ +|+|++++.+ +|.....- +.-.+.||..+.+|+.++.
T Consensus 412 ~iDl~~~~~~~~-----kl~-sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 412 QFDVMDLIRRDY-----KLK-SYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred EEEHHHHHHHhc-----CcC-cCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 578988887654 345 9999999884 45432211 1113688888888888864
No 78
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=97.95 E-value=0.00019 Score=62.59 Aligned_cols=148 Identities=20% Similarity=0.221 Sum_probs=99.3
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhc
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSR 207 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~ 207 (339)
+.+++|+|++|.++...+++.|++.. ++ . ..||.+. +. + .+...+.+++.+
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~i~l~~--~~--~--~~~i~~~-------------------~~--~-~~~~~l~~~l~~- 54 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALAN--GG--G--AYYIPLE-------------------LA--L-LDLAALKEWLED- 54 (178)
T ss_pred CceEEEEEEcCCCcceeeEEEEEEEe--CC--c--EEEEecc-------------------ch--H-HHHHHHHHHHhC-
Confidence 57899999999987677776666553 22 1 1233211 00 1 134446667764
Q ss_pred CCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCC----
Q 019538 208 QKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLV---- 282 (339)
Q Consensus 208 ~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~---- 282 (339)
.+...|+||+ ++|+.+|. ++|+..+. .++||+.+++.+.|... ++++++++..| ++...
T Consensus 55 ----~~~~ki~~d~-K~~~~~l~----~~gi~~~~--~~fDt~laaYLL~p~~~-----~~~l~~l~~~yl~~~~~~~~~ 118 (178)
T cd06140 55 ----EKIPKVGHDA-KRAYVALK----RHGIELAG--VAFDTMLAAYLLDPTRS-----SYDLADLAKRYLGRELPSDEE 118 (178)
T ss_pred ----CCCceeccch-hHHHHHHH----HCCCcCCC--cchhHHHHHHHcCCCCC-----CCCHHHHHHHHcCCCCcchHH
Confidence 2457899999 89998874 57877653 36999999999988642 47999997764 44311
Q ss_pred --CC-----C--C-----ChHHHHHHHHHHHHHHHHhhc-cCHHHHHHhcCCC
Q 019538 283 --GS-----A--H-----RAMADVNCLSLILQRLTFDLK-LSLCDLIERGFTP 320 (339)
Q Consensus 283 --~~-----a--H-----~Al~DA~~ta~L~~~l~~~l~-~tl~~L~~~s~~~ 320 (339)
+. . . .+..||.++..++..+..+++ ..+.+|+...+.|
T Consensus 119 ~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~l~~L~~~iE~P 171 (178)
T cd06140 119 VYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEENEQLELYYEVELP 171 (178)
T ss_pred hcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhh
Confidence 00 0 0 145567788899999998886 5788888887766
No 79
>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=97.93 E-value=0.00018 Score=68.70 Aligned_cols=127 Identities=23% Similarity=0.306 Sum_probs=84.5
Q ss_pred CcEEEEEEecCCCC-----CCCCcEEEEEEEEEcCCee----eeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHH
Q 019538 127 VTAIVFDIETTGFS-----RENERIIEIAFQDLLGGEN----STFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLI 197 (339)
Q Consensus 127 ~~~vviDiETTGl~-----p~~~~IIEIgav~v~~g~i----~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl 197 (339)
.+++.||+||.... +..++|+.|+++..+.+.. ..+..+..+. .... ...+. -.++..+.+
T Consensus 157 l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~-~~~~-------~~~v~--~~~~E~~lL 226 (325)
T PF03104_consen 157 LRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCD-SIED-------NVEVI--YFDSEKELL 226 (325)
T ss_dssp SEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSC-CTTC-------TTEEE--EESSHHHHH
T ss_pred cceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCC-CCCC-------CcEEE--EECCHHHHH
Confidence 58999999998654 5678999999887654321 2222222222 1110 11112 234578899
Q ss_pred HHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC---------------------------------CCC
Q 019538 198 PILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP---------------------------------NNW 244 (339)
Q Consensus 198 ~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p---------------------------------~~~ 244 (339)
..|.+++... ++.+++|||+..||+++|.+.+...|+... ...
T Consensus 227 ~~f~~~i~~~----dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gr 302 (325)
T PF03104_consen 227 EAFLDIIQEY----DPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSRKFSRIDIPGR 302 (325)
T ss_dssp HHHHHHHHHH----S-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCTTEEEEEETTS
T ss_pred HHHHHHHHhc----CCcEEEEecccCCCHHHHHHHHHHhCccccccccccccceeEEeecccccccCCCcceeEEEECCC
Confidence 9999999986 567999999989999999999988854420 011
Q ss_pred ceeeHHHHHHHHHhcCCCCCCCCCCHHHH
Q 019538 245 LFMDTLTLARELMKSGGSNLPSKVSLQAL 273 (339)
Q Consensus 245 ~~iDtl~lar~l~~~~~~~l~~~~~L~~L 273 (339)
..+|++.+++....- . +|+|+++
T Consensus 303 ~~~D~~~~~~~~~~l-----~-sY~L~~V 325 (325)
T PF03104_consen 303 LVLDLYRLARKDYKL-----D-SYSLDNV 325 (325)
T ss_dssp EEEEHHHHHHHHS-------S-S-SHHHH
T ss_pred hHhHHHHHHHhhCCC-----C-CCCCCCC
Confidence 368999999988743 3 8999864
No 80
>PRK05762 DNA polymerase II; Reviewed
Probab=97.93 E-value=0.00016 Score=77.71 Aligned_cols=149 Identities=13% Similarity=0.164 Sum_probs=97.4
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHh
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKS 206 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~ 206 (339)
-++++|||||++. .+|..||.....+..+ ..+.+..+.+ .+.+. ..++..+.+..|.+++.+
T Consensus 155 lrvlsfDIE~~~~----~~i~sI~~~~~~~~~v----i~ig~~~~~~--------~~~v~--~~~sE~~LL~~F~~~i~~ 216 (786)
T PRK05762 155 LKVVSLDIETSNK----GELYSIGLEGCGQRPV----IMLGPPNGEA--------LDFLE--YVADEKALLEKFNAWFAE 216 (786)
T ss_pred CeEEEEEEEEcCC----CceEEeeecCCCCCeE----EEEECCCCCC--------cceEE--EcCCHHHHHHHHHHHHHh
Confidence 4899999999863 3588888752222111 1111111100 01123 334578899999999998
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC--------------CC----------CceeeHHHHHHHHHhcCCC
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP--------------NN----------WLFMDTLTLARELMKSGGS 262 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p--------------~~----------~~~iDtl~lar~l~~~~~~ 262 (339)
. ++.+++|||+..||+++|...+..+|+... .. ...+|++.+.+.....
T Consensus 217 ~----DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~--- 289 (786)
T PRK05762 217 H----DPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWV--- 289 (786)
T ss_pred c----CCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhcc---
Confidence 6 567999999989999999999998887631 00 1268999998876422
Q ss_pred CCCCCCCHHHHHHHhCCCCCC--CC-------------------CChHHHHHHHHHHHHHH
Q 019538 263 NLPSKVSLQALREYYGIPLVG--SA-------------------HRAMADVNCLSLILQRL 302 (339)
Q Consensus 263 ~l~~~~~L~~L~~~~gI~~~~--~a-------------------H~Al~DA~~ta~L~~~l 302 (339)
++ +++|+++++.+..+... .. .-.+.||..+.+|+.++
T Consensus 290 -l~-sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 290 -FD-SFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred -CC-CCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 34 99999999875432210 11 01378999999998853
No 81
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) 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 pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=97.91 E-value=0.00042 Score=58.07 Aligned_cols=133 Identities=27% Similarity=0.371 Sum_probs=81.9
Q ss_pred EEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcC
Q 019538 129 AIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQ 208 (339)
Q Consensus 129 ~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~ 208 (339)
.+++|+|+.+..+...+|..+++..- ++ .+ ++.. . . ....+...+.+++.+
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~---~~--~i~~-----------------~--~--~~~~~~~~l~~~l~~-- 52 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATA-GE---AA--YIPD-----------------E--L--ELEEDLEALKELLED-- 52 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEEC-Cc---EE--EEEc-----------------C--C--CHHHHHHHHHHHHcC--
Confidence 57899998877754566665555421 11 11 2210 0 0 024566667788875
Q ss_pred CCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCC-----
Q 019538 209 KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLV----- 282 (339)
Q Consensus 209 ~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~----- 282 (339)
....+|+||+ +||+.+|.+ .+...+. .++||+.+++.+.|... +++|+++++.| +....
T Consensus 53 ---~~~~~v~~~~-k~d~~~L~~----~~~~~~~--~~~D~~~~ayll~~~~~-----~~~l~~l~~~~l~~~~~~~~~~ 117 (155)
T cd00007 53 ---EDITKVGHDA-KFDLVVLAR----DGIELPG--NIFDTMLAAYLLNPGEG-----SHSLDDLAKEYLGIELDKDEQI 117 (155)
T ss_pred ---CCCcEEeccH-HHHHHHHHH----CCCCCCC--CcccHHHHHHHhCCCCC-----cCCHHHHHHHHcCCCCccHHHH
Confidence 2456999999 899999854 3444432 47999999999987542 45999998876 33311
Q ss_pred -CC------CC-------ChHHHHHHHHHHHHHHHHh
Q 019538 283 -GS------AH-------RAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 283 -~~------aH-------~Al~DA~~ta~L~~~l~~~ 305 (339)
+. .. -|..||.++.+++..+..+
T Consensus 118 ~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 118 YGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred hcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 00 00 1455677777777766653
No 82
>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=97.81 E-value=0.0013 Score=65.71 Aligned_cols=156 Identities=20% Similarity=0.326 Sum_probs=100.5
Q ss_pred CcEEEEEEecCCCC---C--C--CCcEEEEEEEEEcCCee---eeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHH
Q 019538 127 VTAIVFDIETTGFS---R--E--NERIIEIAFQDLLGGEN---STFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDL 196 (339)
Q Consensus 127 ~~~vviDiETTGl~---p--~--~~~IIEIgav~v~~g~i---~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~ev 196 (339)
..++++|+||+... | . .++|+.|+.+.-+++.. ........+... +.++. +. ......+.
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~---~~--~~~~E~~l 72 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKE-----IDGVE---VY--EFNNEKEL 72 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCC-----CCCCe---EE--ecCCHHHH
Confidence 36899999997542 2 2 57899999987765431 122222222222 22221 11 11246788
Q ss_pred HHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC--------------------------------CC
Q 019538 197 IPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN--------------------------------NW 244 (339)
Q Consensus 197 l~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~--------------------------------~~ 244 (339)
+..|.+++... ++.+++|||...||+++|...+...++.... ..
T Consensus 73 L~~f~~~i~~~----dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ 148 (471)
T smart00486 73 LKAFLEFIKKY----DPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGR 148 (471)
T ss_pred HHHHHHHHHHh----CCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccE
Confidence 99999999875 4579999999779999999988876653320 12
Q ss_pred ceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCC-CCCCC-------------------CCChHHHHHHHHHHHHHH
Q 019538 245 LFMDTLTLARELMKSGGSNLPSKVSLQALREYYGI-PLVGS-------------------AHRAMADVNCLSLILQRL 302 (339)
Q Consensus 245 ~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI-~~~~~-------------------aH~Al~DA~~ta~L~~~l 302 (339)
..+|++...+..+. ++ +++|+.+++++.- ....- ....+.||..+.+|+.++
T Consensus 149 ~~~Dl~~~~~~~~k-----l~-~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 149 LVIDLYNLYKNKLK-----LP-SYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEEhHHHHHHHhC-----cc-cCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999988764 34 9999999876532 11100 011256888888888775
No 83
>PHA02528 43 DNA polymerase; Provisional
Probab=97.76 E-value=0.00098 Score=72.25 Aligned_cols=159 Identities=18% Similarity=0.285 Sum_probs=99.1
Q ss_pred CcEEEEEEecCC----CCCC--CCcEEEEEEEEEcCCeeeeEEEEEcCC-CC-------CCCccccCCcHHhhcCCCCCC
Q 019538 127 VTAIVFDIETTG----FSRE--NERIIEIAFQDLLGGENSTFQTLVNPK-RQ-------VPNAHVHGITTDMVCKPDVPR 192 (339)
Q Consensus 127 ~~~vviDiETTG----l~p~--~~~IIEIgav~v~~g~i~~f~~lV~P~-~~-------i~~~~itGIt~e~l~~~~ap~ 192 (339)
-+++.|||||+. .+|. .++|+.||...-.+. .+..+.-+. .+ .++....++ .+. ..++
T Consensus 106 lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~---~~~v~~~~~~~~~~~~~~~~~~~~~~~v---~~~--~~~s 177 (881)
T PHA02528 106 IRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDD---RFYVFDLGSVEEWDAKGDEVPQEILDKV---VYM--PFDT 177 (881)
T ss_pred ccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCC---EEEEEEecCcccccccCCcccccccCCe---eEE--EcCC
Confidence 489999999975 2344 568999998533332 222222111 00 000001111 111 1345
Q ss_pred HHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHh-cCCCC----C-----------------------CCC
Q 019538 193 MEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSR-CSYEV----P-----------------------NNW 244 (339)
Q Consensus 193 ~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r-~gl~~----p-----------------------~~~ 244 (339)
..+.+..|.+|+... ++.+++|||+..||+++|...+.+ .|... . ...
T Consensus 178 E~eLL~~F~~~i~~~----DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GR 253 (881)
T PHA02528 178 EREMLLEYINFWEEN----TPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGI 253 (881)
T ss_pred HHHHHHHHHHHHHHh----CCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcce
Confidence 789999999999876 567999999999999999888874 35331 0 001
Q ss_pred ceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hCCCCCC----------------CCCChHHHHHHHHHHHHH
Q 019538 245 LFMDTLTLARELMKSGGSNLPSKVSLQALREY-YGIPLVG----------------SAHRAMADVNCLSLILQR 301 (339)
Q Consensus 245 ~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~gI~~~~----------------~aH~Al~DA~~ta~L~~~ 301 (339)
..+|.+.+++.+.- ..++ +++|++++++ +|..... -++-.+.||..+.+|+.+
T Consensus 254 v~lD~~dl~k~~~~---~~l~-SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 254 SILDYLDLYKKFTF---TNQP-SYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred EEEeHHHHHHHhhh---cccc-cCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 25678877776421 1345 9999999984 7754331 012247899999999988
No 84
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved 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.
Probab=97.73 E-value=0.00065 Score=60.77 Aligned_cols=145 Identities=20% Similarity=0.154 Sum_probs=86.3
Q ss_pred CcEEEEEEecCCCCC----CCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSR----ENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 127 ~~~vviDiETTGl~p----~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
..+|+||+|+++... ..-.+|||+.- +. -.+|++.. + +...-+...+.+.+
T Consensus 22 ~~vig~D~Ew~~~~~~~~~~~v~LiQiat~----~~----~~lid~~~---------~--------~~~~~~~~~~~L~~ 76 (193)
T cd06146 22 GRVVGIDSEWKPSFLGDSDPRVAILQLATE----DE----VFLLDLLA---------L--------ENLESEDWDRLLKR 76 (193)
T ss_pred CCEEEEECccCCCccCCCCCCceEEEEecC----CC----EEEEEchh---------c--------cccchHHHHHHHHH
Confidence 589999999986542 23457777731 11 12222110 0 00001223334556
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCC------CCCCCCCHHHHHHH
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGS------NLPSKVSLQALREY 276 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~------~l~~~~~L~~L~~~ 276 (339)
++.. .+.+.|||++ .+|..+|.+.+...+-.......++|+..+++.+...... ... .++|.+|++.
T Consensus 77 ll~d-----~~i~KVg~~~-~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~-~~sL~~l~~~ 149 (193)
T cd06146 77 LFED-----PDVLKLGFGF-KQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSK-TKGLADLVQE 149 (193)
T ss_pred HhCC-----CCeeEEEech-HHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcc-cCCHHHHHHH
Confidence 6664 3567899999 8999999765432210000113589999999877643110 012 7899999876
Q ss_pred h-CCCCCC---------------CCCChHHHHHHHHHHHHHHH
Q 019538 277 Y-GIPLVG---------------SAHRAMADVNCLSLILQRLT 303 (339)
Q Consensus 277 ~-gI~~~~---------------~aH~Al~DA~~ta~L~~~l~ 303 (339)
+ |.+.+. .-+-|..||+.+..||.+|.
T Consensus 150 ~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 150 VLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4 543221 23558999999999999886
No 85
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=97.62 E-value=0.00064 Score=69.97 Aligned_cols=150 Identities=23% Similarity=0.289 Sum_probs=103.6
Q ss_pred EEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcC
Q 019538 129 AIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQ 208 (339)
Q Consensus 129 ~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~ 208 (339)
.+++|+||+|+++....++.+++..-. ..++..+. ++ +..-++...+..|+..
T Consensus 24 ~~a~~~et~~l~~~~~~lvg~s~~~~~----~~~yi~~~----------~~-----------~~~~~~~~~l~~~l~~-- 76 (593)
T COG0749 24 NIAFDTETDGLDPHGADLVGLSVASEE----EAAYIPLL----------HG-----------PEQLNVLAALKPLLED-- 76 (593)
T ss_pred cceeeccccccCcccCCeeEEEeeccc----cceeEeec----------cc-----------hhhhhhHHHHHHHhhC--
Confidence 399999999999988888888876532 11111111 01 1122377788889985
Q ss_pred CCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCC-----
Q 019538 209 KPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLV----- 282 (339)
Q Consensus 209 ~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~----- 282 (339)
.....|+||. +||..+|. ++|+. + ....|||.+++.+.+..+ .+.++.|++.| +....
T Consensus 77 ---~~~~kv~~~~-K~d~~~l~----~~Gi~-~--~~~~DtmlasYll~~~~~-----~~~~~~l~~r~l~~~~~~~~~i 140 (593)
T COG0749 77 ---EGIKKVGQNL-KYDYKVLA----NLGIE-P--GVAFDTMLASYLLNPGAG-----AHNLDDLAKRYLGLETITFEDI 140 (593)
T ss_pred ---cccchhcccc-chhHHHHH----HcCCc-c--cchHHHHHHHhccCcCcC-----cCCHHHHHHHhcCCccchhHHh
Confidence 3456899999 89998884 56744 2 247899999999887654 78999998866 22111
Q ss_pred ---C-------------CCCChHHHHHHHHHHHHHHHHhhc--cCHHHHHHhcCCCC
Q 019538 283 ---G-------------SAHRAMADVNCLSLILQRLTFDLK--LSLCDLIERGFTPS 321 (339)
Q Consensus 283 ---~-------------~aH~Al~DA~~ta~L~~~l~~~l~--~tl~~L~~~s~~~~ 321 (339)
+ ..-.+..||..+.+++..+..++. ..+.+|+...+.|-
T Consensus 141 ~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L~~l~~~iE~Pl 197 (593)
T COG0749 141 AGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPVLLELYEEIEMPL 197 (593)
T ss_pred hccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHhccH
Confidence 0 122357899999999999998765 34577887776663
No 86
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved 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. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=97.59 E-value=0.00067 Score=58.88 Aligned_cols=130 Identities=24% Similarity=0.193 Sum_probs=85.2
Q ss_pred CcEEEEEEecCCCCC----CCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSR----ENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLH 202 (339)
Q Consensus 127 ~~~vviDiETTGl~p----~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~ 202 (339)
..+|+||+|+++... ..-.+|+|+. ++ .-.++++.. .......|.+
T Consensus 18 ~~~ig~D~E~~~~~~~~~~~~~~liQl~~----~~----~~~l~~~~~----------------------~~~~~~~l~~ 67 (170)
T cd06141 18 EKVVGFDTEWRPSFRKGKRNKVALLQLAT----ES----RCLLFQLAH----------------------MDKLPPSLKQ 67 (170)
T ss_pred CCEEEEeCccCCccCCCCCCCceEEEEec----CC----cEEEEEhhh----------------------hhcccHHHHH
Confidence 589999999998754 2345677772 11 122222210 0112234556
Q ss_pred HHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCC
Q 019538 203 YVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPL 281 (339)
Q Consensus 203 ~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~ 281 (339)
++.. .+...|+|++ ++|+.+|.+ .+|+... .++|++.+++.+.+... ..+|.+|++.+ |+..
T Consensus 68 ll~~-----~~i~kv~~~~-k~D~~~L~~---~~g~~~~---~~~Dl~~aa~ll~~~~~-----~~~l~~l~~~~l~~~~ 130 (170)
T cd06141 68 LLED-----PSILKVGVGI-KGDARKLAR---DFGIEVR---GVVDLSHLAKRVGPRRK-----LVSLARLVEEVLGLPL 130 (170)
T ss_pred HhcC-----CCeeEEEeee-HHHHHHHHh---HcCCCCC---CeeeHHHHHHHhCCCcC-----CccHHHHHHHHcCccc
Confidence 7764 3567899999 899998854 4566642 35999999998876531 46999998875 5543
Q ss_pred C--C---------------CCCChHHHHHHHHHHHHHHH
Q 019538 282 V--G---------------SAHRAMADVNCLSLILQRLT 303 (339)
Q Consensus 282 ~--~---------------~aH~Al~DA~~ta~L~~~l~ 303 (339)
. . .-|-|..||..+..||.+|.
T Consensus 131 ~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 131 SKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3 1 23558999999999998875
No 87
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=97.57 E-value=4.1e-05 Score=80.49 Aligned_cols=170 Identities=21% Similarity=0.219 Sum_probs=109.5
Q ss_pred CcEEEEEEecCCCCCCCCc----------------EEEEEEEEEcC-Ce-eeeEEEEEcCCCCCCC--ccccCCcHHhhc
Q 019538 127 VTAIVFDIETTGFSRENER----------------IIEIAFQDLLG-GE-NSTFQTLVNPKRQVPN--AHVHGITTDMVC 186 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~----------------IIEIgav~v~~-g~-i~~f~~lV~P~~~i~~--~~itGIt~e~l~ 186 (339)
..+|++|-|..-+.++..| +..|++|+-.| ++ +.--+-||--+..+.+ ++.+||.+.||+
T Consensus 910 g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~PGDLD 989 (1118)
T KOG1275|consen 910 GDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKPGDLD 989 (1118)
T ss_pred CceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCccccC
Confidence 4799999998877643322 22333333321 01 1223345554445555 899999999998
Q ss_pred C----CCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCC
Q 019538 187 K----PDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGS 262 (339)
Q Consensus 187 ~----~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~ 262 (339)
. ....+++-+..++.-.+.- .+++|||.. .-|...| ++..|.. .++||..+.+. +...
T Consensus 990 p~~S~K~Lt~lK~~Y~Kl~~Li~~------GviFVGHGL-~nDFrvI-------Ni~Vp~~-QiiDTv~lf~~--~s~R- 1051 (1118)
T KOG1275|consen 990 PTTSEKRLTTLKVLYLKLRLLIQR------GVIFVGHGL-QNDFRVI-------NIHVPEE-QIIDTVTLFRL--GSQR- 1051 (1118)
T ss_pred CccCcceehhHHHHHHHHHHHHHc------CcEEEcccc-cccceEE-------EEecChh-hheeeeEEEec--cccc-
Confidence 3 1122355566666666653 479999999 8888665 4555533 58899877653 3221
Q ss_pred CCCCCCCHHHHHHH-hCCCCCCCCCChHHHHHHHHHHHHHHHHh-----hccCHHHHHHhcC
Q 019538 263 NLPSKVSLQALREY-YGIPLVGSAHRAMADVNCLSLILQRLTFD-----LKLSLCDLIERGF 318 (339)
Q Consensus 263 ~l~~~~~L~~L~~~-~gI~~~~~aH~Al~DA~~ta~L~~~l~~~-----l~~tl~~L~~~s~ 318 (339)
..+|..|+.+ +|-.....+|+.++||+.+..||++.++- ++..+..+|+...
T Consensus 1052 ----~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~lkeq~~~~~~l~niye~gr 1109 (1118)
T KOG1275|consen 1052 ----MLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLKLKEQGKLESELRNIYECGR 1109 (1118)
T ss_pred ----EEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhhcCc
Confidence 6789999865 56444446999999999999999886652 2356777776653
No 88
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.57 E-value=0.00073 Score=65.57 Aligned_cols=135 Identities=27% Similarity=0.331 Sum_probs=88.7
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHh
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKS 206 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~ 206 (339)
..+|+||+|+.|..+..+++ +.|-+.+|+ ...+|+|-.. + . +.++|. .++..
T Consensus 17 ~~~iAiDTEf~r~~t~~p~L---cLIQi~~~e---~~~lIdpl~~--------~-----~--d~~~l~-------~Ll~d 68 (361)
T COG0349 17 SKAIAIDTEFMRLRTYYPRL---CLIQISDGE---GASLIDPLAG--------I-----L--DLPPLV-------ALLAD 68 (361)
T ss_pred CCceEEecccccccccCCce---EEEEEecCC---CceEeccccc--------c-----c--ccchHH-------HHhcC
Confidence 46999999999999877753 333332221 1445555321 0 1 233333 33433
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hCCCCCCC-
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY-YGIPLVGS- 284 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~gI~~~~~- 284 (339)
...+-|-|++ .||+.+|.+.| |+.+ .+++||...++.. +.. .+++|++|++. +|+..+..
T Consensus 69 -----~~v~KIfHaa-~~DL~~l~~~~---g~~p---~plfdTqiAa~l~-g~~-----~~~gl~~Lv~~ll~v~ldK~~ 130 (361)
T COG0349 69 -----PNVVKIFHAA-RFDLEVLLNLF---GLLP---TPLFDTQIAAKLA-GFG-----TSHGLADLVEELLGVELDKSE 130 (361)
T ss_pred -----Cceeeeeccc-cccHHHHHHhc---CCCC---CchhHHHHHHHHh-CCc-----ccccHHHHHHHHhCCcccccc
Confidence 4578899999 89999998754 4442 2489999888754 322 18999999864 57665521
Q ss_pred --------------CCChHHHHHHHHHHHHHHHHhhc
Q 019538 285 --------------AHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 285 --------------aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
---|..|+..+..|+.+|.+.+.
T Consensus 131 q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 131 QRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred cccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11268999999999999998875
No 89
>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=97.52 E-value=0.0011 Score=61.07 Aligned_cols=141 Identities=21% Similarity=0.261 Sum_probs=90.5
Q ss_pred cEEEEEEecCCCCC-CCCcEEEEEEEEEcC----Ce------eeeEEEEEcCCCC-CCC---ccccCCcHHhhcCCCCCC
Q 019538 128 TAIVFDIETTGFSR-ENERIIEIAFQDLLG----GE------NSTFQTLVNPKRQ-VPN---AHVHGITTDMVCKPDVPR 192 (339)
Q Consensus 128 ~~vviDiETTGl~p-~~~~IIEIgav~v~~----g~------i~~f~~lV~P~~~-i~~---~~itGIt~e~l~~~~ap~ 192 (339)
+++.+-+-|.--.. ...||+.|+++..++ +. ...+...++|... .++ ...-.-....+. -.++
T Consensus 4 ~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~--~~~~ 81 (234)
T cd05776 4 TVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVR--IFEN 81 (234)
T ss_pred EEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEE--EeCC
Confidence 45566666643222 258899999875431 11 1445566677543 222 111011111122 2345
Q ss_pred HHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCC------------CC--------------CCce
Q 019538 193 MEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEV------------PN--------------NWLF 246 (339)
Q Consensus 193 ~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~------------p~--------------~~~~ 246 (339)
..+.+..|..++... ++.++||||...||+++|.+.+...|++. |. ...+
T Consensus 82 E~~LL~~f~~~i~~~----DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~ 157 (234)
T cd05776 82 ERALLNFFLAKLQKI----DPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLL 157 (234)
T ss_pred HHHHHHHHHHHHhhc----CCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchh
Confidence 788999999999976 67899999998999999999998877652 00 1125
Q ss_pred eeHHHHHHHHHhcCCCCCCCCCCHHHHHH-HhCCC
Q 019538 247 MDTLTLARELMKSGGSNLPSKVSLQALRE-YYGIP 280 (339)
Q Consensus 247 iDtl~lar~l~~~~~~~l~~~~~L~~L~~-~~gI~ 280 (339)
+|++..++.+... . +|+|+++++ .+|..
T Consensus 158 ~D~~~~~k~~~~~-----~-sY~L~~va~~~Lg~~ 186 (234)
T cd05776 158 CDTYLSAKELIRC-----K-SYDLTELSQQVLGIE 186 (234)
T ss_pred hccHHHHHHHhCC-----C-CCChHHHHHHHhCcC
Confidence 7899999887642 3 999999988 56753
No 90
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved 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. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=97.51 E-value=0.0026 Score=55.18 Aligned_cols=142 Identities=25% Similarity=0.260 Sum_probs=90.1
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhc
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSR 207 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~ 207 (339)
..+++|+|+.+..+...++.-++...- +. . .++.+. . . .+...|.+++.+
T Consensus 13 ~~l~~~~e~~~~~~~~~~~~~i~l~~~--~~--~--~~i~~~----------------~------~-~~~~~l~~ll~~- 62 (178)
T cd06142 13 GVIAVDTEFMRLNTYYPRLCLIQISTG--GE--V--YLIDPL----------------A------I-GDLSPLKELLAD- 62 (178)
T ss_pred CeEEEECCccCCCcCCCceEEEEEeeC--CC--E--EEEeCC----------------C------c-ccHHHHHHHHcC-
Confidence 589999998776654455555554421 11 1 122210 0 1 133345566764
Q ss_pred CCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCC----
Q 019538 208 QKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLV---- 282 (339)
Q Consensus 208 ~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~---- 282 (339)
.....|+||+ ++|+..|.+. +|+. +. .++|++.+++.+.|.. +.+|+++++.| |+...
T Consensus 63 ----~~i~kv~~d~-K~~~~~L~~~---~gi~-~~--~~~D~~laayLl~p~~------~~~l~~l~~~~l~~~~~~~~~ 125 (178)
T cd06142 63 ----PNIVKVFHAA-REDLELLKRD---FGIL-PQ--NLFDTQIAARLLGLGD------SVGLAALVEELLGVELDKGEQ 125 (178)
T ss_pred ----CCceEEEecc-HHHHHHHHHH---cCCC-CC--CcccHHHHHHHhCCCc------cccHHHHHHHHhCCCCCcccc
Confidence 3467999999 8999888542 2766 32 4699999999887753 45999998754 65411
Q ss_pred -CC----------CCChHHHHHHHHHHHHHHHHhhc-cCHHHHHHh
Q 019538 283 -GS----------AHRAMADVNCLSLILQRLTFDLK-LSLCDLIER 316 (339)
Q Consensus 283 -~~----------aH~Al~DA~~ta~L~~~l~~~l~-~tl~~L~~~ 316 (339)
+. .+.|..||.++.+++..+..+++ ..+.+|++.
T Consensus 126 ~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~~L~~~ 171 (178)
T cd06142 126 RSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEE 171 (178)
T ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcHHHHHH
Confidence 00 01366778899999999998886 556777653
No 91
>PRK10829 ribonuclease D; Provisional
Probab=97.47 E-value=0.0041 Score=61.27 Aligned_cols=132 Identities=20% Similarity=0.190 Sum_probs=87.6
Q ss_pred CcEEEEEEecCCCCCCCC--cEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENE--RIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~--~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
...++||+|+.+.....+ .+|+|+. ++ -..+|+|-. ... +..|.+++
T Consensus 22 ~~~lalDtEf~~~~ty~~~l~LiQl~~----~~----~~~LiD~l~-------------------~~d----~~~L~~ll 70 (373)
T PRK10829 22 FPAIALDTEFVRTRTYYPQLGLIQLYD----GE----QLSLIDPLG-------------------ITD----WSPFKALL 70 (373)
T ss_pred CCeEEEecccccCccCCCceeEEEEec----CC----ceEEEecCC-------------------ccc----hHHHHHHH
Confidence 589999999988765443 3556551 22 124555431 111 23455666
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHH-HhCCCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALRE-YYGIPLVG 283 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~-~~gI~~~~ 283 (339)
.+ .+.+.|.|++ .+|+.+|.+ ..|+.+ ..++||..+++.+--.. ..+|..|++ ++|+..+.
T Consensus 71 ~~-----~~ivKV~H~~-~~Dl~~l~~---~~g~~p---~~~fDTqiaa~~lg~~~------~~gl~~Lv~~~lgv~ldK 132 (373)
T PRK10829 71 RD-----PQVTKFLHAG-SEDLEVFLN---AFGELP---QPLIDTQILAAFCGRPL------SCGFASMVEEYTGVTLDK 132 (373)
T ss_pred cC-----CCeEEEEeCh-HhHHHHHHH---HcCCCc---CCeeeHHHHHHHcCCCc------cccHHHHHHHHhCCccCc
Confidence 65 3567799999 999999855 346542 24899998887553211 679999976 56765441
Q ss_pred ---------------CCCChHHHHHHHHHHHHHHHHhhc
Q 019538 284 ---------------SAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 284 ---------------~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
.-+-|..|+..+..||.+|..++.
T Consensus 133 ~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 133 SESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 234479999999999999988775
No 92
>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=97.42 E-value=0.0026 Score=64.33 Aligned_cols=122 Identities=15% Similarity=0.119 Sum_probs=84.3
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCee-eeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHh
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGEN-STFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKS 206 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i-~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~ 206 (339)
..++||+||+ |...-...+|++..+++.. ..|..++... .....+++.+|.+|+..
T Consensus 285 ~~~ffDiEt~---P~~~~~yL~G~~~~~~~~~~~~~~~fla~~--------------------~~~E~~~~~~f~~~l~~ 341 (457)
T TIGR03491 285 GELIFDIESD---PDENLDYLHGFLVVDKGQENEKYRPFLAED--------------------PNTEELAWQQFLQLLQS 341 (457)
T ss_pred ccEEEEecCC---CCCCCceEEEEEEecCCCCCcceeeeecCC--------------------chHHHHHHHHHHHHHHH
Confidence 5789999998 4445577888877665432 2354444321 12246788999999987
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC----CCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCC
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP----NNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLV 282 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p----~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~ 282 (339)
+ .+..++.||. |....|++.+.++|.... ....++|.....+..+-- ..+ +++|+.++.++|..-.
T Consensus 342 ~----~~~~i~hY~~--~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~---p~~-sysLK~v~~~lg~~~~ 411 (457)
T TIGR03491 342 Y----PDAPIYHYGE--TEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWIL---PIE-SYSLKSIARWLGFEWR 411 (457)
T ss_pred C----CCCeEEeeCH--HHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEEC---CCC-CCCHHHHHHHhCcccC
Confidence 5 2347788885 999999999999887631 111579999887765322 123 8999999999998654
No 93
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=97.39 E-value=0.0075 Score=51.38 Aligned_cols=134 Identities=27% Similarity=0.346 Sum_probs=83.8
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhc
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSR 207 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~ 207 (339)
..+++|+|+++..+...++..++... .++ .++.... . ...+....+.+++..
T Consensus 22 ~~l~~~~e~~~~~~~~~~~~~l~l~~-~~~---~~~i~~~---------------------~--~~~~~~~~l~~~l~~- 73 (172)
T smart00474 22 GEVALDTETTGLNSYSGKLVLIQISV-TGE---GAFIIDP---------------------L--ALGDDLEILKDLLED- 73 (172)
T ss_pred CeEEEeccccCCccCCCCEEEEEEeE-cCC---ceEEEEe---------------------c--cchhhHHHHHHHhcC-
Confidence 58899999887765455665555542 111 1111110 0 012224446667764
Q ss_pred CCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCCC---
Q 019538 208 QKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLVG--- 283 (339)
Q Consensus 208 ~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~~--- 283 (339)
.....|+||. ++|+.+|. ++|+..+ + ++||+.+++.+.|... ..+|+.+++.| |...+.
T Consensus 74 ----~~~~kv~~d~-k~~~~~L~----~~gi~~~-~--~~D~~laayll~p~~~-----~~~l~~l~~~~l~~~~~~~~~ 136 (172)
T smart00474 74 ----ETITKVGHNA-KFDLHVLA----RFGIELE-N--IFDTMLAAYLLLGGPS-----KHGLATLLKEYLGVELDKEEQ 136 (172)
T ss_pred ----CCceEEEech-HHHHHHHH----HCCCccc-c--hhHHHHHHHHHcCCCC-----cCCHHHHHHHHhCCCCCcccC
Confidence 3467999999 89999885 3677754 2 3999999998887542 46999998765 554221
Q ss_pred C--------CC----ChHHHHHHHHHHHHHHHHhh
Q 019538 284 S--------AH----RAMADVNCLSLILQRLTFDL 306 (339)
Q Consensus 284 ~--------aH----~Al~DA~~ta~L~~~l~~~l 306 (339)
. .. .|..||.++.+|+..+..++
T Consensus 137 ~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 137 KSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 01 25667888888888887664
No 94
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=97.36 E-value=0.0059 Score=60.09 Aligned_cols=132 Identities=23% Similarity=0.168 Sum_probs=85.8
Q ss_pred CcEEEEEEecCCCCCCCC--cEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSRENE--RIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~--~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
..+|+||+|+.......+ .+|+|+. ++. ..+|+|-. . . .+..|.+++
T Consensus 18 ~~~ia~DtE~~~~~~y~~~l~LiQia~----~~~----~~liD~~~------------------~-~----~~~~L~~lL 66 (367)
T TIGR01388 18 FPFVALDTEFVRERTFWPQLGLIQVAD----GEQ----LALIDPLV------------------I-I----DWSPLKELL 66 (367)
T ss_pred CCEEEEeccccCCCCCCCcceEEEEee----CCe----EEEEeCCC------------------c-c----cHHHHHHHH
Confidence 479999999987764433 3556653 221 23555421 0 0 123455566
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLVG 283 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~~ 283 (339)
.+ .+.+.|+|++ ++|+.+|.+ .+...|. .++||+..++.+.+.. ..+|..|++.| |+..+.
T Consensus 67 ~d-----~~i~KV~h~~-k~Dl~~L~~----~~~~~~~--~~fDtqlAa~lL~~~~------~~~l~~Lv~~~Lg~~l~K 128 (367)
T TIGR01388 67 RD-----ESVVKVLHAA-SEDLEVFLN----LFGELPQ--PLFDTQIAAAFCGFGM------SMGYAKLVQEVLGVELDK 128 (367)
T ss_pred CC-----CCceEEEeec-HHHHHHHHH----HhCCCCC--CcccHHHHHHHhCCCC------CccHHHHHHHHcCCCCCc
Confidence 64 3467899999 899998854 2333343 4799999998876543 56899997654 665431
Q ss_pred C------CC---------ChHHHHHHHHHHHHHHHHhhc
Q 019538 284 S------AH---------RAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 284 ~------aH---------~Al~DA~~ta~L~~~l~~~l~ 307 (339)
. .. -|..||.++..++..|..++.
T Consensus 129 ~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 129 SESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred ccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 02 378899999999999988775
No 95
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved 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. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=97.33 E-value=0.0023 Score=55.37 Aligned_cols=130 Identities=23% Similarity=0.179 Sum_probs=82.8
Q ss_pred CcEEEEEEecCCCCCCC--CcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFSREN--ERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYV 204 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~--~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l 204 (339)
..+|+||+|+....... -.++||+.- ++.+ .++++.. + +. ....+.+++
T Consensus 13 ~~~ig~D~E~~~~~~~~~~~~liQl~~~---~~~~----~l~d~~~--------------~---~~-----~~~~L~~lL 63 (161)
T cd06129 13 GDVIAFDMEWPPGRRYYGEVALIQLCVS---EEKC----YLFDPLS--------------L---SV-----DWQGLKMLL 63 (161)
T ss_pred CCEEEEECCccCCCCCCCceEEEEEEEC---CCCE----EEEeccc--------------C---cc-----CHHHHHHHh
Confidence 57999999998765432 335666542 1211 2222210 0 10 123345566
Q ss_pred HhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCCC
Q 019538 205 KSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLVG 283 (339)
Q Consensus 205 ~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~~ 283 (339)
.+ .+.+.|+|++ ..|...|.+ .+|+... .++|+..+++.+.+.. +.+|+++++.| |+..+.
T Consensus 64 ~d-----~~i~Kvg~~~-k~D~~~L~~---~~gi~~~---~~~D~~~aa~ll~~~~------~~~L~~l~~~~lg~~l~K 125 (161)
T cd06129 64 EN-----PSIVKALHGI-EGDLWKLLR---DFGEKLQ---RLFDTTIAANLKGLPE------RWSLASLVEHFLGKTLDK 125 (161)
T ss_pred CC-----CCEEEEEecc-HHHHHHHHH---HcCCCcc---cHhHHHHHHHHhCCCC------CchHHHHHHHHhCCCCCc
Confidence 64 3567899999 899988854 2566542 2599999988775432 66999998865 654331
Q ss_pred ---------------CCCChHHHHHHHHHHHHHHH
Q 019538 284 ---------------SAHRAMADVNCLSLILQRLT 303 (339)
Q Consensus 284 ---------------~aH~Al~DA~~ta~L~~~l~ 303 (339)
.-|-|..||+.+..||.+|.
T Consensus 126 ~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 126 SISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred cceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 24558999999999999875
No 96
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=97.07 E-value=0.011 Score=65.61 Aligned_cols=161 Identities=20% Similarity=0.232 Sum_probs=97.5
Q ss_pred cEEEEEEecCCCC-----CCCCcEEEEEEEEEcCCe-e----------eeEEEEEcCCCCCCCccccCCcHHhhcCCCCC
Q 019538 128 TAIVFDIETTGFS-----RENERIIEIAFQDLLGGE-N----------STFQTLVNPKRQVPNAHVHGITTDMVCKPDVP 191 (339)
Q Consensus 128 ~~vviDiETTGl~-----p~~~~IIEIgav~v~~g~-i----------~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap 191 (339)
++++||+|||-+. ...|+|.=|+...--.|. | +-|..-=+ .+.-|-- .+- +.+
T Consensus 247 ~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPK-------pE~eG~F--~v~--Ne~ 315 (2173)
T KOG1798|consen 247 RVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPK-------PEYEGPF--CVF--NEP 315 (2173)
T ss_pred eEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCc-------cccccce--EEe--cCC
Confidence 7999999999874 235788888765311121 1 11111111 1111110 111 345
Q ss_pred CHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC------------CCceeeHHHHHHHHHhc
Q 019538 192 RMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN------------NWLFMDTLTLARELMKS 259 (339)
Q Consensus 192 ~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~------------~~~~iDtl~lar~l~~~ 259 (339)
....++.+|.+.+.+. .+.++|++|+--||++|+.+....+|+.+.. .-++.+-|..+++. ..
T Consensus 316 dEv~Ll~RfFeHiq~~----kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWV-KR 390 (2173)
T KOG1798|consen 316 DEVGLLQRFFEHIQEV----KPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWV-KR 390 (2173)
T ss_pred cHHHHHHHHHHHHHhc----CCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhh-hh
Confidence 5667888998888865 5679999999778999999999999987531 11223334334332 22
Q ss_pred CCCCCC-CCCCHHHHHH-HhCCCCC-------------C---CCCChHHHHHHHHHHHHHHHHh
Q 019538 260 GGSNLP-SKVSLQALRE-YYGIPLV-------------G---SAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 260 ~~~~l~-~~~~L~~L~~-~~gI~~~-------------~---~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
. ..+| |+.+|.++.+ .+|.++. . -+--..+||.+|..||.+....
T Consensus 391 D-SYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP 453 (2173)
T KOG1798|consen 391 D-SYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP 453 (2173)
T ss_pred c-ccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh
Confidence 2 1233 5899999965 4553221 1 2344589999999999887553
No 97
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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 conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=97.00 E-value=0.016 Score=51.93 Aligned_cols=97 Identities=23% Similarity=0.160 Sum_probs=65.5
Q ss_pred HHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCC---CCCCCCCHHHHH
Q 019538 198 PILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGS---NLPSKVSLQALR 274 (339)
Q Consensus 198 ~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~---~l~~~~~L~~L~ 274 (339)
..+.+++.+ .+...|+|++ ++|..+|.+ .+|+... .++||+.+++.+.+.... ... ..+|..++
T Consensus 55 ~~L~~iLe~-----~~i~Kv~h~~-k~D~~~L~~---~~gi~~~---~~fDt~iA~~lL~~~~~~~~~~~~-~~~L~~l~ 121 (197)
T cd06148 55 NGLKDILES-----KKILKVIHDC-RRDSDALYH---QYGIKLN---NVFDTQVADALLQEQETGGFNPDR-VISLVQLL 121 (197)
T ss_pred HHHHHHhcC-----CCccEEEEec-hhHHHHHHH---hcCcccc---ceeeHHHHHHHHHHHhcCCccccc-cccHHHHH
Confidence 445556664 3467899999 899988743 4566542 259999988888764310 011 35888887
Q ss_pred HHh-CCCCC-----------------------CCCCChHHHHHHHHHHHHHHHHhhc
Q 019538 275 EYY-GIPLV-----------------------GSAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 275 ~~~-gI~~~-----------------------~~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
+.| |++.. ..-.-|..||..+..|+..|..++.
T Consensus 122 ~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 122 DKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALI 178 (197)
T ss_pred HHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 654 55431 0123478999999999999999886
No 98
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.79 E-value=0.0026 Score=69.26 Aligned_cols=108 Identities=19% Similarity=0.126 Sum_probs=76.6
Q ss_pred HHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHH
Q 019538 193 MEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQA 272 (339)
Q Consensus 193 ~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~ 272 (339)
...++..|.+|+.. ....+|+||+ +||+.+|. ++|+.... .++||+..++.+.+.. ..+|++
T Consensus 363 ~~~~~~~l~~~l~~-----~~~~~v~~n~-K~d~~~l~----~~gi~~~~--~~~Dt~la~yll~~~~------~~~l~~ 424 (887)
T TIGR00593 363 TILTDDKFARWLLN-----EQIKKIGHDA-KFLMHLLK----REGIELGG--VIFDTMLAAYLLDPAQ------VSTLDT 424 (887)
T ss_pred hHHHHHHHHHHHhC-----CCCcEEEeeH-HHHHHHHH----hCCCCCCC--cchhHHHHHHHcCCCC------CCCHHH
Confidence 34566778888875 3456899999 89999984 57887653 4799999999998754 459999
Q ss_pred HHHHh-CCCC---C---CC------------CCChHHHHHHHHHHHHHHHHhhc-cCHHHHHHhcC
Q 019538 273 LREYY-GIPL---V---GS------------AHRAMADVNCLSLILQRLTFDLK-LSLCDLIERGF 318 (339)
Q Consensus 273 L~~~~-gI~~---~---~~------------aH~Al~DA~~ta~L~~~l~~~l~-~tl~~L~~~s~ 318 (339)
++..| +... . +. ...|..||.++.+|+..+..++. ..+.+|+...+
T Consensus 425 la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~~l~~~iE 490 (887)
T TIGR00593 425 LARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELDENKLLSLYREIE 490 (887)
T ss_pred HHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHH
Confidence 98765 3110 0 00 01367889999999999988875 45566655443
No 99
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=96.71 E-value=0.02 Score=58.30 Aligned_cols=135 Identities=19% Similarity=0.226 Sum_probs=82.5
Q ss_pred CcEEEEEEecCCCC-CC----CCcEEEEEEEEEcCCeeeeEEEEEcC-CC-CCCC-------ccccCCcHHhhcCCCCCC
Q 019538 127 VTAIVFDIETTGFS-RE----NERIIEIAFQDLLGGENSTFQTLVNP-KR-QVPN-------AHVHGITTDMVCKPDVPR 192 (339)
Q Consensus 127 ~~~vviDiETTGl~-p~----~~~IIEIgav~v~~g~i~~f~~lV~P-~~-~i~~-------~~itGIt~e~l~~~~ap~ 192 (339)
.++..+|+|+|+.. |. ..+|..|+..+..++. ..|..+.-. .. +..+ ..+-|+. +. .-++
T Consensus 106 i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~---v~--~f~s 179 (498)
T PHA02524 106 VVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGK-KTYYIFDLVKDVGHWDPKKSVLEKYILDNVV---YM--PFED 179 (498)
T ss_pred ceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCC-ccEEEEeccccccCCCcccccccccccCCeE---EE--EeCC
Confidence 58999999997643 21 2356666665544211 233333211 10 1111 1111211 11 2355
Q ss_pred HHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHh-cCCCC----------CC----------------CCc
Q 019538 193 MEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSR-CSYEV----------PN----------------NWL 245 (339)
Q Consensus 193 ~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r-~gl~~----------p~----------------~~~ 245 (339)
..+.+.+|.+|+.+. ++.+++|||+..||+++|...+.+ .|+.. .. ...
T Consensus 180 E~eLL~~F~~~i~~~----DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv 255 (498)
T PHA02524 180 EVDLLLNYIQLWKAN----TPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIA 255 (498)
T ss_pred HHHHHHHHHHHHHHh----CCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEE
Confidence 789999999999986 567999999999999999888863 55421 00 012
Q ss_pred eeeHHHHHHHH-HhcCCCCCCCCCCHHHHHHH
Q 019538 246 FMDTLTLAREL-MKSGGSNLPSKVSLQALREY 276 (339)
Q Consensus 246 ~iDtl~lar~l-~~~~~~~l~~~~~L~~L~~~ 276 (339)
.+|.+.+++.. +. .++ +++|+.+++.
T Consensus 256 ~iDl~~l~kk~s~~----~l~-sYsL~~Vs~~ 282 (498)
T PHA02524 256 LMDYMDVFKKFSFT----PMP-DYKLGNVGYR 282 (498)
T ss_pred EeEHHHHHHHhhhc----cCC-CCCHHHHHHH
Confidence 57899998865 22 345 9999999874
No 100
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.57 E-value=0.08 Score=59.62 Aligned_cols=140 Identities=18% Similarity=0.129 Sum_probs=89.9
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCC-------e-e--eeEEEEEcCCC-CCCC---ccccCCcHHhhcCCCCCCH
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGG-------E-N--STFQTLVNPKR-QVPN---AHVHGITTDMVCKPDVPRM 193 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g-------~-i--~~f~~lV~P~~-~i~~---~~itGIt~e~l~~~~ap~~ 193 (339)
.++-|++|+.......++++.|+++...+. . . ..|...++|.. .+|. ....|+....+. ...+.
T Consensus 507 ~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~--~~~sE 584 (1172)
T TIGR00592 507 VVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVE--DLATE 584 (1172)
T ss_pred EEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCCCCCchhhhhhhccCCcEEE--EecCH
Confidence 344445554333333578999988865542 1 1 23334455522 1222 233445444555 44556
Q ss_pred HHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC--------------------CCCceeeHHHHH
Q 019538 194 EDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP--------------------NNWLFMDTLTLA 253 (339)
Q Consensus 194 ~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p--------------------~~~~~iDtl~la 253 (339)
.+.+..|+.++... ++.+++|||...||+++|.+.+.+.+++.- ....++|++..+
T Consensus 585 r~lL~~fl~~~~~~----DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~ 660 (1172)
T TIGR00592 585 RALIKKFMAKVKKI----DPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISA 660 (1172)
T ss_pred HHHHHHHHHHHHhc----CCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHH
Confidence 78888998888865 567999999999999999999988776530 112468999998
Q ss_pred HHHHhcCCCCCCCCCCHHHHHHH-hCC
Q 019538 254 RELMKSGGSNLPSKVSLQALREY-YGI 279 (339)
Q Consensus 254 r~l~~~~~~~l~~~~~L~~L~~~-~gI 279 (339)
+..+.. . +|+|++++.. +|.
T Consensus 661 k~~~~~-----~-sy~L~~v~~~~L~~ 681 (1172)
T TIGR00592 661 KELIRC-----K-SYDLSELVQQILKT 681 (1172)
T ss_pred HHHhCc-----C-CCCHHHHHHHHhCC
Confidence 887653 3 9999999874 453
No 101
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=96.40 E-value=0.057 Score=58.40 Aligned_cols=127 Identities=23% Similarity=0.267 Sum_probs=84.3
Q ss_pred CcEEEEEEecCCCC-----CCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFS-----RENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILL 201 (339)
Q Consensus 127 ~~~vviDiETTGl~-----p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~ 201 (339)
.++++||+|+.+.. +..+.++.|+...-.++... ..+. .+...|.. +. ...+-.+.+..|.
T Consensus 154 l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~-----~~~~----~~~~~~~~---v~--~~~~e~e~l~~~~ 219 (792)
T COG0417 154 LRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI-----EVFI----YTSGEGFS---VE--VVISEAELLERFV 219 (792)
T ss_pred ceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc-----cccc----ccCCCCce---eE--EecCHHHHHHHHH
Confidence 47899999998653 23577888887755433110 0000 01111111 22 2234678899999
Q ss_pred HHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC---------------C---CCceeeHHHHHHH-HHhcCCC
Q 019538 202 HYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP---------------N---NWLFMDTLTLARE-LMKSGGS 262 (339)
Q Consensus 202 ~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p---------------~---~~~~iDtl~lar~-l~~~~~~ 262 (339)
.++... ++.++||||+-.||+++|...+..+|++.. . .+..+|+....+. ...
T Consensus 220 ~~i~~~----dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~~---- 291 (792)
T COG0417 220 ELIREY----DPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPLN---- 291 (792)
T ss_pred HHHHhc----CCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhcc----
Confidence 999976 677999999966999999999999888754 1 2357888888873 332
Q ss_pred CCCCCCCHHHHHHHh
Q 019538 263 NLPSKVSLQALREYY 277 (339)
Q Consensus 263 ~l~~~~~L~~L~~~~ 277 (339)
+. .++|...++.+
T Consensus 292 -~~-~ysl~~v~~~~ 304 (792)
T COG0417 292 -LK-SYSLEAVSEAL 304 (792)
T ss_pred -cc-cccHHHHHHHh
Confidence 33 89999997655
No 102
>PHA03036 DNA polymerase; Provisional
Probab=95.98 E-value=0.18 Score=55.40 Aligned_cols=202 Identities=15% Similarity=0.115 Sum_probs=113.0
Q ss_pred ccccchhhhhhhhccchhhhhhhhhhccCc-cCCCcEEEEEEecCCC----CCCCCcEEEEEEEEEc-CCeeeeEEEEEc
Q 019538 94 TINVNKTEISKIQRIQHYDIEQIIAENKDL-AKLVTAIVFDIETTGF----SRENERIIEIAFQDLL-GGENSTFQTLVN 167 (339)
Q Consensus 94 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l-~~~~~~vviDiETTGl----~p~~~~IIEIgav~v~-~g~i~~f~~lV~ 167 (339)
.|.+.+.+...-+...|.+-..-+...-+. .-+..+++||+|.-.. ++..+.|+.|+.+.++ .|. ..--++++
T Consensus 126 ~i~~~~~~~~~~~~y~c~~p~~~f~~~i~~~~~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~~~~-~~~~~l~n 204 (1004)
T PHA03036 126 RIDIDKLEKINNKCYHCDDPKKCFANKIPRFDIPRSYLFLDIECHFDKKFPSVFINPVSHISCCYIDLSGK-EKRFTLIN 204 (1004)
T ss_pred ecCHHHhccccCCceeeCCHHHHhcCcCCCccCcceeEEEEEEeccCCCCCCcccCcceEEEEEEEecCCC-eeEEEEec
Confidence 344444444444455554433334333332 2235899999997632 2446889999975554 222 23334555
Q ss_pred CCC----CCCCccccCCcH-Hhh---c---CCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhc
Q 019538 168 PKR----QVPNAHVHGITT-DMV---C---KPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRC 236 (339)
Q Consensus 168 P~~----~i~~~~itGIt~-e~l---~---~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~ 236 (339)
.+. +..+..+-|+.. +.+ + .--.++..+ +-.+.+++.+. +..+++|+|+..||+++|...+...
T Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sE~~-ml~~~~~i~~~----d~D~i~~yNg~nFD~~Yi~~R~~~L 279 (1004)
T PHA03036 205 EDMLSEDEIEEAVKRGYYEIESLLDMDYSKELILCSEIV-LLRIAKKLLEL----EFDYVVTFNGHNFDLRYISNRLELL 279 (1004)
T ss_pred cccccccccccceeeeeeccccccccCCceeeecCCHHH-HHHHHHHHHhc----CCCEEEeccCCCcchHHHHHHHHHh
Confidence 422 112222222210 001 1 001233344 44667777764 5679999999999999998887765
Q ss_pred CCCC-------------------------------------C--CCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-
Q 019538 237 SYEV-------------------------------------P--NNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY- 276 (339)
Q Consensus 237 gl~~-------------------------------------p--~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~- 276 (339)
.... . ....++|.+...++-+. ++ +|+|+++++.
T Consensus 280 ~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~-----L~-sYkL~~Vsk~~ 353 (1004)
T PHA03036 280 TGEKIIFRSPDGKETVHLCIYERNLSSHKGVGGVANTTYHINNNNGTIFFDLYTFIQKTEK-----LD-SYKLDSISKNA 353 (1004)
T ss_pred ccCceeeccCCCcccccceeeccccccccccCccccceEEecccCCeEEEEhHHHHhhhcC-----cc-cccHHHHHHHh
Confidence 2200 0 11246899988887654 45 9999999876
Q ss_pred hCCC-----CCCC----CCChHHHHHHHHHHHHHHHHhhc
Q 019538 277 YGIP-----LVGS----AHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 277 ~gI~-----~~~~----aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
|+.. .... .-.--.|+...+.+|..++..+.
T Consensus 354 f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl~t~n 393 (1004)
T PHA03036 354 FNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVLSTGN 393 (1004)
T ss_pred hccceeeeecCCceeEEccCcccccccchhhhhhhhcccc
Confidence 4330 0000 00112478888999988888664
No 103
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=95.82 E-value=0.0049 Score=64.50 Aligned_cols=161 Identities=23% Similarity=0.312 Sum_probs=94.6
Q ss_pred CcEEEEEEecCCCC-----CCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHH
Q 019538 127 VTAIVFDIETTGFS-----RENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILL 201 (339)
Q Consensus 127 ~~~vviDiETTGl~-----p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~ 201 (339)
.+++-+|+|+.|-. |..+.||+||-....-|+...|...|-. +.+ -.+|.-.++. ....-++++....
T Consensus 274 lrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~---l~~--capI~G~~V~--~~~~e~elL~~W~ 346 (1066)
T KOG0969|consen 274 LRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFT---LKT--CAPIVGSNVH--SYETEKELLESWR 346 (1066)
T ss_pred ccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhc---ccC--cCCCCCceeE--EeccHHHHHHHHH
Confidence 47889999998753 4458899998765444432222221111 111 1122222233 2223466677777
Q ss_pred HHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCC-CCC--CC------------------------------ceee
Q 019538 202 HYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYE-VPN--NW------------------------------LFMD 248 (339)
Q Consensus 202 ~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~-~p~--~~------------------------------~~iD 248 (339)
.|+.+- ++.+++|+|...||+++|....+..|++ +|. .. ..+|
T Consensus 347 ~firev----DPDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqfD 422 (1066)
T KOG0969|consen 347 KFIREV----DPDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQFD 422 (1066)
T ss_pred HHHHhc----CCCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeeeh
Confidence 777754 5679999999999999988777766664 221 00 1456
Q ss_pred HHHHHHHHHhcCCCCCCCCCCHHHHHH-HhCCCCCCCCCCh-------------------HHHHHHHHHHHHHHHH
Q 019538 249 TLTLARELMKSGGSNLPSKVSLQALRE-YYGIPLVGSAHRA-------------------MADVNCLSLILQRLTF 304 (339)
Q Consensus 249 tl~lar~l~~~~~~~l~~~~~L~~L~~-~~gI~~~~~aH~A-------------------l~DA~~ta~L~~~l~~ 304 (339)
.+....+=++ +. +|+|..++. ++|-+.++.+|.- +-||+.=.+|+.+|+.
T Consensus 423 llqvi~Rd~K-----Lr-SytLNaVs~hFL~EQKEDV~~siItdLQng~~~TRRRlA~YCLkDAYLPlRLlekLM~ 492 (1066)
T KOG0969|consen 423 LLQVILRDYK-----LR-SYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQTRRRLAVYCLKDAYLPLRLLEKLMV 492 (1066)
T ss_pred HHHHHHHhhh-----hh-hcchhhhHHHhhhhhcccccccchhhhhcCcHHHHHHHHHHHhhhhcchHHHHHHHHH
Confidence 6655444333 23 888888854 4554444333432 4677777777777654
No 104
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=95.76 E-value=0.072 Score=47.21 Aligned_cols=133 Identities=25% Similarity=0.238 Sum_probs=81.3
Q ss_pred cEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhc
Q 019538 128 TAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKSR 207 (339)
Q Consensus 128 ~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~ 207 (339)
..+++|+|+....+...+++.+++.. .++ .| +|.+ +. .......|.+++.+
T Consensus 25 ~~l~~~~e~~~~~~~~~~~~~l~l~~-~~~---~~--~i~~----------------l~------~~~~~~~L~~~L~~- 75 (192)
T cd06147 25 KEIAVDLEHHSYRSYLGFTCLMQIST-REE---DY--IVDT----------------LK------LRDDMHILNEVFTD- 75 (192)
T ss_pred CeEEEEeEecCCccCCCceEEEEEec-CCC---cE--EEEe----------------cc------cccchHHHHHHhcC-
Confidence 48899998876655456666655552 221 11 2221 01 11122335566764
Q ss_pred CCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CCCCCC---
Q 019538 208 QKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GIPLVG--- 283 (339)
Q Consensus 208 ~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI~~~~--- 283 (339)
.+...|+|+. +.|+..|.+ ++|+... . . +|++..++.+.|. . . +|+.+++.| +.....
T Consensus 76 ----~~i~kv~~d~-K~~~~~L~~---~~gi~~~-~-~-fD~~laaYLL~p~-~-----~-~l~~l~~~yl~~~~~k~~~ 137 (192)
T cd06147 76 ----PNILKVFHGA-DSDIIWLQR---DFGLYVV-N-L-FDTGQAARVLNLP-R-----H-SLAYLLQKYCNVDADKKYQ 137 (192)
T ss_pred ----CCceEEEech-HHHHHHHHH---HhCCCcC-c-h-HHHHHHHHHhCCC-c-----c-cHHHHHHHHhCCCcchhhh
Confidence 3467899999 899988742 5677654 2 3 9999999998875 2 4 899997765 443100
Q ss_pred ----CCC--------ChHHHHHHHHHHHHHHHHhhc
Q 019538 284 ----SAH--------RAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 284 ----~aH--------~Al~DA~~ta~L~~~l~~~l~ 307 (339)
..+ .+..||.++..++..+..+++
T Consensus 138 ~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~ 173 (192)
T cd06147 138 LADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELL 173 (192)
T ss_pred ccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 011 145567778888888888775
No 105
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=94.40 E-value=0.24 Score=44.97 Aligned_cols=183 Identities=15% Similarity=0.141 Sum_probs=103.6
Q ss_pred hhhhhhhccCccCCCcEEEEEEecCCCC--C-------------------CCCcEEEEEEEEEc--CCee-----eeEEE
Q 019538 113 IEQIIAENKDLAKLVTAIVFDIETTGFS--R-------------------ENERIIEIAFQDLL--GGEN-----STFQT 164 (339)
Q Consensus 113 ~~~~~~~~~~l~~~~~~vviDiETTGl~--p-------------------~~~~IIEIgav~v~--~g~i-----~~f~~ 164 (339)
++.++..-..+-.--++|-+|+|..|.- | +.-.||++|...-+ |+.. =.|+.
T Consensus 28 L~~Em~~I~qLi~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF 107 (299)
T COG5228 28 LYSEMAVIRQLISRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNF 107 (299)
T ss_pred HHHHHHHHHHHHHhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEE
Confidence 3444433333322248999999998852 1 01259999988665 3322 35666
Q ss_pred EEcCCCCCCC------ccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhc-CCCCCceEEEEECCcchhHHHHHHHHHhcC
Q 019538 165 LVNPKRQVPN------AHVHGITTDMVCKPDVPRMEDLIPILLHYVKSR-QKPGGYILFVAHNARSFDVPFLINEFSRCS 237 (339)
Q Consensus 165 lV~P~~~i~~------~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~-~~~~~~~~lV~hN~~~FD~~fL~~~~~r~g 237 (339)
-.++...+-. -.-.||.-+.-++.|.. ..+|.+.+.+- ....+.+++|.+.. .+|..+|.+.+....
T Consensus 108 ~F~l~~dmya~ESieLL~ksgIdFkkHe~~GI~-----v~eF~elLm~SGLvm~e~VtWitfHs-aYDfgyLikilt~~p 181 (299)
T COG5228 108 EFDLKKDMYATESIELLRKSGIDFKKHENLGID-----VFEFSELLMDSGLVMDESVTWITFHS-AYDFGYLIKILTNDP 181 (299)
T ss_pred EecchhhhcchHHHHHHHHcCCChhhHhhcCCC-----HHHHHHHHhccCceeccceEEEEeec-chhHHHHHHHHhcCC
Confidence 6777665432 23356665544432332 12334443321 11224678999999 899999988775433
Q ss_pred CCCCCCCceeeHHHHHHHHHhcCCC-------CCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHh
Q 019538 238 YEVPNNWLFMDTLTLARELMKSGGS-------NLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 238 l~~p~~~~~iDtl~lar~l~~~~~~-------~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
+ |.+ .=|-..+...++|.-.. -+..+..|.+++.-+++...|..|.|-.||+.|+..|-.....
T Consensus 182 l--P~~--~EdFy~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~ 252 (299)
T COG5228 182 L--PNN--KEDFYWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFS 252 (299)
T ss_pred C--Ccc--HHHHHHHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhh
Confidence 3 322 22333333333332100 0000345666666777877788999999999999988665543
No 106
>PRK05761 DNA polymerase I; Reviewed
Probab=93.72 E-value=0.34 Score=52.42 Aligned_cols=101 Identities=18% Similarity=0.231 Sum_probs=65.8
Q ss_pred CHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCC-CC------ceeeHHHHHHHH----Hh-c
Q 019538 192 RMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPN-NW------LFMDTLTLAREL----MK-S 259 (339)
Q Consensus 192 ~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~-~~------~~iDtl~lar~l----~~-~ 259 (339)
+..+.+..|.+++.+. .+.|.+|+..||+++|...+.++|+.... .. ..+|....+... +. .
T Consensus 209 ~E~eLL~~f~~~i~~~------dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~ 282 (787)
T PRK05761 209 SEKELLAELFDIILEY------PPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFY 282 (787)
T ss_pred CHHHHHHHHHHHHHhc------CCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeecc
Confidence 3678999999999975 24566999899999999999999986441 00 125665543221 00 0
Q ss_pred CCCCCCCCCCHHHHHH-HhCCCCCC------------CCCChHHHHHHHHHHH
Q 019538 260 GGSNLPSKVSLQALRE-YYGIPLVG------------SAHRAMADVNCLSLIL 299 (339)
Q Consensus 260 ~~~~l~~~~~L~~L~~-~~gI~~~~------------~aH~Al~DA~~ta~L~ 299 (339)
..-.++ +++|+.+++ .+|..... -+.-.+.||..+.+|.
T Consensus 283 ~~~~~~-~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 283 GKYRHR-EARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ceeecc-cCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 111223 689999988 66754320 1223589999999984
No 107
>PHA02563 DNA polymerase; Provisional
Probab=93.28 E-value=0.5 Score=49.65 Aligned_cols=79 Identities=18% Similarity=0.219 Sum_probs=48.8
Q ss_pred CcEEEEEEecCCCCCCCCcEEEEEEEEEcCCeeeeEEEEEcCCCCCCCccccCCcHHhhcCCCCCCHHHHHHHHHHHHHh
Q 019538 127 VTAIVFDIETTGFSRENERIIEIAFQDLLGGENSTFQTLVNPKRQVPNAHVHGITTDMVCKPDVPRMEDLIPILLHYVKS 206 (339)
Q Consensus 127 ~~~vviDiETTGl~p~~~~IIEIgav~v~~g~i~~f~~lV~P~~~i~~~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~ 206 (339)
..+++.|+||++.+. .......+.+ + +.+ |..+. + .+.+.+|.+|+..
T Consensus 12 ~~~~~~DfET~t~~~-~~~~~~~~~~--d-~~~--~~s~~----------------------~----~~~~~~f~~~i~~ 59 (630)
T PHA02563 12 RKILACDFETTTINK-DCRRWFWGEI--D-VED--FPSYY----------------------G----GNSFDEFLQWIED 59 (630)
T ss_pred ceEEEEEEEecccCC-cceeeeeeEe--c-cce--eceee----------------------c----cccHHHHHHHHhh
Confidence 579999999998863 3334444433 2 211 11111 1 1223466777762
Q ss_pred cCCCCCceEEEEECCcchhHHHHHHHHHhcCC
Q 019538 207 RQKPGGYILFVAHNARSFDVPFLINEFSRCSY 238 (339)
Q Consensus 207 ~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl 238 (339)
........++..||. .||..||...+.+++.
T Consensus 60 ~~~k~~~~~vYfHN~-~FD~~Fil~~L~~~~~ 90 (630)
T PHA02563 60 TTYKETECIIYFHNL-KFDGSFILKWLLRNGF 90 (630)
T ss_pred ccccccceEEEEecC-CccHHHHHHHHHhhcc
Confidence 212224679999998 9999999998888764
No 108
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy 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. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=93.22 E-value=0.66 Score=38.56 Aligned_cols=64 Identities=23% Similarity=0.290 Sum_probs=45.4
Q ss_pred HHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-C
Q 019538 200 LLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-G 278 (339)
Q Consensus 200 ~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-g 278 (339)
+.+++.+ .....|+||+ ++|..+|. +.|+..+. .++||+.+++.+.|... +.+|+.|++.| +
T Consensus 45 l~~~l~~-----~~~~kv~~d~-K~~~~~L~----~~~~~~~~--~~~D~~laayLl~p~~~-----~~~l~~l~~~~l~ 107 (150)
T cd09018 45 LKPLLED-----EKALKVGQNL-KYDRGILL----NYFIELRG--IAFDTMLEAYILNSVAG-----RWDMDSLVERWLG 107 (150)
T ss_pred HHHHhcC-----CCCceeeecH-HHHHHHHH----HcCCccCC--cchhHHHHHHHhCCCCC-----CCCHHHHHHHHhC
Confidence 4556664 2457899999 89998874 45665543 47999999999987531 34899997765 5
Q ss_pred CC
Q 019538 279 IP 280 (339)
Q Consensus 279 I~ 280 (339)
..
T Consensus 108 ~~ 109 (150)
T cd09018 108 HK 109 (150)
T ss_pred CC
Confidence 54
No 109
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=89.58 E-value=3 Score=37.85 Aligned_cols=110 Identities=16% Similarity=0.124 Sum_probs=67.1
Q ss_pred cEEEEEEEEEc--CCeeeeEEEEEcCCCCCCC---------ccccCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCCc
Q 019538 145 RIIEIAFQDLL--GGENSTFQTLVNPKRQVPN---------AHVHGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGY 213 (339)
Q Consensus 145 ~IIEIgav~v~--~g~i~~f~~lV~P~~~i~~---------~~itGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~ 213 (339)
-..|||++.+. +|.++.|+.+|+|+....- ..-|+|..+-.+. +...+..++.++..|+.......+.
T Consensus 9 ~PaEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~-~~~d~~~l~~~l~~fl~~~~~~~~~ 87 (213)
T PF13017_consen 9 VPAEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNAL-GESDYSELYNELLNFLKPNKGGEKM 87 (213)
T ss_pred EeEEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCccc-ccCCHHHHHHHHHHHhhhcCCCCCc
Confidence 46899998765 7777999999999854321 2456666553331 4446899999999999976432234
Q ss_pred eEEEEECCcchhH--HHHHHHHHhcCCCCCCCCceeeHHHHHHHHHh
Q 019538 214 ILFVAHNARSFDV--PFLINEFSRCSYEVPNNWLFMDTLTLARELMK 258 (339)
Q Consensus 214 ~~lV~hN~~~FD~--~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~ 258 (339)
.++++-.- .... ..|++.+...+.... +.+.+...+...+..
T Consensus 88 ~~i~~~~~-~~~~V~~cl~~La~~a~~~~~--~~v~~~~~lf~~l~~ 131 (213)
T PF13017_consen 88 PPIFTKRD-QIPRVQSCLKWLAKKAGEDND--FKVYDFEYLFFDLKN 131 (213)
T ss_pred ceEEEeHh-HHHHHHHHHHHHHHhcCCCcc--eEeecHHHHHHHHHH
Confidence 45555443 2332 345555555555432 345555555444433
No 110
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=88.72 E-value=1.1 Score=37.75 Aligned_cols=64 Identities=22% Similarity=0.256 Sum_probs=46.2
Q ss_pred HHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-C
Q 019538 200 LLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-G 278 (339)
Q Consensus 200 ~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-g 278 (339)
|.+|+.+ .....++||. +.++.+| .++|+.... ..+|++..++.+.|... ...++++++.| +
T Consensus 45 l~~~l~~-----~~~~ki~~d~-K~~~~~l----~~~gi~l~~--~~fD~~LAaYLL~p~~~-----~~~l~~la~~yl~ 107 (151)
T cd06128 45 LKPLLED-----EKALKVGQNL-KYDRVIL----ANYGIELRG--IAFDTMLEAYLLDPVAG-----RHDMDSLAERWLK 107 (151)
T ss_pred HHHHHcC-----CCCCEEeeeh-HHHHHHH----HHCCCCCCC--cchhHHHHHHHcCCCCC-----CCCHHHHHHHHcC
Confidence 5567764 2345799999 7888776 467887653 36999999999998641 25899998776 5
Q ss_pred CC
Q 019538 279 IP 280 (339)
Q Consensus 279 I~ 280 (339)
+.
T Consensus 108 ~~ 109 (151)
T cd06128 108 EK 109 (151)
T ss_pred CC
Confidence 43
No 111
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=82.84 E-value=11 Score=31.47 Aligned_cols=46 Identities=24% Similarity=0.279 Sum_probs=32.4
Q ss_pred HhhcCCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHH
Q 019538 183 DMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFS 234 (339)
Q Consensus 183 e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~ 234 (339)
+.|+..+..+..+.++.|.+.+... ...+|++|. .|....|+....
T Consensus 47 efL~~~~~DPr~~~~~~L~~~i~~~-----~g~ivvyN~-sfE~~rL~ela~ 92 (130)
T PF11074_consen 47 EFLADPGEDPRRELIEALIKAIGSI-----YGSIVVYNK-SFEKTRLKELAE 92 (130)
T ss_pred HHhccCCCCchHHHHHHHHHHhhhh-----cCeEEEech-HHHHHHHHHHHH
Confidence 3344334555778888888888752 158999999 899998866443
No 112
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=69.37 E-value=4.4 Score=43.63 Aligned_cols=37 Identities=32% Similarity=0.454 Sum_probs=27.3
Q ss_pred ceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHH
Q 019538 213 YILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLAR 254 (339)
Q Consensus 213 ~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar 254 (339)
..++||||+ .||+.-++.+.. +.-. ...++|||.+.-
T Consensus 241 e~liVGHNV-sfDRaRirEeY~---i~~S-k~rFlDTMSlHi 277 (1075)
T KOG3657|consen 241 EQLIVGHNV-SFDRARIREEYN---INGS-KIRFLDTMSLHI 277 (1075)
T ss_pred CceEEeccc-cchHHHHHHHHh---cccc-ceeeeechhhhh
Confidence 469999999 999999877543 3322 346899998643
No 113
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=58.60 E-value=47 Score=37.36 Aligned_cols=159 Identities=19% Similarity=0.229 Sum_probs=92.9
Q ss_pred CcEEEEEEecCCCCCC-CCcEEEEEEEEEc-----CCe-----eeeEEEEEcCCCCCCC--------ccccCCcHHhhcC
Q 019538 127 VTAIVFDIETTGFSRE-NERIIEIAFQDLL-----GGE-----NSTFQTLVNPKRQVPN--------AHVHGITTDMVCK 187 (339)
Q Consensus 127 ~~~vviDiETTGl~p~-~~~IIEIgav~v~-----~g~-----i~~f~~lV~P~~~i~~--------~~itGIt~e~l~~ 187 (339)
..+..+-++|+-.... ..+|+-|++.... .+. ...|-.+++|..-+-+ .+.+++ .
T Consensus 529 l~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~v-----~- 602 (1429)
T KOG0970|consen 529 LTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSKV-----V- 602 (1429)
T ss_pred eeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHhccCce-----E-
Confidence 4778888888754432 3788888876443 121 1567788888754322 122221 1
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCC-----------CCC--------------
Q 019538 188 PDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYE-----------VPN-------------- 242 (339)
Q Consensus 188 ~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~-----------~p~-------------- 242 (339)
-..+....+.-|+.-+... +..++||||...|++..|...+..+.++ +|.
T Consensus 603 -~~~sErALLs~fla~~~~~----dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~ 677 (1429)
T KOG0970|consen 603 -LHNSERALLSHFLAMLNKE----DPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFII 677 (1429)
T ss_pred -EecCHHHHHHHHHHHhhcc----CCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccc
Confidence 1122344556666666543 6679999996599999997777665544 110
Q ss_pred -CCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHh-CC-----CCCC-------C------CCChHHHHHHHHHHHHHH
Q 019538 243 -NWLFMDTLTLARELMKSGGSNLPSKVSLQALREYY-GI-----PLVG-------S------AHRAMADVNCLSLILQRL 302 (339)
Q Consensus 243 -~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~-gI-----~~~~-------~------aH~Al~DA~~ta~L~~~l 302 (339)
....-|+-..++.+.+.. +|+|.+|++.. +. +... . -.....|+...++|+.++
T Consensus 678 aGRl~CD~~~~a~~lik~~------S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s~~L~~ll~~~~~d~~~~l~i~~~l 751 (1429)
T KOG0970|consen 678 AGRLMCDLNLAARELIKAQ------SYSLSELSQQILKEERKEINANEIPKMYEDSKSLTYLLEHTITDAELILQIMFRL 751 (1429)
T ss_pred cceEEeehHHHHHhhhccc------cccHHHHHHHHHhhhcccCCHhHhhhhccChHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 001235655566666644 89999998642 22 1110 0 112367888888888765
No 114
>PF09281 Taq-exonuc: Taq polymerase, exonuclease; InterPro: IPR015361 This domain is found in prokaryotic Taq DNA polymerase (thermostable), where it assumes a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase []. ; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 4DF4_A 3T3F_A 1QSY_A 3OJS_A 3PO5_A 3OJU_A 1QTM_A 1QSS_A 3PY8_A 4DFJ_A ....
Probab=56.11 E-value=90 Score=26.28 Aligned_cols=69 Identities=20% Similarity=0.027 Sum_probs=42.0
Q ss_pred HHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHh
Q 019538 226 VPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREYYGIPLVGSAHRAMADVNCLSLILQRLTFD 305 (339)
Q Consensus 226 ~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~~gI~~~~~aH~Al~DA~~ta~L~~~l~~~ 305 (339)
-+-|.-...+.|+..++. =|.|.+++.+.|. +.....++++|+-..- .-+|-.-|.++.+|++.|..+
T Consensus 70 AK~LAv~a~~~G~~v~PG---DDPlLlAYLlDPs-------Nt~p~~varRY~~~~W--~~dA~~RA~~t~~L~~~L~pr 137 (138)
T PF09281_consen 70 AKDLAVHALREGVVVEPG---DDPLLLAYLLDPS-------NTNPEGVARRYLGGEW--PEDAATRALATARLLRALPPR 137 (138)
T ss_dssp HHHHHHHHHHTT----B------HHHHHHHH-TT---------SHHHHHHHH-TS-----SSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCcccCCC---CCcchhhhhcCcc-------CCChHHHHHHhcCCCC--CccHHHHHHHHHHHHHHhhhc
Confidence 344444456778876532 4999999999987 6688889998843221 356888999999999988764
Q ss_pred h
Q 019538 306 L 306 (339)
Q Consensus 306 l 306 (339)
+
T Consensus 138 L 138 (138)
T PF09281_consen 138 L 138 (138)
T ss_dssp T
T ss_pred C
Confidence 3
No 115
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.61 E-value=14 Score=42.05 Aligned_cols=91 Identities=18% Similarity=0.183 Sum_probs=52.9
Q ss_pred CcEEEEEEecCC---------CCCCCCcEEEEEEEEEc----CCeeeeEEE---EEcCCCCCCCccccCCcHHhhcCCCC
Q 019538 127 VTAIVFDIETTG---------FSRENERIIEIAFQDLL----GGENSTFQT---LVNPKRQVPNAHVHGITTDMVCKPDV 190 (339)
Q Consensus 127 ~~~vviDiETTG---------l~p~~~~IIEIgav~v~----~g~i~~f~~---lV~P~~~i~~~~itGIt~e~l~~~~a 190 (339)
-+.+.||+|..+ .++..|.||+|+...+. .|....+.. .+.+- ..+.|... . ..
T Consensus 198 ~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~v---~--~~ 267 (1172)
T TIGR00592 198 LKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWDYESEPEARVVTWKKPD-----KPTTGSYV---E--SV 267 (1172)
T ss_pred ccccccccccccccccccCcccccccccccccccccccccccccCCCccchhhhccCcc-----ccCCCccc---e--ec
Confidence 478899999653 33456889999864211 111000000 01111 12223222 2 23
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHH
Q 019538 191 PRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLIN 231 (339)
Q Consensus 191 p~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~ 231 (339)
++..+.+..|.+++.+. +..+++|+|...||++++..
T Consensus 268 ~~E~~~L~~f~~~i~~~----dpdii~gYNi~~FD~pyl~~ 304 (1172)
T TIGR00592 268 SEEISMIKRFWDVIDQE----DTDVEITVNGDNFDLVYLAD 304 (1172)
T ss_pred cchHHHHhhHHHHHhhc----CcchhcccccccCccceecC
Confidence 44567778888888764 45589999999999998865
No 116
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=43.04 E-value=62 Score=36.53 Aligned_cols=58 Identities=10% Similarity=0.093 Sum_probs=41.5
Q ss_pred cCCcHHhhcCCCCCCHHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCC
Q 019538 178 HGITTDMVCKPDVPRMEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVP 241 (339)
Q Consensus 178 tGIt~e~l~~~~ap~~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p 241 (339)
+||+.-.+. -..+..+.+.++.+++... +..+++||-...+-++||....+..|++++
T Consensus 724 ~~~~~~~V~--~~~sE~elf~ev~~~i~q~----DPDIl~GyEi~~~SWGyl~eR~~~l~~di~ 781 (1488)
T KOG0968|consen 724 GGIYGCRVV--VMESELELFEEVAKLIVQY----DPDILLGYEIHNLSWGYLIERAKLLGIDIS 781 (1488)
T ss_pred CCcCCceEE--EehhHHHHHHHHHHHHHhc----CcceeeeeeecccchHHHHHHHHHhcchHH
Confidence 555543333 2333566778888888876 567999999988899999887777887754
No 117
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=33.15 E-value=63 Score=33.87 Aligned_cols=96 Identities=31% Similarity=0.320 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHHhcCCCCCceEEEEECCcchhHHHHHHHHHhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHH
Q 019538 193 MEDLIPILLHYVKSRQKPGGYILFVAHNARSFDVPFLINEFSRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQA 272 (339)
Q Consensus 193 ~~evl~~~~~~l~~~~~~~~~~~lV~hN~~~FD~~fL~~~~~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~ 272 (339)
+.+++.-+.+++.. ...+-|-|++ .-|+-||++-| |+.. ...+||....+.+- ++ .++|.+
T Consensus 250 l~~~i~~l~e~fsd-----p~ivkvfhga-D~diiwlqrdf---giyv---vnLfdt~~a~r~L~------~~-r~sL~~ 310 (687)
T KOG2206|consen 250 LRDHIGILNEVFSD-----PGIVKVFHGA-DTDIIWLQRDF---GIYV---VNLFDTIQASRLLG------LP-RPSLAY 310 (687)
T ss_pred HHHHHHHhhhhccC-----CCeEEEEecC-ccchhhhhccc---eEEE---EechhhHHHHHHhC------CC-cccHHH
Confidence 55666655555543 4578899999 99999997643 4432 24689999998763 34 889999
Q ss_pred HHHHh-CCCCCC---------------CCCChHHHHHHHHHHHHHHHHhhc
Q 019538 273 LREYY-GIPLVG---------------SAHRAMADVNCLSLILQRLTFDLK 307 (339)
Q Consensus 273 L~~~~-gI~~~~---------------~aH~Al~DA~~ta~L~~~l~~~l~ 307 (339)
|.+.+ |+.... ----|-.|+..+..+|..|..++.
T Consensus 311 ll~~~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~ 361 (687)
T KOG2206|consen 311 LLECVCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELK 361 (687)
T ss_pred HHHHHHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHH
Confidence 98754 332220 011245677788888887776554
No 118
>KOG3506 consensus 40S ribosomal protein S29 [Translation, ribosomal structure and biogenesis]
Probab=30.76 E-value=17 Score=25.73 Aligned_cols=14 Identities=29% Similarity=0.551 Sum_probs=12.5
Q ss_pred hhhhhhhhhhcCCC
Q 019538 26 RESFHSFSRRYGHS 39 (339)
Q Consensus 26 ~~~~~~~~~~~~~~ 39 (339)
|.++||+.++||=+
T Consensus 24 Csn~~gLIrKYGL~ 37 (56)
T KOG3506|consen 24 CSNRHGLIRKYGLN 37 (56)
T ss_pred eccchhHHHHhhhH
Confidence 89999999999953
No 119
>PF06471 NSP11: NSP11; InterPro: IPR009466 This region of coronavirus polyproteins encodes the NSP11 protein.; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0008168 methyltransferase activity, 0016896 exoribonuclease activity, producing 5'-phosphomonoesters; PDB: 2RHB_D 2H85_A 2OZK_A 2GTH_A 2GTI_A.
Probab=30.71 E-value=17 Score=37.11 Aligned_cols=105 Identities=15% Similarity=0.207 Sum_probs=0.0
Q ss_pred cEEEEEEecC---CCCCCCCcEEEEEEE------EEcCCee-eeEEEEEcCCCC-CCC-ccccCCcHHhhcCCCCCCHHH
Q 019538 128 TAIVFDIETT---GFSRENERIIEIAFQ------DLLGGEN-STFQTLVNPKRQ-VPN-AHVHGITTDMVCKPDVPRMED 195 (339)
Q Consensus 128 ~~vviDiETT---Gl~p~~~~IIEIgav------~v~~g~i-~~f~~lV~P~~~-i~~-~~itGIt~e~l~~~~ap~~~e 195 (339)
--|.||+|.. |.+-...-.+|+|.- ..-.|.+ .+.-..+.|-.. +|+ .+..++-+-|-. |.| +.-
T Consensus 89 ~WiGfDVEgAHa~~~nvGTNlPLQvGFStGvdFvV~peG~v~te~G~~~~~v~AkaPPGeQF~HL~plmrk--g~p-W~V 165 (593)
T PF06471_consen 89 GWIGFDVEGAHACGPNVGTNLPLQVGFSTGVDFVVQPEGCVVTETGTCFKPVPAKAPPGEQFKHLIPLMRK--GQP-WSV 165 (593)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhcccceeeccccccccCcCcceeecccCCceeEEccceEEEecCCceeeeecCCCCchhhhHhhHHHHhc--CCC-chh
Confidence 4588999953 434344556777753 1123433 455555565433 555 777777777766 665 666
Q ss_pred HHHHHHHHHHhcC-CCCCceEEEEECCcchhHHHHHHHHHhcC
Q 019538 196 LIPILLHYVKSRQ-KPGGYILFVAHNARSFDVPFLINEFSRCS 237 (339)
Q Consensus 196 vl~~~~~~l~~~~-~~~~~~~lV~hN~~~FD~~fL~~~~~r~g 237 (339)
+-.++.+.+.+.. ...+..++|.|.. .|++.-++. |-+.|
T Consensus 166 VR~rIVqml~D~l~~~SD~vvFVtWA~-glELTtmrY-FvKiG 206 (593)
T PF06471_consen 166 VRKRIVQMLSDYLDGLSDYVVFVTWAH-GLELTTMRY-FVKIG 206 (593)
T ss_dssp -------------------------------------------
T ss_pred hHHHHHHHHHHhccCCCCEEEEEEccC-ceehhhhhh-hhhhC
Confidence 6666666665432 1224567899988 899987743 44444
No 120
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=24.56 E-value=3.1e+02 Score=28.59 Aligned_cols=68 Identities=24% Similarity=0.152 Sum_probs=43.4
Q ss_pred HhcCCCCCCCCceeeHHHHHHHHHhcCCCCCCCCCCHHHHHHH-hCCCCCC--------------CCCChHHHHHHHHHH
Q 019538 234 SRCSYEVPNNWLFMDTLTLARELMKSGGSNLPSKVSLQALREY-YGIPLVG--------------SAHRAMADVNCLSLI 298 (339)
Q Consensus 234 ~r~gl~~p~~~~~iDtl~lar~l~~~~~~~l~~~~~L~~L~~~-~gI~~~~--------------~aH~Al~DA~~ta~L 298 (339)
.++|+.+. .++||+..++.+.+...+ . ..+++.+++. +++.... ...-|..|+..+..|
T Consensus 63 ~~~Gv~~~---~~fDT~LAa~lL~~~~~~--~-~~~l~~la~~~l~~~l~k~~~~sdw~rpls~~q~~YAa~Dv~~l~~L 136 (553)
T PRK14975 63 LAAGVRVE---RCHDLMLASQLLLGSEGR--A-GSSLSAAAARALGEGLDKPPQTSALSDPPDEEQLLYAAADADVLLEL 136 (553)
T ss_pred HHCCCccC---CCchHHHHHHHcCCCCCc--C-CCCHHHHHHHHhCCCCCChhhhccccccchHHHHHHHHHHhHHHHHH
Confidence 45566533 278888888877654210 1 4578888664 4444221 112367889999999
Q ss_pred HHHHHHhhc
Q 019538 299 LQRLTFDLK 307 (339)
Q Consensus 299 ~~~l~~~l~ 307 (339)
|..+..++.
T Consensus 137 ~~~L~~qL~ 145 (553)
T PRK14975 137 YAVLADQLN 145 (553)
T ss_pred HHHHHHHHH
Confidence 999988876
Done!