Query 023805
Match_columns 277
No_of_seqs 223 out of 1390
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 06:47:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023805.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023805hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09146 DNA polymerase III su 100.0 4E-31 8.6E-36 231.5 23.3 177 6-189 40-230 (239)
2 PRK06063 DNA polymerase III su 100.0 1.5E-30 3.2E-35 236.4 25.2 174 5-188 7-181 (313)
3 PRK05711 DNA polymerase III su 100.0 1.1E-30 2.4E-35 228.5 22.0 167 12-185 3-175 (240)
4 TIGR01406 dnaQ_proteo DNA poly 100.0 1.5E-30 3.2E-35 226.3 21.7 164 14-184 1-170 (225)
5 smart00479 EXOIII exonuclease 100.0 3.3E-30 7.1E-35 213.4 22.4 166 14-187 1-168 (169)
6 PRK07740 hypothetical protein; 100.0 3.1E-30 6.8E-35 226.8 22.9 173 8-188 54-228 (244)
7 PRK09145 DNA polymerase III su 100.0 3.8E-30 8.3E-35 220.5 22.3 167 11-184 27-199 (202)
8 PRK07748 sporulation inhibitor 100.0 2.7E-30 5.8E-35 222.2 20.9 172 12-187 3-181 (207)
9 TIGR00573 dnaq exonuclease, DN 100.0 3.9E-30 8.5E-35 222.7 21.5 171 10-187 4-178 (217)
10 PRK06310 DNA polymerase III su 100.0 7.2E-30 1.6E-34 225.3 22.6 168 10-186 4-174 (250)
11 PRK07942 DNA polymerase III su 100.0 5.8E-30 1.3E-34 223.7 21.7 171 11-187 4-181 (232)
12 cd06131 DNA_pol_III_epsilon_Ec 100.0 8.8E-30 1.9E-34 211.5 21.2 161 15-182 1-166 (167)
13 cd06130 DNA_pol_III_epsilon_li 100.0 7.2E-30 1.6E-34 209.3 20.0 155 15-180 1-155 (156)
14 PRK08517 DNA polymerase III su 100.0 2.1E-29 4.6E-34 222.7 23.1 168 8-186 63-231 (257)
15 PRK06807 DNA polymerase III su 100.0 1.9E-29 4.2E-34 228.7 22.7 168 10-186 5-172 (313)
16 PRK06195 DNA polymerase III su 100.0 2.9E-29 6.3E-34 228.0 22.5 165 14-188 2-166 (309)
17 PRK06309 DNA polymerase III su 100.0 3.1E-29 6.7E-34 219.2 21.2 163 13-186 2-166 (232)
18 PRK07247 DNA polymerase III su 100.0 1.1E-28 2.3E-33 209.8 21.3 163 12-186 4-169 (195)
19 PRK06722 exonuclease; Provisio 100.0 6.3E-29 1.4E-33 221.0 20.6 171 11-184 3-179 (281)
20 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 4.6E-29 1E-33 209.5 17.2 157 15-181 1-176 (177)
21 PRK07883 hypothetical protein; 100.0 1.1E-28 2.5E-33 239.3 22.1 176 7-190 9-186 (557)
22 PRK05168 ribonuclease T; Provi 100.0 3.3E-28 7.1E-33 209.7 21.8 170 11-187 15-202 (211)
23 cd06133 ERI-1_3'hExo_like DEDD 100.0 2.2E-28 4.7E-33 204.2 19.6 166 15-182 1-175 (176)
24 TIGR01298 RNaseT ribonuclease 100.0 4.1E-28 8.9E-33 207.5 21.5 168 13-187 8-193 (200)
25 cd06134 RNaseT DEDDh 3'-5' exo 100.0 6.5E-28 1.4E-32 204.6 20.5 165 14-185 6-188 (189)
26 PRK05601 DNA polymerase III su 100.0 1.8E-27 3.8E-32 216.4 23.8 170 7-185 40-248 (377)
27 PRK07246 bifunctional ATP-depe 100.0 1.9E-27 4.1E-32 240.0 22.7 166 11-187 5-171 (820)
28 cd06138 ExoI_N N-terminal DEDD 100.0 1.6E-27 3.5E-32 201.2 17.1 161 16-180 1-183 (183)
29 COG2176 PolC DNA polymerase II 100.0 1.9E-28 4.2E-33 243.1 12.8 173 9-190 417-590 (1444)
30 PRK08074 bifunctional ATP-depe 100.0 8.1E-27 1.7E-31 238.7 23.1 168 12-187 2-170 (928)
31 PTZ00315 2'-phosphotransferase 100.0 3.8E-26 8.2E-31 218.3 25.3 176 12-189 55-258 (582)
32 cd06127 DEDDh DEDDh 3'-5' exon 100.0 9.6E-27 2.1E-31 189.2 18.3 157 16-180 1-159 (159)
33 TIGR01405 polC_Gram_pos DNA po 99.9 1.1E-26 2.4E-31 239.7 22.3 170 11-189 188-358 (1213)
34 TIGR01407 dinG_rel DnaQ family 99.9 3E-26 6.6E-31 233.1 22.6 165 14-187 1-166 (850)
35 cd06149 ISG20 DEDDh 3'-5' exon 99.9 1.5E-26 3.3E-31 190.5 13.9 149 16-180 1-157 (157)
36 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 1.2E-26 2.5E-31 192.1 12.2 144 16-179 1-160 (161)
37 PRK07983 exodeoxyribonuclease 99.9 2E-25 4.4E-30 193.0 19.5 147 15-186 2-154 (219)
38 cd06145 REX1_like DEDDh 3'-5' 99.9 1.2E-25 2.6E-30 183.9 13.9 143 16-180 1-150 (150)
39 cd06144 REX4_like DEDDh 3'-5' 99.9 1.1E-25 2.5E-30 184.4 13.6 148 16-180 1-152 (152)
40 PRK09182 DNA polymerase III su 99.9 1.1E-24 2.3E-29 196.0 20.1 165 7-185 31-200 (294)
41 COG0847 DnaQ DNA polymerase II 99.9 1.8E-24 4E-29 190.1 20.7 165 13-185 13-181 (243)
42 cd06135 Orn DEDDh 3'-5' exonuc 99.9 4.4E-25 9.4E-30 184.7 14.6 158 15-186 1-172 (173)
43 PRK05359 oligoribonuclease; Pr 99.9 2.3E-24 4.9E-29 181.5 17.8 161 12-188 2-177 (181)
44 PF00929 RNase_T: Exonuclease; 99.9 6.3E-27 1.4E-31 190.8 -1.0 160 16-179 1-164 (164)
45 PRK11779 sbcB exonuclease I; P 99.9 2.2E-23 4.9E-28 197.7 20.3 173 11-185 4-197 (476)
46 PRK00448 polC DNA polymerase I 99.9 7.9E-23 1.7E-27 213.6 19.6 171 9-188 415-586 (1437)
47 KOG0542 Predicted exonuclease 99.9 8.1E-22 1.7E-26 168.4 12.9 174 13-188 56-244 (280)
48 COG5018 KapD Inhibitor of the 99.8 4.9E-20 1.1E-24 148.6 8.0 179 12-193 3-193 (210)
49 KOG2249 3'-5' exonuclease [Rep 99.8 4.1E-19 8.8E-24 153.1 14.0 161 10-187 102-267 (280)
50 cd06143 PAN2_exo DEDDh 3'-5' e 99.7 8.1E-16 1.8E-20 127.3 13.6 151 13-180 5-174 (174)
51 COG1949 Orn Oligoribonuclease 99.5 8.9E-14 1.9E-18 112.0 11.0 160 10-188 3-180 (184)
52 KOG3242 Oligoribonuclease (3'- 99.5 2.1E-13 4.5E-18 110.8 10.1 165 11-189 24-202 (208)
53 COG2925 SbcB Exonuclease I [DN 99.5 9.7E-13 2.1E-17 118.9 13.7 174 10-185 6-200 (475)
54 KOG2248 3'-5' exonuclease [Rep 99.4 4.7E-13 1E-17 123.5 10.8 157 9-186 212-375 (380)
55 cd05160 DEDDy_DNA_polB_exo DED 99.3 4.6E-11 9.9E-16 101.8 15.3 138 15-167 1-167 (199)
56 cd06125 DnaQ_like_exo DnaQ-lik 99.1 1.5E-09 3.2E-14 82.0 11.3 79 16-138 1-83 (96)
57 PF13482 RNase_H_2: RNase_H su 99.0 1.9E-09 4.2E-14 88.8 8.9 115 16-163 1-116 (164)
58 cd06139 DNA_polA_I_Ecoli_like_ 98.9 4.9E-08 1.1E-12 82.1 15.6 145 10-188 2-172 (193)
59 COG3359 Predicted exonuclease 98.9 3.9E-08 8.5E-13 84.7 14.1 150 11-189 96-272 (278)
60 cd05780 DNA_polB_Kod1_like_exo 98.9 7.9E-08 1.7E-12 81.9 14.4 129 14-166 4-159 (195)
61 cd05781 DNA_polB_B3_exo DEDDy 98.8 1.6E-07 3.4E-12 79.6 13.7 117 14-162 4-144 (188)
62 KOG4793 Three prime repair exo 98.7 4.8E-08 1E-12 85.0 8.8 198 4-209 4-237 (318)
63 cd05779 DNA_polB_epsilon_exo D 98.7 7.1E-07 1.5E-11 76.6 15.1 146 14-165 3-171 (204)
64 PRK05755 DNA polymerase I; Pro 98.7 3.4E-07 7.3E-12 94.4 14.7 135 12-188 314-471 (880)
65 cd05785 DNA_polB_like2_exo Unc 98.7 3.6E-07 7.9E-12 78.6 12.2 119 14-162 10-168 (207)
66 cd05782 DNA_polB_like1_exo Unc 98.5 3E-06 6.6E-11 72.9 12.7 74 87-162 79-169 (208)
67 cd05777 DNA_polB_delta_exo DED 98.4 1.8E-05 4E-10 69.0 15.6 136 13-162 7-182 (230)
68 cd05783 DNA_polB_B1_exo DEDDy 98.4 1.4E-05 3.1E-10 68.5 14.4 79 84-162 71-170 (204)
69 PF01612 DNA_pol_A_exo1: 3'-5' 98.4 3E-05 6.5E-10 63.9 15.8 89 89-186 65-175 (176)
70 PF10108 DNA_pol_B_exo2: Predi 98.3 1.2E-05 2.5E-10 68.9 13.0 126 31-184 8-171 (209)
71 cd05784 DNA_polB_II_exo DEDDy 98.3 2.5E-05 5.4E-10 66.5 14.7 127 14-166 4-157 (193)
72 PHA02570 dexA exonuclease; Pro 98.3 2.1E-05 4.5E-10 67.4 12.6 159 16-183 4-196 (220)
73 PF04857 CAF1: CAF1 family rib 98.2 1.1E-05 2.3E-10 72.0 10.4 161 12-180 21-261 (262)
74 cd00007 35EXOc 3'-5' exonuclea 98.1 0.00029 6.3E-09 56.4 15.1 65 87-159 40-106 (155)
75 KOG1275 PAB-dependent poly(A) 98.0 3.5E-06 7.5E-11 83.9 4.0 162 8-184 905-1090(1118)
76 cd06129 RNaseD_like DEDDy 3'-5 98.0 0.00024 5.1E-09 58.5 13.5 129 12-183 12-160 (161)
77 cd06146 mut-7_like_exo DEDDy 3 97.9 0.00039 8.4E-09 59.1 13.2 143 10-183 19-192 (193)
78 cd06141 WRN_exo DEDDy 3'-5' ex 97.9 0.00049 1.1E-08 56.8 13.5 129 12-183 17-169 (170)
79 TIGR01388 rnd ribonuclease D. 97.9 0.00056 1.2E-08 63.9 15.3 132 12-188 17-168 (367)
80 PRK10829 ribonuclease D; Provi 97.8 0.0006 1.3E-08 63.7 14.7 135 11-190 20-174 (373)
81 COG0349 Rnd Ribonuclease D [Tr 97.8 0.00033 7.1E-09 64.4 11.9 136 12-191 16-171 (361)
82 cd06140 DNA_polA_I_Bacillus_li 97.8 0.0011 2.4E-08 55.0 14.2 133 13-188 3-158 (178)
83 PRK05762 DNA polymerase II; Re 97.7 0.00074 1.6E-08 69.1 14.7 145 12-182 154-348 (786)
84 cd05778 DNA_polB_zeta_exo inac 97.6 0.0029 6.2E-08 55.3 15.3 168 14-185 5-222 (231)
85 PTZ00166 DNA polymerase delta 97.6 0.0011 2.3E-08 69.8 14.4 158 12-183 263-483 (1054)
86 smart00474 35EXOc 3'-5' exonuc 97.6 0.008 1.7E-07 48.8 16.3 88 90-186 64-171 (172)
87 PHA02528 43 DNA polymerase; Pr 97.5 0.0027 5.9E-08 65.4 15.2 98 84-181 176-323 (881)
88 COG0749 PolA DNA polymerase I 97.5 0.0011 2.4E-08 64.8 11.5 136 15-191 24-185 (593)
89 KOG0304 mRNA deadenylase subun 97.5 0.0027 5.9E-08 54.2 11.9 173 10-184 21-237 (239)
90 smart00486 POLBc DNA polymeras 97.4 0.0038 8.3E-08 59.4 13.5 156 13-182 3-220 (471)
91 cd06148 Egl_like_exo DEDDy 3'- 97.3 0.0036 7.9E-08 53.3 11.6 140 9-189 6-180 (197)
92 TIGR03491 RecB family nuclease 97.3 0.0071 1.5E-07 58.2 14.7 120 12-162 283-409 (457)
93 cd06142 RNaseD_exo DEDDy 3'-5' 97.2 0.025 5.5E-07 46.5 15.1 91 90-189 53-163 (178)
94 cd05776 DNA_polB_alpha_exo ina 97.1 0.0059 1.3E-07 53.4 10.3 146 14-162 4-186 (234)
95 PF03104 DNA_pol_B_exo1: DNA p 97.0 0.0032 7E-08 57.1 8.8 130 12-155 156-325 (325)
96 cd06147 Rrp6p_like_exo DEDDy 3 96.3 0.24 5.1E-06 41.7 14.3 89 91-189 67-175 (192)
97 cd09018 DEDDy_polA_RNaseD_like 96.2 0.072 1.6E-06 42.4 10.6 62 93-162 45-109 (150)
98 TIGR00593 pola DNA polymerase 96.1 0.043 9.2E-07 57.0 10.6 93 86-187 363-478 (887)
99 PHA02524 43A DNA polymerase su 96.1 0.068 1.5E-06 51.7 11.2 76 83-158 177-282 (498)
100 KOG1798 DNA polymerase epsilon 96.0 0.19 4.1E-06 53.7 14.2 159 12-185 245-453 (2173)
101 TIGR00592 pol2 DNA polymerase 95.7 0.28 6E-06 52.7 14.8 143 15-162 508-682 (1172)
102 COG0417 PolB DNA polymerase el 95.1 0.5 1.1E-05 48.7 13.9 129 12-160 153-305 (792)
103 PHA03036 DNA polymerase; Provi 94.8 0.73 1.6E-05 48.2 14.1 169 11-185 158-391 (1004)
104 cd06128 DNA_polA_exo DEDDy 3'- 94.7 0.13 2.9E-06 41.3 7.0 62 93-162 45-109 (151)
105 PRK05761 DNA polymerase I; Rev 94.4 0.29 6.3E-06 50.3 10.1 94 86-179 210-334 (787)
106 PHA02563 DNA polymerase; Provi 91.2 1.4 3E-05 44.2 9.4 34 90-124 50-90 (630)
107 KOG4793 Three prime repair exo 91.2 0.35 7.5E-06 42.9 4.6 87 102-188 201-293 (318)
108 COG5228 POP2 mRNA deadenylase 88.3 0.68 1.5E-05 39.9 4.1 167 11-188 40-255 (299)
109 PF00843 Arena_nucleocap: Aren 81.7 3.1 6.7E-05 39.4 5.4 146 9-177 368-529 (533)
110 KOG0969 DNA polymerase delta, 79.1 0.7 1.5E-05 46.6 0.4 104 10-125 271-380 (1066)
111 PF13017 Maelstrom: piRNA path 78.6 42 0.00091 28.8 11.8 105 31-140 7-127 (213)
112 KOG3657 Mitochondrial DNA poly 74.6 3 6.5E-05 42.6 3.3 38 98-140 240-277 (1075)
113 PF11074 DUF2779: Domain of un 69.9 22 0.00048 28.1 6.8 36 85-121 56-93 (130)
114 PF09281 Taq-exonuc: Taq polym 65.0 29 0.00063 27.5 6.3 66 115-186 73-138 (138)
115 KOG0970 DNA polymerase alpha, 64.5 68 0.0015 34.4 10.5 139 14-158 530-706 (1429)
116 PRK14975 bifunctional 3'-5' ex 40.6 1.4E+02 0.0029 29.6 8.2 66 119-188 62-146 (553)
117 TIGR00592 pol2 DNA polymerase 26.9 35 0.00075 37.1 1.6 34 84-117 268-304 (1172)
118 PF12096 DUF3572: Protein of u 22.2 1.4E+02 0.0031 22.0 3.6 47 69-126 27-73 (88)
119 COG2251 Predicted nuclease (Re 21.0 1.5E+02 0.0034 28.5 4.5 91 87-179 339-436 (474)
No 1
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=4e-31 Score=231.54 Aligned_cols=177 Identities=19% Similarity=0.285 Sum_probs=154.4
Q ss_pred CCCCCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCC
Q 023805 6 PSQAAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPE 85 (277)
Q Consensus 6 ~~~~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~ 85 (277)
...+.....|++||+||||+++ ..++|||||+|.++++.+...++|+++|+|.. ++++.+.++||||+++++++++
T Consensus 40 ~~~~~~~~~~vviD~ETTGl~p--~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt~e~l~~ap~ 115 (239)
T PRK09146 40 PDTPLSEVPFVALDFETTGLDA--EQDAIVSIGLVPFTLQRIRCRQARHWVVKPRR--PLEEESVVIHGITHSELQDAPD 115 (239)
T ss_pred CCCCcccCCEEEEEeECCCCCC--CCCcEEEEEEEEEECCeEeecceEEEEECCCC--CCChhhhhhcCCCHHHHhCCCC
Confidence 3446667899999999999998 67899999999999987665688999999998 8999999999999999999999
Q ss_pred HHHHHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCC-CCCCCCceeehHHHHHHHhCC------------CCCCCCH
Q 023805 86 FEEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGK-PAPVPVGMIDSLGVLTEKFGR------------RAGNMKM 152 (277)
Q Consensus 86 f~ev~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~-~~p~~~~~iDt~~l~~~~~~~------------~~~~~~L 152 (277)
|.+++.+|.+++++.++||||+ .||+.||++++.+++. ..+. .++||+.++.+.+.. ...+++|
T Consensus 116 ~~evl~~l~~~~~~~~lVaHna-~FD~~fL~~~l~~~~~~~~~~--~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L 192 (239)
T PRK09146 116 LERILDELLEALAGKVVVVHYR-RIERDFLDQALRNRIGEGIEF--PVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRL 192 (239)
T ss_pred HHHHHHHHHHHhCCCEEEEECH-HHHHHHHHHHHHHhcCCCCCC--ceechHHHHHHHcccccccccchhccCCCCCCCH
Confidence 9999999999999999999999 9999999999987543 3333 489999988765421 1267899
Q ss_pred HHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHhhhcc
Q 023805 153 ATLASYFGLG-QQKHRSLDDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 153 ~~La~~~gi~-~~~H~Al~DA~~t~~l~~~l~~~l~~~ 189 (277)
++++++||++ ..+|+|++||.+|++|+.+++.+.+.+
T Consensus 193 ~~l~~~~gl~~~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 193 ADSRLRYGLPAYSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred HHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 9999999999 689999999999999999999887653
No 2
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=1.5e-30 Score=236.40 Aligned_cols=174 Identities=22% Similarity=0.329 Sum_probs=152.7
Q ss_pred CCCCCCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCC
Q 023805 5 IPSQAAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAP 84 (277)
Q Consensus 5 ~~~~~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~ 84 (277)
.+++...+..|++||+||||+++ ..++|||||++.++.++. +.++|+.+|+|.. ++.+..+||||+++|++++
T Consensus 7 ~~~~~~~~~~fvvlD~ETTGl~p--~~d~IIeIgav~v~~~g~-i~~~~~~lv~P~~----~~~~~~IhGIt~e~l~~ap 79 (313)
T PRK06063 7 GRPASHYPRGWAVVDVETSGFRP--GQARIISLAVLGLDADGN-VEQSVVTLLNPGV----DPGPTHVHGLTAEMLEGQP 79 (313)
T ss_pred CCCCcCCCCCEEEEEEECCCCCC--CCCEEEEEEEEEEECCce-eeeEEEEEECcCC----CCCCeecCCCCHHHHhCCC
Confidence 34556778899999999999998 668999999999986443 3589999999975 4567899999999999999
Q ss_pred CHHHHHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-C
Q 023805 85 EFEEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-Q 163 (277)
Q Consensus 85 ~f~ev~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~ 163 (277)
+|.+++.+|.+|+++.++||||+ .||+.||.+++.+++.+.|.. .++||+.+++ .+.+...+++|++|+++||++ .
T Consensus 80 ~f~ev~~~l~~~l~~~~lVaHNa-~FD~~fL~~~~~r~g~~~~~~-~~ldTl~lar-~~~~~~~~~kL~~l~~~~gi~~~ 156 (313)
T PRK06063 80 QFADIAGEVAELLRGRTLVAHNV-AFDYSFLAAEAERAGAELPVD-QVMCTVELAR-RLGLGLPNLRLETLAAHWGVPQQ 156 (313)
T ss_pred CHHHHHHHHHHHcCCCEEEEeCH-HHHHHHHHHHHHHcCCCCCCC-CEEehHHHHH-HhccCCCCCCHHHHHHHcCCCCC
Confidence 99999999999999999999999 999999999999999887753 4899998775 455666789999999999999 7
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhhc
Q 023805 164 QKHRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 164 ~~H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
++|+|++||++|++|+.+++++...
T Consensus 157 ~~H~Al~DA~ata~l~~~ll~~~~~ 181 (313)
T PRK06063 157 RPHDALDDARVLAGILRPSLERARE 181 (313)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 8999999999999999999887644
No 3
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=1.1e-30 Score=228.49 Aligned_cols=167 Identities=26% Similarity=0.372 Sum_probs=145.9
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
...+|+||+||||+++. ..++|||||+|.+.++... .++|+.||+|.. ++++.+.++||||.++|+++|+|.+++.
T Consensus 3 ~~r~vvlDtETTGldp~-~~drIIEIGaV~v~~~~~~-~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev~~ 78 (240)
T PRK05711 3 IMRQIVLDTETTGLNQR-EGHRIIEIGAVELINRRLT-GRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEVAD 78 (240)
T ss_pred CCeEEEEEeeCCCcCCC-CCCeEEEEEEEEEECCEEe-ccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHHHH
Confidence 45799999999999972 2579999999999987653 478999999988 8999999999999999999999999999
Q ss_pred HHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCC---CCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCC---CC
Q 023805 92 KIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPV---PVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQ---QK 165 (277)
Q Consensus 92 ~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~---~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~---~~ 165 (277)
+|.+|+++.++|+||+ .||+.||++++.++|...|. ...++||+.++++.+ |. ..++|+.||++||++. ..
T Consensus 79 ~f~~fi~~~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~-p~-~~~~L~aL~~~~gi~~~~r~~ 155 (240)
T PRK05711 79 EFLDFIRGAELIIHNA-PFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMF-PG-KRNSLDALCKRYGIDNSHRTL 155 (240)
T ss_pred HHHHHhCCCEEEEEcc-HHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHc-CC-CCCCHHHHHHHCCCCCCCCCC
Confidence 9999999999999999 99999999999999865552 235899998876554 44 3579999999999983 46
Q ss_pred CChHHHHHHHHHHHHHHHHh
Q 023805 166 HRSLDDVRMNLEVLKHCATV 185 (277)
Q Consensus 166 H~Al~DA~~t~~l~~~l~~~ 185 (277)
|+|+.||.++++||.+|...
T Consensus 156 H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 156 HGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred CCHHHHHHHHHHHHHHHHCc
Confidence 99999999999999998764
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=99.97 E-value=1.5e-30 Score=226.32 Aligned_cols=164 Identities=23% Similarity=0.376 Sum_probs=142.6
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHH
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKI 93 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l 93 (277)
.+|+||+||||+++. ..++|||||+|.+.++.. ..++|+.||+|.. .+++.+.++||||.++|+++|+|.+++.+|
T Consensus 1 r~vvlD~ETTGl~p~-~~d~IIEIgav~~~~~~~-~~~~f~~~i~P~~--~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f 76 (225)
T TIGR01406 1 RQIILDTETTGLDPK-GGHRIVEIGAVELVNRML-TGDNFHVYVNPER--DMPAEAAKVHGITDEFLADKPKFKEIADEF 76 (225)
T ss_pred CEEEEEeeCCCcCCC-CCCeEEEEEEEEEECCcE-ecceEEEEECcCC--CCCHHHHhccCCCHHHHhCCCCHHHHHHHH
Confidence 479999999999972 237999999999887654 3478999999998 799999999999999999999999999999
Q ss_pred HHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCC---CCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCC---CCCC
Q 023805 94 FSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAP---VPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQ---QKHR 167 (277)
Q Consensus 94 ~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p---~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~---~~H~ 167 (277)
.+|+++.++|+||+ .||+.||+.++.++|...+ ....++||+.+++..+ |. .+++|+.||++||++. ..|+
T Consensus 77 ~~fi~~~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~-p~-~~~~L~~L~~~~gi~~~~r~~H~ 153 (225)
T TIGR01406 77 LDFIGGSELVIHNA-AFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERF-PG-QRNSLDALCKRFKVDNSHRTLHG 153 (225)
T ss_pred HHHhCCCEEEEEec-HHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHc-CC-CCCCHHHHHHhcCCCCCCCCCcC
Confidence 99999999999999 9999999999999984322 1246999998876554 54 3689999999999982 4699
Q ss_pred hHHHHHHHHHHHHHHHH
Q 023805 168 SLDDVRMNLEVLKHCAT 184 (277)
Q Consensus 168 Al~DA~~t~~l~~~l~~ 184 (277)
|++||.++++||.+|..
T Consensus 154 Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 154 ALLDAHLLAEVYLALTG 170 (225)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 99999999999999876
No 5
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.97 E-value=3.3e-30 Score=213.41 Aligned_cols=166 Identities=27% Similarity=0.392 Sum_probs=148.5
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHH
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKI 93 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l 93 (277)
.+|+||+||||+++ ..++|+|||++.++++. +.+.|+.+|+|.. ++++++.++||||+++++++++|.+++.+|
T Consensus 1 ~~v~~D~Ettg~~~--~~~~Iieig~v~~~~~~--~~~~f~~~v~p~~--~i~~~~~~~~Git~~~l~~~~~~~~~~~~~ 74 (169)
T smart00479 1 TLVVIDCETTGLDP--GKDEIIEIAAVDVDGGR--IIVVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLEEL 74 (169)
T ss_pred CEEEEEeeCCCCCC--CCCeEEEEEEEEEECCE--eEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 38999999999987 56899999999999986 3578999999976 899999999999999999999999999999
Q ss_pred HHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CC-CCChHHH
Q 023805 94 FSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQ-KHRSLDD 171 (277)
Q Consensus 94 ~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~-~H~Al~D 171 (277)
.+|+.+.++++||+..||+.+|+.++.+.++..|....++|+..++.... +.. +.+|++++++||++ .. +|+|++|
T Consensus 75 ~~~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~-~~~-~~~L~~l~~~~~~~~~~~~H~A~~D 152 (169)
T smart00479 75 LEFLKGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALN-PGR-KYSLKKLAERLGLEVIGRAHRALDD 152 (169)
T ss_pred HHHhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHC-CCC-CCCHHHHHHHCCCCCCCCCcCcHHH
Confidence 99999999999998899999999999999998877667999998775444 333 79999999999999 44 4999999
Q ss_pred HHHHHHHHHHHHHhhh
Q 023805 172 VRMNLEVLKHCATVLF 187 (277)
Q Consensus 172 A~~t~~l~~~l~~~l~ 187 (277)
|++|++|+.+++.+++
T Consensus 153 a~~t~~l~~~~~~~~~ 168 (169)
T smart00479 153 ARATAKLFKKLVERLL 168 (169)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999988653
No 6
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=3.1e-30 Score=226.81 Aligned_cols=173 Identities=23% Similarity=0.318 Sum_probs=151.2
Q ss_pred CCCCCCcEEEEEeccCCCCCCCCC-CceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCH
Q 023805 8 QAAGTAEIVFFDLETTVPRRAGQR-FWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEF 86 (277)
Q Consensus 8 ~~~~~~~~v~~D~ETTg~~~~~~~-~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f 86 (277)
++....++|+||+||||+++ .. ++|||||+|.++++.+ +.++|+.+|+|.. ++++.+.++||||+++++++++|
T Consensus 54 ~~~~~~~~vv~D~ETTGl~p--~~~deIIeIgaV~~~~~~i-~~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~ 128 (244)
T PRK07740 54 IPLTDLPFVVFDLETTGFSP--QQGDEILSIGAVKTKGGEV-ETDTFYSLVKPKR--PIPEHILELTGITAEDVAFAPPL 128 (244)
T ss_pred CCccCCCEEEEEEeCCCCCC--CCCCeEEEEEEEEEECCEE-EEEEEEEEeCcCC--CCChhheeccCCCHHHHhCCCCH
Confidence 45566789999999999987 43 7999999999998865 4689999999998 89999999999999999999999
Q ss_pred HHHHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCC
Q 023805 87 EEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQK 165 (277)
Q Consensus 87 ~ev~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~ 165 (277)
.+++.+|.+|++++++||||+ .||+.||+.++.+... .++...++|++.++. .+.+..++++|++++++||++ ..+
T Consensus 129 ~evl~~f~~fi~~~~lVahna-~fD~~fL~~~~~~~~~-~~~~~~~iDt~~l~r-~l~~~~~~~sL~~l~~~~gi~~~~~ 205 (244)
T PRK07740 129 AEVLHRFYAFIGAGVLVAHHA-GHDKAFLRHALWRTYR-QPFTHRLIDTMFLTK-LLAHERDFPTLDDALAYYGIPIPRR 205 (244)
T ss_pred HHHHHHHHHHhCCCEEEEeCH-HHHHHHHHHHHHHhcC-CCcCCCeechHHHHH-HHcCCCCCCCHHHHHHHCCcCCCCC
Confidence 999999999999999999999 9999999998876542 344456999998764 455656689999999999999 678
Q ss_pred CChHHHHHHHHHHHHHHHHhhhc
Q 023805 166 HRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 166 H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
|+|++||++|++|+.+++..+..
T Consensus 206 H~Al~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 206 HHALGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999887643
No 7
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.8e-30 Score=220.47 Aligned_cols=167 Identities=18% Similarity=0.287 Sum_probs=145.1
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVA 90 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~ 90 (277)
.+..+|+||+||||+++ ..++|||||+|.++++.+...+.|+.+|+|.. .+++++.++||||++++++++++.+++
T Consensus 27 ~~~~~vviD~ETTGl~~--~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~--~i~~~~~~ihGIt~~~l~~~~~~~~vl 102 (202)
T PRK09145 27 PPDEWVALDCETTGLDP--RRAEIVSIAAVKIRGNRILTSERLELLVRPPQ--SLSAESIKIHRLRHQDLEDGLSEEEAL 102 (202)
T ss_pred CCCCEEEEEeECCCCCC--CCCceEEEEEEEEECCEEeecCceEEEECCCC--CCCHhHhhhcCcCHHHHhcCCCHHHHH
Confidence 55689999999999987 56899999999999887665578999999997 899999999999999999999999999
Q ss_pred HHHHHHhCCCEEEEeCCchhHHHHHHHHHHH-hCCCCCCCCceeehHHHHHHHhC---C-CCCCCCHHHHHHHhCCC-CC
Q 023805 91 DKIFSILNGRVWAGHNIRRFDCARIKEAFAE-IGKPAPVPVGMIDSLGVLTEKFG---R-RAGNMKMATLASYFGLG-QQ 164 (277)
Q Consensus 91 ~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~-~g~~~p~~~~~iDt~~l~~~~~~---~-~~~~~~L~~La~~~gi~-~~ 164 (277)
.+|.+|+++.++||||+ .||+.+|..++.+ .+...+. .++|+..++..... + ...+++|++++++||++ ..
T Consensus 103 ~~~~~~i~~~~lv~hn~-~fD~~fL~~~~~~~~~~~~~~--~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~ 179 (202)
T PRK09145 103 RQLLAFIGNRPLVGYYL-EFDVAMLNRYVRPLLGIPLPN--PLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLG 179 (202)
T ss_pred HHHHHHHcCCeEEEeCH-HHHHHHHHHHHHHhcCCCCCC--CeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCC
Confidence 99999999999999999 9999999999986 4555443 48999877643322 2 23468999999999998 67
Q ss_pred CCChHHHHHHHHHHHHHHHH
Q 023805 165 KHRSLDDVRMNLEVLKHCAT 184 (277)
Q Consensus 165 ~H~Al~DA~~t~~l~~~l~~ 184 (277)
+|+|++||++|++||.++..
T Consensus 180 ~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 180 RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCcHHHHHHHHHHHHHHHh
Confidence 89999999999999998865
No 8
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.97 E-value=2.7e-30 Score=222.22 Aligned_cols=172 Identities=21% Similarity=0.268 Sum_probs=146.1
Q ss_pred CCcEEEEEeccCCCCCC----CCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHH
Q 023805 12 TAEIVFFDLETTVPRRA----GQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFE 87 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~----~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ 87 (277)
+.+||+||+||||+++. +..++|||||+|.++++.+ .++|+.||+|...+.++++++++||||+++|+++++|.
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i--~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ 80 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEV--EDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFE 80 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcC--hhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHH
Confidence 45799999999996531 1247999999999997743 58999999998755689999999999999999999999
Q ss_pred HHHHHHHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC--CC
Q 023805 88 EVADKIFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG--QQ 164 (277)
Q Consensus 88 ev~~~l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~--~~ 164 (277)
+++.+|.+|+++ ..+++|++ .||+.+|++++.++|++.|+...++|+..++...+ +....++|.+++++||++ +.
T Consensus 81 evl~~f~~~~~~~~~~iv~~~-~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~-~~~~~~~L~~~~~~~gi~~~~~ 158 (207)
T PRK07748 81 ELVEKLAEYDKRCKPTIVTWG-NMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFF-GERNQTGLWKAIEEYGKEGTGK 158 (207)
T ss_pred HHHHHHHHHhCcCCeEEEEEC-HHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHh-CcCCCCCHHHHHHHcCCCCCCC
Confidence 999999999988 46666777 99999999999999998776567899886654443 444568999999999999 35
Q ss_pred CCChHHHHHHHHHHHHHHHHhhh
Q 023805 165 KHRSLDDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 165 ~H~Al~DA~~t~~l~~~l~~~l~ 187 (277)
+|+|++||++|++|+.+++....
T Consensus 159 ~H~Al~DA~~ta~l~~~l~~~~~ 181 (207)
T PRK07748 159 HHCALDDAMTTYNIFKLVEKDKE 181 (207)
T ss_pred CcChHHHHHHHHHHHHHHHhCcc
Confidence 89999999999999999998753
No 9
>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=3.9e-30 Score=222.71 Aligned_cols=171 Identities=20% Similarity=0.260 Sum_probs=147.2
Q ss_pred CCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 10 AGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
.....||+||+||||+++ ..+ |||||++.+.++... .++|+.+|+|.. ++++.+..+||||+++|+++++|.++
T Consensus 4 l~~~~fvv~D~ETTGl~~--~~~-IIeIgav~v~~~~~~-~~~f~~li~P~~--~i~~~a~~ihGIt~e~l~~~p~~~ev 77 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYA--GHD-IIEIGAVEIINRRIT-GNKFHTYIKPDR--PIDPDAIKIHGITDDMLKDKPDFKEI 77 (217)
T ss_pred EEecCEEEEEecCCCCCC--CCC-EEEEEEEEEECCCEe-eeEEEEEECcCC--CCCHHHHhhcCCCHHHHcCCCCHHHH
Confidence 456789999999999987 556 999999998766543 589999999997 89999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCC-CCCCCCHHHHHHHhCCC-C--CC
Q 023805 90 ADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGR-RAGNMKMATLASYFGLG-Q--QK 165 (277)
Q Consensus 90 ~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~-~~~~~~L~~La~~~gi~-~--~~ 165 (277)
+.+|.+|+++.++||||+ .||+.||..++.+.+...+....++|++.++...... ...+++|..++++||++ . .+
T Consensus 78 ~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~ 156 (217)
T TIGR00573 78 AEDFADYIRGAELVIHNA-SFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRAL 156 (217)
T ss_pred HHHHHHHhCCCEEEEecc-HHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCccc
Confidence 999999999999999999 9999999999998876545445689998776544321 12468999999999998 3 68
Q ss_pred CChHHHHHHHHHHHHHHHHhhh
Q 023805 166 HRSLDDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 166 H~Al~DA~~t~~l~~~l~~~l~ 187 (277)
|+|++||.+|++|+.+++.+..
T Consensus 157 H~Al~DA~~ta~l~~~l~~~~~ 178 (217)
T TIGR00573 157 HGALADAFILAKLYLVMTGKQT 178 (217)
T ss_pred CCHHHHHHHHHHHHHHHHhcch
Confidence 9999999999999999988653
No 10
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=7.2e-30 Score=225.28 Aligned_cols=168 Identities=26% Similarity=0.390 Sum_probs=149.7
Q ss_pred CCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 10 AGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
.++..+|+||+||||+++ ..++|||||+|.++++.. .+.|+.+|+|.. +|++.+..+||||+++|+++|+|.++
T Consensus 4 l~~~~~v~~D~ETTGl~~--~~d~IIEIa~v~v~~~~~--~~~~~~li~P~~--~I~~~a~~ihgIt~e~v~~~p~~~ev 77 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDV--KKDRIIEFAAIRFTFDEV--IDSVEFLINPER--VVSAESQRIHHISDAMLRDKPKIAEV 77 (250)
T ss_pred ccCCcEEEEEEeCCCCCC--CCCeEEEEEEEEEECCeE--EEEEEEEECcCC--CCCHhhhhccCcCHHHHhCCCCHHHH
Confidence 455789999999999987 678999999999998754 478999999998 89999999999999999999999999
Q ss_pred HHHHHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCCCCC-CCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCC
Q 023805 90 ADKIFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKPAPV-PVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKH 166 (277)
Q Consensus 90 ~~~l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~-~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H 166 (277)
+.+|.+|+++ .++||||+ .||+.+|.+++.++|++.+. ...+|||+.++. .+ +...+++|+.|+++||++ ..+|
T Consensus 78 ~~~~~~fl~~~~~lvghn~-~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar-~~-~~~~~~~L~~l~~~~g~~~~~aH 154 (250)
T PRK06310 78 FPQIKGFFKEGDYIVGHSV-GFDLQVLSQESERIGETFLSKHYYIIDTLRLAK-EY-GDSPNNSLEALAVHFNVPYDGNH 154 (250)
T ss_pred HHHHHHHhCCCCEEEEECH-HHHHHHHHHHHHHcCCCccccCCcEEehHHHHH-hc-ccCCCCCHHHHHHHCCCCCCCCc
Confidence 9999999986 89999999 99999999999999988764 257999998765 33 344578999999999999 6799
Q ss_pred ChHHHHHHHHHHHHHHHHhh
Q 023805 167 RSLDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 167 ~Al~DA~~t~~l~~~l~~~l 186 (277)
+|++||.+|++|+.++++++
T Consensus 155 ~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 155 RAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ChHHHHHHHHHHHHHHHHhc
Confidence 99999999999999998754
No 11
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=5.8e-30 Score=223.66 Aligned_cols=171 Identities=22% Similarity=0.219 Sum_probs=144.6
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhC-CCCHHHH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVES-APEFEEV 89 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~-a~~f~ev 89 (277)
....|++||+||||+++ ..++|||||++.++.++. +++.|+.+|+|.. ++++.+.++||||++++.. ++++.++
T Consensus 4 ~~~~~vv~D~ETTGl~p--~~d~Iieig~v~v~~~g~-~~~~~~~lv~P~~--~i~~~a~~IhGIt~e~l~~~g~~~~~v 78 (232)
T PRK07942 4 HPGPLAAFDLETTGVDP--ETARIVTAALVVVDADGE-VVESREWLADPGV--EIPEEASAVHGITTEYARAHGRPAAEV 78 (232)
T ss_pred ccCcEEEEEeccCCCCC--CCCeeEEEEEEEEeCCCc-cccceEEEECCCC--CCCHHHHHHhCCCHHHHHhhCCCHHHH
Confidence 45689999999999998 678999999999985332 2478999999988 8999999999999999975 6788888
Q ss_pred HHHHHHHh-----CCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-C
Q 023805 90 ADKIFSIL-----NGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-Q 163 (277)
Q Consensus 90 ~~~l~~~l-----~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~ 163 (277)
+.+|.+++ .+.++||||+ .||+.+|.+++.++|...+....++|++.+.........++++|++|+++||++ .
T Consensus 79 l~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~~ 157 (232)
T PRK07942 79 LAEIADALREAWARGVPVVVFNA-PYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRLD 157 (232)
T ss_pred HHHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCCC
Confidence 88888776 4679999999 999999999999999875544458999976644332234578999999999999 6
Q ss_pred CCCChHHHHHHHHHHHHHHHHhhh
Q 023805 164 QKHRSLDDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 164 ~~H~Al~DA~~t~~l~~~l~~~l~ 187 (277)
.+|+|++||.+|++|+.+++++..
T Consensus 158 ~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 158 NAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred CCCChHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999988654
No 12
>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=8.8e-30 Score=211.47 Aligned_cols=161 Identities=24% Similarity=0.386 Sum_probs=140.0
Q ss_pred EEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHH
Q 023805 15 IVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIF 94 (277)
Q Consensus 15 ~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~ 94 (277)
+|+||+||||+++. ..++|||||++.++++.. ..++|+.+|+|.. .+++.+.++||||+++++++++|.+++.+|.
T Consensus 1 ~v~~D~ETTGl~~~-~~~~iieig~v~v~~~~~-~~~~~~~~v~P~~--~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~ 76 (167)
T cd06131 1 QIVLDTETTGLDPR-EGHRIIEIGCVELINRRL-TGNTFHVYINPER--DIPEEAFKVHGITDEFLADKPKFAEIADEFL 76 (167)
T ss_pred CEEEEeeCCCCCCC-CCCeEEEEEEEEEECCcE-eccEEEEEECCCC--CCCHHHHHHhCCCHHHHhcCCCHHHHHHHHH
Confidence 58999999999861 346999999999988654 3468999999998 7999999999999999999999999999999
Q ss_pred HHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCC--CCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCC---CCCChH
Q 023805 95 SILNGRVWAGHNIRRFDCARIKEAFAEIGKPAP--VPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQ---QKHRSL 169 (277)
Q Consensus 95 ~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p--~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~---~~H~Al 169 (277)
+|+++.++|+||+ .||+.+|++++.++++..+ .+..++||+.++...+ +. ..++|++++++||++. .+|+|+
T Consensus 77 ~~l~~~~lv~hn~-~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~-~~-~~~~L~~l~~~~~i~~~~~~~H~Al 153 (167)
T cd06131 77 DFIRGAELVIHNA-SFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKF-PG-KPNSLDALCKRFGIDNSHRTLHGAL 153 (167)
T ss_pred HHHCCCeEEEeCh-HHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHc-CC-CCCCHHHHHHHCCCCCCCCCCCChH
Confidence 9999999999999 9999999999999887543 2357999998775544 43 4689999999999982 579999
Q ss_pred HHHHHHHHHHHHH
Q 023805 170 DDVRMNLEVLKHC 182 (277)
Q Consensus 170 ~DA~~t~~l~~~l 182 (277)
+||+++++|+.+|
T Consensus 154 ~Da~~~a~l~~~l 166 (167)
T cd06131 154 LDAELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999876
No 13
>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=7.2e-30 Score=209.26 Aligned_cols=155 Identities=29% Similarity=0.432 Sum_probs=139.3
Q ss_pred EEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHH
Q 023805 15 IVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIF 94 (277)
Q Consensus 15 ~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~ 94 (277)
||+||+||||..+ ++|||||++.++++.. +++|+.+|+|.. ++++++.++||||+++++++++|.+++++|.
T Consensus 1 ~v~~D~Ettg~~~----~~ii~ig~v~~~~~~~--~~~~~~~i~p~~--~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~ 72 (156)
T cd06130 1 FVAIDFETANADR----ASACSIGLVKVRDGQI--VDTFYTLIRPPT--RFDPFNIAIHGITPEDVADAPTFPEVWPEIK 72 (156)
T ss_pred CEEEEEeCCCCCC----CceEEEEEEEEECCEE--EEEEEEEeCcCC--CCChhhccccCcCHHHHhcCCCHHHHHHHHH
Confidence 6899999998653 6899999999997654 489999999998 8999999999999999999999999999999
Q ss_pred HHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCCCCCChHHHHHH
Q 023805 95 SILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQQKHRSLDDVRM 174 (277)
Q Consensus 95 ~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~~~H~Al~DA~~ 174 (277)
+|+++.++||||+ .||+.+|++++.++|+..+ ...++|++.++.+.+ +..++++|+.++++||++..+|+|++||++
T Consensus 73 ~~l~~~~lv~hn~-~fD~~~l~~~~~~~g~~~~-~~~~idt~~~~~~~~-~~~~~~~L~~l~~~~g~~~~~H~Al~Da~~ 149 (156)
T cd06130 73 PFLGGSLVVAHNA-SFDRSVLRAALEAYGLPPP-PYQYLCTVRLARRVW-PLLPNHKLNTVAEHLGIELNHHDALEDARA 149 (156)
T ss_pred HHhCCCEEEEeCh-HHhHHHHHHHHHHcCCCCC-CCCEEEHHHHHHHHh-ccCCCCCHHHHHHHcCCCccCcCchHHHHH
Confidence 9999999999999 9999999999999998866 346999998776554 556789999999999999339999999999
Q ss_pred HHHHHH
Q 023805 175 NLEVLK 180 (277)
Q Consensus 175 t~~l~~ 180 (277)
+++|+.
T Consensus 150 ta~l~~ 155 (156)
T cd06130 150 CAEILL 155 (156)
T ss_pred HHHHHh
Confidence 999984
No 14
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=2.1e-29 Score=222.67 Aligned_cols=168 Identities=24% Similarity=0.405 Sum_probs=149.4
Q ss_pred CCCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHH
Q 023805 8 QAAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFE 87 (277)
Q Consensus 8 ~~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ 87 (277)
.+..+..|++||+||||.++ ..++|||||+|.++++.. +++|+.+|+|. .+++.+.++||||++++++++++.
T Consensus 63 ~~~~~~~~vv~DiETTG~~~--~~~~IIEIGAv~v~~g~i--~~~f~~~v~p~---~ip~~~~~itGIt~e~l~~ap~~~ 135 (257)
T PRK08517 63 TPIKDQVFCFVDIETNGSKP--KKHQIIEIGAVKVKNGEI--IDRFESFVKAK---EVPEYITELTGITYEDLENAPSLK 135 (257)
T ss_pred CCCCCCCEEEEEEeCCCCCC--CCCeEEEEEEEEEECCEE--EEEEEEEECCC---CCChhhhhhcCcCHHHHcCCCCHH
Confidence 45677899999999999987 567999999999987644 47899999996 589999999999999999999999
Q ss_pred HHHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCC
Q 023805 88 EVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKH 166 (277)
Q Consensus 88 ev~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H 166 (277)
+++.+|.+|+++.++||||+ .||+.||.+++.++|.... ...++||+.++...+ + ..+++|++|+++||++ ..+|
T Consensus 136 evl~~f~~fl~~~v~VaHNa-~FD~~fL~~~l~r~g~~~~-~~~~ldtl~la~~~~-~-~~~~~L~~L~~~lgi~~~~~H 211 (257)
T PRK08517 136 EVLEEFRLFLGDSVFVAHNV-NFDYNFISRSLEEIGLGPL-LNRKLCTIDLAKRTI-E-SPRYGLSFLKELLGIEIEVHH 211 (257)
T ss_pred HHHHHHHHHHCCCeEEEECH-HHHHHHHHHHHHHcCCCCC-CCCcEehHHHHHHHc-c-CCCCCHHHHHHHcCcCCCCCC
Confidence 99999999999999999999 9999999999999998754 345899998876554 3 2468999999999999 5899
Q ss_pred ChHHHHHHHHHHHHHHHHhh
Q 023805 167 RSLDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 167 ~Al~DA~~t~~l~~~l~~~l 186 (277)
+|++||.+|++|+..++.++
T Consensus 212 rAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 212 RAYADALAAYEIFKICLLNL 231 (257)
T ss_pred ChHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999875
No 15
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.9e-29 Score=228.66 Aligned_cols=168 Identities=25% Similarity=0.383 Sum_probs=152.1
Q ss_pred CCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 10 AGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
..+.++|+||+||||+++ ..++|||||++.++++.+ +++|+.+|+|.. ++++.++++||||+++|+++++|.++
T Consensus 5 ~~~~~~Vv~DlETTGl~p--~~~eIIEIgaV~v~~g~i--~~~f~~lVkP~~--~I~~~a~~ihGIT~e~l~~~~~~~ev 78 (313)
T PRK06807 5 SLPLDYVVIDFETTGFNP--YNDKIIQVAAVKYRNHEL--VDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPTIEEV 78 (313)
T ss_pred CCCCCEEEEEEECCCCCC--CCCeEEEEEEEEEECCEE--EEEEEEEECcCC--CCCHhhhccCCCCHHHHhCCCCHHHH
Confidence 467799999999999987 678999999999997643 589999999998 89999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCCCCCChH
Q 023805 90 ADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQQKHRSL 169 (277)
Q Consensus 90 ~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~~~H~Al 169 (277)
+.+|.+|+++.++||||+ .||+.+|.+++.++|++.+. ..++|++.++.. +.+...+++|++|+++||++.++|+|+
T Consensus 79 l~~f~~fl~~~~lVaHNa-~FD~~fL~~~~~~~gl~~~~-~~~iDtl~la~~-~~~~~~~~kL~~L~~~lgi~~~~H~Al 155 (313)
T PRK06807 79 LPLFLAFLHTNVIVAHNA-SFDMRFLKSNVNMLGLPEPK-NKVIDTVFLAKK-YMKHAPNHKLETLKRMLGIRLSSHNAF 155 (313)
T ss_pred HHHHHHHHcCCeEEEEcH-HHHHHHHHHHHHHcCCCCCC-CCEeeHHHHHHH-HhCCCCCCCHHHHHHHcCCCCCCcChH
Confidence 999999999999999999 99999999999999997654 359999987654 446667899999999999998899999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 023805 170 DDVRMNLEVLKHCATVL 186 (277)
Q Consensus 170 ~DA~~t~~l~~~l~~~l 186 (277)
+||.+|++|+.++....
T Consensus 156 ~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 156 DDCITCAAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 99999999999998865
No 16
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.9e-29 Score=227.97 Aligned_cols=165 Identities=23% Similarity=0.342 Sum_probs=146.8
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHH
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKI 93 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l 93 (277)
+|++||+||||.. .++|||||++.++++.+ ++.|+++|+|... .+++.+.++||||+++|+++++|.+++.+|
T Consensus 2 ~~vviD~ETTg~~----~d~IieIgav~v~~g~i--~~~f~~lv~P~~~-~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~ 74 (309)
T PRK06195 2 NFVAIDFETANEK----RNSPCSIGIVVVKDGEI--VEKVHYLIKPKEM-RFMPINIGIHGIRPHMVEDELEFDKIWEKI 74 (309)
T ss_pred cEEEEEEeCCCCC----CCceEEEEEEEEECCEE--EEEEEEEECCCCC-CCChhheeccCcCHHHHhCCCCHHHHHHHH
Confidence 6999999999753 47899999999988754 4789999999852 578889999999999999999999999999
Q ss_pred HHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCCCCCChHHHHH
Q 023805 94 FSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQQKHRSLDDVR 173 (277)
Q Consensus 94 ~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~~~H~Al~DA~ 173 (277)
.+|+++.++||||+ .||+.+|++++.+++++.|.. .++||+.++.+ +.+...+++|.+|+++||++..+|+|++||+
T Consensus 75 ~~fl~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~-~~idT~~lar~-l~~~~~~~~L~~L~~~~gi~~~~H~Al~DA~ 151 (309)
T PRK06195 75 KHYFNNNLVIAHNA-SFDISVLRKTLELYNIPMPSF-EYICTMKLAKN-FYSNIDNARLNTVNNFLGYEFKHHDALADAM 151 (309)
T ss_pred HHHhCCCEEEEECc-HHHHHHHHHHHHHhCCCCCCC-CEEEHHHHHHH-HcCCCCcCCHHHHHHHcCCCCcccCCHHHHH
Confidence 99999999999999 999999999999999887753 59999987754 4566678999999999999977999999999
Q ss_pred HHHHHHHHHHHhhhc
Q 023805 174 MNLEVLKHCATVLFL 188 (277)
Q Consensus 174 ~t~~l~~~l~~~l~~ 188 (277)
+|++|+.++++++..
T Consensus 152 ata~l~~~l~~~~~~ 166 (309)
T PRK06195 152 ACSNILLNISKELNS 166 (309)
T ss_pred HHHHHHHHHHHHhcc
Confidence 999999999987643
No 17
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.1e-29 Score=219.16 Aligned_cols=163 Identities=27% Similarity=0.408 Sum_probs=144.3
Q ss_pred CcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHH
Q 023805 13 AEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADK 92 (277)
Q Consensus 13 ~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~ 92 (277)
..+++||+||||+++ ..++|||||++ +.. ..+.|+.+|+|.. +|++.+.++||||+++|+++|+|.+++.+
T Consensus 2 ~~~vv~D~ETTGl~~--~~d~IIeig~v--~~~---~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~~ 72 (232)
T PRK06309 2 PALIFYDTETTGTQI--DKDRIIEIAAY--NGV---TSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQK 72 (232)
T ss_pred CcEEEEEeeCCCCCC--CCCEEEEEEEE--cCc---cccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 469999999999987 67899999995 322 2368999999998 89999999999999999999999999999
Q ss_pred HHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCCChHH
Q 023805 93 IFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKHRSLD 170 (277)
Q Consensus 93 l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H~Al~ 170 (277)
|.+|+++ .++||||+..||+.+|.+++.++|++.+. ..++||+.++.. +.+...+++|+.++++||++ ..+|+|++
T Consensus 73 ~~~fi~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~-~~~iDt~~l~~~-~~~~~~~~~L~~l~~~~~~~~~~aH~Al~ 150 (232)
T PRK06309 73 FIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPPT-LRTIDSLKWAQK-YRPDLPKHNLQYLRQVYGFEENQAHRALD 150 (232)
T ss_pred HHHHHcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCC-CcEEeHHHHHHH-HcCCCCCCCHHHHHHHcCCCCCCCCCcHH
Confidence 9999985 69999995489999999999999998765 469999988754 55666679999999999998 78999999
Q ss_pred HHHHHHHHHHHHHHhh
Q 023805 171 DVRMNLEVLKHCATVL 186 (277)
Q Consensus 171 DA~~t~~l~~~l~~~l 186 (277)
||.+|++|+.++++++
T Consensus 151 Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 151 DVITLHRVFSALVGDL 166 (232)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999999865
No 18
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.1e-28 Score=209.83 Aligned_cols=163 Identities=21% Similarity=0.247 Sum_probs=137.2
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
..+||+||+||||+++ .++|||||+|.++++.. +++|+.+|+|.. +++.+++++||||+++|+++|+|.+++.
T Consensus 4 ~~~~vvlD~EtTGl~~---~~eIIeIgaV~v~~g~~--~~~f~~lv~P~~--~i~~~~~~lhGIt~~~v~~ap~~~evl~ 76 (195)
T PRK07247 4 LETYIAFDLEFNTVNG---VSHIIQVSAVKYDDHKE--VDSFDSYVYTDV--PLQSFINGLTGITADKIADAPKVEEVLA 76 (195)
T ss_pred CCeEEEEEeeCCCCCC---CCeEEEEEEEEEECCEE--EEEEEEEECCCC--CCCccceecCCCCHHHHhCCCCHHHHHH
Confidence 3589999999999875 47899999999998754 478999999998 8999999999999999999999999999
Q ss_pred HHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHH-HHh--CCCCCCCCHHHHHHHhCCCCCCCCh
Q 023805 92 KIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLT-EKF--GRRAGNMKMATLASYFGLGQQKHRS 168 (277)
Q Consensus 92 ~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~-~~~--~~~~~~~~L~~La~~~gi~~~~H~A 168 (277)
+|.+|+++.++||||+..||+.+|.+ .|...+.. ..+|+...+. +.. .+...+++|.+||++||++..+|+|
T Consensus 77 ~f~~f~~~~~lVaHNa~~fD~~fL~~----~g~~~~~~-~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~~~HrA 151 (195)
T PRK07247 77 AFKEFVGELPLIGYNAQKSDLPILAE----NGLDLSDQ-YQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKGRGHNS 151 (195)
T ss_pred HHHHHHCCCeEEEEeCcHhHHHHHHH----cCCCcCCC-ceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCCCCcCC
Confidence 99999999999999993489999864 46554322 3577765431 111 2455789999999999999778999
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 023805 169 LDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 169 l~DA~~t~~l~~~l~~~l 186 (277)
++||++|+.|+.++++..
T Consensus 152 l~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 152 LEDARMTARVYESFLESD 169 (195)
T ss_pred HHHHHHHHHHHHHHHhhc
Confidence 999999999999998854
No 19
>PRK06722 exonuclease; Provisional
Probab=99.97 E-value=6.3e-29 Score=221.04 Aligned_cols=171 Identities=15% Similarity=0.238 Sum_probs=144.5
Q ss_pred CCCcEEEEEeccCCCCCC-CCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 11 GTAEIVFFDLETTVPRRA-GQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~-~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
....|++||+|||+.... ...++|||||+|.++++.+.++++|+.+|+|.. +++++++++||||++||+++|+|.++
T Consensus 3 ~~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--~I~~~i~~LTGIT~emV~~AP~f~eV 80 (281)
T PRK06722 3 NATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--RLTRHTTKLTGITKKDLIGVEKFPQI 80 (281)
T ss_pred CCCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--cCCHhHhhhcCCCHHHHcCCCCHHHH
Confidence 457899999999953221 134799999999999886666789999999998 89999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCC--CceeehHHHHHHHhCCC-CCCCCHHHHHHHhCCC--CC
Q 023805 90 ADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVP--VGMIDSLGVLTEKFGRR-AGNMKMATLASYFGLG--QQ 164 (277)
Q Consensus 90 ~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~--~~~iDt~~l~~~~~~~~-~~~~~L~~La~~~gi~--~~ 164 (277)
+.+|.+|+++..+|+||+ .||+.||.+++.++|++.|.. ..++|+..++...+... ...++|++++++||++ +.
T Consensus 81 l~ef~~fig~~~lvahna-~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~~g~ 159 (281)
T PRK06722 81 IEKFIQFIGEDSIFVTWG-KEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEGK 159 (281)
T ss_pred HHHHHHHHCCCcEEEEEe-HHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCCCCC
Confidence 999999999888888888 999999999999999887653 24688887664433211 1347899999999999 46
Q ss_pred CCChHHHHHHHHHHHHHHHH
Q 023805 165 KHRSLDDVRMNLEVLKHCAT 184 (277)
Q Consensus 165 ~H~Al~DA~~t~~l~~~l~~ 184 (277)
+|+|++||.+|++|+.+|++
T Consensus 160 ~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 160 QHRALADAENTANILLKAYS 179 (281)
T ss_pred CcCcHHHHHHHHHHHHHHhc
Confidence 89999999999999999985
No 20
>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=99.96 E-value=4.6e-29 Score=209.52 Aligned_cols=157 Identities=26% Similarity=0.362 Sum_probs=132.1
Q ss_pred EEEEEeccCCCC-CCCCCCceEEEEEEEEECCeee-----------eeceEEEeecCCCCCCCCchhhhhcCCCHHHHhC
Q 023805 15 IVFFDLETTVPR-RAGQRFWVLEFGAIIVCPRKLV-----------ELESFSTLIKPKDLSAVALKSSRCDGITREAVES 82 (277)
Q Consensus 15 ~v~~D~ETTg~~-~~~~~~~IieIg~v~v~~~~~~-----------~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~ 82 (277)
|++||+||||++ + ..++|||||++.++++.+. +.++|+++|+|.. +|++.++++||||.+++.+
T Consensus 1 ~vv~D~ETTGl~~~--~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~--~I~~~a~~IhGIt~e~l~~ 76 (177)
T cd06136 1 FVFLDLETTGLPKH--NRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR--AISPGASEITGLSNDLLEH 76 (177)
T ss_pred CeEEeeecCCCCCC--CCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC--cCChhHHHHhCcCHHHHhc
Confidence 689999999998 4 4689999999999976431 2468999999998 8999999999999999999
Q ss_pred CCCHHH-HHHHHHHHhC---C-CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHH
Q 023805 83 APEFEE-VADKIFSILN---G-RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLAS 157 (277)
Q Consensus 83 a~~f~e-v~~~l~~~l~---~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~ 157 (277)
+++|.+ +.+.+.+|+. + .++||||+..||+.||++++.++|...+....++||+.++.... + +|++|++
T Consensus 77 ~~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~-~-----~L~~l~~ 150 (177)
T cd06136 77 KAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD-Q-----SLGSLYK 150 (177)
T ss_pred CCCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-h-----hHHHHHH
Confidence 998764 5566666663 3 58999997479999999999999998774456899998776543 2 8999998
Q ss_pred -HhCCC-CCCCChHHHHHHHHHHHHH
Q 023805 158 -YFGLG-QQKHRSLDDVRMNLEVLKH 181 (277)
Q Consensus 158 -~~gi~-~~~H~Al~DA~~t~~l~~~ 181 (277)
+||++ ..+|+|++||.+|++|+.+
T Consensus 151 ~~~~~~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 151 RLFGQEPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHhCCCcccccchHHHHHHHHHHHhh
Confidence 48999 7899999999999999875
No 21
>PRK07883 hypothetical protein; Validated
Probab=99.96 E-value=1.1e-28 Score=239.35 Aligned_cols=176 Identities=30% Similarity=0.373 Sum_probs=157.1
Q ss_pred CCCCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCH
Q 023805 7 SQAAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEF 86 (277)
Q Consensus 7 ~~~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f 86 (277)
..+.....||+||+||||+++ ..++|||||+|.++++.+ ++.|+.+|+|.. .+++++.++||||+++++++++|
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~p--~~~~IIEIgaV~v~~g~i--v~~f~~lV~P~~--~i~~~~~~itGIt~e~l~~ap~~ 82 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGSP--AGDAITEIGAVKVRGGEV--LGEFATLVNPGR--PIPPFITVLTGITTAMVAGAPPI 82 (557)
T ss_pred CCCCcCCCEEEEEEecCCCCC--CCCeEEEEEEEEEECCEE--EEEEEEEECCCC--CCChhHHhhcCCCHHHHhCCCCH
Confidence 345667899999999999988 668999999999997754 478999999987 89999999999999999999999
Q ss_pred HHHHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCC-CCCCCCHHHHHHHhCCC-CC
Q 023805 87 EEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGR-RAGNMKMATLASYFGLG-QQ 164 (277)
Q Consensus 87 ~ev~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~-~~~~~~L~~La~~~gi~-~~ 164 (277)
.+++.+|.+|+++.++||||+ .||+.+|+.++.++|++.+. ..++||+.++...+.+ ...+++|++|+++||++ ..
T Consensus 83 ~evl~~f~~fl~~~~lVaHNa-~FD~~fL~~~~~r~g~~~~~-~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~~ 160 (557)
T PRK07883 83 EEVLPAFLEFARGAVLVAHNA-PFDIGFLRAAAARCGYPWPG-PPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTTP 160 (557)
T ss_pred HHHHHHHHHHhcCCEEEEeCc-HHHHHHHHHHHHHcCCCCCC-CCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccCC
Confidence 999999999999999999999 99999999999999998764 3589999887665532 55789999999999999 78
Q ss_pred CCChHHHHHHHHHHHHHHHHhhhccc
Q 023805 165 KHRSLDDVRMNLEVLKHCATVLFLES 190 (277)
Q Consensus 165 ~H~Al~DA~~t~~l~~~l~~~l~~~~ 190 (277)
+|+|++||.+|++|+.+++.++...+
T Consensus 161 ~H~Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 161 THRALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999886433
No 22
>PRK05168 ribonuclease T; Provisional
Probab=99.96 E-value=3.3e-28 Score=209.74 Aligned_cols=170 Identities=18% Similarity=0.204 Sum_probs=142.3
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEEC---CeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHH-HhCCCCH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCP---RKLVELESFSTLIKPKDLSAVALKSSRCDGITREA-VESAPEF 86 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~---~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~-l~~a~~f 86 (277)
....+++||+||||+++ ..++|||||+|.+.. +.+...++|+.+|+|.....+++.+.++||||+++ +++++++
T Consensus 15 ~~~~~vv~D~ETTGl~~--~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~ 92 (211)
T PRK05168 15 RGFLPVVIDVETAGFNA--KTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSE 92 (211)
T ss_pred cCCceEEEEeeCCCCCC--CCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCCh
Confidence 45578999999999998 678999999999873 33334589999999954347999999999999886 8889999
Q ss_pred HHHHHHHHHHhC---------CCEEEEeCCchhHHHHHHHHHHHhCCCC-CC-CCceeehHHHHHHHhCCCCCCCCHHHH
Q 023805 87 EEVADKIFSILN---------GRVWAGHNIRRFDCARIKEAFAEIGKPA-PV-PVGMIDSLGVLTEKFGRRAGNMKMATL 155 (277)
Q Consensus 87 ~ev~~~l~~~l~---------~~~lv~hn~~~fD~~~L~~~~~~~g~~~-p~-~~~~iDt~~l~~~~~~~~~~~~~L~~L 155 (277)
.+++.++.+|+. +.++||||+ .||+.||.+++.++++.. ++ +..++||+.+++..+ + ..+|..+
T Consensus 93 ~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~-~---~~~L~~l 167 (211)
T PRK05168 93 KEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLAL-G---QTVLAKA 167 (211)
T ss_pred HHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHc-C---CCCHHHH
Confidence 999888888774 579999999 999999999999998753 22 235899998876543 3 3689999
Q ss_pred HHHhCCC---CCCCChHHHHHHHHHHHHHHHHhhh
Q 023805 156 ASYFGLG---QQKHRSLDDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 156 a~~~gi~---~~~H~Al~DA~~t~~l~~~l~~~l~ 187 (277)
+++||++ ..+|+|++||.+|++|+.++++++.
T Consensus 168 ~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 168 CQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred HHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 9999998 3689999999999999999999874
No 23
>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=99.96 E-value=2.2e-28 Score=204.22 Aligned_cols=166 Identities=22% Similarity=0.271 Sum_probs=144.0
Q ss_pred EEEEEeccCCCCCC---CCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 15 IVFFDLETTVPRRA---GQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 15 ~v~~D~ETTg~~~~---~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
||+||+||||+++. ...++|||||+|.+++++..++++|+.+|+|.....+++++.++||||.++++++++|.+++.
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 68999999999861 123799999999999987656789999999998667899999999999999999999999999
Q ss_pred HHHHHhCCC--EEEEeCCchhHHHHHHHHHHHhCCC--CCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-C-CC
Q 023805 92 KIFSILNGR--VWAGHNIRRFDCARIKEAFAEIGKP--APVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-Q-QK 165 (277)
Q Consensus 92 ~l~~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~--~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~-~~ 165 (277)
+|.+|+++. .+++|+. .||..++..++.+.+.. .+....++|+..++...+ +...+++|.+++++||++ . ..
T Consensus 81 ~~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~-~~~~~~~L~~l~~~~gi~~~~~~ 158 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFY-GLKKRTGLSKALEYLGLEFEGRH 158 (176)
T ss_pred HHHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHh-CCCCCCCHHHHHHHCCCCCCCCC
Confidence 999999987 6777777 99999988888888775 445567999998887655 444689999999999998 4 79
Q ss_pred CChHHHHHHHHHHHHHH
Q 023805 166 HRSLDDVRMNLEVLKHC 182 (277)
Q Consensus 166 H~Al~DA~~t~~l~~~l 182 (277)
|+|++||+++++|+.+|
T Consensus 159 H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 159 HRGLDDARNIARILKRL 175 (176)
T ss_pred cCcHHHHHHHHHHHHHh
Confidence 99999999999999987
No 24
>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=4.1e-28 Score=207.49 Aligned_cols=168 Identities=19% Similarity=0.205 Sum_probs=139.2
Q ss_pred CcEEEEEeccCCCCCCCCCCceEEEEEEEEEC---CeeeeeceEEEeecCCCCCCCCchhhhhcCCCHH-HHhCCCCHHH
Q 023805 13 AEIVFFDLETTVPRRAGQRFWVLEFGAIIVCP---RKLVELESFSTLIKPKDLSAVALKSSRCDGITRE-AVESAPEFEE 88 (277)
Q Consensus 13 ~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~---~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e-~l~~a~~f~e 88 (277)
..+++||+||||+++ ..++|||||+|.+.. +.+...++|+.+|+|....++++.+.++||||++ ++++++++.+
T Consensus 8 ~~~vv~D~ETTGl~~--~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~~ 85 (200)
T TIGR01298 8 YLPVVVDVETGGFNA--KTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEYE 85 (200)
T ss_pred CeeEEEEeeCCCCCC--CCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchHH
Confidence 468999999999998 568999999999863 3333346799999985434799999999999976 6899999888
Q ss_pred HHHHHHHHh---------CCCEEEEeCCchhHHHHHHHHHHHhCCCC-CC-CCceeehHHHHHHHhCCCCCCCCHHHHHH
Q 023805 89 VADKIFSIL---------NGRVWAGHNIRRFDCARIKEAFAEIGKPA-PV-PVGMIDSLGVLTEKFGRRAGNMKMATLAS 157 (277)
Q Consensus 89 v~~~l~~~l---------~~~~lv~hn~~~fD~~~L~~~~~~~g~~~-p~-~~~~iDt~~l~~~~~~~~~~~~~L~~La~ 157 (277)
++.++..++ ++.++||||+ .||+.||++++++++... +. +..++||+.+++..+ + ..+|..+++
T Consensus 86 ~~~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~-~---~~~L~~l~~ 160 (200)
T TIGR01298 86 ALHEIFKVVRKAMKASGCQRAILVGHNA-NFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY-G---QTVLAKACQ 160 (200)
T ss_pred HHHHHHHHHHHHHHhcccCCCEEEEECc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc-C---cccHHHHHH
Confidence 888887776 5679999999 999999999999998752 22 235899998875443 3 468999999
Q ss_pred HhCCC---CCCCChHHHHHHHHHHHHHHHHhhh
Q 023805 158 YFGLG---QQKHRSLDDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 158 ~~gi~---~~~H~Al~DA~~t~~l~~~l~~~l~ 187 (277)
+||++ .++|+|++||.+|++|+.+++.++.
T Consensus 161 ~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 161 AAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred HcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 99998 3789999999999999999998764
No 25
>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=6.5e-28 Score=204.58 Aligned_cols=165 Identities=21% Similarity=0.230 Sum_probs=133.6
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECC---eeeeeceEEEeecCCCCCCCCchhhhhcCCCHHH-HhCCCCHHHH
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPR---KLVELESFSTLIKPKDLSAVALKSSRCDGITREA-VESAPEFEEV 89 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~---~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~-l~~a~~f~ev 89 (277)
..|+||+||||+++ ..++|||||+|.+.++ .+...++|+++|+|....++++.+.++||||+++ ++.++...++
T Consensus 6 ~~vv~D~ETTGl~~--~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~ 83 (189)
T cd06134 6 LPVVVDVETGGFNP--QTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEA 83 (189)
T ss_pred eeEEEEecCCCCCC--CCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHH
Confidence 57999999999998 6789999999999742 2234589999999953337999999999999986 5666666666
Q ss_pred HHHHHHHhC---------CCEEEEeCCchhHHHHHHHHHHHhCCC-CCC-CCceeehHHHHHHHhCCCCCCCCHHHHHHH
Q 023805 90 ADKIFSILN---------GRVWAGHNIRRFDCARIKEAFAEIGKP-APV-PVGMIDSLGVLTEKFGRRAGNMKMATLASY 158 (277)
Q Consensus 90 ~~~l~~~l~---------~~~lv~hn~~~fD~~~L~~~~~~~g~~-~p~-~~~~iDt~~l~~~~~~~~~~~~~L~~La~~ 158 (277)
+.+|.+++. +.++||||+ .||+.||++++.++|+. .++ +..++||+.+++..+ + +.+|+++|++
T Consensus 84 ~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~-~---~~~L~~l~~~ 158 (189)
T cd06134 84 LKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAY-G---QTVLAKACQA 158 (189)
T ss_pred HHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHh-C---CCcHHHHHHH
Confidence 666555542 579999999 99999999999999983 332 235899998876543 3 4689999999
Q ss_pred hCCC---CCCCChHHHHHHHHHHHHHHHHh
Q 023805 159 FGLG---QQKHRSLDDVRMNLEVLKHCATV 185 (277)
Q Consensus 159 ~gi~---~~~H~Al~DA~~t~~l~~~l~~~ 185 (277)
||++ ..+|+|++||.+|++|+.+|+++
T Consensus 159 ~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 159 AGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 9998 36899999999999999999874
No 26
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.8e-27 Score=216.37 Aligned_cols=170 Identities=17% Similarity=0.272 Sum_probs=141.3
Q ss_pred CCCCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCH
Q 023805 7 SQAAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEF 86 (277)
Q Consensus 7 ~~~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f 86 (277)
+++.....||+||+||||+++ ..++|||||+|.+..++. +.++|+++|+|.. .+. ...+||||+++|+++++|
T Consensus 40 ~~~~~~~~fVvlDiETTGLdp--~~drIIeIgAV~i~~~g~-ive~f~tLVnP~~--~~~--p~~LHGIT~e~La~AP~f 112 (377)
T PRK05601 40 QEAIEAAPFVAVSIQTSGIHP--STSRLITIDAVTLTADGE-EVEHFHAVLNPGE--DPG--PFHLHGLSAEEFAQGKRF 112 (377)
T ss_pred CCCCCCCCEEEEEEECCCCCC--CCCeEEEEEEEEEEcCCE-EEEEEEEEECcCC--CCC--CccccCCCHHHHhcCCCH
Confidence 345566789999999999998 678999999999985443 3589999999987 333 347999999999999999
Q ss_pred HHHHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCC--------------------------CCCCCCceeehHHHHH
Q 023805 87 EEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGK--------------------------PAPVPVGMIDSLGVLT 140 (277)
Q Consensus 87 ~ev~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~--------------------------~~p~~~~~iDt~~l~~ 140 (277)
.+++.+|.+|++++++|+||+ .||+.||..++++... ..|.+..++||+.+++
T Consensus 113 ~eVl~el~~fL~g~vLVaHNA-~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR 191 (377)
T PRK05601 113 SQILKPLDRLIDGRTLILHNA-PRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR 191 (377)
T ss_pred HHHHHHHHHHhCCCEEEEECc-HHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH
Confidence 999999999999999999999 9999999999877522 1234456999998765
Q ss_pred HHhCCCCCCCCHHHHHHHhCCCC-----------CCCChH--HHHHHHHHHHHHHHHh
Q 023805 141 EKFGRRAGNMKMATLASYFGLGQ-----------QKHRSL--DDVRMNLEVLKHCATV 185 (277)
Q Consensus 141 ~~~~~~~~~~~L~~La~~~gi~~-----------~~H~Al--~DA~~t~~l~~~l~~~ 185 (277)
.+.+.+.+++|.+||++||++. ..|+++ +||+.+++|+.+..+.
T Consensus 192 -rl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 192 -RQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred -HHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 5557778999999999999973 347777 6999999999887443
No 27
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.9e-27 Score=240.00 Aligned_cols=166 Identities=20% Similarity=0.380 Sum_probs=149.9
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVA 90 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~ 90 (277)
...+||+||+||||+++ .++|||||+|.+.++.+ +++|+++|+|.. +++++++++||||+++++++|+|++++
T Consensus 5 ~~~~~vvvD~ETTGl~~---~d~IIeIgaV~v~~g~i--~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~ 77 (820)
T PRK07246 5 KLRKYAVVDLEATGAGP---NASIIQVGIVIIEGGEI--IDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFSQVA 77 (820)
T ss_pred cCCCEEEEEEecCCcCC---CCeEEEEEEEEEECCEE--EEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHHHHH
Confidence 45689999999999986 37999999999998754 489999999998 899999999999999999999999999
Q ss_pred HHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCCChH
Q 023805 91 DKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKHRSL 169 (277)
Q Consensus 91 ~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H~Al 169 (277)
.+|.+|+++.++||||+ .||+.+|.+++.+.|.+.+.+ ++||+.++. .+.+...+++|.+||++||++ ..+|+|+
T Consensus 78 ~~~~~~l~~~~lVaHN~-~FD~~fL~~~~~~~g~~~~~~--~iDT~~la~-~~~p~~~~~~L~~L~~~lgl~~~~~H~Al 153 (820)
T PRK07246 78 RHIYDLIEDCIFVAHNV-KFDANLLAEALFLEGYELRTP--RVDTVELAQ-VFFPTLEKYSLSHLSRELNIDLADAHTAI 153 (820)
T ss_pred HHHHHHhCCCEEEEECc-HHHHHHHHHHHHHcCCCCCCC--ceeHHHHHH-HHhCCCCCCCHHHHHHHcCCCCCCCCCHH
Confidence 99999999999999999 999999999998888776544 899998764 556777789999999999999 6889999
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 023805 170 DDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 170 ~DA~~t~~l~~~l~~~l~ 187 (277)
+||++|++|+.++++++.
T Consensus 154 ~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 154 ADARATAELFLKLLQKIE 171 (820)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 999999999999998763
No 28
>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=1.6e-27 Score=201.20 Aligned_cols=161 Identities=24% Similarity=0.221 Sum_probs=134.7
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhC-CCCHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVES-APEFEEVADKIF 94 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~-a~~f~ev~~~l~ 94 (277)
++||+||||+++ ..++|||||+|.++++.... ++|+.+++|.....+++.+..+||||+++|++ ++++.+++.+|.
T Consensus 1 ~~~D~ETTGl~~--~~d~Iieig~v~v~~~~~~~-~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~ 77 (183)
T cd06138 1 LFYDYETFGLNP--SFDQILQFAAIRTDENFNEI-EPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIH 77 (183)
T ss_pred CEEEeecCCCCC--CCCceEEEEEEEECCCCCCc-cceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHH
Confidence 589999999998 67899999999998764443 88999999986435788899999999999999 899999999999
Q ss_pred HHhC--CCEEEEeC-CchhHHHHHHHHHHHhCCCCCC-----CCceeehHHHHHHHh--CC----------CCCCCCHHH
Q 023805 95 SILN--GRVWAGHN-IRRFDCARIKEAFAEIGKPAPV-----PVGMIDSLGVLTEKF--GR----------RAGNMKMAT 154 (277)
Q Consensus 95 ~~l~--~~~lv~hn-~~~fD~~~L~~~~~~~g~~~p~-----~~~~iDt~~l~~~~~--~~----------~~~~~~L~~ 154 (277)
+|+. +.++|||| + .||+.||+.++.+++...+. ...++|++.++.... .+ ...+++|++
T Consensus 78 ~~~~~~~~~lVahn~~-~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~ 156 (183)
T cd06138 78 RLFNTPGTCIVGYNNI-RFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLED 156 (183)
T ss_pred HHHccCCCcEEeeCch-hhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHH
Confidence 9995 46899997 6 99999999999999875431 224689987775432 12 235789999
Q ss_pred HHHHhCCC-CCCCChHHHHHHHHHHHH
Q 023805 155 LASYFGLG-QQKHRSLDDVRMNLEVLK 180 (277)
Q Consensus 155 La~~~gi~-~~~H~Al~DA~~t~~l~~ 180 (277)
|+++||++ ..+|+|++||++|++|++
T Consensus 157 l~~~~gi~~~~~H~Al~Da~~ta~l~~ 183 (183)
T cd06138 157 LAQANGIEHSNAHDALSDVEATIALAK 183 (183)
T ss_pred HHHHCCCCccccccHHHHHHHHHHHhC
Confidence 99999999 789999999999999863
No 29
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.95 E-value=1.9e-28 Score=243.14 Aligned_cols=173 Identities=24% Similarity=0.350 Sum_probs=158.6
Q ss_pred CCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHH
Q 023805 9 AAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEE 88 (277)
Q Consensus 9 ~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~e 88 (277)
.....+||+||+||||+++ ..++|||||++.+.++.+ ++.|+.+++|.. +++...+++||||++||+++++..+
T Consensus 417 ~l~datyVVfDiETTGLs~--~~d~iIE~aAvKikng~i--Id~f~~Fi~P~~--pl~~~~telTgITdeml~~a~~i~~ 490 (1444)
T COG2176 417 KLDDATYVVFDIETTGLSP--VYDEIIEIAAVKIKNGRI--IDKFQFFIKPGR--PLSATITELTGITDEMLENAPEIEE 490 (1444)
T ss_pred ccccccEEEEEeecCCcCc--ccchhhhheeeeeeCCcc--hHHHHHhcCCCC--cCchhhhhccccCHHHHcCCccHHH
Confidence 4667789999999999998 778999999999999865 489999999999 9999999999999999999999999
Q ss_pred HHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCCC
Q 023805 89 VADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKHR 167 (277)
Q Consensus 89 v~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H~ 167 (277)
|+.+|.+|++++++|+||+ +||+.||+..+++++++. ..+++|||+.++ +.++|.+++++|..||+.||+. ..+|+
T Consensus 491 vL~kf~~~~~d~IlVAHNa-sFD~gFl~~~~~k~~~~~-~~~pvIDTL~la-r~L~P~~ksh~Lg~l~kk~~v~le~hHR 567 (1444)
T COG2176 491 VLEKFREFIGDSILVAHNA-SFDMGFLNTNYEKYGLEP-LTNPVIDTLELA-RALNPEFKSHRLGTLCKKLGVELERHHR 567 (1444)
T ss_pred HHHHHHHHhcCcEEEeccC-ccchhHHHHHHHHhCCcc-ccCchhhHHHHH-HHhChhhhhcchHHHHHHhCccHHHhhh
Confidence 9999999999999999999 999999999999999874 334699999765 6788999999999999999999 88999
Q ss_pred hHHHHHHHHHHHHHHHHhhhccc
Q 023805 168 SLDDVRMNLEVLKHCATVLFLES 190 (277)
Q Consensus 168 Al~DA~~t~~l~~~l~~~l~~~~ 190 (277)
|.+||.+|+.|+..+++.+..-+
T Consensus 568 A~yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 568 ADYDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred hhhhHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999988765543
No 30
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=8.1e-27 Score=238.72 Aligned_cols=168 Identities=26% Similarity=0.402 Sum_probs=151.1
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
.++||+||+||||.++. ..++|||||+|.++++.+ +++|+.+|+|.. ++++++.++||||+++|+++++|.+++.
T Consensus 2 ~~~~vvvD~ETTG~~p~-~~d~IIeigav~v~~~~i--~~~f~~~v~P~~--~i~~~~~~ltGIt~~~l~~ap~f~ev~~ 76 (928)
T PRK08074 2 SKRFVVVDLETTGNSPK-KGDKIIQIAAVVVEDGEI--LERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVAP 76 (928)
T ss_pred CCCEEEEEEeCCCCCCC-CCCcEEEEEEEEEECCEE--EEEEEEEECcCC--CCCHHHhhcCCCCHHHHhcCCCHHHHHH
Confidence 35799999999998762 237999999999988755 579999999998 8999999999999999999999999999
Q ss_pred HHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCCChHH
Q 023805 92 KIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKHRSLD 170 (277)
Q Consensus 92 ~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H~Al~ 170 (277)
+|.+|+++.++||||+ .||+.||+++|.+.|.+.+ ...+|||+.++. .+.|...+++|++|+++||++ ..+|+|++
T Consensus 77 ~l~~~l~~~~~VaHN~-~FD~~fL~~~~~~~g~~~~-~~~~iDt~~la~-~~~p~~~~~~L~~l~~~l~i~~~~~H~Al~ 153 (928)
T PRK08074 77 EIVELLEGAYFVAHNV-HFDLNFLNEELERAGYTEI-HCPKLDTVELAR-ILLPTAESYKLRDLSEELGLEHDQPHRADS 153 (928)
T ss_pred HHHHHhCCCeEEEECh-HHHHHHHHHHHHHcCCCCC-CCCeeeHHHHHH-HhcCCCCCCCHHHHHHhCCCCCCCCCChHH
Confidence 9999999999999999 9999999999999998754 346999998764 556777889999999999999 78999999
Q ss_pred HHHHHHHHHHHHHHhhh
Q 023805 171 DVRMNLEVLKHCATVLF 187 (277)
Q Consensus 171 DA~~t~~l~~~l~~~l~ 187 (277)
||.+|++|+.+++.++.
T Consensus 154 DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 154 DAEVTAELFLQLLNKLE 170 (928)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999998764
No 31
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.95 E-value=3.8e-26 Score=218.29 Aligned_cols=176 Identities=18% Similarity=0.190 Sum_probs=144.2
Q ss_pred CCcEEEEEeccCCCCCC-CCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHH
Q 023805 12 TAEIVFFDLETTVPRRA-GQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVA 90 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~-~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~ 90 (277)
-..|++||+||||.++. ...++|||||+|.++.....+++.|+.||+|...+.++++|+++||||+++|+++++|.+++
T Consensus 55 ~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl 134 (582)
T PTZ00315 55 FDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVY 134 (582)
T ss_pred CCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHH
Confidence 46899999999998752 13479999999999844444568999999998766799999999999999999999999999
Q ss_pred HHHHHHhCCC----------EEEEeCCchhHHH-HHHHHHH---HhCCCCCCCCceeehHHHHHHHhCC-----------
Q 023805 91 DKIFSILNGR----------VWAGHNIRRFDCA-RIKEAFA---EIGKPAPVPVGMIDSLGVLTEKFGR----------- 145 (277)
Q Consensus 91 ~~l~~~l~~~----------~lv~hn~~~fD~~-~L~~~~~---~~g~~~p~~~~~iDt~~l~~~~~~~----------- 145 (277)
.+|.+|+.+. .+++||+ .||+. ||..++. +++++..+ ..|+|+...+.+.+.+
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~~~~~~g~p~~f-~~widLk~~lar~l~p~~~~~~~~~~~ 212 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMRVSGQQGTPLSF-QRWCNLKKYMSQLGFGNGSGCGGGATP 212 (582)
T ss_pred HHHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHHHhhhcCCCccc-ceEEEhHHHHHHHhCcccccccccccc
Confidence 9999999653 5899999 99995 8988887 34665443 3477764344455444
Q ss_pred CCCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHhhhcc
Q 023805 146 RAGNMKMATLASYFGLG--QQKHRSLDDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 146 ~~~~~~L~~La~~~gi~--~~~H~Al~DA~~t~~l~~~l~~~l~~~ 189 (277)
....++|.++++++|++ +.+|+|++||+++++|+.+|+..+...
T Consensus 213 ~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~ 258 (582)
T PTZ00315 213 PLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVI 258 (582)
T ss_pred ccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEE
Confidence 34568999999999998 578999999999999999999987553
No 32
>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=99.95 E-value=9.6e-27 Score=189.23 Aligned_cols=157 Identities=31% Similarity=0.486 Sum_probs=139.0
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIFS 95 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~~ 95 (277)
|+||+||||+++ ..++|+|||++.++.+ ..+.+.|+.+|+|.. .+++.+.++|||+++++++++++.+++.+|.+
T Consensus 1 v~~D~Ettg~~~--~~~~iiei~~v~~~~~-~~~~~~~~~~i~p~~--~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~ 75 (159)
T cd06127 1 VVFDTETTGLDP--KKDRIIEIGAVKVDGG-IEIVERFETLVNPGR--PIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75 (159)
T ss_pred CeEEeeCCCcCC--CCCeEEEEEEEEEECC-cChhhhhheeeCcCC--cCCHhheeccCCCHHHHhcCCCHHHHHHHHHH
Confidence 589999999987 6789999999999987 444688999999998 78999999999999999999999999999999
Q ss_pred HhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHH-HHHhCCC-CCCCChHHHHH
Q 023805 96 ILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATL-ASYFGLG-QQKHRSLDDVR 173 (277)
Q Consensus 96 ~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~L-a~~~gi~-~~~H~Al~DA~ 173 (277)
|+.+.++||||+ .||..+|+..+.+++. .+....++|++.++...+ +.....++..+ +++++++ ..+|+|++||+
T Consensus 76 ~l~~~~~v~~n~-~fD~~~l~~~~~~~~~-~~~~~~~iDt~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~H~Al~Da~ 152 (159)
T cd06127 76 FLGGRVLVAHNA-SFDLRFLNRELRRLGG-PPLPNPWIDTLRLARRLL-PGLRSHRLGLLLAERYGIPLEGAHRALADAL 152 (159)
T ss_pred HHCCCEEEEeCc-HhhHHHHHHHHHHhCC-CCCCCCeeEHHHHHHHHc-CCCCcCchHHHHHHHcCCCCCCCCCcHHHHH
Confidence 999999999999 9999999999999983 344567999998876555 44556889998 8899998 78999999999
Q ss_pred HHHHHHH
Q 023805 174 MNLEVLK 180 (277)
Q Consensus 174 ~t~~l~~ 180 (277)
++++|+.
T Consensus 153 ~t~~l~~ 159 (159)
T cd06127 153 ATAELLL 159 (159)
T ss_pred HHHHHhC
Confidence 9999873
No 33
>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=1.1e-26 Score=239.70 Aligned_cols=170 Identities=26% Similarity=0.414 Sum_probs=153.8
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVA 90 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~ 90 (277)
...+||+||+||||+++ ..++|||||+|.++++.. +++|+.+|+|.. ++++.+.++||||+++|++++++.+++
T Consensus 188 ~~~~~VVfDiETTGL~~--~~d~IIEIGAVkv~~g~i--id~f~~~V~P~~--~I~~~~~~ltGIT~e~L~~ap~~~evl 261 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSP--QYDEIIEFGAVKVKNGRI--IDKFQFFIKPHE--PLSAFVTELTGITQDMLENAPEIEEVL 261 (1213)
T ss_pred cCCcEEEEEeEecCCCC--CCCeEEEEEEEEEECCeE--EEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHH
Confidence 46689999999999998 678999999999998744 589999999998 899999999999999999999999999
Q ss_pred HHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCCChH
Q 023805 91 DKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKHRSL 169 (277)
Q Consensus 91 ~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H~Al 169 (277)
.+|.+|+++.++||||+ .||+.+|++.+.++|++. +...++||+.++. .+.+..++++|++||++||++ ..+|+|+
T Consensus 262 ~~f~~fl~~~iLVaHNa-~FD~~fL~~~~~r~g~~~-~~~~~IDTl~lar-~l~p~~k~~kL~~Lak~lgi~~~~~HrAl 338 (1213)
T TIGR01405 262 EKFKEFFKDSILVAHNA-SFDIGFLNTNFEKVGLEP-LENPVIDTLELAR-ALNPEYKSHRLGNICKKLGVDLDDHHRAD 338 (1213)
T ss_pred HHHHHHhCCCeEEEECh-HHHHHHHHHHHHHcCCCc-cCCCEeEHHHHHH-HHhccCCCCCHHHHHHHcCCCCCCCcCHH
Confidence 99999999999999998 999999999999999863 3456999998764 556777889999999999999 6799999
Q ss_pred HHHHHHHHHHHHHHHhhhcc
Q 023805 170 DDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 170 ~DA~~t~~l~~~l~~~l~~~ 189 (277)
+||.+|++|+..+++.+...
T Consensus 339 ~DA~aTa~I~~~ll~~l~~~ 358 (1213)
T TIGR01405 339 YDAEATAKVFKVMVEQLKEK 358 (1213)
T ss_pred HHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999887543
No 34
>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=3e-26 Score=233.15 Aligned_cols=165 Identities=22% Similarity=0.383 Sum_probs=149.0
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHH
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKI 93 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l 93 (277)
+||+||+||||+++ ..++|||||+|.++++.+ ++.|+++|+|.. ++++++.++||||+++++++++|.+++.+|
T Consensus 1 ~~vvvD~ETTG~~~--~~~~IIeig~v~v~~~~i--~~~f~~~v~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l 74 (850)
T TIGR01407 1 RYAVVDLETTGTQL--SFDKIIQIGIVVVEDGEI--VDTFHTDVNPNE--PIPPFIQELTGISDNMLQQAPYFSQVAQEI 74 (850)
T ss_pred CEEEEEEECCCCCC--CCCeEEEEEEEEEECCEE--EEEEEEEeCCCC--CCChhhhhhcCcCHHHHhCCCCHHHHHHHH
Confidence 48999999999987 668999999999987754 479999999997 899999999999999999999999999999
Q ss_pred HHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCCChHHHH
Q 023805 94 FSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKHRSLDDV 172 (277)
Q Consensus 94 ~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H~Al~DA 172 (277)
.+|+++.++||||+ .||+.+|.+++.++|.+.. ...++||+.++. .+.+...+++|.+|+++||++ ..+|+|++||
T Consensus 75 ~~~l~~~~~VahN~-~fD~~fL~~~~~~~g~~~~-~~~~iDt~~l~~-~~~p~~~~~~L~~l~~~~gi~~~~~H~Al~DA 151 (850)
T TIGR01407 75 YDLLEDGIFVAHNV-HFDLNFLAKALKDCGYEPL-PKPRIDTVELAQ-IFFPTEESYQLSELSEALGLTHENPHRADSDA 151 (850)
T ss_pred HHHhCCCEEEEeCc-HHHHHHHHHHHHHcCCCCC-CCCeEeHHHHHH-HhcCCCCCCCHHHHHHHCCCCCCCCCChHHHH
Confidence 99999999999999 9999999999999998732 345899998764 556766789999999999999 7899999999
Q ss_pred HHHHHHHHHHHHhhh
Q 023805 173 RMNLEVLKHCATVLF 187 (277)
Q Consensus 173 ~~t~~l~~~l~~~l~ 187 (277)
.+|++|+.++++++.
T Consensus 152 ~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 152 QATAELLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999988764
No 35
>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=99.94 E-value=1.5e-26 Score=190.54 Aligned_cols=149 Identities=24% Similarity=0.311 Sum_probs=122.9
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIFS 95 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~~ 95 (277)
|+|||||||+++.+..++|++|+++.+++.. .|+++|+|.. +++++.+++||||+++++++++|++++.+|.+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~-----~~~~lv~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~ 73 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDV-----LYDKYIRPEG--PVTDYRTRWSGIRRQHLVNATPFAVAQKEILK 73 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCE-----EEEEeECCCC--ccCccceECCCCCHHHHhcCCCHHHHHHHHHH
Confidence 5899999999984335789999998764432 2889999998 89999999999999999999999999999999
Q ss_pred HhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHH--HHHH-hCCCCCCCCHHHHHHHh---CCC--CCCCC
Q 023805 96 ILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGV--LTEK-FGRRAGNMKMATLASYF---GLG--QQKHR 167 (277)
Q Consensus 96 ~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l--~~~~-~~~~~~~~~L~~La~~~---gi~--~~~H~ 167 (277)
+++++++||||+ .||+.+|+.. .+ ...++||..+ +.+. ..|...+++|+.|+++| +++ .+.|+
T Consensus 74 ~l~~~vlV~Hn~-~~D~~~l~~~-------~~-~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~ 144 (157)
T cd06149 74 ILKGKVVVGHAI-HNDFKALKYF-------HP-KHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHS 144 (157)
T ss_pred HcCCCEEEEeCc-HHHHHHhccc-------CC-CcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcC
Confidence 999999999999 9999999733 22 1237888754 3322 25556779999999999 676 35799
Q ss_pred hHHHHHHHHHHHH
Q 023805 168 SLDDVRMNLEVLK 180 (277)
Q Consensus 168 Al~DA~~t~~l~~ 180 (277)
|++||++|++||+
T Consensus 145 Al~DA~at~~l~~ 157 (157)
T cd06149 145 SVEDARATMELYK 157 (157)
T ss_pred cHHHHHHHHHHhC
Confidence 9999999999985
No 36
>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=1.2e-26 Score=192.07 Aligned_cols=144 Identities=21% Similarity=0.305 Sum_probs=121.9
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCC-------HHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPE-------FEE 88 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~-------f~e 88 (277)
|+||+||||+++ ..++|+|||+|.+.++.+ .|+.+|+|.. +++++.+++||||+++|+++++ |++
T Consensus 1 v~lD~EttGl~~--~~d~ii~Ig~V~v~~g~i----~~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~ 72 (161)
T cd06137 1 VALDCEMVGLAD--GDSEVVRISAVDVLTGEV----LIDSLVRPSV--RVTDWRTRFSGVTPADLEEAAKAGKTIFGWEA 72 (161)
T ss_pred CEEEeeeeeEcC--CCCEEEEEEEEEcCCCeE----EEeccccCCC--CCCccceeccCCCHHHHhhhhhcCCccccHHH
Confidence 589999999998 568999999999966543 2889999997 8999999999999999998874 468
Q ss_pred HHHHHHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCC---CCCCHHHHHHH-hCCC-
Q 023805 89 VADKIFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRA---GNMKMATLASY-FGLG- 162 (277)
Q Consensus 89 v~~~l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~---~~~~L~~La~~-~gi~- 162 (277)
++++|.+|+++ .++||||+ .||+.||+.. ...++||+.++.+.. +.. .+++|.+||++ ||++
T Consensus 73 ~~~~~~~~i~~~~vlVgHn~-~fD~~fL~~~----------~~~~iDT~~l~~~~~-~~~~~~~~~~L~~L~~~~~~~~~ 140 (161)
T cd06137 73 ARAALWKFIDPDTILVGHSL-QNDLDALRMI----------HTRVVDTAILTREAV-KGPLAKRQWSLRTLCRDFLGLKI 140 (161)
T ss_pred HHHHHHHhcCCCcEEEeccH-HHHHHHHhCc----------CCCeeEehhhhhhcc-CCCcCCCCccHHHHHHHHCCchh
Confidence 99999999998 89999999 9999999742 124899998876544 443 57999999986 6876
Q ss_pred ---CCCCChHHHHHHHHHHH
Q 023805 163 ---QQKHRSLDDVRMNLEVL 179 (277)
Q Consensus 163 ---~~~H~Al~DA~~t~~l~ 179 (277)
...|+|++||++|++|+
T Consensus 141 ~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 141 QGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred cCCCCCCCcHHHHHHHHHHh
Confidence 25799999999999987
No 37
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=2e-25 Score=193.00 Aligned_cols=147 Identities=20% Similarity=0.252 Sum_probs=126.7
Q ss_pred EEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHH
Q 023805 15 IVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIF 94 (277)
Q Consensus 15 ~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~ 94 (277)
+++||+||||+++ +|||||++.+.++.+ .+.|+.+|+|.. ++++.+.++||||+++++++|+|.+++..
T Consensus 2 ~~vlD~ETTGl~~-----~IieIg~v~v~~~~i--~~~~~~lv~P~~--~i~~~~~~ihgIt~e~v~~ap~~~ev~~~-- 70 (219)
T PRK07983 2 LRVIDTETCGLQG-----GIVEIASVDVIDGKI--VNPMSHLVRPDR--PISPQAMAIHRITEAMVADKPWIEDVIPH-- 70 (219)
T ss_pred eEEEEEECCCCCC-----CCEEEEEEEEECCEE--EEEEEEEECcCC--CCCHHHhhcCCCCHHHHcCCCCHHHHHHH--
Confidence 6899999999864 399999999987654 478999999998 89999999999999999999999999887
Q ss_pred HHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC------CCCCCh
Q 023805 95 SILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG------QQKHRS 168 (277)
Q Consensus 95 ~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~------~~~H~A 168 (277)
|+++.++||||+ .||+.+|.. ....++||+.++++ +.|+.. ++|+.|+++||++ ..+|+|
T Consensus 71 -~~~~~~lVaHNa-~FD~~~L~~----------~~~~~idTl~lar~-l~p~~~-~~l~~L~~~~~l~~~~~~~~~aHrA 136 (219)
T PRK07983 71 -YYGSEWYVAHNA-SFDRRVLPE----------MPGEWICTMKLARR-LWPGIK-YSNMALYKSRKLNVQTPPGLHHHRA 136 (219)
T ss_pred -HcCCCEEEEeCc-HhhHHHHhC----------cCCCcEeHHHHHHH-HccCCC-CCHHHHHHHcCCCCCCCCCCCCCcH
Confidence 567889999999 999999852 12348999988765 456655 8999999999975 368999
Q ss_pred HHHHHHHHHHHHHHHHhh
Q 023805 169 LDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 169 l~DA~~t~~l~~~l~~~l 186 (277)
++||.+|++|+.++++..
T Consensus 137 l~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 137 LYDCYITAALLIDIMNTS 154 (219)
T ss_pred HHHHHHHHHHHHHHHHHc
Confidence 999999999999998753
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=1.2e-25 Score=183.85 Aligned_cols=143 Identities=22% Similarity=0.322 Sum_probs=120.2
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCC-CHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAP-EFEEVADKIF 94 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~-~f~ev~~~l~ 94 (277)
+++||||+|... . ++|++|+++.++++ ..|+.||+|.. +++++.+++||||++||++++ +|++++.+|.
T Consensus 1 ~~iD~E~~g~~~--g-~ei~~i~~v~~~~~-----~~f~~lv~P~~--~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~ 70 (150)
T cd06145 1 FALDCEMCYTTD--G-LELTRVTVVDENGK-----VVLDELVKPDG--EIVDYNTRFSGITEEMLENVTTTLEDVQKKLL 70 (150)
T ss_pred CEEeeeeeeecC--C-CEEEEEEEEeCCCC-----EEEEEeECCCC--ccchhccCcCCCCHHHhccCCCCHHHHHHHHH
Confidence 589999999886 3 89999999977443 24999999998 899999999999999999995 9999999999
Q ss_pred HHhC-CCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CC--C--CCCCCh
Q 023805 95 SILN-GRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GL--G--QQKHRS 168 (277)
Q Consensus 95 ~~l~-~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi--~--~~~H~A 168 (277)
+|++ +.++||||+ .||+.||+.. ...++||+.+++... +...+++|+.||++| +. + ...|+|
T Consensus 71 ~fl~~~~vlVgHn~-~fD~~fL~~~----------~~~~iDT~~l~r~~~-~~~~~~~L~~L~~~~~~~~i~~~~~~H~A 138 (150)
T cd06145 71 SLISPDTILVGHSL-ENDLKALKLI----------HPRVIDTAILFPHPR-GPPYKPSLKNLAKKYLGRDIQQGEGGHDS 138 (150)
T ss_pred HHhCCCCEEEEcCh-HHHHHHhhcc----------CCCEEEcHHhccccC-CCCCChhHHHHHHHHCCcceeCCCCCCCc
Confidence 9997 789999999 9999999731 123899998765433 334478999999977 53 3 378999
Q ss_pred HHHHHHHHHHHH
Q 023805 169 LDDVRMNLEVLK 180 (277)
Q Consensus 169 l~DA~~t~~l~~ 180 (277)
++||+++++|++
T Consensus 139 l~DA~~t~~l~~ 150 (150)
T cd06145 139 VEDARAALELVK 150 (150)
T ss_pred HHHHHHHHHHhC
Confidence 999999999874
No 39
>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=1.1e-25 Score=184.40 Aligned_cols=148 Identities=23% Similarity=0.325 Sum_probs=116.4
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIFS 95 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~~ 95 (277)
|+||+||||+++ . +++++|+.+.+.+.... ..|+.+|+|.. +++.++.++||||+++++++++|.+++.+|.+
T Consensus 1 v~lD~EttGl~~--~-~~~~~i~~v~~v~~~~~--~~~~~~v~P~~--~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~ 73 (152)
T cd06144 1 VALDCEMVGVGP--D-GSESALARVSIVNEDGN--VVYDTYVKPQE--PVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAE 73 (152)
T ss_pred CEEEEEeecccC--C-CCEEEEEEEEEEeCCCC--EEEEEEECCCC--CCCcccccCCCCCHHHHcCCCCHHHHHHHHHH
Confidence 589999999987 2 25666655443332222 23999999987 79999999999999999999999999999999
Q ss_pred HhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCC-CCCCCHHHHHHH-hCCC--CCCCChHHH
Q 023805 96 ILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRR-AGNMKMATLASY-FGLG--QQKHRSLDD 171 (277)
Q Consensus 96 ~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~-~~~~~L~~La~~-~gi~--~~~H~Al~D 171 (277)
|+++.++||||+ .||+.+|+ ...+. ..++|+..+. ....+. ..+++|+.||++ +|++ ..+|+|++|
T Consensus 74 ~l~~~vlVgHn~-~fD~~~L~-------~~~~~-~~~~dt~~l~-~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~D 143 (152)
T cd06144 74 LLKGRILVGHAL-KNDLKVLK-------LDHPK-KLIRDTSKYK-PLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVED 143 (152)
T ss_pred HhCCCEEEEcCc-HHHHHHhc-------CcCCC-ccEEEeEEee-ccccccCCCChhHHHHHHHHcCcccCCCCcCcHHH
Confidence 999999999999 99999996 22222 2478887542 222221 467999999997 5987 368999999
Q ss_pred HHHHHHHHH
Q 023805 172 VRMNLEVLK 180 (277)
Q Consensus 172 A~~t~~l~~ 180 (277)
|++|++||+
T Consensus 144 A~at~~l~~ 152 (152)
T cd06144 144 ARAAMRLYR 152 (152)
T ss_pred HHHHHHHhC
Confidence 999999974
No 40
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1.1e-24 Score=195.99 Aligned_cols=165 Identities=21% Similarity=0.208 Sum_probs=132.5
Q ss_pred CCCCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEEC---Cee-eeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhC
Q 023805 7 SQAAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCP---RKL-VELESFSTLIKPKDLSAVALKSSRCDGITREAVES 82 (277)
Q Consensus 7 ~~~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~---~~~-~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~ 82 (277)
++......+|+||+||||+++ ..++|||||+|.++. +.+ .+.+.|+.+++|.. +|++.++.+||||.+++++
T Consensus 31 ~~~~~~~~~vvlD~ETTGLd~--~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~--~I~~~~t~IhGIt~e~v~~ 106 (294)
T PRK09182 31 PRGEFVRLGVILDTETTGLDP--RKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR--PIPPEITRLTGITDEMVAG 106 (294)
T ss_pred CCCCCCCeEEEEEeeCCCCCC--CCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC--CCCHHHHHhcCCCHHHHhc
Confidence 445667789999999999998 678999999999983 322 34588999999998 8999999999999999999
Q ss_pred CCCHHHHHHHHHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCC
Q 023805 83 APEFEEVADKIFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGL 161 (277)
Q Consensus 83 a~~f~ev~~~l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi 161 (277)
++...+ .|.+|++. .++||||+ .||+.||...+..... ..+.|++..+.+. .+..++++|++|+.+||.
T Consensus 107 ~~~~~~---~l~~fl~~~~vlVAHNA-~FD~~fL~~~~~~~~~-----~~~~ct~~~i~~~-~~~~~~~kL~~La~~~g~ 176 (294)
T PRK09182 107 QTIDPA---AVDALIAPADLIIAHNA-GFDRPFLERFSPVFAT-----KPWACSVSEIDWS-ARGFEGTKLGYLAGQAGF 176 (294)
T ss_pred CCCcHH---HHHHHhcCCCEEEEeCH-HHHHHHHHHHHHhccC-----CcccccHHHHhhc-cccCCCCCHHHHHHHcCC
Confidence 886544 35556755 59999999 9999999877654322 2367887544332 345578999999999996
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHh
Q 023805 162 GQQKHRSLDDVRMNLEVLKHCATV 185 (277)
Q Consensus 162 ~~~~H~Al~DA~~t~~l~~~l~~~ 185 (277)
...+|+|++||.+|++|+..++..
T Consensus 177 ~~~aHrAl~Da~Ata~ll~~~l~~ 200 (294)
T PRK09182 177 FHEGHRAVDDCQALLELLARPLPE 200 (294)
T ss_pred CCCCcChHHHHHHHHHHHHHHHhh
Confidence 578999999999999999987654
No 41
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.93 E-value=1.8e-24 Score=190.07 Aligned_cols=165 Identities=27% Similarity=0.401 Sum_probs=148.9
Q ss_pred CcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHH
Q 023805 13 AEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADK 92 (277)
Q Consensus 13 ~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~ 92 (277)
..+++||+||||.++ ..++|||||+|.+.++.+.. ..|+.+|+|.. ++++...++||||.+++.++|.|.+++.+
T Consensus 13 ~~~vv~D~ETtg~~~--~~~~iieIgav~~~~~~i~~-~~~~~~v~P~~--~i~~~~~~i~git~e~l~~~p~~~~v~~~ 87 (243)
T COG0847 13 TRFVVIDLETTGLNP--KKDRIIEIGAVTLEDGRIVE-RSFHTLVNPER--PIPPEIFKIHGITDEMLADAPKFAEVLPE 87 (243)
T ss_pred CcEEEEecccCCCCC--CCCceEEEEeEEEECCeeec-ceeEEEECCCC--CCChhhhhhcCCCHHHHhcCCCHHHHHHH
Confidence 578999999999987 67899999999999987653 55999999966 79999999999999999999999999999
Q ss_pred HHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC---CCCCCh
Q 023805 93 IFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG---QQKHRS 168 (277)
Q Consensus 93 l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~---~~~H~A 168 (277)
|.+|+++ ..+|+||+ .||+.+|..++..++...+ ...++|++.++.. ..++...++|+.||.++|++ ...|+|
T Consensus 88 ~~~~i~~~~~~Vahna-~fD~~fl~~~~~~~~~~~~-~~~~~~t~~~~r~-~~~~~~~~~L~~l~~~~gi~~~~~~~H~A 164 (243)
T COG0847 88 FLDFIGGLRLLVAHNA-AFDVGFLRVESERLGIEIP-GDPVLDTLALARR-HFPGFDRSSLDALAERLGIDRNPFHPHRA 164 (243)
T ss_pred HHHHHCCCCeEEEEch-hhcHHHHHHHHHHcCCCcc-cCceehHHHHHHH-HcCCCccchHHHHHHHcCCCcCCcCCcch
Confidence 9999999 99999999 9999999999999999876 4458999987754 44666789999999999999 467999
Q ss_pred HHHHHHHHHHHHHHHHh
Q 023805 169 LDDVRMNLEVLKHCATV 185 (277)
Q Consensus 169 l~DA~~t~~l~~~l~~~ 185 (277)
+.||.++++++..+...
T Consensus 165 l~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 165 LFDALALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999999999999885
No 42
>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=99.93 E-value=4.4e-25 Score=184.73 Aligned_cols=158 Identities=18% Similarity=0.236 Sum_probs=127.8
Q ss_pred EEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCC--CCCCchhhhhc---CCCHHHHhCCCCHHHH
Q 023805 15 IVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDL--SAVALKSSRCD---GITREAVESAPEFEEV 89 (277)
Q Consensus 15 ~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~--~~i~~~~~~~~---GIt~e~l~~a~~f~ev 89 (277)
+++||+||||+++ ..++|||||+|.++++.+.+.++|+.+|+|... ..+++++.++| ||+++++++++++.++
T Consensus 1 lv~iD~ETTGl~p--~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~v 78 (173)
T cd06135 1 LVWIDLEMTGLDP--EKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQA 78 (173)
T ss_pred CEEEEEecCCCCC--CCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHH
Confidence 5899999999998 678999999999998776667899999999872 12346677775 9999999999999999
Q ss_pred HHHHHHHhCC------CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHH--HHHHhCCCCCCCCHHHHHHHhCC
Q 023805 90 ADKIFSILNG------RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGV--LTEKFGRRAGNMKMATLASYFGL 161 (277)
Q Consensus 90 ~~~l~~~l~~------~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l--~~~~~~~~~~~~~L~~La~~~gi 161 (277)
+.+|.+|+++ .+++|||+ .||+.||++++.+++... .+..+|+..+ +.+.+.|+..+ +++
T Consensus 79 l~~~~~f~~~~~~~~~~~lvgh~~-~FD~~fL~~~~~~~~~~~--~~~~~D~~~l~~l~~~l~p~~~~---------~~~ 146 (173)
T cd06135 79 EAELLEFIKKYVPKGKSPLAGNSV-HQDRRFLDKYMPELEEYL--HYRILDVSSIKELARRWYPEIYR---------KAP 146 (173)
T ss_pred HHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHHhccC--CcchhhHHHHHHHHHHhCcHhhh---------cCC
Confidence 9999999964 58899999 999999999999988433 3347887332 33455554322 566
Q ss_pred C-CCCCChHHHHHHHHHHHHHHHHhh
Q 023805 162 G-QQKHRSLDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 162 ~-~~~H~Al~DA~~t~~l~~~l~~~l 186 (277)
. ...|+|++||.+++.+++++.+.+
T Consensus 147 ~~~~~HrAl~Da~~~~~~~~~~~~~~ 172 (173)
T cd06135 147 KKKGTHRALDDIRESIAELKYYRENI 172 (173)
T ss_pred CCCCCcchHHHHHHHHHHHHHHHHHh
Confidence 5 678999999999999999988743
No 43
>PRK05359 oligoribonuclease; Provisional
Probab=99.93 E-value=2.3e-24 Score=181.50 Aligned_cols=161 Identities=20% Similarity=0.241 Sum_probs=133.5
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCC--CCCCchhhhhc---CCCHHHHhCCCCH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDL--SAVALKSSRCD---GITREAVESAPEF 86 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~--~~i~~~~~~~~---GIt~e~l~~a~~f 86 (277)
..+||+||+||||+++ ..++|+|||+|.++++.....+.|+.+|+|... ..+++++..+| |||.+++++++++
T Consensus 2 ~~~~vvlD~ETTGLdp--~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~ 79 (181)
T PRK05359 2 EDNLIWIDLEMTGLDP--ERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSE 79 (181)
T ss_pred CCcEEEEEeecCCCCC--CCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCH
Confidence 5689999999999998 678999999999988765544679999999862 13578888887 8999999999999
Q ss_pred HHHHHHHHHHhC------CCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceee--hH-HHHHHHhCCCCCCCCHHHHHH
Q 023805 87 EEVADKIFSILN------GRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMID--SL-GVLTEKFGRRAGNMKMATLAS 157 (277)
Q Consensus 87 ~ev~~~l~~~l~------~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iD--t~-~l~~~~~~~~~~~~~L~~La~ 157 (277)
.+++.+|.+|++ +.+++|||+ .||+.||++.+.+.+..+.+. ++| ++ .++ +.+.|+.
T Consensus 80 ~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~~~~~~~~~l~~~--~~Dv~tl~~l~-r~~~P~~---------- 145 (181)
T PRK05359 80 AEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLARYMPELEAYFHYR--NLDVSTLKELA-RRWKPEI---------- 145 (181)
T ss_pred HHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHhcccCCCc--ccchhHHHHHH-HHhChhh----------
Confidence 999999999995 478999999 999999999998888765544 666 55 444 4565642
Q ss_pred HhCCC-CCCCChHHHHHHHHHHHHHHHHhhhc
Q 023805 158 YFGLG-QQKHRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 158 ~~gi~-~~~H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
+++++ ...|+|++|++.+.+.++++.+.++.
T Consensus 146 ~~~~~~~~~HRal~D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 146 LNGFKKQGTHRALADIRESIAELKYYREHFFK 177 (181)
T ss_pred hhCCCCcCCcccHHHHHHHHHHHHHHHHHhcc
Confidence 35776 67899999999999999999987765
No 44
>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=99.92 E-value=6.3e-27 Score=190.82 Aligned_cols=160 Identities=34% Similarity=0.547 Sum_probs=132.0
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIFS 95 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~~ 95 (277)
|+||+||||+++ ..++|+|||++.++++...+...|+.+|+|.....++++++++||||.+++++++++.+++.+|.+
T Consensus 1 v~~D~Ettg~~~--~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLDP--RQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSSTT--TTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHH
T ss_pred cEEEeEcCCCCC--CCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhh
Confidence 689999999987 678999999999999875445789999999994459999999999999999999999999999999
Q ss_pred HhC-CCEEEEeCCchhHHHHHHHHHHHh-CCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CC-CCChHHH
Q 023805 96 ILN-GRVWAGHNIRRFDCARIKEAFAEI-GKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQ-KHRSLDD 171 (277)
Q Consensus 96 ~l~-~~~lv~hn~~~fD~~~L~~~~~~~-g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~-~H~Al~D 171 (277)
|++ ..++||||. .||..++...+.+. +...|....++|++.+....+ +....++|+.|+++|+++ .. +|+|++|
T Consensus 79 ~~~~~~~~v~~n~-~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~l~~~~~~~~~~~~H~Al~D 156 (164)
T PF00929_consen 79 FLKKNDILVGHNA-SFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALF-PNRKKYSLDDLAEYFGIPFDGTAHDALDD 156 (164)
T ss_dssp HHHHHTEEEETTC-CHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHH-HHHHHHSHHHHHHHTTSSSTSTTTSHHHH
T ss_pred hhhcccccccccc-cchhhHHHHhhhhcccccccccchhhhhhHHHHHHh-hccccCCHHHHHHHcCCCCCCCCcChHHH
Confidence 998 689999998 99999988888776 333331123566665443333 222238999999999999 33 6999999
Q ss_pred HHHHHHHH
Q 023805 172 VRMNLEVL 179 (277)
Q Consensus 172 A~~t~~l~ 179 (277)
|++|++||
T Consensus 157 a~~t~~l~ 164 (164)
T PF00929_consen 157 ARATAELF 164 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHhCcC
Confidence 99999986
No 45
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.91 E-value=2.2e-23 Score=197.75 Aligned_cols=173 Identities=18% Similarity=0.116 Sum_probs=137.3
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCC-CCHHHH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESA-PEFEEV 89 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a-~~f~ev 89 (277)
...+|+++|+||||+++ ..++|||||+|.++.+...+.+.|..+++|.....+++.+..+||||++++.+. .+..++
T Consensus 4 ~~~~fvv~D~ETTGLdP--~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~ 81 (476)
T PRK11779 4 MQPTFLWHDYETFGANP--ALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEF 81 (476)
T ss_pred CCCcEEEEEEECCCCCC--CCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHH
Confidence 45679999999999998 678999999999998765555789999999864345788999999999999665 478999
Q ss_pred HHHHHHHhC--CCEEEEeCCchhHHHHHHHHHHHhCCC-----CCCCCceeehHHHHHH--HhC------C----CCCCC
Q 023805 90 ADKIFSILN--GRVWAGHNIRRFDCARIKEAFAEIGKP-----APVPVGMIDSLGVLTE--KFG------R----RAGNM 150 (277)
Q Consensus 90 ~~~l~~~l~--~~~lv~hn~~~fD~~~L~~~~~~~g~~-----~p~~~~~iDt~~l~~~--~~~------~----~~~~~ 150 (277)
+.+|.+++. +.++||||...||..|++..+.+..+. +......+|++.++.. .+. | +..++
T Consensus 82 ~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~ 161 (476)
T PRK11779 82 AARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSF 161 (476)
T ss_pred HHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCC
Confidence 999999995 679999984399999999998665432 1121223455444432 221 1 23679
Q ss_pred CHHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHh
Q 023805 151 KMATLASYFGLG-QQKHRSLDDVRMNLEVLKHCATV 185 (277)
Q Consensus 151 ~L~~La~~~gi~-~~~H~Al~DA~~t~~l~~~l~~~ 185 (277)
+|+.|+++||++ ..+|+|+.||.+|++|++.+.++
T Consensus 162 rLe~L~~~~gI~~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 162 KLEHLTKANGIEHENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred cHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHh
Confidence 999999999999 78999999999999999998876
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.90 E-value=7.9e-23 Score=213.64 Aligned_cols=171 Identities=25% Similarity=0.326 Sum_probs=153.0
Q ss_pred CCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHH
Q 023805 9 AAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEE 88 (277)
Q Consensus 9 ~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~e 88 (277)
......+|+||+||||+++ ..++|+|||++.++.+.. ++.|+.+|+|.. ++++.++++||||++++.+++++.+
T Consensus 415 ~L~~~~~VVfDLETTGL~~--~~deIIEIgAV~V~~G~i--ie~F~~~V~P~~--~I~~~~~~LTGIT~e~L~~aps~~E 488 (1437)
T PRK00448 415 DLKDATYVVFDVETTGLSA--VYDEIIEIGAVKIKNGEI--IDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEE 488 (1437)
T ss_pred hhccCcEEEEEhhhcCCCC--chhhhheeeeEEEeCCeE--eeeEEEEECCCC--CCCHHHHHHhCCCHHHHcCCCCHHH
Confidence 4455689999999999987 678999999999997754 489999999998 8999999999999999999999999
Q ss_pred HHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCCCC
Q 023805 89 VADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQKHR 167 (277)
Q Consensus 89 v~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~H~ 167 (277)
++.+|.+|+++.++||||+ .||+.+|+..+.+.|++.+. ..++|++.++. .+.+...+++|..||++||+. ..+|+
T Consensus 489 aL~~f~~figg~vLVAHNa-~FD~~fL~~~l~rlgl~~l~-~~~IDTLelar-~l~p~~k~~kL~~LAk~lGL~~~~~Hr 565 (1437)
T PRK00448 489 VLPKFKEFCGDSILVAHNA-SFDVGFINTNYEKLGLEKIK-NPVIDTLELSR-FLYPELKSHRLNTLAKKFGVELEHHHR 565 (1437)
T ss_pred HHHHHHHHhCCCEEEEeCc-cccHHHHHHHHHHcCCcccc-ccceeHHHHHH-HHcCccccccHHHHHHHcCCCCCCCcC
Confidence 9999999999999999999 99999999999999986432 35899998764 555667789999999999999 67899
Q ss_pred hHHHHHHHHHHHHHHHHhhhc
Q 023805 168 SLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 168 Al~DA~~t~~l~~~l~~~l~~ 188 (277)
|++||.+|++|+.++++.+..
T Consensus 566 Al~DA~aTa~lf~~ll~~l~~ 586 (1437)
T PRK00448 566 ADYDAEATAYLLIKFLKDLKE 586 (1437)
T ss_pred hHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999988754
No 47
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.87 E-value=8.1e-22 Score=168.43 Aligned_cols=174 Identities=17% Similarity=0.202 Sum_probs=144.0
Q ss_pred CcEEEEEeccCCCCCCC--CCCceEEEEEEEEECCeeeeec-eEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 13 AEIVFFDLETTVPRRAG--QRFWVLEFGAIIVCPRKLVELE-SFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 13 ~~~v~~D~ETTg~~~~~--~~~~IieIg~v~v~~~~~~~~~-sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
+-++++|+|+|+...++ ...+|||+.+|.++.-...+++ +|+.||+|..++.++.+|+.+|||.++.|+.+++|.+|
T Consensus 56 dYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~v 135 (280)
T KOG0542|consen 56 DYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQV 135 (280)
T ss_pred ceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHH
Confidence 45799999999976432 3469999999966653333344 99999999999999999999999999999999999999
Q ss_pred HHHHHHHhCC--------CEEEEeCCchhHHH-HHHHHHHHhCCCCCC-CCceeehHHHHHHHhCCCCCCCCHHHHHHHh
Q 023805 90 ADKIFSILNG--------RVWAGHNIRRFDCA-RIKEAFAEIGKPAPV-PVGMIDSLGVLTEKFGRRAGNMKMATLASYF 159 (277)
Q Consensus 90 ~~~l~~~l~~--------~~lv~hn~~~fD~~-~L~~~~~~~g~~~p~-~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~ 159 (277)
+++|..||.. ..-..... .+|+. +|..+|+..++..|. .++|||+...+...+.. ....++..+.++|
T Consensus 136 l~~f~~Wlr~~~~~~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~-~~~t~it~mLe~~ 213 (280)
T KOG0542|consen 136 LSEFDSWLRKDSLGDKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNR-PAPTNITGMLEHY 213 (280)
T ss_pred HHHHHHHHHHhhcccccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcC-ccccCHHHHHHHh
Confidence 9999999942 22233344 99996 899999999999884 45899999888766643 2467999999999
Q ss_pred CCC--CCCCChHHHHHHHHHHHHHHHHhhhc
Q 023805 160 GLG--QQKHRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 160 gi~--~~~H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
|++ +.+|++++||+++++|+.+|+..+..
T Consensus 214 gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~ 244 (280)
T KOG0542|consen 214 GLQFEGRAHSGIDDARNIARIAQKMIRDGAE 244 (280)
T ss_pred CCcccCCcccCchhHHHHHHHHHHHHhCCcE
Confidence 998 89999999999999999999986544
No 48
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.81 E-value=4.9e-20 Score=148.61 Aligned_cols=179 Identities=24% Similarity=0.346 Sum_probs=143.6
Q ss_pred CCcEEEEEeccCCCCCC--CCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 12 TAEIVFFDLETTVPRRA--GQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~--~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
..-+++||+|+|..... ....+||||+|.+++.-.-.+++.|++||+|...+.++.+|..++||++..+++++-|..+
T Consensus 3 ~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v 82 (210)
T COG5018 3 TNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMV 82 (210)
T ss_pred CceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHH
Confidence 35689999999976431 1457999999988875444457999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCC------CEEEEeCCchhHHHHHHHHHHHhCCC-CCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC
Q 023805 90 ADKIFSILNG------RVWAGHNIRRFDCARIKEAFAEIGKP-APVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG 162 (277)
Q Consensus 90 ~~~l~~~l~~------~~lv~hn~~~fD~~~L~~~~~~~g~~-~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~ 162 (277)
+++|..||.. ..|+.+ +.+|++.|.+.+..+++. .++...++|...-+...+ ....-.+|..+++.||.+
T Consensus 83 ~E~f~r~L~~h~Pr~~~~wa~w--G~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~-~~pr~tgln~ale~~G~s 159 (210)
T COG5018 83 FEDFIRKLNEHDPRKNSTWATW--GNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVF-GDPRLTGLNKALEEYGDS 159 (210)
T ss_pred HHHHHHHHHhcCcccCCccccc--cchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHh-cCCccccHHHHHHHhccc
Confidence 9999999953 246644 399999999999999988 444557999985544433 333347899999999998
Q ss_pred --CCCCChHHHHHHHHHHHHHHHHh-hhcccCCC
Q 023805 163 --QQKHRSLDDVRMNLEVLKHCATV-LFLESSLP 193 (277)
Q Consensus 163 --~~~H~Al~DA~~t~~l~~~l~~~-l~~~~~l~ 193 (277)
+..|+|++||+++++|++.++.. -++|..-+
T Consensus 160 f~G~~HraldDArn~~rl~klv~~~~~~~e~~~~ 193 (210)
T COG5018 160 FTGTHHRALDDARNAYRLFKLVEQDKQYLEKPKP 193 (210)
T ss_pred cCCchhhhHHHHHHHHHHHHHHcchhhhccCCCC
Confidence 78999999999999999988753 34444333
No 49
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.81 E-value=4.1e-19 Score=153.11 Aligned_cols=161 Identities=19% Similarity=0.301 Sum_probs=129.7
Q ss_pred CCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 10 AGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
.....+|++|||+.|..+.|..+.+..+++|-+.++.+ |+.||+|.. +|++|.+.++||+++.+.++.+|+.+
T Consensus 102 ~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~Vv-----yDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~a 174 (280)
T KOG2249|consen 102 GSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVV-----YDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVA 174 (280)
T ss_pred cccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEe-----eeeecCCCc--ccccceeeecccCHHHhccCccHHHH
Confidence 33446999999999999877777888888877776643 889999999 89999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHH--HHHHhCCCCCCCCHHHHHH-HhCCC--CC
Q 023805 90 ADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGV--LTEKFGRRAGNMKMATLAS-YFGLG--QQ 164 (277)
Q Consensus 90 ~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l--~~~~~~~~~~~~~L~~La~-~~gi~--~~ 164 (277)
..++.++|.++++|||.. ..|+..|.....+.- +-||... +.+.+ ......+|..|++ .+|++ ..
T Consensus 175 Q~ev~klL~gRIlVGHaL-hnDl~~L~l~hp~s~--------iRDTs~~~pl~k~~-~~~~tpSLK~Lt~~~Lg~~IQ~G 244 (280)
T KOG2249|consen 175 QKEVLKLLKGRILVGHAL-HNDLQALKLEHPRSM--------IRDTSKYPPLMKLL-SKKATPSLKKLTEALLGKDIQVG 244 (280)
T ss_pred HHHHHHHHhCCEEecccc-ccHHHHHhhhCchhh--------hcccccCchHHHHh-hccCCccHHHHHHHHhchhhhcc
Confidence 999999999999999999 999998875443322 3354421 11111 2335789999999 56765 56
Q ss_pred CCChHHHHHHHHHHHHHHHHhhh
Q 023805 165 KHRSLDDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 165 ~H~Al~DA~~t~~l~~~l~~~l~ 187 (277)
.|++.+||+++++||+.+..+..
T Consensus 245 eHsSvEDA~AtM~LY~~vk~qwe 267 (280)
T KOG2249|consen 245 EHSSVEDARATMELYKRVKVQWE 267 (280)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHH
Confidence 69999999999999998876543
No 50
>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=99.68 E-value=8.1e-16 Score=127.26 Aligned_cols=151 Identities=19% Similarity=0.273 Sum_probs=111.7
Q ss_pred CcEEEEEeccCCCCCCCCC-------CceEEEEEEEEE--CCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCC
Q 023805 13 AEIVFFDLETTVPRRAGQR-------FWVLEFGAIIVC--PRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESA 83 (277)
Q Consensus 13 ~~~v~~D~ETTg~~~~~~~-------~~IieIg~v~v~--~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a 83 (277)
.+||.++.|+++..++|.. .++..+++|-.+ ..+.+ -|+.||+|.. +|.++.++++|||+++++++
T Consensus 5 ~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~v---llD~~VkP~~--~V~DYrT~~SGIt~~~L~~a 79 (174)
T cd06143 5 AEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVP---FIDDYISTTE--PVVDYLTRFSGIKPGDLDPK 79 (174)
T ss_pred eeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCE---EEeeeECCCC--CccCcCccccccCHHHcCcc
Confidence 3555566655554443332 357777776521 11112 3789999998 99999999999999999876
Q ss_pred C------CHHHHHHHHHHHhC-CCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHH
Q 023805 84 P------EFEEVADKIFSILN-GRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLA 156 (277)
Q Consensus 84 ~------~f~ev~~~l~~~l~-~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La 156 (277)
. +++++..++.+++. +.++|||.. ..|+..|+ +..|. ..++||..++. .+.....+|..|+
T Consensus 80 ~~~~~~~t~~~v~~~l~~li~~~tILVGHsL-~nDL~aL~-------l~hp~-~~viDTa~l~~---~~~~r~~sLk~La 147 (174)
T cd06143 80 TSSKNLTTLKSAYLKLRLLVDLGCIFVGHGL-AKDFRVIN-------IQVPK-EQVIDTVELFH---LPGQRKLSLRFLA 147 (174)
T ss_pred ccccccCCHHHHHHHHHHHcCCCCEEEeccc-hhHHHHhc-------CcCCC-cceEEcHHhcc---CCCCCChhHHHHH
Confidence 4 69999999999994 789999999 99998875 54443 24899985542 1333468999999
Q ss_pred H-HhCCC--CCCCChHHHHHHHHHHHH
Q 023805 157 S-YFGLG--QQKHRSLDDVRMNLEVLK 180 (277)
Q Consensus 157 ~-~~gi~--~~~H~Al~DA~~t~~l~~ 180 (277)
+ ++|.. ...|++.+||+++++|++
T Consensus 148 ~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 148 WYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 9 45655 578999999999999984
No 51
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.53 E-value=8.9e-14 Score=111.95 Aligned_cols=160 Identities=19% Similarity=0.229 Sum_probs=119.6
Q ss_pred CCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCC--CCCCchhhhhc---CCCHHHHhCCC
Q 023805 10 AGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDL--SAVALKSSRCD---GITREAVESAP 84 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~--~~i~~~~~~~~---GIt~e~l~~a~ 84 (277)
...+++|.+|+|+||+++ ..++||||++++.|.+.....+-+...|+-... ..+++++++.| |++....++..
T Consensus 3 ~~~~nLiWIDlEMTGLd~--~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~ 80 (184)
T COG1949 3 ANKNNLIWIDLEMTGLDP--ERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTV 80 (184)
T ss_pred CcCCceEEEeeeeccCCc--CcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhc
Confidence 356789999999999999 789999999999998876655556666655442 46788888877 67777778888
Q ss_pred CHHHHHHHHHHHhCC------CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHH
Q 023805 85 EFEEVADKIFSILNG------RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASY 158 (277)
Q Consensus 85 ~f~ev~~~l~~~l~~------~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~ 158 (277)
+..++-.++.+||++ .++.|.++ .-|+.||...+.+..--+.+ +++|. .+|.+||.+
T Consensus 81 t~~~aE~~~l~flkkwvp~~~spicGNSI-~qDRrFl~r~MP~Le~yfHY--R~lDV--------------STlKELa~R 143 (184)
T COG1949 81 TEAEAEAQTLDFLKKWVPKGVSPICGNSI-AQDRRFLFRYMPKLEAYFHY--RYLDV--------------STLKELARR 143 (184)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCCccchh-hHHHHHHHHHhhhHHHHhhh--HhhhH--------------HHHHHHHHh
Confidence 999998888888853 47778777 99999999887553322222 23333 345555554
Q ss_pred h------CCC-CCCCChHHHHHHHHHHHHHHHHhhhc
Q 023805 159 F------GLG-QQKHRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 159 ~------gi~-~~~H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
+ |.. +..|+|++|.+-...-+++..+.++.
T Consensus 144 W~P~i~~~~~K~~~H~Al~DI~ESI~EL~~YR~~f~~ 180 (184)
T COG1949 144 WNPEILAGFKKGGTHRALDDIRESIAELRYYREHFLK 180 (184)
T ss_pred hCcHhhhccccccchhHHHHHHHHHHHHHHHHHHhcc
Confidence 4 333 57899999999999999988887655
No 52
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.49 E-value=2.1e-13 Score=110.82 Aligned_cols=165 Identities=16% Similarity=0.195 Sum_probs=125.7
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCC--CCCCchhhhhc---CCCHHHHhCCCC
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDL--SAVALKSSRCD---GITREAVESAPE 85 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~--~~i~~~~~~~~---GIt~e~l~~a~~ 85 (277)
..+.+|.+|||+||++. ..+.|+||++++.+++.....+-+...|+-+.. ..+++||.+-| |+|...+++..+
T Consensus 24 l~q~lVWiD~EMTGLdv--ekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~t 101 (208)
T KOG3242|consen 24 LKQPLVWIDCEMTGLDV--EKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKIT 101 (208)
T ss_pred ccCceEEEeeecccccc--ccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhcc
Confidence 46789999999999998 789999999999998877666667777776553 56788999877 688888999999
Q ss_pred HHHHHHHHHHHhCC------CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHH--HHHHhCCCCCCCCHHHHHH
Q 023805 86 FEEVADKIFSILNG------RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGV--LTEKFGRRAGNMKMATLAS 157 (277)
Q Consensus 86 f~ev~~~l~~~l~~------~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l--~~~~~~~~~~~~~L~~La~ 157 (277)
+.|+-.++.+|++. +++.|.++ -.|+.||..++....-.+++. +||+..+ +.+..+|...
T Consensus 102 l~~aEnevl~yikk~ip~~~~~laGNSV-~~DrlFl~k~mPk~~~~lhyr--ivDVStIkeL~~Rw~P~~~--------- 169 (208)
T KOG3242|consen 102 LADAENEVLEYIKKHIPKGKCPLAGNSV-YMDRLFLKKYMPKLIKHLHYR--IVDVSTIKELARRWYPDIK--------- 169 (208)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCccCcch-hhHHHHHHHHhHHHHHhccee--eeeHHHHHHHHHHhCchhh---------
Confidence 99999999999953 46667666 999999999998766555543 7775432 1122223211
Q ss_pred HhCCC-CCCCChHHHHHHHHHHHHHHHHhhhcc
Q 023805 158 YFGLG-QQKHRSLDDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 158 ~~gi~-~~~H~Al~DA~~t~~l~~~l~~~l~~~ 189 (277)
.+.-. ...|+|++|.+-...-+++..+.+++-
T Consensus 170 ~~aPkK~~~HrAldDI~ESI~ELq~Yr~nifkk 202 (208)
T KOG3242|consen 170 ARAPKKKATHRALDDIRESIKELQYYRENIFKK 202 (208)
T ss_pred ccCcccccccchHHHHHHHHHHHHHHHHHhccC
Confidence 01111 467999999999999999999988773
No 53
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.46 E-value=9.7e-13 Score=118.88 Aligned_cols=174 Identities=19% Similarity=0.111 Sum_probs=139.0
Q ss_pred CCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHh-CCCCHHH
Q 023805 10 AGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVE-SAPEFEE 88 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~-~a~~f~e 88 (277)
.....|++.|.||.|.+| ..+++.+|++|..|.+..++.+-...|++|.+..--.|.+.-+||||+.... .+.+-.+
T Consensus 6 ~~~~tF~~yDYETfG~~P--a~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~ 83 (475)
T COG2925 6 TKQPTFLFYDYETFGVHP--ALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAA 83 (475)
T ss_pred CCCCcEEEEehhhcCCCc--ccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHH
Confidence 345689999999999998 7789999999999998888888888999999865557888889999998874 5668888
Q ss_pred HHHHHHHHh--CCCEEEEeCCchhHHHHHHHHHHHhCCC-----CCCCCceeehHHHHH--HHhCC----------CCCC
Q 023805 89 VADKIFSIL--NGRVWAGHNIRRFDCARIKEAFAEIGKP-----APVPVGMIDSLGVLT--EKFGR----------RAGN 149 (277)
Q Consensus 89 v~~~l~~~l--~~~~lv~hn~~~fD~~~L~~~~~~~g~~-----~p~~~~~iDt~~l~~--~~~~~----------~~~~ 149 (277)
....+..-+ .+.+++|+|..+||-.+.+..|.+.=++ +...+.-+|.+.+.+ +.+.| +..+
T Consensus 84 F~~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pS 163 (475)
T COG2925 84 FAARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPS 163 (475)
T ss_pred HHHHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcc
Confidence 889988888 4578999999999998888777664333 333334455555543 33333 2468
Q ss_pred CCHHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHh
Q 023805 150 MKMATLASYFGLG-QQKHRSLDDVRMNLEVLKHCATV 185 (277)
Q Consensus 150 ~~L~~La~~~gi~-~~~H~Al~DA~~t~~l~~~l~~~ 185 (277)
++|+.|.+.-|++ ..+|+|+.|+++|+.+.+.+..+
T Consensus 164 FkLEhLt~ANgieH~nAHdAmsDVyATIamAklvk~~ 200 (475)
T COG2925 164 FKLEHLTKANGIEHSNAHDAMSDVYATIAMAKLVKTA 200 (475)
T ss_pred hhhHHHhhccccccchhhHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999 89999999999999988877553
No 54
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.45 E-value=4.7e-13 Score=123.51 Aligned_cols=157 Identities=21% Similarity=0.326 Sum_probs=123.5
Q ss_pred CCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCC-CHH
Q 023805 9 AAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAP-EFE 87 (277)
Q Consensus 9 ~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~-~f~ 87 (277)
.....+++++|||+..... . -++.++++|-.+...+ |..+|+|.. +|.++.+.++|||.+++++++ +++
T Consensus 212 v~~~~~i~AlDCEm~~te~--g-~el~RVt~VD~~~~vi-----~D~fVkP~~--~VvDy~T~~SGIT~~~~e~~t~tl~ 281 (380)
T KOG2248|consen 212 VSKSPNIFALDCEMVVTEN--G-LELTRVTAVDRDGKVI-----LDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLE 281 (380)
T ss_pred CCCCCCeEEEEeeeeeecc--c-eeeEEeeeeeccCcEE-----eEEeecCCC--cccccccccccccHHHHhcCccCHH
Confidence 3555789999999986654 2 6899999987776642 779999999 999999999999999998665 999
Q ss_pred HHHHHHHHHhC-CCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHH-HhCCC---
Q 023805 88 EVADKIFSILN-GRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLAS-YFGLG--- 162 (277)
Q Consensus 88 ev~~~l~~~l~-~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~-~~gi~--- 162 (277)
++.++|..|+. +.++|||+. ..|+..|+- ..+ .+|||..++.+..++.....+|.+|++ ++|..
T Consensus 282 dvq~~l~~~~~~~TILVGHSL-enDL~aLKl-------~H~---~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~ 350 (380)
T KOG2248|consen 282 DVQKELLELISKNTILVGHSL-ENDLKALKL-------DHP---SVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQE 350 (380)
T ss_pred HHHHHHHhhcCcCcEEEeech-hhHHHHHhh-------hCC---ceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhc
Confidence 99999999994 679999999 999998873 223 389998555444433122356899998 44443
Q ss_pred -CCCCChHHHHHHHHHHHHHHHHhh
Q 023805 163 -QQKHRSLDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 163 -~~~H~Al~DA~~t~~l~~~l~~~l 186 (277)
...|++..||.++++|++......
T Consensus 351 ~~~~HdS~eDA~acm~Lv~~k~~~~ 375 (380)
T KOG2248|consen 351 GVGGHDSVEDALACMKLVKLKIKNS 375 (380)
T ss_pred cCCCCccHHHHHHHHHHHHHHHhcc
Confidence 356999999999999999877643
No 55
>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=99.34 E-value=4.6e-11 Score=101.82 Aligned_cols=138 Identities=19% Similarity=0.167 Sum_probs=101.2
Q ss_pred EEEEEeccCCC----CCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHH
Q 023805 15 IVFFDLETTVP----RRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVA 90 (277)
Q Consensus 15 ~v~~D~ETTg~----~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~ 90 (277)
+++||+||+|. ++ ..++|++||++....+... .+.....+.. ...+ ||+..++...++..+++
T Consensus 1 v~~~DIEt~~~~~~p~~--~~d~Ii~I~~~~~~~g~~~---~~~~~~~~~~--~~~~------~i~~~~v~~~~~E~~lL 67 (199)
T cd05160 1 VLSFDIETTPPVGGPEP--DRDPIICITYADSFDGVKV---VFLLKTSTVG--DDIE------FIDGIEVEYFADEKELL 67 (199)
T ss_pred CccEEEeecCCCCCcCC--CCCCEEEEEEEEeeCCcee---eEEEeecccC--CcCC------CCCCceEEEeCCHHHHH
Confidence 47899999997 54 5689999999887444432 1222222221 1111 78888888899999999
Q ss_pred HHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCC-C--------------------CCceeehHHHHHHHhCCC
Q 023805 91 DKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAP-V--------------------PVGMIDSLGVLTEKFGRR 146 (277)
Q Consensus 91 ~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p-~--------------------~~~~iDt~~l~~~~~~~~ 146 (277)
..|.++++. .+++|||+..||+++|...+..+|++.. . ....+|++.++...+ +
T Consensus 68 ~~f~~~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~-~- 145 (199)
T cd05160 68 KRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDF-K- 145 (199)
T ss_pred HHHHHHHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhc-C-
Confidence 999999976 5999999999999999999999998762 0 113789998775544 3
Q ss_pred CCCCCHHHHHHHhCCC-CCCCC
Q 023805 147 AGNMKMATLASYFGLG-QQKHR 167 (277)
Q Consensus 147 ~~~~~L~~La~~~gi~-~~~H~ 167 (277)
..+++|+++|+.++.. ...++
T Consensus 146 l~sy~L~~v~~~~l~~~k~~~~ 167 (199)
T cd05160 146 LKSYTLDAVAEELLGEGKEKVD 167 (199)
T ss_pred cccCCHHHHHHHHhCCCCCcCC
Confidence 7789999999977655 33343
No 56
>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=99.10 E-value=1.5e-09 Score=82.03 Aligned_cols=79 Identities=25% Similarity=0.342 Sum_probs=60.8
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIFS 95 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~~ 95 (277)
++||+||+|.++ ..++|+.|++...+++. .| ++ . |.+
T Consensus 1 ~~~DiEt~~~~~--~~~~i~~i~~~~~~~~~-----~~--~~--------~--------------------------f~~ 37 (96)
T cd06125 1 IAIDTEATGLDG--AVHEIIEIALADVNPED-----TA--VI--------D--------------------------LKD 37 (96)
T ss_pred CEEEEECCCCCC--CCCcEEEEEEEEccCCC-----EE--Ee--------h--------------------------HHH
Confidence 479999999887 67899999987543221 12 11 0 667
Q ss_pred HhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCCC-CCceeehHHH
Q 023805 96 ILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAPV-PVGMIDSLGV 138 (277)
Q Consensus 96 ~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p~-~~~~iDt~~l 138 (277)
|+++ .++|+||+ .||+.+|.+++.+++.+.|. ...++||+.+
T Consensus 38 ~l~~~~~~v~V~hn~-~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 38 ILRDKPLAILVGHNG-SFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHhhCCCCEEEEeCc-HHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 7755 48999999 99999999999999998774 4579999965
No 57
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.99 E-value=1.9e-09 Score=88.80 Aligned_cols=115 Identities=21% Similarity=0.358 Sum_probs=64.2
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHHH
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIFS 95 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~~ 95 (277)
++||+||||+++ ..+.|+-||++.++++... .|..+..... +. ++.+.++.+
T Consensus 1 l~~DIET~Gl~~--~~~~i~liG~~~~~~~~~~---~~~~~~~~~~----------------~e-------e~~~~~~~~ 52 (164)
T PF13482_consen 1 LFFDIETTGLSP--DNDTIYLIGVADFDDDEII---TFIQWFAEDP----------------DE-------EEIILEFFE 52 (164)
T ss_dssp --EEEEESS-GG---G---EEEEEEE-ETTTTE----EEEE-GGGH----------------HH-------HHHHHH--H
T ss_pred CcEEecCCCCCC--CCCCEEEEEEEEeCCCceE---EeeHhhccCc----------------HH-------HHHHHHHHH
Confidence 589999999987 5677999999988876532 1333332221 00 223333224
Q ss_pred Hh-CCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCC
Q 023805 96 IL-NGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQ 163 (277)
Q Consensus 96 ~l-~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~ 163 (277)
++ +...+++||+..||.++|++.+.+++++.+ ...+|++..+.+... .+++|..+++.+|+..
T Consensus 53 ~l~~~~~iv~yng~~FD~p~L~~~~~~~~~~~~--~~~iDl~~~~~~~~~---~~~~Lk~ve~~lg~~~ 116 (164)
T PF13482_consen 53 LLDEADNIVTYNGKNFDIPFLKRRAKRYGLPPP--FNHIDLLKIIKKHFL---ESYSLKNVEKFLGIER 116 (164)
T ss_dssp HHHTT--EEESSTTTTHHHHHHHHH-HHHH--G--GGEEEHHHHHT-TTS---CCTT--SHHH------
T ss_pred HHhcCCeEEEEeCcccCHHHHHHHHHHcCCCcc--cchhhHHHHHHhccC---CCCCHHHHhhhccccc
Confidence 55 557899999889999999999988887753 459999987754433 6789999999999984
No 58
>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=98.94 E-value=4.9e-08 Score=82.12 Aligned_cols=145 Identities=17% Similarity=0.170 Sum_probs=99.4
Q ss_pred CCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 10 AGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
.+...++++|+|++|..+ ...+|+.+++..- ++ ..|..-+.+. .. .++..+.++
T Consensus 2 ~~~~~~~a~d~e~~~~~~--~~~~i~~l~~~~~-~~-----~~~~~~~~~~---~~---------------~~~~~~~~~ 55 (193)
T cd06139 2 LEKAKVFAFDTETTSLDP--MQAELVGISFAVE-PG-----EAYYIPLGHD---YG---------------GEQLPREEV 55 (193)
T ss_pred CccCCeEEEEeecCCCCc--CCCeEEEEEEEcC-CC-----CEEEEecCCC---cc---------------ccCCCHHHH
Confidence 356678999999999876 4567887776422 11 1232212211 11 133456788
Q ss_pred HHHHHHHhCCC--EEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC----
Q 023805 90 ADKIFSILNGR--VWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG---- 162 (277)
Q Consensus 90 ~~~l~~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~---- 162 (277)
+..|.+++.+. .+|+||+ +||+.+|. ++|+..+. .++||+ ++.+.+++...+.+|+++++.| +..
T Consensus 56 ~~~l~~~l~~~~~~~v~hn~-k~d~~~l~----~~gi~~~~--~~~Dt~-l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~ 127 (193)
T cd06139 56 LAALKPLLEDPSIKKVGQNL-KFDLHVLA----NHGIELRG--PAFDTM-LASYLLNPGRRRHGLDDLAERYLGHKTISF 127 (193)
T ss_pred HHHHHHHHhCCCCcEEeecc-HHHHHHHH----HCCCCCCC--CcccHH-HHHHHhCCCCCCCCHHHHHHHHhCCCCccH
Confidence 99999999764 7999999 99999885 45776543 379999 6778888876457999999965 322
Q ss_pred ----C---------------CCCChHHHHHHHHHHHHHHHHhhhc
Q 023805 163 ----Q---------------QKHRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 163 ----~---------------~~H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
+ ..|.+..||..+.+|+..+.+.+..
T Consensus 128 ~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 128 EDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 1135788899999999998887643
No 59
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.92 E-value=3.9e-08 Score=84.67 Aligned_cols=150 Identities=16% Similarity=0.176 Sum_probs=103.3
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVA 90 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~ 90 (277)
+..+++|||+||||++. ..+.|+-+|...+.++...+-+ .+ -|..+ .| .-++
T Consensus 96 ~~e~~~FFDiETTGL~~--ag~~I~~~g~a~~~~~~~~Vrq---~~-lp~p~--------------~E--------~avl 147 (278)
T COG3359 96 EAEDVAFFDIETTGLDR--AGNTITLVGGARGVDDTMHVRQ---HF-LPAPE--------------EE--------VAVL 147 (278)
T ss_pred cccceEEEeeeccccCC--CCCeEEEEEEEEccCceEEEEe---ec-CCCcc--------------hh--------hHHH
Confidence 35679999999999997 4566777777766666544311 11 12210 00 1234
Q ss_pred HHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC-CCC----
Q 023805 91 DKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG-QQK---- 165 (277)
Q Consensus 91 ~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~-~~~---- 165 (277)
+.|.....-..+|.+|+..||.++++. +.+..+++.....-+|.+..++++....+.+.+|+++-+.+|+. ...
T Consensus 148 e~fl~~~~~~~lvsfNGkaFD~PfikR-~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~edtdG~ 226 (278)
T COG3359 148 ENFLHDPDFNMLVSFNGKAFDIPFIKR-MVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREEDTDGY 226 (278)
T ss_pred HHHhcCCCcceEEEecCcccCcHHHHH-HHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHHHhCccccccCCCc
Confidence 443333333589999999999999994 77777777666668999987776665567789999999999886 110
Q ss_pred ----------------------CChHHHHHHHHHHHHHHHHhhhcc
Q 023805 166 ----------------------HRSLDDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 166 ----------------------H~Al~DA~~t~~l~~~l~~~l~~~ 189 (277)
+.--.|+.++..|+.++..++..+
T Consensus 227 ~~p~lyr~~~~~~dp~ll~~l~~hN~eDvlnL~~i~~h~~~~i~~~ 272 (278)
T COG3359 227 DGPELYRLYRRYGDPGLLDGLVLHNREDVLNLPTIIKHVSKKILED 272 (278)
T ss_pred chHHHHHHHHHcCCHHHHHHHHHccHHHHHhHHHHHHHHHHHHHHH
Confidence 333578999999998888876553
No 60
>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=98.87 E-value=7.9e-08 Score=81.86 Aligned_cols=129 Identities=17% Similarity=0.163 Sum_probs=87.2
Q ss_pred cEEEEEeccCCCC--CCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 14 EIVFFDLETTVPR--RAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 14 ~~v~~D~ETTg~~--~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
.+++||+||++.. |....+.|+.||++....+.+. .+ .+.. . . .+..-.+-.+++.
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~------~~-~~~~---~-~-----------~v~~~~~E~~lL~ 61 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVI------TW-KKFD---L-P-----------FVEVVKTEKEMIK 61 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEE------Ee-cCCC---C-C-----------eEEEeCCHHHHHH
Confidence 6899999998421 2225689999998653222111 11 1111 0 0 1112233378999
Q ss_pred HHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCCCC---------------------CceeehHHHHHHHhCCCC
Q 023805 92 KIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAPVP---------------------VGMIDSLGVLTEKFGRRA 147 (277)
Q Consensus 92 ~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~---------------------~~~iDt~~l~~~~~~~~~ 147 (277)
.|.+++.. .+++|||+..||+++|..-+..+|+..+.. ...+|+..++.+. ...
T Consensus 62 ~F~~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~--~~l 139 (195)
T cd05780 62 RFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT--LNL 139 (195)
T ss_pred HHHHHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhh--CCC
Confidence 99999965 689999998999999999999999875531 1378999877653 356
Q ss_pred CCCCHHHHHH-HhCCCCCCC
Q 023805 148 GNMKMATLAS-YFGLGQQKH 166 (277)
Q Consensus 148 ~~~~L~~La~-~~gi~~~~H 166 (277)
.+++|+++++ .+|.+...+
T Consensus 140 ~sy~L~~v~~~~Lg~~k~d~ 159 (195)
T cd05780 140 TRYTLERVYEELFGIEKEDV 159 (195)
T ss_pred CcCcHHHHHHHHhCCCCCcC
Confidence 7899999988 778774443
No 61
>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=98.79 E-value=1.6e-07 Score=79.64 Aligned_cols=117 Identities=14% Similarity=0.120 Sum_probs=84.1
Q ss_pred cEEEEEeccCCCC--CCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 14 EIVFFDLETTVPR--RAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 14 ~~v~~D~ETTg~~--~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
++++||+||++.. |....+.|+.||+...++.. . .+.. ...+-.+++.
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~-~------~~~~-----------------------~~~~E~~lL~ 53 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDV-E------FILA-----------------------EGLDDRKIIR 53 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCE-E------EEEe-----------------------cCCCHHHHHH
Confidence 6799999998421 22256899999986644331 1 1110 0122378999
Q ss_pred HHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCCCC--C-----------------ceeehHHHHHHHhCCCCCC
Q 023805 92 KIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAPVP--V-----------------GMIDSLGVLTEKFGRRAGN 149 (277)
Q Consensus 92 ~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~--~-----------------~~iDt~~l~~~~~~~~~~~ 149 (277)
.|.++++. .+++|||+..||+++|..-+..+|+..+.. . ..+|...++.+.. .+++
T Consensus 54 ~F~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~--~l~~ 131 (188)
T cd05781 54 EFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP--EVKV 131 (188)
T ss_pred HHHHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC--CCCC
Confidence 99999964 589999999999999999999999765421 0 1789998776543 3678
Q ss_pred CCHHHHHHHhCCC
Q 023805 150 MKMATLASYFGLG 162 (277)
Q Consensus 150 ~~L~~La~~~gi~ 162 (277)
++|+++|+++|..
T Consensus 132 y~L~~Va~~Lg~~ 144 (188)
T cd05781 132 KTLENVAEYLGVM 144 (188)
T ss_pred CCHHHHHHHHCCC
Confidence 9999999999875
No 62
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=98.74 E-value=4.8e-08 Score=85.04 Aligned_cols=198 Identities=17% Similarity=0.133 Sum_probs=139.5
Q ss_pred CCCCCCCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCee------------------eeeceEEEeecCCCCCCC
Q 023805 4 FIPSQAAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKL------------------VELESFSTLIKPKDLSAV 65 (277)
Q Consensus 4 ~~~~~~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~------------------~~~~sf~~~v~P~~~~~i 65 (277)
...+|...-..++|+|+|+||+.. ....|.|+....|....+ ..++..+.++.|.. ..
T Consensus 4 i~~se~pr~~tf~fldleat~lp~--~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~ 79 (318)
T KOG4793|consen 4 ISISEVPRLRTFSFLDLEATGLPG--WIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VT 79 (318)
T ss_pred cccCcCCceeEEEeeeeccccCCc--ccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--Cc
Confidence 345666777899999999999875 556788877655431100 12344556667776 78
Q ss_pred CchhhhhcCCCHHHHh--CCCCHH-HHHHHHHHHhCC----CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHH
Q 023805 66 ALKSSRCDGITREAVE--SAPEFE-EVADKIFSILNG----RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGV 138 (277)
Q Consensus 66 ~~~~~~~~GIt~e~l~--~a~~f~-ev~~~l~~~l~~----~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l 138 (277)
++.+.+++|++++.+. ...-|+ ++.+-+..|+.. ..+|+||...||+..|.+++++.|+..|-....+|++..
T Consensus 80 ~p~aeeitgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa 159 (318)
T KOG4793|consen 80 RPIAEEITGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPA 159 (318)
T ss_pred ChhhhhhcccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHH
Confidence 8999999999997653 233444 455666777754 478999999999999999999999998865568888865
Q ss_pred HHHHhCC--------CCCCCCHHHHHHHh-CC-C-CCCCChHHHHHHHHHHHHHHHHhhhcccCCCccccccccCCcccc
Q 023805 139 LTEKFGR--------RAGNMKMATLASYF-GL-G-QQKHRSLDDVRMNLEVLKHCATVLFLESSLPNTFNSNLQSSLTVT 207 (277)
Q Consensus 139 ~~~~~~~--------~~~~~~L~~La~~~-gi-~-~~~H~Al~DA~~t~~l~~~l~~~l~~~~~l~~~~~~~~~~~~~~~ 207 (277)
+..+-.. ...+++|..+..+| +- + ...|.+..|+....-+++....++.-|+. ..... |+..+++
T Consensus 160 ~~ald~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~d---eqa~p-w~~ir~l 235 (318)
T KOG4793|consen 160 LNALDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSD---EQARP-WLLIRPL 235 (318)
T ss_pred HHHHhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHh---hcCCC-cccccch
Confidence 5433221 13567888887755 43 2 46799999999999999999999888774 22233 4435555
Q ss_pred cc
Q 023805 208 TR 209 (277)
Q Consensus 208 ~~ 209 (277)
.-
T Consensus 236 ~~ 237 (318)
T KOG4793|consen 236 YL 237 (318)
T ss_pred hh
Confidence 53
No 63
>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=98.70 E-value=7.1e-07 Score=76.56 Aligned_cols=146 Identities=13% Similarity=0.126 Sum_probs=88.0
Q ss_pred cEEEEEeccCCC---CCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCC-chhhhhcCCCHHHHhCCCCHHHH
Q 023805 14 EIVFFDLETTVP---RRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVA-LKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 14 ~~v~~D~ETTg~---~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~-~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
.+++||+|+.+. .|+...+.|++|+++.-..+... . ....+.+... .+. ..+..+.|. -.+..-.+-.++
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~-~--~~~~~~~~~~-~~~~~~~~~~~~~--~~v~~~~~E~~l 76 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLI-V--NREIVSEDIE-DFEYTPKPEYEGP--FKVFNEPDEKAL 76 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEE-e--cccccccccc-cccccCCCCCCCc--eEEecCCCHHHH
Confidence 589999999752 23336789999998764433211 0 0000000000 000 000001110 001112355789
Q ss_pred HHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCC--C---CC----------ceeehHHHHHHHhCCCCCCCC
Q 023805 90 ADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAP--V---PV----------GMIDSLGVLTEKFGRRAGNMK 151 (277)
Q Consensus 90 ~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p--~---~~----------~~iDt~~l~~~~~~~~~~~~~ 151 (277)
+.+|.+++.. .+++|||+..||+++|..-+..+|+... . .. ..+|.+.++++......++++
T Consensus 77 L~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sys 156 (204)
T cd05779 77 LQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQG 156 (204)
T ss_pred HHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCcc
Confidence 9999999965 4899999999999999999999887744 1 00 268999877654433345899
Q ss_pred HHHHHH-HhCCCCCC
Q 023805 152 MATLAS-YFGLGQQK 165 (277)
Q Consensus 152 L~~La~-~~gi~~~~ 165 (277)
|+++|+ .+|.++..
T Consensus 157 Ld~Va~~~Lg~~K~~ 171 (204)
T cd05779 157 LKAVTKAKLGYDPVE 171 (204)
T ss_pred HHHHHHHHhCCCcCc
Confidence 999999 58887433
No 64
>PRK05755 DNA polymerase I; Provisional
Probab=98.68 E-value=3.4e-07 Score=94.41 Aligned_cols=135 Identities=17% Similarity=0.212 Sum_probs=98.4
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
...+++||+||+|+++ ...+|+.|++. +.++. . .+|.+.. +. .+++.
T Consensus 314 ~~~~~a~DtEt~~l~~--~~~~i~~i~ls-~~~g~-----~--~~ip~~~-------------i~----------~~~l~ 360 (880)
T PRK05755 314 AAGLFAFDTETTSLDP--MQAELVGLSFA-VEPGE-----A--AYIPLDQ-------------LD----------REVLA 360 (880)
T ss_pred ccCeEEEEeccCCCCc--ccccEEEEEEE-eCCCc-----E--EEEeccc-------------cc----------HHHHH
Confidence 3568999999999987 56788888863 33321 1 2332211 11 15777
Q ss_pred HHHHHhCCC--EEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCCC-----
Q 023805 92 KIFSILNGR--VWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLGQ----- 163 (277)
Q Consensus 92 ~l~~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~~----- 163 (277)
.|.+++.+. .+|+||+ +||+.+|.. +|+..+. .++||+ ++.+++++... ++|+.|++.| |++.
T Consensus 361 ~l~~~L~d~~v~kV~HNa-kfDl~~L~~----~gi~~~~--~~~DT~-iAa~Ll~~~~~-~~L~~L~~~ylg~~~~~~~~ 431 (880)
T PRK05755 361 ALKPLLEDPAIKKVGQNL-KYDLHVLAR----YGIELRG--IAFDTM-LASYLLDPGRR-HGLDSLAERYLGHKTISFEE 431 (880)
T ss_pred HHHHHHhCCCCcEEEecc-HhHHHHHHh----CCCCcCC--CcccHH-HHHHHcCCCCC-CCHHHHHHHHhCCCccchHH
Confidence 888899764 4899999 999999873 4776543 489999 67788888654 8999999976 5441
Q ss_pred ---------------CCCChHHHHHHHHHHHHHHHHhhhc
Q 023805 164 ---------------QKHRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 164 ---------------~~H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
..|.|..|+..+++|+..+.+.+..
T Consensus 432 ~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 432 VAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred hcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 2267899999999999999987644
No 65
>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=98.67 E-value=3.6e-07 Score=78.57 Aligned_cols=119 Identities=20% Similarity=0.262 Sum_probs=82.2
Q ss_pred cEEEEEeccCCCC------CCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHH
Q 023805 14 EIVFFDLETTVPR------RAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFE 87 (277)
Q Consensus 14 ~~v~~D~ETTg~~------~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ 87 (277)
++++||+|+.... +....+.|+.||.. +.++.. ..+.. ...+-.
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~--~~~~~~------~~~~~----------------------~~~~E~ 59 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALR--DNRGWE------EVLHA----------------------EDAAEK 59 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecc--cCCCce------eeecc----------------------CCCCHH
Confidence 6899999996532 21244689999874 222111 11100 123447
Q ss_pred HHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCCC----------------------------C-Cceeeh
Q 023805 88 EVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAPV----------------------------P-VGMIDS 135 (277)
Q Consensus 88 ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p~----------------------------~-~~~iDt 135 (277)
+++..|.+++.+ .+++|||+..||+++|..-+..+|+..+. + ...+|+
T Consensus 60 ~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl 139 (207)
T cd05785 60 ELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDT 139 (207)
T ss_pred HHHHHHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEc
Confidence 899999999965 68999999999999999999999987631 0 123799
Q ss_pred HHHHHHHh--CCCCCCCCHHHHHHHhCCC
Q 023805 136 LGVLTEKF--GRRAGNMKMATLASYFGLG 162 (277)
Q Consensus 136 ~~l~~~~~--~~~~~~~~L~~La~~~gi~ 162 (277)
+.++.+.- ...+.+++|+++|++||+.
T Consensus 140 ~~~~~~~~~~~~~l~sysL~~Va~~~g~~ 168 (207)
T cd05785 140 YFLVQLFDVSSRDLPSYGLKAVAKHFGLA 168 (207)
T ss_pred HHHHHhhcccccCCCCCCHHHHHHHhccc
Confidence 87665421 2356789999999999874
No 66
>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=98.48 E-value=3e-06 Score=72.91 Aligned_cols=74 Identities=19% Similarity=0.288 Sum_probs=59.4
Q ss_pred HHHHHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCC---------------ceeehHHHHHHHhCCCCCC
Q 023805 87 EEVADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPV---------------GMIDSLGVLTEKFGRRAGN 149 (277)
Q Consensus 87 ~ev~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~---------------~~iDt~~l~~~~~~~~~~~ 149 (277)
.+++..|.+++.+ .++|+||+..||+++|..-+..+|+..|... ..+|++.+++. + ....+
T Consensus 79 ~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~-~-~~~~~ 156 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAF-Y-GARAR 156 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhc-c-CccCC
Confidence 6789999888854 5899999999999999999999999765321 27899876642 2 22468
Q ss_pred CCHHHHHHHhCCC
Q 023805 150 MKMATLASYFGLG 162 (277)
Q Consensus 150 ~~L~~La~~~gi~ 162 (277)
++|+.+|+.+|++
T Consensus 157 ~~L~~va~~lG~~ 169 (208)
T cd05782 157 ASLDLLAKLLGIP 169 (208)
T ss_pred CCHHHHHHHhCCC
Confidence 9999999999996
No 67
>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=98.38 E-value=1.8e-05 Score=69.04 Aligned_cols=136 Identities=15% Similarity=0.148 Sum_probs=85.8
Q ss_pred CcEEEEEeccCCC---CCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 13 AEIVFFDLETTVP---RRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 13 ~~~v~~D~ETTg~---~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
-++++||+|+... .|+...+.|+.|+++...++........-..+.+.. .+. | ..+..-.+-.+.
T Consensus 7 l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~--~~~-------~---~~v~~~~~E~eL 74 (230)
T cd05777 7 LRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCA--PIV-------G---AQVFSFETEEEL 74 (230)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCC--CCC-------C---CEEEEECCHHHH
Confidence 3689999999742 233366899999998665442111111111122211 111 1 111122355789
Q ss_pred HHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCC--C-------------------------------CCcee
Q 023805 90 ADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAP--V-------------------------------PVGMI 133 (277)
Q Consensus 90 ~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p--~-------------------------------~~~~i 133 (277)
+..|.+++.. .+++|||+..||+.+|.+-++.+|+... . .--.+
T Consensus 75 L~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~i 154 (230)
T cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQF 154 (230)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEee
Confidence 9999999965 5999999999999999988888876521 0 00346
Q ss_pred ehHHHHHHHhCCCCCCCCHHHHHH-HhCCC
Q 023805 134 DSLGVLTEKFGRRAGNMKMATLAS-YFGLG 162 (277)
Q Consensus 134 Dt~~l~~~~~~~~~~~~~L~~La~-~~gi~ 162 (277)
|+..++.+.. .+.+++|+++|+ .+|..
T Consensus 155 D~~~~~~~~~--kl~sy~L~~Va~~~Lg~~ 182 (230)
T cd05777 155 DLLQVIQRDY--KLRSYSLNSVSAHFLGEQ 182 (230)
T ss_pred eHHHHHHHhc--CcccCcHHHHHHHHhCCC
Confidence 8887775543 578999999999 44543
No 68
>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=98.37 E-value=1.4e-05 Score=68.54 Aligned_cols=79 Identities=20% Similarity=0.320 Sum_probs=59.2
Q ss_pred CCHHHHHHHHHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCC---CCC----------CCceeehHHHHHH------Hh
Q 023805 84 PEFEEVADKIFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKP---APV----------PVGMIDSLGVLTE------KF 143 (277)
Q Consensus 84 ~~f~ev~~~l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~---~p~----------~~~~iDt~~l~~~------~~ 143 (277)
.+-.+++.+|.+++.+ .+++|||+..||+++|..-+.++|+. .|. ....+|.+..++. .+
T Consensus 71 ~~E~~lL~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~ 150 (204)
T cd05783 71 DSEKELIREAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAF 150 (204)
T ss_pred CCHHHHHHHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhh
Confidence 3447899999999964 68999999999999999999999987 211 1246888776543 12
Q ss_pred CCCCCCCCHHHHHHHh-CCC
Q 023805 144 GRRAGNMKMATLASYF-GLG 162 (277)
Q Consensus 144 ~~~~~~~~L~~La~~~-gi~ 162 (277)
+....+++|+++|+++ |.+
T Consensus 151 ~~~~~~~~L~~Va~~~lg~~ 170 (204)
T cd05783 151 GNKYREYTLDAVAKALLGEG 170 (204)
T ss_pred ccccccCcHHHHHHHhcCCC
Confidence 2245789999999966 555
No 69
>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=98.37 E-value=3e-05 Score=63.87 Aligned_cols=89 Identities=16% Similarity=0.323 Sum_probs=65.5
Q ss_pred HHHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHH-hC-CC--
Q 023805 89 VADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASY-FG-LG-- 162 (277)
Q Consensus 89 v~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~-~g-i~-- 162 (277)
+...|.++|.+ ...||||+ +||+.+|.+. +|+... .++|++ ++.+.+++... ++|++|+.. +| +.
T Consensus 65 ~~~~l~~ll~~~~i~kv~~n~-~~D~~~L~~~---~~i~~~---~~~D~~-l~~~~l~~~~~-~~L~~L~~~~l~~~~~~ 135 (176)
T PF01612_consen 65 ILDALKELLEDPNIIKVGHNA-KFDLKWLYRS---FGIDLK---NVFDTM-LAAYLLDPTRS-YSLKDLAEEYLGNIDLD 135 (176)
T ss_dssp HHHHHHHHHTTTTSEEEESSH-HHHHHHHHHH---HTS--S---SEEEHH-HHHHHTTTSTT-SSHHHHHHHHHSEEE-G
T ss_pred hHHHHHHHHhCCCccEEEEEE-echHHHHHHH---hccccC---Cccchh-hhhhccccccc-ccHHHHHHHHhhhccCc
Confidence 56777888864 58999999 9999998865 577644 389995 88888876544 999999884 46 22
Q ss_pred --C---C-C----------CChHHHHHHHHHHHHHHHHhh
Q 023805 163 --Q---Q-K----------HRSLDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 163 --~---~-~----------H~Al~DA~~t~~l~~~l~~~l 186 (277)
. . . .-|..||..+.+|+..+..++
T Consensus 136 ~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 136 KKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp HCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred HHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 1 1 235679999999999988765
No 70
>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=98.35 E-value=1.2e-05 Score=68.91 Aligned_cols=126 Identities=15% Similarity=0.173 Sum_probs=88.2
Q ss_pred CCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHHHHhCC--CEEEEeCCc
Q 023805 31 RFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIFSILNG--RVWAGHNIR 108 (277)
Q Consensus 31 ~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~~~l~~--~~lv~hn~~ 108 (277)
.++||.|+++..+++....+.++ -.+.. ...+++..|.+++.+ ..+|+||+.
T Consensus 8 f~kIV~Is~~~~~~~~~~~v~s~---~~~~~-----------------------~E~~lL~~F~~~~~~~~p~LVs~NG~ 61 (209)
T PF10108_consen 8 FHKIVCISVVYADDDGQFKVKSL---GGPDD-----------------------DEKELLQDFFDLVEKYNPQLVSFNGR 61 (209)
T ss_pred CCCeEEEEEEEEecCCcEEEEec---cCCCC-----------------------CHHHHHHHHHHHHHhCCCeEEecCCc
Confidence 46899999997775432221222 11111 126899999999964 579999999
Q ss_pred hhHHHHHHHHHHHhCCCCCCC----------------CceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCCCC-------
Q 023805 109 RFDCARIKEAFAEIGKPAPVP----------------VGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQQK------- 165 (277)
Q Consensus 109 ~fD~~~L~~~~~~~g~~~p~~----------------~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~~~------- 165 (277)
.||+++|..-.-.+|++.|.. ..-+|++++.. .+ ......+|+.||..+|+++..
T Consensus 62 ~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~-~~-g~~~~~sLd~la~~lgiPgK~~idGs~V 139 (209)
T PF10108_consen 62 GFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLS-FY-GAKARTSLDELAALLGIPGKDDIDGSQV 139 (209)
T ss_pred cCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHh-cc-CccccCCHHHHHHHcCCCCCCCCCHHHH
Confidence 999999999988999987631 12478887642 22 233468999999999998311
Q ss_pred -------------CChHHHHHHHHHHHHHHHH
Q 023805 166 -------------HRSLDDVRMNLEVLKHCAT 184 (277)
Q Consensus 166 -------------H~Al~DA~~t~~l~~~l~~ 184 (277)
.--..||.+|+.|+.++.-
T Consensus 140 ~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 140 AELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2236799999999987754
No 71
>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=98.33 E-value=2.5e-05 Score=66.49 Aligned_cols=127 Identities=17% Similarity=0.230 Sum_probs=81.1
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHH
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKI 93 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l 93 (277)
++++||+||++.. .|..||......+.+. .+-.+.. .. |. .+.--.+-.+++..|
T Consensus 4 ~~~~fDIE~~~~~------~i~~i~~~~~~~~~i~------~~~~~~~---~~-------~~---~v~~~~~E~~lL~~f 58 (193)
T cd05784 4 KVVSLDIETSMDG------ELYSIGLYGEGQERVL------MVGDPED---DA-------PD---NIEWFADEKSLLLAL 58 (193)
T ss_pred cEEEEEeecCCCC------CEEEEEeecCCCCEEE------EECCCCC---CC-------CC---EEEEECCHHHHHHHH
Confidence 6899999998643 5888887432222211 1111111 10 00 011123447899999
Q ss_pred HHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCCCC----------------------C-ceeehHHHHHHHhCCCC
Q 023805 94 FSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAPVP----------------------V-GMIDSLGVLTEKFGRRA 147 (277)
Q Consensus 94 ~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~----------------------~-~~iDt~~l~~~~~~~~~ 147 (277)
.+++.. .+++|||+..||+++|.+-+..+|+..... . -.+|+..++++.. ...
T Consensus 59 ~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~-~kl 137 (193)
T cd05784 59 IAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTAT-YHF 137 (193)
T ss_pred HHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHcc-CCC
Confidence 999965 489999999999999999999988875310 0 2688887665422 257
Q ss_pred CCCCHHHHHH-HhCCCCCCC
Q 023805 148 GNMKMATLAS-YFGLGQQKH 166 (277)
Q Consensus 148 ~~~~L~~La~-~~gi~~~~H 166 (277)
.+++|+++|+ .+|..+..+
T Consensus 138 ~sy~L~~Va~~~Lg~~K~~~ 157 (193)
T cd05784 138 ESFSLENVAQELLGEGKLIH 157 (193)
T ss_pred CcCCHHHHHHHHhCCCcccc
Confidence 8999999999 455554333
No 72
>PHA02570 dexA exonuclease; Provisional
Probab=98.26 E-value=2.1e-05 Score=67.39 Aligned_cols=159 Identities=17% Similarity=0.141 Sum_probs=91.4
Q ss_pred EEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCC-----------CCCchhhh-hcCCCHHH---H
Q 023805 16 VFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLS-----------AVALKSSR-CDGITREA---V 80 (277)
Q Consensus 16 v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~-----------~i~~~~~~-~~GIt~e~---l 80 (277)
+.||+||-|..+ ..-|++||+|.+++... .+.+|+.+|.....- .++..... +..-+.|. |
T Consensus 4 lMIDlETmG~~p---~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L 79 (220)
T PHA02570 4 FIIDFETFGNTP---DGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNL 79 (220)
T ss_pred EEEEeeccCCCC---CceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhc
Confidence 689999999876 46899999999997655 457787776532100 11111111 11122221 2
Q ss_pred h---CCCCHHHHHHHHHHHhCC------CEEEEeCCchhHHHHHHHHHHHh----C--CCCCCC-CceeehHHHHHH-Hh
Q 023805 81 E---SAPEFEEVADKIFSILNG------RVWAGHNIRRFDCARIKEAFAEI----G--KPAPVP-VGMIDSLGVLTE-KF 143 (277)
Q Consensus 81 ~---~a~~f~ev~~~l~~~l~~------~~lv~hn~~~fD~~~L~~~~~~~----g--~~~p~~-~~~iDt~~l~~~-~~ 143 (277)
. ...++.+++.+|.+|+.. ...+--|...||+..|+.++++. + .+.|.. +..-|+..+... ++
T Consensus 80 ~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~~~l 159 (220)
T PHA02570 80 KPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEATLL 159 (220)
T ss_pred cCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhhhhc
Confidence 1 235789999999999952 13444465699999999999888 6 444431 123344433332 23
Q ss_pred CCCCCCCCHHHHHHHhC-CC-CCCCChHHHHHHHHHHHHHHH
Q 023805 144 GRRAGNMKMATLASYFG-LG-QQKHRSLDDVRMNLEVLKHCA 183 (277)
Q Consensus 144 ~~~~~~~~L~~La~~~g-i~-~~~H~Al~DA~~t~~l~~~l~ 183 (277)
.++....-| .-| ++ -.+|+|+.||..-+..+.+-.
T Consensus 160 ~r~~~~cp~-----~~g~l~gfv~H~sihDcakd~lml~y~~ 196 (220)
T PHA02570 160 TRGMTTCPL-----PKGTLDGFVAHDSIHDCAKDILMLIYAK 196 (220)
T ss_pred cCCcccCCC-----cCccccchhhcccHHHHHHHHHHHHHHH
Confidence 333210000 001 12 267999998766665554433
No 73
>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=98.22 E-value=1.1e-05 Score=71.97 Aligned_cols=161 Identities=19% Similarity=0.263 Sum_probs=91.9
Q ss_pred CCcEEEEEeccCCCCCCC-------------------CCCceEEEEEEEE-ECCeeee----eceEEEeecCCCCCCCCc
Q 023805 12 TAEIVFFDLETTVPRRAG-------------------QRFWVLEFGAIIV-CPRKLVE----LESFSTLIKPKDLSAVAL 67 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~-------------------~~~~IieIg~v~v-~~~~~~~----~~sf~~~v~P~~~~~i~~ 67 (277)
...||+||+|.||+.... ....|+|+|+..+ +.+.... ...|..++-|......+.
T Consensus 21 ~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~ 100 (262)
T PF04857_consen 21 KADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQA 100 (262)
T ss_dssp HSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEH
T ss_pred hCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecc
Confidence 346999999999976421 2357999999999 3333221 233444433433211122
Q ss_pred hhhh---hcCCCHHHH-hCCCCHHHHHH-----HHHH---Hh----C-CCEEEEeCCchhHHHHHHHHHHHhCCCCC---
Q 023805 68 KSSR---CDGITREAV-ESAPEFEEVAD-----KIFS---IL----N-GRVWAGHNIRRFDCARIKEAFAEIGKPAP--- 127 (277)
Q Consensus 68 ~~~~---~~GIt~e~l-~~a~~f~ev~~-----~l~~---~l----~-~~~lv~hn~~~fD~~~L~~~~~~~g~~~p--- 127 (277)
.+.+ -+|+.-+.+ ..+.++....+ ++.. ++ + +.+|||||. -+|+.+|.+.|-. ++|
T Consensus 101 ~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~-~~Dl~~l~~~f~~---~LP~t~ 176 (262)
T PF04857_consen 101 SSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNG-LYDLMYLYKKFIG---PLPETL 176 (262)
T ss_dssp HHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESST-HHHHHHHHHHHTT---S--SSH
T ss_pred hhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeCh-HhHHHHHHHHhcC---CCCCCH
Confidence 2222 356665443 34444443331 1111 11 1 269999999 9999998877644 433
Q ss_pred ----------CCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC--------------------------CCCCChHHH
Q 023805 128 ----------VPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG--------------------------QQKHRSLDD 171 (277)
Q Consensus 128 ----------~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~--------------------------~~~H~Al~D 171 (277)
++ .++||.-++.. .. ....+|+.|++.++.. ...|.|-.|
T Consensus 177 ~eF~~~~~~~FP-~i~DtK~la~~-~~--~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyD 252 (262)
T PF04857_consen 177 EEFKELLRELFP-RIYDTKYLAEE-CP--GKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYD 252 (262)
T ss_dssp HHHHHHHHHHSS-SEEEHHHHHTS-TT--TS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHH
T ss_pred HHHHHHHHHHCc-ccccHHHHHHh-cc--ccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchH
Confidence 22 38899855432 21 3467999999988743 237999999
Q ss_pred HHHHHHHHH
Q 023805 172 VRMNLEVLK 180 (277)
Q Consensus 172 A~~t~~l~~ 180 (277)
|.+|+.++.
T Consensus 253 A~mTg~~F~ 261 (262)
T PF04857_consen 253 AYMTGCVFI 261 (262)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHc
Confidence 999999875
No 74
>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=98.06 E-value=0.00029 Score=56.37 Aligned_cols=65 Identities=20% Similarity=0.353 Sum_probs=49.4
Q ss_pred HHHHHHHHHHhCCC--EEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh
Q 023805 87 EEVADKIFSILNGR--VWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF 159 (277)
Q Consensus 87 ~ev~~~l~~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~ 159 (277)
..+...|.+|+.+. .+|+||+ +||+.+|.. .+...+. .++|++ ++.+.+++...+.+|+.+++.|
T Consensus 40 ~~~~~~l~~~l~~~~~~~v~~~~-k~d~~~L~~----~~~~~~~--~~~D~~-~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 40 EEDLEALKELLEDEDITKVGHDA-KFDLVVLAR----DGIELPG--NIFDTM-LAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred HHHHHHHHHHHcCCCCcEEeccH-HHHHHHHHH----CCCCCCC--CcccHH-HHHHHhCCCCCcCCHHHHHHHH
Confidence 45777788888764 5899999 999998863 3444433 379998 7889998866346999999976
No 75
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=98.04 E-value=3.5e-06 Score=83.92 Aligned_cols=162 Identities=17% Similarity=0.237 Sum_probs=110.6
Q ss_pred CCCCCCcEEEEEeccCCCCC-------CCCC-------CceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhc
Q 023805 8 QAAGTAEIVFFDLETTVPRR-------AGQR-------FWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCD 73 (277)
Q Consensus 8 ~~~~~~~~v~~D~ETTg~~~-------~~~~-------~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~ 73 (277)
|-...+++|.+|-|..-++. .|.. -.+-.|++|.-.+ -.+.+---+-||-..+ .+.++.+++.
T Consensus 905 EmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeG-p~eGiPFiDDYv~T~d--~VvDYLTqyS 981 (1118)
T KOG1275|consen 905 EMPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEG-PNEGIPFIDDYVSTDD--KVVDYLTQYS 981 (1118)
T ss_pred ccCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccC-CCCCCccccceecchh--HHHHHHHHhc
Confidence 44667789999999877654 1111 1233455554441 1111122334666666 7999999999
Q ss_pred CCCHHHHhCC------CCHHHHHHHHHHHh-CCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCC
Q 023805 74 GITREAVESA------PEFEEVADKIFSIL-NGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRR 146 (277)
Q Consensus 74 GIt~e~l~~a------~~f~ev~~~l~~~l-~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~ 146 (277)
||-+.||... .++.-++.++.-++ .+.++|||.. ..|++.|+ +..|. .++|||..++ +.+.
T Consensus 982 GI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL-~nDFrvIN-------i~Vp~-~QiiDTv~lf---~~~s 1049 (1118)
T KOG1275|consen 982 GIKPGDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGL-QNDFRVIN-------IHVPE-EQIIDTVTLF---RLGS 1049 (1118)
T ss_pred CCCccccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccc-cccceEEE-------EecCh-hhheeeeEEE---eccc
Confidence 9999999643 36666777777666 4789999999 88887664 44443 3589998543 2333
Q ss_pred CCCCCHHHHHHHh-C--CCCCCCChHHHHHHHHHHHHHHHH
Q 023805 147 AGNMKMATLASYF-G--LGQQKHRSLDDVRMNLEVLKHCAT 184 (277)
Q Consensus 147 ~~~~~L~~La~~~-g--i~~~~H~Al~DA~~t~~l~~~l~~ 184 (277)
....+|..||-++ | |+..+|++.+||+.++.|+++.++
T Consensus 1050 ~R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1050 QRMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred ccEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHH
Confidence 4468999999855 4 447899999999999999987653
No 76
>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=97.99 E-value=0.00024 Score=58.49 Aligned_cols=129 Identities=20% Similarity=0.227 Sum_probs=83.0
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
...++.||+|+.........-.++||+. .++.. .++.+.. .. ....
T Consensus 12 ~~~~ig~D~E~~~~~~~~~~~~liQl~~---~~~~~-------~l~d~~~---~~---------------------~~~~ 57 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYYGEVALIQLCV---SEEKC-------YLFDPLS---LS---------------------VDWQ 57 (161)
T ss_pred CCCEEEEECCccCCCCCCCceEEEEEEE---CCCCE-------EEEeccc---Cc---------------------cCHH
Confidence 5679999999987653112335666654 10211 3344332 00 0223
Q ss_pred HHHHHhCCC--EEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC--C---
Q 023805 92 KIFSILNGR--VWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG--Q--- 163 (277)
Q Consensus 92 ~l~~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~--~--- 163 (277)
.|.+++.+. +.|+|++ +.|+..|.. .+|+... .++|+. ++.+.+++. .+.+|+.+++.| |+. +
T Consensus 58 ~L~~lL~d~~i~Kvg~~~-k~D~~~L~~---~~gi~~~---~~~D~~-~aa~ll~~~-~~~~L~~l~~~~lg~~l~K~~~ 128 (161)
T cd06129 58 GLKMLLENPSIVKALHGI-EGDLWKLLR---DFGEKLQ---RLFDTT-IAANLKGLP-ERWSLASLVEHFLGKTLDKSIS 128 (161)
T ss_pred HHHHHhCCCCEEEEEecc-HHHHHHHHH---HcCCCcc---cHhHHH-HHHHHhCCC-CCchHHHHHHHHhCCCCCccce
Confidence 455677654 5699999 999988753 2466542 268999 577777764 346999999965 654 1
Q ss_pred ------------CCCChHHHHHHHHHHHHHHH
Q 023805 164 ------------QKHRSLDDVRMNLEVLKHCA 183 (277)
Q Consensus 164 ------------~~H~Al~DA~~t~~l~~~l~ 183 (277)
+-+-|..||..+..|+.+|.
T Consensus 129 ~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 129 CADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 11778999999999998874
No 77
>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=97.88 E-value=0.00039 Score=59.11 Aligned_cols=143 Identities=14% Similarity=0.099 Sum_probs=86.1
Q ss_pred CCCCcEEEEEeccCCCCCCC--CCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHH
Q 023805 10 AGTAEIVFFDLETTVPRRAG--QRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFE 87 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~~~~--~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ 87 (277)
.....++.||+|.+.....+ ..-.++||+. .+.. .+|.+.. +.. - .-+
T Consensus 19 l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat----~~~~-------~lid~~~---~~~-------~---------~~~ 68 (193)
T cd06146 19 LEAGRVVGIDSEWKPSFLGDSDPRVAILQLAT----EDEV-------FLLDLLA---LEN-------L---------ESE 68 (193)
T ss_pred hccCCEEEEECccCCCccCCCCCCceEEEEec----CCCE-------EEEEchh---ccc-------c---------chH
Confidence 45678999999998654311 2346777763 2211 2333322 000 0 012
Q ss_pred HHHHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCC---------CCCCCCHHHHH
Q 023805 88 EVADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGR---------RAGNMKMATLA 156 (277)
Q Consensus 88 ev~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~---------~~~~~~L~~La 156 (277)
.....+..+|.+ -+.|||++ ++|..+|...+...+........++|+..++...... .....+|..|+
T Consensus 69 ~~~~~L~~ll~d~~i~KVg~~~-~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~ 147 (193)
T cd06146 69 DWDRLLKRLFEDPDVLKLGFGF-KQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLV 147 (193)
T ss_pred HHHHHHHHHhCCCCeeEEEech-HHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHH
Confidence 344456778865 35699999 9999999865532211011234599999666443321 12468999999
Q ss_pred HHh-CCC--C---------------CCCChHHHHHHHHHHHHHHH
Q 023805 157 SYF-GLG--Q---------------QKHRSLDDVRMNLEVLKHCA 183 (277)
Q Consensus 157 ~~~-gi~--~---------------~~H~Al~DA~~t~~l~~~l~ 183 (277)
+.+ |.+ + +-+-|..||..+..|+.+|.
T Consensus 148 ~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 148 QEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 955 543 1 11778999999999999875
No 78
>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=97.88 E-value=0.00049 Score=56.85 Aligned_cols=129 Identities=19% Similarity=0.278 Sum_probs=84.1
Q ss_pred CCcEEEEEeccCCCCCC--CCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHH
Q 023805 12 TAEIVFFDLETTVPRRA--GQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEV 89 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~--~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev 89 (277)
...++.||+|+++.... ...-.+++|+. ++ ...++.+.. + ..+
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~~----~~-------~~~l~~~~~---~---------------------~~~ 61 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLAT----ES-------RCLLFQLAH---M---------------------DKL 61 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEec----CC-------cEEEEEhhh---h---------------------hcc
Confidence 67899999999876431 12345777762 11 123343332 0 123
Q ss_pred HHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC-C--
Q 023805 90 ADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG-Q-- 163 (277)
Q Consensus 90 ~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~-~-- 163 (277)
...|.+++.+ ...|+|++ ++|+..|.. .+|+... .++|+. ++.+.+++.....+|..|++.| |.. .
T Consensus 62 ~~~l~~ll~~~~i~kv~~~~-k~D~~~L~~---~~g~~~~---~~~Dl~-~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~ 133 (170)
T cd06141 62 PPSLKQLLEDPSILKVGVGI-KGDARKLAR---DFGIEVR---GVVDLS-HLAKRVGPRRKLVSLARLVEEVLGLPLSKP 133 (170)
T ss_pred cHHHHHHhcCCCeeEEEeee-HHHHHHHHh---HcCCCCC---CeeeHH-HHHHHhCCCcCCccHHHHHHHHcCcccCCC
Confidence 3456667754 46799999 999988753 4466532 369999 5667887754446999999976 553 1
Q ss_pred ----------------CCCChHHHHHHHHHHHHHHH
Q 023805 164 ----------------QKHRSLDDVRMNLEVLKHCA 183 (277)
Q Consensus 164 ----------------~~H~Al~DA~~t~~l~~~l~ 183 (277)
+-|-|..||..+.+|+..|.
T Consensus 134 k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 134 KKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 11678899999999998774
No 79
>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=97.88 E-value=0.00056 Score=63.91 Aligned_cols=132 Identities=17% Similarity=0.102 Sum_probs=84.8
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
...+++||+|+.........-.+|+|+. ++. ..+|.|-. + ..+.
T Consensus 17 ~~~~ia~DtE~~~~~~y~~~l~LiQia~----~~~-------~~liD~~~---~----------------------~~~~ 60 (367)
T TIGR01388 17 TFPFVALDTEFVRERTFWPQLGLIQVAD----GEQ-------LALIDPLV---I----------------------IDWS 60 (367)
T ss_pred cCCEEEEeccccCCCCCCCcceEEEEee----CCe-------EEEEeCCC---c----------------------ccHH
Confidence 4579999999987653111224566653 221 24555543 0 0123
Q ss_pred HHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC--CC--
Q 023805 92 KIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG--QQ-- 164 (277)
Q Consensus 92 ~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~--~~-- 164 (277)
.|.+++.+ .+.|+|++ ++|+.+|.. .+...+. .++||+ ++.+.+++.. +.+|..|++.| |+. +.
T Consensus 61 ~L~~lL~d~~i~KV~h~~-k~Dl~~L~~----~~~~~~~--~~fDtq-lAa~lL~~~~-~~~l~~Lv~~~Lg~~l~K~~~ 131 (367)
T TIGR01388 61 PLKELLRDESVVKVLHAA-SEDLEVFLN----LFGELPQ--PLFDTQ-IAAAFCGFGM-SMGYAKLVQEVLGVELDKSES 131 (367)
T ss_pred HHHHHHCCCCceEEEeec-HHHHHHHHH----HhCCCCC--CcccHH-HHHHHhCCCC-CccHHHHHHHHcCCCCCcccc
Confidence 45567754 45799999 999988763 3333443 389999 7888888754 36999998855 654 11
Q ss_pred ----CC---------ChHHHHHHHHHHHHHHHHhhhc
Q 023805 165 ----KH---------RSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 165 ----~H---------~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
.. -|..||..+..|+..+.+++..
T Consensus 132 ~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~ 168 (367)
T TIGR01388 132 RTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEE 168 (367)
T ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 01 3778899999999998877643
No 80
>PRK10829 ribonuclease D; Provisional
Probab=97.83 E-value=0.0006 Score=63.73 Aligned_cols=135 Identities=18% Similarity=0.125 Sum_probs=88.7
Q ss_pred CCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHH
Q 023805 11 GTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVA 90 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~ 90 (277)
....+++||+|+.........-.+|+|+ +++. ..+|.|-. ++ -+
T Consensus 20 ~~~~~lalDtEf~~~~ty~~~l~LiQl~----~~~~-------~~LiD~l~-------------~~------------d~ 63 (373)
T PRK10829 20 RAFPAIALDTEFVRTRTYYPQLGLIQLY----DGEQ-------LSLIDPLG-------------IT------------DW 63 (373)
T ss_pred hcCCeEEEecccccCccCCCceeEEEEe----cCCc-------eEEEecCC-------------cc------------ch
Confidence 4567899999998765411123455554 1221 25666654 11 12
Q ss_pred HHHHHHhCCC--EEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHH-HhCCC--C--
Q 023805 91 DKIFSILNGR--VWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLAS-YFGLG--Q-- 163 (277)
Q Consensus 91 ~~l~~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~-~~gi~--~-- 163 (277)
..|.++|.+. +.|.|++ .+|+.+|.. .+|+.+ ..++||. ++...++.. .+.+|..|++ ++|+. +
T Consensus 64 ~~L~~ll~~~~ivKV~H~~-~~Dl~~l~~---~~g~~p---~~~fDTq-iaa~~lg~~-~~~gl~~Lv~~~lgv~ldK~~ 134 (373)
T PRK10829 64 SPFKALLRDPQVTKFLHAG-SEDLEVFLN---AFGELP---QPLIDTQ-ILAAFCGRP-LSCGFASMVEEYTGVTLDKSE 134 (373)
T ss_pred HHHHHHHcCCCeEEEEeCh-HhHHHHHHH---HcCCCc---CCeeeHH-HHHHHcCCC-ccccHHHHHHHHhCCccCccc
Confidence 4566677653 4589999 999998854 346642 2389998 676777543 2589999988 66774 1
Q ss_pred -------------CCCChHHHHHHHHHHHHHHHHhhhccc
Q 023805 164 -------------QKHRSLDDVRMNLEVLKHCATVLFLES 190 (277)
Q Consensus 164 -------------~~H~Al~DA~~t~~l~~~l~~~l~~~~ 190 (277)
+-+-|..||..+..|+..|.+.+...+
T Consensus 135 ~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g 174 (373)
T PRK10829 135 SRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAG 174 (373)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 116789999999999999988765433
No 81
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.79 E-value=0.00033 Score=64.44 Aligned_cols=136 Identities=20% Similarity=0.223 Sum_probs=91.1
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
...+|++|+|+.+..+ ..++ ++.|-+.++.. ..+|+|... + .-+.
T Consensus 16 ~~~~iAiDTEf~r~~t--~~p~---LcLIQi~~~e~------~~lIdpl~~--~----------------------~d~~ 60 (361)
T COG0349 16 GSKAIAIDTEFMRLRT--YYPR---LCLIQISDGEG------ASLIDPLAG--I----------------------LDLP 60 (361)
T ss_pred CCCceEEecccccccc--cCCc---eEEEEEecCCC------ceEeccccc--c----------------------cccc
Confidence 3568999999999876 4442 44444444432 366777641 1 1122
Q ss_pred HHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHH-HhCCC--CCC-
Q 023805 92 KIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLAS-YFGLG--QQK- 165 (277)
Q Consensus 92 ~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~-~~gi~--~~~- 165 (277)
-|..++.+ .+-|=|++ +||+.+|.+.| |+. |.+ +|||. ++.+..+-.. +++|++|++ ++|++ +..
T Consensus 61 ~l~~Ll~d~~v~KIfHaa-~~DL~~l~~~~---g~~-p~p--lfdTq-iAa~l~g~~~-~~gl~~Lv~~ll~v~ldK~~q 131 (361)
T COG0349 61 PLVALLADPNVVKIFHAA-RFDLEVLLNLF---GLL-PTP--LFDTQ-IAAKLAGFGT-SHGLADLVEELLGVELDKSEQ 131 (361)
T ss_pred hHHHHhcCCceeeeeccc-cccHHHHHHhc---CCC-CCc--hhHHH-HHHHHhCCcc-cccHHHHHHHHhCCccccccc
Confidence 34456644 35688999 99999887665 333 333 89999 6766665444 899999999 45665 111
Q ss_pred --------------CChHHHHHHHHHHHHHHHHhhhcccC
Q 023805 166 --------------HRSLDDVRMNLEVLKHCATVLFLESS 191 (277)
Q Consensus 166 --------------H~Al~DA~~t~~l~~~l~~~l~~~~~ 191 (277)
.-|..||..+..|+.++.+.+..++-
T Consensus 132 ~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r 171 (361)
T COG0349 132 RSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGR 171 (361)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 45789999999999999888766553
No 82
>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=97.78 E-value=0.0011 Score=55.01 Aligned_cols=133 Identities=12% Similarity=0.033 Sum_probs=85.0
Q ss_pred CcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHH
Q 023805 13 AEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADK 92 (277)
Q Consensus 13 ~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~ 92 (277)
.+.+.+|+|+++.++ ...+++.|++. .++. . .+|.+.. . + .+...
T Consensus 3 ~~~~~~~~~~~~~~~--~~~~l~~i~l~--~~~~-----~--~~i~~~~--~----------~------------~~~~~ 47 (178)
T cd06140 3 ADEVALYVELLGENY--HTADIIGLALA--NGGG-----A--YYIPLEL--A----------L------------LDLAA 47 (178)
T ss_pred CCceEEEEEEcCCCc--ceeeEEEEEEE--eCCc-----E--EEEeccc--h----------H------------HHHHH
Confidence 467899999999875 44566655543 2221 1 3343221 0 0 13455
Q ss_pred HHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC-C-----
Q 023805 93 IFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG-Q----- 163 (277)
Q Consensus 93 l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~-~----- 163 (277)
+.+++.+ ...++||. ++|+.+|. ++|+..+.. ++|++ ++.++++|...++++++++..| +.+ .
T Consensus 48 l~~~l~~~~~~ki~~d~-K~~~~~l~----~~gi~~~~~--~fDt~-laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~~ 119 (178)
T cd06140 48 LKEWLEDEKIPKVGHDA-KRAYVALK----RHGIELAGV--AFDTM-LAAYLLDPTRSSYDLADLAKRYLGRELPSDEEV 119 (178)
T ss_pred HHHHHhCCCCceeccch-hHHHHHHH----HCCCcCCCc--chhHH-HHHHHcCCCCCCCCHHHHHHHHcCCCCcchHHh
Confidence 6677754 46899999 99998764 568776643 79999 8999999976657999998865 443 1
Q ss_pred --C-----C--C-----ChHHHHHHHHHHHHHHHHhhhc
Q 023805 164 --Q-----K--H-----RSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 164 --~-----~--H-----~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
. . . .+..||..+.+++..+.+++..
T Consensus 120 ~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~ 158 (178)
T cd06140 120 YGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELEE 158 (178)
T ss_pred cCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 0 0 1334466677777777666543
No 83
>PRK05762 DNA polymerase II; Reviewed
Probab=97.73 E-value=0.00074 Score=69.12 Aligned_cols=145 Identities=15% Similarity=0.182 Sum_probs=93.6
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
+-.+++||+|++.. .+|..|++.-...+ .-..+.+.. ... .+.+....+-.+++.
T Consensus 154 ~lrvlsfDIE~~~~------~~i~sI~~~~~~~~-------~vi~ig~~~--~~~----------~~~v~~~~sE~~LL~ 208 (786)
T PRK05762 154 PLKVVSLDIETSNK------GELYSIGLEGCGQR-------PVIMLGPPN--GEA----------LDFLEYVADEKALLE 208 (786)
T ss_pred CCeEEEEEEEEcCC------CceEEeeecCCCCC-------eEEEEECCC--CCC----------cceEEEcCCHHHHHH
Confidence 34789999999753 25777776411111 112222222 110 001223345578999
Q ss_pred HHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCC--------------CCC----------ceeehHHHHHHHhC
Q 023805 92 KIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAP--------------VPV----------GMIDSLGVLTEKFG 144 (277)
Q Consensus 92 ~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p--------------~~~----------~~iDt~~l~~~~~~ 144 (277)
.|.+++.. .+++|||+..||+++|..-+..+|+... ... ..+|+..++....
T Consensus 209 ~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~- 287 (786)
T PRK05762 209 KFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSAT- 287 (786)
T ss_pred HHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhh-
Confidence 99999965 5999999999999999999988888642 000 2689998776544
Q ss_pred CCCCCCCHHHHHHHhCCC-CCCCC----------------------hHHHHHHHHHHHHHH
Q 023805 145 RRAGNMKMATLASYFGLG-QQKHR----------------------SLDDVRMNLEVLKHC 182 (277)
Q Consensus 145 ~~~~~~~L~~La~~~gi~-~~~H~----------------------Al~DA~~t~~l~~~l 182 (277)
..+.+++|+++|+++..+ ...|+ .+.||..+.+|+.++
T Consensus 288 ~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 288 WVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred ccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 356789999999966443 22111 367888888888743
No 84
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=97.65 E-value=0.0029 Score=55.34 Aligned_cols=168 Identities=10% Similarity=0.052 Sum_probs=98.2
Q ss_pred cEEEEEeccCC---CCCCCCCCceEEEEEEEEECCeeeee--ce-EEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHH
Q 023805 14 EIVFFDLETTV---PRRAGQRFWVLEFGAIIVCPRKLVEL--ES-FSTLIKPKDLSAVALKSSRCDGITREAVESAPEFE 87 (277)
Q Consensus 14 ~~v~~D~ETTg---~~~~~~~~~IieIg~v~v~~~~~~~~--~s-f~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ 87 (277)
.++.||+|+.+ ..|+...+.|+.|+.+.-++...... .. ...++.+... ..... .....+....+.--.+-.
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~-~~~~~~~~~~v~~~~~E~ 82 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKS-NASNG-RIRSGLSGIPVEVVESEL 82 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccc-hhhhh-ccccCCCCCeEEEeCCHH
Confidence 57899999853 22334678999999885554432211 01 1122222220 00000 000111112223344567
Q ss_pred HHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCC---------------------CC-----------Cce
Q 023805 88 EVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAP---------------------VP-----------VGM 132 (277)
Q Consensus 88 ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p---------------------~~-----------~~~ 132 (277)
+.+.+|.+++.. .+++|||+..||+.+|.+-+...++..- +. --.
T Consensus 83 ~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi~ 162 (231)
T cd05778 83 ELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHI 162 (231)
T ss_pred HHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEEE
Confidence 888998888854 6999999999999999887776655421 00 024
Q ss_pred eehHHHHHHHhCCCCCCCCHHHHHH-HhCCCC--CCCChHHHH------HHHHHHHHHHHHh
Q 023805 133 IDSLGVLTEKFGRRAGNMKMATLAS-YFGLGQ--QKHRSLDDV------RMNLEVLKHCATV 185 (277)
Q Consensus 133 iDt~~l~~~~~~~~~~~~~L~~La~-~~gi~~--~~H~Al~DA------~~t~~l~~~l~~~ 185 (277)
+|+..++++.+ .+.+++|++++. .+|.+. -.+..+.+. ....++++++++.
T Consensus 163 lD~~~~~r~~~--kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d 222 (231)
T cd05778 163 LNVWRLMRSEL--ALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKR 222 (231)
T ss_pred eEhHHHHHHHc--CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHH
Confidence 67887765543 567899999999 567653 334445554 3456677777664
No 85
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.63 E-value=0.0011 Score=69.76 Aligned_cols=158 Identities=15% Similarity=0.128 Sum_probs=97.1
Q ss_pred CCcEEEEEeccCCC----CCCCCCCceEEEEEEEEECCeee-eeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCH
Q 023805 12 TAEIVFFDLETTVP----RRAGQRFWVLEFGAIIVCPRKLV-ELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEF 86 (277)
Q Consensus 12 ~~~~v~~D~ETTg~----~~~~~~~~IieIg~v~v~~~~~~-~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f 86 (277)
+-.+++||+||.+. .|....+.||+|+.+....+... ....+-..+.+ +..+.|. .+..-.+-
T Consensus 263 plrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~---------c~~i~g~---~V~~f~sE 330 (1054)
T PTZ00166 263 PLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE---------CASIAGA---NVLSFETE 330 (1054)
T ss_pred CcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc---------cccCCCc---eEEEeCCH
Confidence 34689999999763 23235689999999866543221 11111111111 1111111 12222345
Q ss_pred HHHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCC----------C------------CC-----------C
Q 023805 87 EEVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPA----------P------------VP-----------V 130 (277)
Q Consensus 87 ~ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~----------p------------~~-----------~ 130 (277)
.+.+..|.+++.. .+++|||+..||+.+|..-++..|+.. + +. -
T Consensus 331 ~eLL~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR 410 (1054)
T PTZ00166 331 KELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGR 410 (1054)
T ss_pred HHHHHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeE
Confidence 7888998888854 699999999999999988877766541 0 00 0
Q ss_pred ceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCCCC--C-------------------CChHHHHHHHHHHHHHHH
Q 023805 131 GMIDSLGVLTEKFGRRAGNMKMATLASYF-GLGQQ--K-------------------HRSLDDVRMNLEVLKHCA 183 (277)
Q Consensus 131 ~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~~~--~-------------------H~Al~DA~~t~~l~~~l~ 183 (277)
-.+|+..++.+. ..+.+++|++++.++ |.+.. . .-.+.||..+.+|+.++.
T Consensus 411 ~~iDl~~~~~~~--~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 411 IQFDVMDLIRRD--YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred EEEEHHHHHHHh--cCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 357888776544 357899999999954 54311 1 113578888888887763
No 86
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=97.58 E-value=0.008 Score=48.82 Aligned_cols=88 Identities=17% Similarity=0.271 Sum_probs=61.5
Q ss_pred HHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC-CC-
Q 023805 90 ADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG-QQ- 164 (277)
Q Consensus 90 ~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~-~~- 164 (277)
...+.+++.+ ...|+||. ++|+.+|. ++|+..+. ++|++ ++.+++.|.....+|+.+++.| +.. ..
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~-k~~~~~L~----~~gi~~~~---~~D~~-laayll~p~~~~~~l~~l~~~~l~~~~~~~ 134 (172)
T smart00474 64 LEILKDLLEDETITKVGHNA-KFDLHVLA----RFGIELEN---IFDTM-LAAYLLLGGPSKHGLATLLKEYLGVELDKE 134 (172)
T ss_pred HHHHHHHhcCCCceEEEech-HHHHHHHH----HCCCcccc---hhHHH-HHHHHHcCCCCcCCHHHHHHHHhCCCCCcc
Confidence 4556677764 46899999 99998886 36776543 58998 7888888865546999999865 543 11
Q ss_pred --------C---C----ChHHHHHHHHHHHHHHHHhh
Q 023805 165 --------K---H----RSLDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 165 --------~---H----~Al~DA~~t~~l~~~l~~~l 186 (277)
. . .+..||..+.+|+..+.+++
T Consensus 135 ~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 135 EQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred cCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0 14566777777777776654
No 87
>PHA02528 43 DNA polymerase; Provisional
Probab=97.51 E-value=0.0027 Score=65.45 Aligned_cols=98 Identities=13% Similarity=0.196 Sum_probs=70.2
Q ss_pred CCHHHHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHH-hCCCC----C-C------------C----------Cce
Q 023805 84 PEFEEVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAE-IGKPA----P-V------------P----------VGM 132 (277)
Q Consensus 84 ~~f~ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~-~g~~~----p-~------------~----------~~~ 132 (277)
.+-.+.+..|.+|+.. .+++|||+..||++.|..-+++ .|... . . . ...
T Consensus 176 ~sE~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~ 255 (881)
T PHA02528 176 DTEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISI 255 (881)
T ss_pred CCHHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEE
Confidence 4557899999999954 6999999999999999887764 35331 0 0 0 025
Q ss_pred eehHHHHHHHhCCCCCCCCHHHHHH-HhCCCCCC------------------CChHHHHHHHHHHHHH
Q 023805 133 IDSLGVLTEKFGRRAGNMKMATLAS-YFGLGQQK------------------HRSLDDVRMNLEVLKH 181 (277)
Q Consensus 133 iDt~~l~~~~~~~~~~~~~L~~La~-~~gi~~~~------------------H~Al~DA~~t~~l~~~ 181 (277)
+|...++.......+.+++|+++|+ .+|.+... +-.+.||..+.+|+.+
T Consensus 256 lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 256 LDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred EeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 6777666554344577999999999 57876322 2347899999999887
No 88
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=97.50 E-value=0.0011 Score=64.84 Aligned_cols=136 Identities=18% Similarity=0.230 Sum_probs=94.6
Q ss_pred EEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHHHHH
Q 023805 15 IVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVADKIF 94 (277)
Q Consensus 15 ~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~~l~ 94 (277)
.+++|+||+++++ ....++.+++..-. . . .|| |... + .+. -++...+.
T Consensus 24 ~~a~~~et~~l~~--~~~~lvg~s~~~~~-~------~--~yi-~~~~-----------~--~~~-------~~~~~~l~ 71 (593)
T COG0749 24 NIAFDTETDGLDP--HGADLVGLSVASEE-E------A--AYI-PLLH-----------G--PEQ-------LNVLAALK 71 (593)
T ss_pred cceeeccccccCc--ccCCeeEEEeeccc-c------c--eeE-eecc-----------c--hhh-------hhhHHHHH
Confidence 3899999999998 55677777765333 1 1 222 2110 0 111 12778889
Q ss_pred HHhCCC--EEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCCCC-------
Q 023805 95 SILNGR--VWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLGQQ------- 164 (277)
Q Consensus 95 ~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~~~------- 164 (277)
.|+.+. ..++||. +||..+|. ++|+. +. ..+|++ ++.|.+.+..+.+.+++|+++| +....
T Consensus 72 ~~l~~~~~~kv~~~~-K~d~~~l~----~~Gi~-~~--~~~Dtm-lasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~ 142 (593)
T COG0749 72 PLLEDEGIKKVGQNL-KYDYKVLA----NLGIE-PG--VAFDTM-LASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAG 142 (593)
T ss_pred HHhhCcccchhcccc-chhHHHHH----HcCCc-cc--chHHHH-HHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhc
Confidence 999764 5999999 99997775 66754 22 378999 8999999988889999999977 32210
Q ss_pred ----------------CCChHHHHHHHHHHHHHHHHhhhcccC
Q 023805 165 ----------------KHRSLDDVRMNLEVLKHCATVLFLESS 191 (277)
Q Consensus 165 ----------------~H~Al~DA~~t~~l~~~l~~~l~~~~~ 191 (277)
.-.+..||..+.++...+..++.....
T Consensus 143 kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~ 185 (593)
T COG0749 143 KGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPV 185 (593)
T ss_pred cccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 133567899999999988876655443
No 89
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=97.45 E-value=0.0027 Score=54.16 Aligned_cols=173 Identities=13% Similarity=0.134 Sum_probs=106.4
Q ss_pred CCCCcEEEEEeccCCCC--CCC-----------------CCCceEEEEEEEEECCeeee---eceEEEeec---CCCC--
Q 023805 10 AGTAEIVFFDLETTVPR--RAG-----------------QRFWVLEFGAIIVCPRKLVE---LESFSTLIK---PKDL-- 62 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~--~~~-----------------~~~~IieIg~v~v~~~~~~~---~~sf~~~v~---P~~~-- 62 (277)
...-.+|++|+|..|.- +.+ +.-.+||+|.-..+.++... .+.+....+ +...
T Consensus 21 v~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~ 100 (239)
T KOG0304|consen 21 VKDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMY 100 (239)
T ss_pred HHhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCCCCCceeEEecccCCchhhcc
Confidence 34557899999997731 111 22469999999998644322 123333332 2211
Q ss_pred CCCCchhhhhcCCCHHHHhC-CCCHHHHHHHHHHH---hC-CCEEEEeCCchhHHHHHHHHHHHhCCCCC----------
Q 023805 63 SAVALKSSRCDGITREAVES-APEFEEVADKIFSI---LN-GRVWAGHNIRRFDCARIKEAFAEIGKPAP---------- 127 (277)
Q Consensus 63 ~~i~~~~~~~~GIt~e~l~~-a~~f~ev~~~l~~~---l~-~~~lv~hn~~~fD~~~L~~~~~~~g~~~p---------- 127 (277)
..-+-...+-+||.-+..+. +....+..+.+..- +. +-.||.+.. .||+..|.+.+-...++..
T Consensus 101 a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs-~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~ 179 (239)
T KOG0304|consen 101 AQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHS-GYDFGYLLKILTGKPLPETEEEFFEIVRQ 179 (239)
T ss_pred chhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeec-cchHHHHHHHHcCCCCcchHHHHHHHHHH
Confidence 11222333456887776643 44444444444332 22 358999998 9999998877655443321
Q ss_pred CCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHH
Q 023805 128 VPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG--QQKHRSLDDVRMNLEVLKHCAT 184 (277)
Q Consensus 128 ~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~--~~~H~Al~DA~~t~~l~~~l~~ 184 (277)
+...++|+..++..- ....-..+|+.+|+.++++ +..|.|-.|+..|+.++.++.+
T Consensus 180 ~fp~vYDiK~l~~~c-~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 180 LFPFVYDVKYLMKFC-EGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HcchhhhHHHHHHhh-hhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 011356776544322 1112357899999999999 7899999999999999998865
No 90
>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=97.37 E-value=0.0038 Score=59.37 Aligned_cols=156 Identities=17% Similarity=0.216 Sum_probs=96.7
Q ss_pred CcEEEEEeccCCCC---CCCC--CCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHH
Q 023805 13 AEIVFFDLETTVPR---RAGQ--RFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFE 87 (277)
Q Consensus 13 ~~~v~~D~ETTg~~---~~~~--~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ 87 (277)
-.+++||+||+... |... .+.|+.|+.+..+...............+.. .++ ++. +..-....
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~-------~~~---~~~~~~E~ 70 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK--EID-------GVE---VYEFNNEK 70 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC--CCC-------CCe---EEecCCHH
Confidence 46899999997542 2212 5789999998877654221112222222322 122 111 11112446
Q ss_pred HHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCCC--------------------------------CCce
Q 023805 88 EVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAPV--------------------------------PVGM 132 (277)
Q Consensus 88 ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p~--------------------------------~~~~ 132 (277)
+.+..|.+++.. .+++|||...||+.+|...+...++.... ..-.
T Consensus 71 ~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 150 (471)
T smart00486 71 ELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLV 150 (471)
T ss_pred HHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEE
Confidence 788888888854 59999999889999999888776654320 1246
Q ss_pred eehHHHHHHHhCCCCCCCCHHHHHHHhCC-CCCC---------------------CChHHHHHHHHHHHHHH
Q 023805 133 IDSLGVLTEKFGRRAGNMKMATLASYFGL-GQQK---------------------HRSLDDVRMNLEVLKHC 182 (277)
Q Consensus 133 iDt~~l~~~~~~~~~~~~~L~~La~~~gi-~~~~---------------------H~Al~DA~~t~~l~~~l 182 (277)
+|+..++...+ ...+++|+.+++++.- +... .-.+.|+..+.+|+.++
T Consensus 151 ~Dl~~~~~~~~--kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 151 IDLYNLYKNKL--KLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEhHHHHHHHh--CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88887776655 3678999999986533 2211 11255788888887775
No 91
>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=97.34 E-value=0.0036 Score=53.26 Aligned_cols=140 Identities=13% Similarity=0.126 Sum_probs=87.5
Q ss_pred CCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHH
Q 023805 9 AAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEE 88 (277)
Q Consensus 9 ~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~e 88 (277)
......+++||+|+.+.+..+ .-.+++|+.- .+.+ .++.+.. +. . ..
T Consensus 6 ~l~~~~~i~~D~E~~~~~~~~-~~~LiQia~~---~~~v-------~l~D~~~---~~----------~---------~~ 52 (197)
T cd06148 6 HLKKQKVIGLDCEGVNLGRKG-KLCLVQIATR---TGQI-------YLFDILK---LG----------S---------IV 52 (197)
T ss_pred hhhhCCEEEEEcccccCCCCC-CEEEEEEeeC---CCcE-------EEEEhhh---cc----------c---------hh
Confidence 455678999999998766521 2345555431 1211 3333332 00 0 11
Q ss_pred HHHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCC-------CCCHHHHHHHh
Q 023805 89 VADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAG-------NMKMATLASYF 159 (277)
Q Consensus 89 v~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~-------~~~L~~La~~~ 159 (277)
..+.+.+++.+ ...|+|++ ++|+.+|. ..+|+... .++|+. ++.+.+++... ..+|..+++.|
T Consensus 53 ~~~~L~~iLe~~~i~Kv~h~~-k~D~~~L~---~~~gi~~~---~~fDt~-iA~~lL~~~~~~~~~~~~~~~L~~l~~~~ 124 (197)
T cd06148 53 FINGLKDILESKKILKVIHDC-RRDSDALY---HQYGIKLN---NVFDTQ-VADALLQEQETGGFNPDRVISLVQLLDKY 124 (197)
T ss_pred HHHHHHHHhcCCCccEEEEec-hhHHHHHH---HhcCcccc---ceeeHH-HHHHHHHHHhcCCccccccccHHHHHHHh
Confidence 23456667754 35699999 99998874 24566543 268998 77777765321 35888888854
Q ss_pred -CCCC-------------------------CCCChHHHHHHHHHHHHHHHHhhhcc
Q 023805 160 -GLGQ-------------------------QKHRSLDDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 160 -gi~~-------------------------~~H~Al~DA~~t~~l~~~l~~~l~~~ 189 (277)
|++. .-.-|..||..+..|+..+.+.+...
T Consensus 125 l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 125 LYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred hCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 5421 11567899999999999999887554
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=97.32 E-value=0.0071 Score=58.20 Aligned_cols=120 Identities=11% Similarity=0.178 Sum_probs=83.0
Q ss_pred CCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHHHHH
Q 023805 12 TAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEEVAD 91 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ev~~ 91 (277)
....++||+||+. ...-...+|++..+++... +.|..++.... .. ..+++.
T Consensus 283 ~~~~~ffDiEt~P-----~~~~~yL~G~~~~~~~~~~--~~~~~fla~~~--------------~~--------E~~~~~ 333 (457)
T TIGR03491 283 APGELIFDIESDP-----DENLDYLHGFLVVDKGQEN--EKYRPFLAEDP--------------NT--------EELAWQ 333 (457)
T ss_pred CCccEEEEecCCC-----CCCCceEEEEEEecCCCCC--cceeeeecCCc--------------hH--------HHHHHH
Confidence 3567899999983 2345678888766554221 23655554433 01 146778
Q ss_pred HHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCC----CCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCC
Q 023805 92 KIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAP----VPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLG 162 (277)
Q Consensus 92 ~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p----~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~ 162 (277)
+|.+|+.. ..++.+| .|....|++...+++.... ....++|...+.+..+.-..++++|+.++..+|.+
T Consensus 334 ~f~~~l~~~~~~~i~hY~--~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~~ 409 (457)
T TIGR03491 334 QFLQLLQSYPDAPIYHYG--ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGFE 409 (457)
T ss_pred HHHHHHHHCCCCeEEeeC--HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCcc
Confidence 88888853 4677777 7889999999999887631 11157999988776654455789999999999997
No 93
>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=97.21 E-value=0.025 Score=46.53 Aligned_cols=91 Identities=21% Similarity=0.227 Sum_probs=63.2
Q ss_pred HHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC-CCC
Q 023805 90 ADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG-QQK 165 (277)
Q Consensus 90 ~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~-~~~ 165 (277)
...|..++.+ ...|+||+ ++|+..|... +|+. .. .++|++ ++.+.+++... .+|+++++.| ++. ...
T Consensus 53 ~~~l~~ll~~~~i~kv~~d~-K~~~~~L~~~---~gi~-~~--~~~D~~-laayLl~p~~~-~~l~~l~~~~l~~~~~~~ 123 (178)
T cd06142 53 LSPLKELLADPNIVKVFHAA-REDLELLKRD---FGIL-PQ--NLFDTQ-IAARLLGLGDS-VGLAALVEELLGVELDKG 123 (178)
T ss_pred HHHHHHHHcCCCceEEEecc-HHHHHHHHHH---cCCC-CC--CcccHH-HHHHHhCCCcc-ccHHHHHHHHhCCCCCcc
Confidence 3445667754 46899999 9999887532 2666 32 379998 88999998654 5999999854 554 110
Q ss_pred ----------------CChHHHHHHHHHHHHHHHHhhhcc
Q 023805 166 ----------------HRSLDDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 166 ----------------H~Al~DA~~t~~l~~~l~~~l~~~ 189 (277)
+.+..||..+.+++..+.+++...
T Consensus 124 ~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~ 163 (178)
T cd06142 124 EQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEE 163 (178)
T ss_pred cccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHc
Confidence 125667888888888888776543
No 94
>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=97.06 E-value=0.0059 Score=53.45 Aligned_cols=146 Identities=14% Similarity=0.169 Sum_probs=86.8
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECCeee-------eeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCH
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLV-------ELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEF 86 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~-------~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f 86 (277)
.++.|-+-|.- ++.....||+.|+++...+=... ....+...++|......+..-...-......+.--.+-
T Consensus 4 ~v~sls~~T~~-n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~E 82 (234)
T cd05776 4 TVMSLSIKTVL-NSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENE 82 (234)
T ss_pred EEEEEEeEEEe-cCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCCH
Confidence 34556666642 22123579999998876521100 01334556666652111111111111111112334466
Q ss_pred HHHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCC------------CC--------------CCceeehHH
Q 023805 87 EEVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPA------------PV--------------PVGMIDSLG 137 (277)
Q Consensus 87 ~ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~------------p~--------------~~~~iDt~~ 137 (277)
.+.+..|.+++.. .+++|||...||+.+|.+-+...+++. |. .--.+|+..
T Consensus 83 ~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~ 162 (234)
T cd05776 83 RALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYL 162 (234)
T ss_pred HHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHH
Confidence 7888998888864 699999999999999998888777652 10 002577887
Q ss_pred HHHHHhCCCCCCCCHHHHHH-HhCCC
Q 023805 138 VLTEKFGRRAGNMKMATLAS-YFGLG 162 (277)
Q Consensus 138 l~~~~~~~~~~~~~L~~La~-~~gi~ 162 (277)
.+.... ...+|+|+++|+ .+|.+
T Consensus 163 ~~k~~~--~~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 163 SAKELI--RCKSYDLTELSQQVLGIE 186 (234)
T ss_pred HHHHHh--CCCCCChHHHHHHHhCcC
Confidence 664443 367999999999 67765
No 95
>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=97.04 E-value=0.0032 Score=57.14 Aligned_cols=130 Identities=14% Similarity=0.128 Sum_probs=79.3
Q ss_pred CCcEEEEEeccCCCC---CCCCCCceEEEEEEEEECCeeee-eceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHH
Q 023805 12 TAEIVFFDLETTVPR---RAGQRFWVLEFGAIIVCPRKLVE-LESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFE 87 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~---~~~~~~~IieIg~v~v~~~~~~~-~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~ 87 (277)
+-.+++||+||.... |....++|+.|+++....+.... ...+..+..+.. ... ...+....+-.
T Consensus 156 ~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~---~~~---------~~~v~~~~~E~ 223 (325)
T PF03104_consen 156 PLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDS---IED---------NVEVIYFDSEK 223 (325)
T ss_dssp GSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCC---TTC---------TTEEEEESSHH
T ss_pred ccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCC---CCC---------CcEEEEECCHH
Confidence 447899999997654 12356899999998775532111 122223322221 110 11111123447
Q ss_pred HHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCC-------C--------------------------CCCc
Q 023805 88 EVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPA-------P--------------------------VPVG 131 (277)
Q Consensus 88 ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~-------p--------------------------~~~~ 131 (277)
+++..|.+++.. .+++|||+..||+.+|..-+...|+.. . ..--
T Consensus 224 ~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gr~ 303 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSRKFSRIDIPGRL 303 (325)
T ss_dssp HHHHHHHHHHHHHS-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCTTEEEEEETTSE
T ss_pred HHHHHHHHHHHhcCCcEEEEecccCCCHHHHHHHHHHhCccccccccccccceeEEeecccccccCCCcceeEEEECCCh
Confidence 899999888853 699999999999999999888885442 0 0013
Q ss_pred eeehHHHHHHHhCCCCCCCCHHHH
Q 023805 132 MIDSLGVLTEKFGRRAGNMKMATL 155 (277)
Q Consensus 132 ~iDt~~l~~~~~~~~~~~~~L~~L 155 (277)
.+|+..++...+ .+.+++|+++
T Consensus 304 ~~D~~~~~~~~~--~l~sY~L~~V 325 (325)
T PF03104_consen 304 VLDLYRLARKDY--KLDSYSLDNV 325 (325)
T ss_dssp EEEHHHHHHHHS----SS-SHHHH
T ss_pred HhHHHHHHHhhC--CCCCCCCCCC
Confidence 578887776555 5677888764
No 96
>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=96.26 E-value=0.24 Score=41.70 Aligned_cols=89 Identities=10% Similarity=0.093 Sum_probs=60.9
Q ss_pred HHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC--C--
Q 023805 91 DKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG--Q-- 163 (277)
Q Consensus 91 ~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~--~-- 163 (277)
..|.+|+.+ ...++||. +.|+..|.+ ++|+.... .+|++ ++.++++|. . .+|+.+++.| +.. .
T Consensus 67 ~~L~~~L~~~~i~kv~~d~-K~~~~~L~~---~~gi~~~~---~fD~~-laaYLL~p~-~-~~l~~l~~~yl~~~~~k~~ 136 (192)
T cd06147 67 HILNEVFTDPNILKVFHGA-DSDIIWLQR---DFGLYVVN---LFDTG-QAARVLNLP-R-HSLAYLLQKYCNVDADKKY 136 (192)
T ss_pred HHHHHHhcCCCceEEEech-HHHHHHHHH---HhCCCcCc---hHHHH-HHHHHhCCC-c-ccHHHHHHHHhCCCcchhh
Confidence 346667754 57899999 999987642 55776542 38999 889999997 5 4999999866 443 0
Q ss_pred -----CCC--------ChHHHHHHHHHHHHHHHHhhhcc
Q 023805 164 -----QKH--------RSLDDVRMNLEVLKHCATVLFLE 189 (277)
Q Consensus 164 -----~~H--------~Al~DA~~t~~l~~~l~~~l~~~ 189 (277)
..+ .+..||..+.+|...+..++..+
T Consensus 137 ~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 137 QLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred hccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 111 13445666777777777776443
No 97
>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=96.24 E-value=0.072 Score=42.36 Aligned_cols=62 Identities=16% Similarity=0.226 Sum_probs=45.4
Q ss_pred HHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC
Q 023805 93 IFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG 162 (277)
Q Consensus 93 l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~ 162 (277)
+.+++.+ ...++||. ++|+.+|. +.|+..+.. ++|++ ++.++++|..++.+|+.|++.| +..
T Consensus 45 l~~~l~~~~~~kv~~d~-K~~~~~L~----~~~~~~~~~--~~D~~-laayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKALKVGQNL-KYDRGILL----NYFIELRGI--AFDTM-LEAYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCCceeeecH-HHHHHHHH----HcCCccCCc--chhHH-HHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence 5567754 56899999 99998875 456665433 79999 7889999865235999998865 543
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=96.10 E-value=0.043 Score=56.96 Aligned_cols=93 Identities=14% Similarity=0.012 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC
Q 023805 86 FEEVADKIFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG 162 (277)
Q Consensus 86 f~ev~~~l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~ 162 (277)
...+...|..||.+ ...++||. +||+.+|. ++|+.... .++||+ ++.++++++.. .+|+.++..| +.+
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~-K~d~~~l~----~~gi~~~~--~~~Dt~-la~yll~~~~~-~~l~~la~~yl~~~ 433 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDA-KFLMHLLK----REGIELGG--VIFDTM-LAAYLLDPAQV-STLDTLARRYLVEE 433 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeH-HHHHHHHH----hCCCCCCC--cchhHH-HHHHHcCCCCC-CCHHHHHHHHcCcc
Confidence 34567778888865 45899999 99998875 67877654 379999 88999988654 5999999866 321
Q ss_pred --------CC-----C-------CChHHHHHHHHHHHHHHHHhhh
Q 023805 163 --------QQ-----K-------HRSLDDVRMNLEVLKHCATVLF 187 (277)
Q Consensus 163 --------~~-----~-------H~Al~DA~~t~~l~~~l~~~l~ 187 (277)
+. . ..+..||..+.+|+..+..++.
T Consensus 434 ~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 434 LILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred cccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 00 0 1356789999999988877663
No 99
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=96.09 E-value=0.068 Score=51.73 Aligned_cols=76 Identities=13% Similarity=0.173 Sum_probs=54.9
Q ss_pred CCCHHHHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHH-hCCCCC-----C---------------------CCce
Q 023805 83 APEFEEVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAE-IGKPAP-----V---------------------PVGM 132 (277)
Q Consensus 83 a~~f~ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~-~g~~~p-----~---------------------~~~~ 132 (277)
-.+-.+++.+|.+|+.. .+++|||+..||++.|..-+.. +|+... + ....
T Consensus 177 f~sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~ 256 (498)
T PHA02524 177 FEDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIAL 256 (498)
T ss_pred eCCHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEE
Confidence 34567899999999965 6999999999999998877753 555310 0 0035
Q ss_pred eehHHHHHHHhCCCCCCCCHHHHHHH
Q 023805 133 IDSLGVLTEKFGRRAGNMKMATLASY 158 (277)
Q Consensus 133 iDt~~l~~~~~~~~~~~~~L~~La~~ 158 (277)
+|.+.++.+.-...+.+++|+++++.
T Consensus 257 iDl~~l~kk~s~~~l~sYsL~~Vs~~ 282 (498)
T PHA02524 257 MDYMDVFKKFSFTPMPDYKLGNVGYR 282 (498)
T ss_pred eEHHHHHHHhhhccCCCCCHHHHHHH
Confidence 78887776432346789999999873
No 100
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=95.95 E-value=0.19 Score=53.70 Aligned_cols=159 Identities=13% Similarity=0.123 Sum_probs=91.3
Q ss_pred CCcEEEEEeccCCCC---CCCCCCceEEEEEEEEECCeeee---------eceEEEeecCCCCCCCCchhhhhcCCCHHH
Q 023805 12 TAEIVFFDLETTVPR---RAGQRFWVLEFGAIIVCPRKLVE---------LESFSTLIKPKDLSAVALKSSRCDGITREA 79 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~---~~~~~~~IieIg~v~v~~~~~~~---------~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~ 79 (277)
+..+++||+|||-+. |+...++|.=|+.. +++.+..+ ++-|..-=+|+. +....+.
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISYM-iDGqGfLItNREiVs~DIedfEYTPKpE~-----eG~F~v~------ 312 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISYM-IDGQGFLITNREIVSEDIEDFEYTPKPEY-----EGPFCVF------ 312 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEEE-ecCceEEEechhhhccchhhcccCCcccc-----ccceEEe------
Confidence 346899999999864 32345667666543 44444322 111211111111 0001111
Q ss_pred HhCCCCHHHHHHHHHHHhC---CCEEEEeCCchhHHHHHHHHHHHhCCCCCC------------CCceeehHHHHHHHhC
Q 023805 80 VESAPEFEEVADKIFSILN---GRVWAGHNIRRFDCARIKEAFAEIGKPAPV------------PVGMIDSLGVLTEKFG 144 (277)
Q Consensus 80 l~~a~~f~ev~~~l~~~l~---~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~------------~~~~iDt~~l~~~~~~ 144 (277)
+.+.-..++..|.+-+. -.++|.+|+.-||++|+.+-...+|+.... ...+..-+.-+ +...
T Consensus 313 --Ne~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcf-rWVK 389 (2173)
T KOG1798|consen 313 --NEPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCF-RWVK 389 (2173)
T ss_pred --cCCcHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhh-hhhh
Confidence 22233456666655553 368999999999999999999999887431 11223333222 2222
Q ss_pred C----CCCCCCHHHHHH-HhCCC---------------CC---CCChHHHHHHHHHHHHHHHHh
Q 023805 145 R----RAGNMKMATLAS-YFGLG---------------QQ---KHRSLDDVRMNLEVLKHCATV 185 (277)
Q Consensus 145 ~----~~~~~~L~~La~-~~gi~---------------~~---~H~Al~DA~~t~~l~~~l~~~ 185 (277)
+ ..++.+|..+.+ .+|.. +. +.-+..||.+|.-|+.+...-
T Consensus 390 RDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP 453 (2173)
T KOG1798|consen 390 RDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP 453 (2173)
T ss_pred hcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh
Confidence 2 247889998887 56553 11 245688999999999877654
No 101
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.69 E-value=0.28 Score=52.68 Aligned_cols=143 Identities=12% Similarity=0.057 Sum_probs=85.2
Q ss_pred EEEEEeccCCCCCCCCCCceEEEEEEEEECCee-------eeeceEEEeecCCCCCCCC-chhhhhcCCCHHHHhCCCCH
Q 023805 15 IVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKL-------VELESFSTLIKPKDLSAVA-LKSSRCDGITREAVESAPEF 86 (277)
Q Consensus 15 ~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~-------~~~~sf~~~v~P~~~~~i~-~~~~~~~GIt~e~l~~a~~f 86 (277)
++.|++| .++|.....+++.|+++....... .....+...++|... .++ .+.....|+....|..-.+-
T Consensus 508 vLdFsi~--SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~-~~p~~~~~~~~~~~~~~L~~~~sE 584 (1172)
T TIGR00592 508 VLDFSMK--SLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDC-SFPLDLKGEFPGKKPSLVEDLATE 584 (1172)
T ss_pred EEEeeeE--EecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCC-CCCchhhhhhhccCCcEEEEecCH
Confidence 3445566 344432456899998887664211 000123333444210 111 11122334444445555566
Q ss_pred HHHHHHHHHHhC---CCEEEEeCCchhHHHHHHHHHHHhCCCCCC--------------------CCceeehHHHHHHHh
Q 023805 87 EEVADKIFSILN---GRVWAGHNIRRFDCARIKEAFAEIGKPAPV--------------------PVGMIDSLGVLTEKF 143 (277)
Q Consensus 87 ~ev~~~l~~~l~---~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~--------------------~~~~iDt~~l~~~~~ 143 (277)
.+.+..|.+++. -.+++|||...||+..|..-+...+++.-. .--++|+...+...+
T Consensus 585 r~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~ 664 (1172)
T TIGR00592 585 RALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELI 664 (1172)
T ss_pred HHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHh
Confidence 788888888885 369999999999999998888777765310 113578887765544
Q ss_pred CCCCCCCCHHHHHH-HhCCC
Q 023805 144 GRRAGNMKMATLAS-YFGLG 162 (277)
Q Consensus 144 ~~~~~~~~L~~La~-~~gi~ 162 (277)
...+++|.+++. .+|.+
T Consensus 665 --~~~sy~L~~v~~~~L~~~ 682 (1172)
T TIGR00592 665 --RCKSYDLSELVQQILKTE 682 (1172)
T ss_pred --CcCCCCHHHHHHHHhCCC
Confidence 367899999998 44543
No 102
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=95.09 E-value=0.5 Score=48.69 Aligned_cols=129 Identities=17% Similarity=0.171 Sum_probs=79.9
Q ss_pred CCcEEEEEeccCCCCC---CCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHH
Q 023805 12 TAEIVFFDLETTVPRR---AGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEE 88 (277)
Q Consensus 12 ~~~~v~~D~ETTg~~~---~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~e 88 (277)
.-.+++||+|+..... ++..+.++.|+...-..+... ..+.. ....|.. +....+-.+
T Consensus 153 ~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~--------~~~~~--------~~~~~~~---v~~~~~e~e 213 (792)
T COG0417 153 PLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI--------EVFIY--------TSGEGFS---VEVVISEAE 213 (792)
T ss_pred CceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc--------ccccc--------cCCCCce---eEEecCHHH
Confidence 3467999999976432 223456777766544433211 00000 0000000 222233468
Q ss_pred HHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCCC---------------C---CCceeehHHHHHHHhCCCC
Q 023805 89 VADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPAP---------------V---PVGMIDSLGVLTEKFGRRA 147 (277)
Q Consensus 89 v~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~p---------------~---~~~~iDt~~l~~~~~~~~~ 147 (277)
++..|.+++.. .+++|||...||++.|..-+..+|++.. . ....+|....+.. -...+
T Consensus 214 ~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~-~~~~~ 292 (792)
T COG0417 214 LLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRR-RPLNL 292 (792)
T ss_pred HHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhh-hhccc
Confidence 99999998843 6999999988999999999999998865 1 1136788766542 12345
Q ss_pred CCCCHHHHHHHhC
Q 023805 148 GNMKMATLASYFG 160 (277)
Q Consensus 148 ~~~~L~~La~~~g 160 (277)
.+++|+..++.+.
T Consensus 293 ~~ysl~~v~~~~l 305 (792)
T COG0417 293 KSYSLEAVSEALL 305 (792)
T ss_pred ccccHHHHHHHhc
Confidence 6899999987653
No 103
>PHA03036 DNA polymerase; Provisional
Probab=94.82 E-value=0.73 Score=48.20 Aligned_cols=169 Identities=13% Similarity=0.076 Sum_probs=93.8
Q ss_pred CCCcEEEEEeccCC--CCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCC-HH---HHhC--
Q 023805 11 GTAEIVFFDLETTV--PRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGIT-RE---AVES-- 82 (277)
Q Consensus 11 ~~~~~v~~D~ETTg--~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt-~e---~l~~-- 82 (277)
-+..+++||+|+-. ..|....+-|+.|+++.++..+.+ ..| ++++.+......+.-..+-|.. -+ ++.+
T Consensus 158 ~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~~~~~--~~~-~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (1004)
T PHA03036 158 IPRSYLFLDIECHFDKKFPSVFINPVSHISCCYIDLSGKE--KRF-TLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSK 234 (1004)
T ss_pred CcceeEEEEEEeccCCCCCCcccCcceEEEEEEEecCCCe--eEE-EEeccccccccccccceeeeeeccccccccCCce
Confidence 45578999999853 223234577999998777765432 223 5555543211112122222220 00 1111
Q ss_pred ---CCCHHHHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCCC------------------------------
Q 023805 83 ---APEFEEVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKPA------------------------------ 126 (277)
Q Consensus 83 ---a~~f~ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~~------------------------------ 126 (277)
-.+-.+++ .+.+++.. .+++|+|+..||++.|..-++....+.
T Consensus 235 ~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~gg~ 313 (1004)
T PHA03036 235 ELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKGVGGV 313 (1004)
T ss_pred eeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHHHHHHHhccCceeeccCCCcccccceeeccccccccccCcc
Confidence 12334444 44555533 699999999999998877666642200
Q ss_pred -------C--CCCceeehHHHHHHHhCCCCCCCCHHHHHHH-hCCC-------CCC----CChHHHHHHHHHHHHHHHHh
Q 023805 127 -------P--VPVGMIDSLGVLTEKFGRRAGNMKMATLASY-FGLG-------QQK----HRSLDDVRMNLEVLKHCATV 185 (277)
Q Consensus 127 -------p--~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~-~gi~-------~~~----H~Al~DA~~t~~l~~~l~~~ 185 (277)
. ...-++|.+.++.+.+ .+.+++|+++++. |+.. ... -.--.|+...+.+|..++..
T Consensus 314 ~~~t~~i~~~~G~i~fDLy~~i~k~~--~L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl~t 391 (1004)
T PHA03036 314 ANTTYHINNNNGTIFFDLYTFIQKTE--KLDSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVLST 391 (1004)
T ss_pred ccceEEecccCCeEEEEhHHHHhhhc--CcccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhhcc
Confidence 0 1114678887665443 5678999999995 5431 000 11124677777777766653
No 104
>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=94.71 E-value=0.13 Score=41.28 Aligned_cols=62 Identities=19% Similarity=0.270 Sum_probs=46.6
Q ss_pred HHHHhCC--CEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHh-CCC
Q 023805 93 IFSILNG--RVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYF-GLG 162 (277)
Q Consensus 93 l~~~l~~--~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~-gi~ 162 (277)
|.+|+.+ ...++||. ++++.+| .++|+..... .+|++ |+.++++|...+..++++++.| +..
T Consensus 45 l~~~l~~~~~~ki~~d~-K~~~~~l----~~~gi~l~~~--~fD~~-LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNL-KYDRVIL----ANYGIELRGI--AFDTM-LEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeeh-HHHHHHH----HHCCCCCCCc--chhHH-HHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 5667764 45789999 8888775 4678876543 68999 8999999976523999999976 443
No 105
>PRK05761 DNA polymerase I; Reviewed
Probab=94.36 E-value=0.29 Score=50.30 Aligned_cols=94 Identities=16% Similarity=0.245 Sum_probs=65.4
Q ss_pred HHHHHHHHHHHhCC-CEEEEeCCchhHHHHHHHHHHHhCCCCCCCC-------ceeehHHHHHHH------hCCC--CCC
Q 023805 86 FEEVADKIFSILNG-RVWAGHNIRRFDCARIKEAFAEIGKPAPVPV-------GMIDSLGVLTEK------FGRR--AGN 149 (277)
Q Consensus 86 f~ev~~~l~~~l~~-~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~-------~~iDt~~l~~~~------~~~~--~~~ 149 (277)
-.+++..|.+++.. .+.|.+|+..||++.|..-+..+|+...... ..+|....+... +... ..+
T Consensus 210 E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~~ 289 (787)
T PRK05761 210 EKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRHRE 289 (787)
T ss_pred HHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeeccc
Confidence 37899999999965 5777799999999999999999998754111 126665443211 0111 237
Q ss_pred CCHHHHHH-HhCCCCCC--------------CChHHHHHHHHHHH
Q 023805 150 MKMATLAS-YFGLGQQK--------------HRSLDDVRMNLEVL 179 (277)
Q Consensus 150 ~~L~~La~-~~gi~~~~--------------H~Al~DA~~t~~l~ 179 (277)
++|+.+++ .+|.++.. .-.+.||..+.+|.
T Consensus 290 ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 290 ARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred CChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 89999999 77776311 23588999999984
No 106
>PHA02563 DNA polymerase; Provisional
Probab=91.25 E-value=1.4 Score=44.16 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=26.6
Q ss_pred HHHHHHHhC-------CCEEEEeCCchhHHHHHHHHHHHhCC
Q 023805 90 ADKIFSILN-------GRVWAGHNIRRFDCARIKEAFAEIGK 124 (277)
Q Consensus 90 ~~~l~~~l~-------~~~lv~hn~~~fD~~~L~~~~~~~g~ 124 (277)
+++|.+|+. +.++..||. .||-.||...+.+.+.
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN~-~FD~~Fil~~L~~~~~ 90 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHNL-KFDGSFILKWLLRNGF 90 (630)
T ss_pred HHHHHHHHhhccccccceEEEEecC-CccHHHHHHHHHhhcc
Confidence 446666665 458899996 9999999998887664
No 107
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=91.20 E-value=0.35 Score=42.92 Aligned_cols=87 Identities=20% Similarity=0.153 Sum_probs=63.3
Q ss_pred EEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHH---hCC-CCCCCCHHHHHHHhCCC--CCCCChHHHHHHH
Q 023805 102 WAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEK---FGR-RAGNMKMATLASYFGLG--QQKHRSLDDVRMN 175 (277)
Q Consensus 102 lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~---~~~-~~~~~~L~~La~~~gi~--~~~H~Al~DA~~t 175 (277)
...||+-.|++.|..+++-+.+.+.+-++..|+.+-.+..- ..| -...++++.||.++... ..+|+|+.|+..+
T Consensus 201 e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~~ 280 (318)
T KOG4793|consen 201 EGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPTPKLVSSLEALATYYSLTPELDAHRALSDVLLL 280 (318)
T ss_pred ecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCCCccchhHHHHHHHhhcCcccchhhhccccchh
Confidence 34566668999999999988777766665567766322111 223 22457899999988775 7899999999999
Q ss_pred HHHHHHHHHhhhc
Q 023805 176 LEVLKHCATVLFL 188 (277)
Q Consensus 176 ~~l~~~l~~~l~~ 188 (277)
-++++++-..+..
T Consensus 281 ~k~~q~~~idlla 293 (318)
T KOG4793|consen 281 SKVFQKLTIDLLA 293 (318)
T ss_pred hhHHHHhhhhhhh
Confidence 9999988766544
No 108
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=88.31 E-value=0.68 Score=39.88 Aligned_cols=167 Identities=14% Similarity=0.098 Sum_probs=91.9
Q ss_pred CCCcEEEEEeccCCCCC--CC-----------------CCCceEEEEEEEEECCeeee--ece--EEEeecCCCCCCCCc
Q 023805 11 GTAEIVFFDLETTVPRR--AG-----------------QRFWVLEFGAIIVCPRKLVE--LES--FSTLIKPKDLSAVAL 67 (277)
Q Consensus 11 ~~~~~v~~D~ETTg~~~--~~-----------------~~~~IieIg~v~v~~~~~~~--~~s--f~~~v~P~~~~~i~~ 67 (277)
.+-++|.+|+|..|.-. -| +.-.||++|..+-|.++... ..+ |+.-..+... -...
T Consensus 40 ~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~d-mya~ 118 (299)
T COG5228 40 SRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKD-MYAT 118 (299)
T ss_pred HhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhh-hcch
Confidence 34578999999988421 01 22369999999888655432 122 4444444442 1122
Q ss_pred hhhh---hcCCCHHHHhC-CCCHHHHHHHHHHHh--------CCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeeh
Q 023805 68 KSSR---CDGITREAVES-APEFEEVADKIFSIL--------NGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDS 135 (277)
Q Consensus 68 ~~~~---~~GIt~e~l~~-a~~f~ev~~~l~~~l--------~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt 135 (277)
+..+ -.||.-+.-+. +.... +|.+.| ..-+||.+.. .||+.+|-..+-...+ |.. .=|.
T Consensus 119 ESieLL~ksgIdFkkHe~~GI~v~----eF~elLm~SGLvm~e~VtWitfHs-aYDfgyLikilt~~pl--P~~--~EdF 189 (299)
T COG5228 119 ESIELLRKSGIDFKKHENLGIDVF----EFSELLMDSGLVMDESVTWITFHS-AYDFGYLIKILTNDPL--PNN--KEDF 189 (299)
T ss_pred HHHHHHHHcCCChhhHhhcCCCHH----HHHHHHhccCceeccceEEEEeec-chhHHHHHHHHhcCCC--Ccc--HHHH
Confidence 2222 23555443322 22222 233333 2248999888 9999998877654333 321 2233
Q ss_pred HHHHHHHhCCCC------------CCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHhhhc
Q 023805 136 LGVLTEKFGRRA------------GNMKMATLASYFGLG--QQKHRSLDDVRMNLEVLKHCATVLFL 188 (277)
Q Consensus 136 ~~l~~~~~~~~~------------~~~~L~~La~~~gi~--~~~H~Al~DA~~t~~l~~~l~~~l~~ 188 (277)
..+.. .+.|+. .+-.|++++.-+++. +..|-|-.||..|+..+-.....++-
T Consensus 190 y~~l~-~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F~ 255 (299)
T COG5228 190 YWWLH-QYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFT 255 (299)
T ss_pred HHHHH-HHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhheec
Confidence 33322 222321 123466666666666 67899999999999988755554433
No 109
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=81.73 E-value=3.1 Score=39.44 Aligned_cols=146 Identities=16% Similarity=0.173 Sum_probs=72.6
Q ss_pred CCCCCcEEEEEeccCCCCCCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCHHH
Q 023805 9 AAGTAEIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEFEE 88 (277)
Q Consensus 9 ~~~~~~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f~e 88 (277)
...+..-.++|+|... +..+|+++ +.+..... .++|=+|.+....-..+...|||.-.+|+++.| -
T Consensus 368 ~Ldp~~ttWiDIEG~p-------~DPVElAi--yQP~sg~Y---iHcyR~P~D~K~FK~~SKysHGillkDl~~aqP--G 433 (533)
T PF00843_consen 368 KLDPNATTWIDIEGPP-------NDPVELAI--YQPSSGNY---IHCYREPHDEKQFKNQSKYSHGILLKDLENAQP--G 433 (533)
T ss_dssp CS-TTS-EEEEEESET-------TSESEEEE--EETTTTEE---EEEE---S-HHHHHHHHHHTT-B-GGGCTTB-T--T
T ss_pred hCCCCCCeeEecCCCC-------CCCeEEEE--eccCCCcE---EEEecCCcchhhhcccccccccccHHHHhhhcc--c
Confidence 3556677899999432 34789877 44444322 445666766334455677789999999998876 5
Q ss_pred HHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCC---CCHHHHHHHh-CC---
Q 023805 89 VADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGN---MKMATLASYF-GL--- 161 (277)
Q Consensus 89 v~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~---~~L~~La~~~-gi--- 161 (277)
....+...|....++.--. .-|+..|- ..+|..- ..+||+. +-... .+.+.+ -+...||... |+
T Consensus 434 L~S~vi~~LP~~MVlT~QG-sDDIrkLl---d~hGRrD---iKlvDV~-lt~eq-aR~FEd~VWd~f~~LC~~H~GvVv~ 504 (533)
T PF00843_consen 434 LTSAVIELLPKNMVLTCQG-SDDIRKLL---DMHGRRD---IKLVDVK-LTSEQ-ARKFEDQVWDRFGHLCKKHTGVVVK 504 (533)
T ss_dssp HHHHHHHHS-TT-EEEESS-HHHHHHHH---HCTT-TT---SEEEE-----HHH-HTTTHHHHHHHHGGG---B-S-EEE
T ss_pred hHHHHHHhCCcCcEEEeeC-hHHHHHHH---HhcCCCc---ceEEEee-cCHHH-HHHHHHHHHHHHHHHHHhcCceEEe
Confidence 6677777887776666666 88887654 3444332 2478887 33222 222211 1122344422 33
Q ss_pred ------C---CCCCChHHHHHHHHH
Q 023805 162 ------G---QQKHRSLDDVRMNLE 177 (277)
Q Consensus 162 ------~---~~~H~Al~DA~~t~~ 177 (277)
. .++|+||-||.+--.
T Consensus 505 KKKkg~~~~~t~PHCALlDCiMf~a 529 (533)
T PF00843_consen 505 KKKKGKKPESTNPHCALLDCIMFEA 529 (533)
T ss_dssp --SSSS-EEE-----HHHHHHHHHH
T ss_pred cccCCCCCCCCCchHHHHHHHHHHh
Confidence 1 258999999987543
No 110
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=79.06 E-value=0.7 Score=46.63 Aligned_cols=104 Identities=16% Similarity=0.198 Sum_probs=57.1
Q ss_pred CCCCcEEEEEeccCCCC---CCCCCCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchhhhhcCCCHHHHhCCCCH
Q 023805 10 AGTAEIVFFDLETTVPR---RAGQRFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKSSRCDGITREAVESAPEF 86 (277)
Q Consensus 10 ~~~~~~v~~D~ETTg~~---~~~~~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~l~~a~~f 86 (277)
..+-.++.||+|+.|-. |...-+-+|+|+-+..-.+... -|...+-.-. ...+|.-.++-...+-
T Consensus 271 ~APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~---pf~rnvf~l~---------~capI~G~~V~~~~~e 338 (1066)
T KOG0969|consen 271 IAPLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENE---PFVRNVFTLK---------TCAPIVGSNVHSYETE 338 (1066)
T ss_pred cccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCc---hHHHhhhccc---------CcCCCCCceeEEeccH
Confidence 34557889999998743 2123456777775443322211 1211111111 0122333333333334
Q ss_pred HHHHHHHHHHh---CCCEEEEeCCchhHHHHHHHHHHHhCCC
Q 023805 87 EEVADKIFSIL---NGRVWAGHNIRRFDCARIKEAFAEIGKP 125 (277)
Q Consensus 87 ~ev~~~l~~~l---~~~~lv~hn~~~fD~~~L~~~~~~~g~~ 125 (277)
.+++.....|+ .-.+++|+|+..||++.|-.-.+-.|++
T Consensus 339 ~elL~~W~~firevDPDvI~GYNi~nFDiPYll~RA~~L~Ie 380 (1066)
T KOG0969|consen 339 KELLESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIE 380 (1066)
T ss_pred HHHHHHHHHHHHhcCCCeEecccccccccceecChHhhcCcc
Confidence 55665555555 4579999999999999876555555554
No 111
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=78.63 E-value=42 Score=28.83 Aligned_cols=105 Identities=11% Similarity=0.094 Sum_probs=61.8
Q ss_pred CCceEEEEEEEEECCeeeeeceEEEeecCCCCCCCCchh-------hhhcCCCHHHHhCC-CCHHHHHHHHHHHhCC---
Q 023805 31 RFWVLEFGAIIVCPRKLVELESFSTLIKPKDLSAVALKS-------SRCDGITREAVESA-PEFEEVADKIFSILNG--- 99 (277)
Q Consensus 31 ~~~IieIg~v~v~~~~~~~~~sf~~~v~P~~~~~i~~~~-------~~~~GIt~e~l~~a-~~f~ev~~~l~~~l~~--- 99 (277)
..-.+|||++.+.-..+. .+.|+.+|+|... ...+. ...|+|..+-.+.+ ..+..++.+|.+||+.
T Consensus 7 ~y~PaEiai~~fSL~~GI-~~~~H~~I~Pg~~--p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~ 83 (213)
T PF13017_consen 7 EYVPAEIAICKFSLKEGI-IDSFHTFINPGQI--PLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNKG 83 (213)
T ss_pred cEEeEEEEEEEEecCCcc-chhhhcccCCCCC--CcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcCC
Confidence 346889999999866653 5999999999972 22222 23456655544444 4899999999999943
Q ss_pred --C--EEEEeCC-chhHHHHHHHHHHHhCCCCCCCCceeehHHHHH
Q 023805 100 --R--VWAGHNI-RRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLT 140 (277)
Q Consensus 100 --~--~lv~hn~-~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~ 140 (277)
. +++.-.- .......|+..+...+....+ .+.+...++-
T Consensus 84 ~~~~~~i~~~~~~~~~V~~cl~~La~~a~~~~~~--~v~~~~~lf~ 127 (213)
T PF13017_consen 84 GEKMPPIFTKRDQIPRVQSCLKWLAKKAGEDNDF--KVYDFEYLFF 127 (213)
T ss_pred CCCcceEEEeHhHHHHHHHHHHHHHHhcCCCcce--EeecHHHHHH
Confidence 1 3332211 022233455555555554432 2445544443
No 112
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=74.62 E-value=3 Score=42.60 Aligned_cols=38 Identities=26% Similarity=0.559 Sum_probs=27.6
Q ss_pred CCCEEEEeCCchhHHHHHHHHHHHhCCCCCCCCceeehHHHHH
Q 023805 98 NGRVWAGHNIRRFDCARIKEAFAEIGKPAPVPVGMIDSLGVLT 140 (277)
Q Consensus 98 ~~~~lv~hn~~~fD~~~L~~~~~~~g~~~p~~~~~iDt~~l~~ 140 (277)
++.++||||+ .||+..+++++- +.- ....++||+.|.-
T Consensus 240 ke~liVGHNV-sfDRaRirEeY~---i~~-Sk~rFlDTMSlHi 277 (1075)
T KOG3657|consen 240 KEQLIVGHNV-SFDRARIREEYN---ING-SKIRFLDTMSLHI 277 (1075)
T ss_pred CCceEEeccc-cchHHHHHHHHh---ccc-cceeeeechhhhh
Confidence 4579999999 999999987664 322 1235889987653
No 113
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=69.90 E-value=22 Score=28.12 Aligned_cols=36 Identities=17% Similarity=0.124 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHhC-C-CEEEEeCCchhHHHHHHHHHHH
Q 023805 85 EFEEVADKIFSILN-G-RVWAGHNIRRFDCARIKEAFAE 121 (277)
Q Consensus 85 ~f~ev~~~l~~~l~-~-~~lv~hn~~~fD~~~L~~~~~~ 121 (277)
+-.+.++.|.+.+. . ..+|++|. .|...+|++..+.
T Consensus 56 Pr~~~~~~L~~~i~~~~g~ivvyN~-sfE~~rL~ela~~ 93 (130)
T PF11074_consen 56 PRRELIEALIKAIGSIYGSIVVYNK-SFEKTRLKELAEL 93 (130)
T ss_pred chHHHHHHHHHHhhhhcCeEEEech-HHHHHHHHHHHHH
Confidence 45678888888884 4 68999999 9999998865443
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=64.97 E-value=29 Score=27.51 Aligned_cols=66 Identities=14% Similarity=0.045 Sum_probs=41.3
Q ss_pred HHHHHHHhCCCCCCCCceeehHHHHHHHhCCCCCCCCHHHHHHHhCCCCCCCChHHHHHHHHHHHHHHHHhh
Q 023805 115 IKEAFAEIGKPAPVPVGMIDSLGVLTEKFGRRAGNMKMATLASYFGLGQQKHRSLDDVRMNLEVLKHCATVL 186 (277)
Q Consensus 115 L~~~~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~gi~~~~H~Al~DA~~t~~l~~~l~~~l 186 (277)
|-....+-|+..+. --|-+ |..|++.|. +.....++++|+-..-..+|-..|.++.+|++.|..++
T Consensus 73 LAv~a~~~G~~v~P---GDDPl-LlAYLlDPs--Nt~p~~varRY~~~~W~~dA~~RA~~t~~L~~~L~prL 138 (138)
T PF09281_consen 73 LAVHALREGVVVEP---GDDPL-LLAYLLDPS--NTNPEGVARRYLGGEWPEDAATRALATARLLRALPPRL 138 (138)
T ss_dssp HHHHHHHTT----B------HH-HHHHHH-TT----SHHHHHHHH-TS---SSHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhcCcccCC---CCCcc-hhhhhcCcc--CCChHHHHHHhcCCCCCccHHHHHHHHHHHHHHhhhcC
Confidence 33344566776654 34777 788999885 57899999999877777899999999999999887653
No 115
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=64.53 E-value=68 Score=34.44 Aligned_cols=139 Identities=13% Similarity=0.203 Sum_probs=76.7
Q ss_pred cEEEEEeccCCCCCCCCCCceEEEEEEEEECCeee-------eeceEEEeecCCCCCCCCchhhhhcCCCHHH---HhCC
Q 023805 14 EIVFFDLETTVPRRAGQRFWVLEFGAIIVCPRKLV-------ELESFSTLIKPKDLSAVALKSSRCDGITREA---VESA 83 (277)
Q Consensus 14 ~~v~~D~ETTg~~~~~~~~~IieIg~v~v~~~~~~-------~~~sf~~~v~P~~~~~i~~~~~~~~GIt~e~---l~~a 83 (277)
.+..+-++|+-... ...++|+.|++.....-.+. ...-|..+++|.. .+-|...+ .+.... +.-.
T Consensus 530 ~llsL~i~T~~N~k-~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~--~~fP~g~~--ela~~k~~~v~~~ 604 (1429)
T KOG0970|consen 530 TLLSLNIRTSMNPK-QNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPG--TSFPLGLK--ELAKQKLSKVVLH 604 (1429)
T ss_pred eEEEeeeeehhccc-cchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCC--CcCCchHH--HHHHhccCceEEe
Confidence 67788888874332 23478888887665422111 1244777888875 22222111 111111 1122
Q ss_pred CCHHHHHHHHHHHhCC---CEEEEeCCchhHHHHHHHHHHHhCCC-----------CC--CC------------Cceeeh
Q 023805 84 PEFEEVADKIFSILNG---RVWAGHNIRRFDCARIKEAFAEIGKP-----------AP--VP------------VGMIDS 135 (277)
Q Consensus 84 ~~f~ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~~~~~~g~~-----------~p--~~------------~~~iDt 135 (277)
.+-.-.+..|.+-++. .++||||+..|++..|...+....++ +| +. ...+|-
T Consensus 605 ~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~CD 684 (1429)
T KOG0970|consen 605 NSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMCD 684 (1429)
T ss_pred cCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccceEEee
Confidence 3444455666555543 69999996699999886655444443 11 00 123333
Q ss_pred HHHHHHHhCCCCCCCCHHHHHHH
Q 023805 136 LGVLTEKFGRRAGNMKMATLASY 158 (277)
Q Consensus 136 ~~l~~~~~~~~~~~~~L~~La~~ 158 (277)
..++.+-+-+ ..+++|++|.+.
T Consensus 685 ~~~~a~~lik-~~S~~LseL~q~ 706 (1429)
T KOG0970|consen 685 LNLAARELIK-AQSYSLSELSQQ 706 (1429)
T ss_pred hHHHHHhhhc-cccccHHHHHHH
Confidence 3566655544 458999999883
No 116
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=40.64 E-value=1.4e+02 Score=29.65 Aligned_cols=66 Identities=18% Similarity=0.155 Sum_probs=46.1
Q ss_pred HHHhCCCCCCCCceeehHHHHHHHhCCCCC--CCCHHHHHHHh-CCC--C--CC------------CChHHHHHHHHHHH
Q 023805 119 FAEIGKPAPVPVGMIDSLGVLTEKFGRRAG--NMKMATLASYF-GLG--Q--QK------------HRSLDDVRMNLEVL 179 (277)
Q Consensus 119 ~~~~g~~~p~~~~~iDt~~l~~~~~~~~~~--~~~L~~La~~~-gi~--~--~~------------H~Al~DA~~t~~l~ 179 (277)
+.++|+.+. .++||+ ++.+++++... +.++..++..| ++. + .. .-|..|+..+..|+
T Consensus 62 L~~~Gv~~~---~~fDT~-LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~rpls~~q~~YAa~Dv~~l~~L~ 137 (553)
T PRK14975 62 LLAAGVRVE---RCHDLM-LASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALSDPPDEEQLLYAAADADVLLELY 137 (553)
T ss_pred HHHCCCccC---CCchHH-HHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhccccccchHHHHHHHHHHhHHHHHHH
Confidence 445676643 289999 88899987653 57999998854 554 1 01 23677888899998
Q ss_pred HHHHHhhhc
Q 023805 180 KHCATVLFL 188 (277)
Q Consensus 180 ~~l~~~l~~ 188 (277)
..+.+++..
T Consensus 138 ~~L~~qL~~ 146 (553)
T PRK14975 138 AVLADQLNR 146 (553)
T ss_pred HHHHHHHHh
Confidence 888877644
No 117
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.93 E-value=35 Score=37.07 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHHhCC---CEEEEeCCchhHHHHHHH
Q 023805 84 PEFEEVADKIFSILNG---RVWAGHNIRRFDCARIKE 117 (277)
Q Consensus 84 ~~f~ev~~~l~~~l~~---~~lv~hn~~~fD~~~L~~ 117 (277)
++..+.+..+.+++.+ .+++|+|+..||++.+..
T Consensus 268 ~~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~~ 304 (1172)
T TIGR00592 268 SEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLAD 304 (1172)
T ss_pred cchHHHHhhHHHHHhhcCcchhcccccccCccceecC
Confidence 4446677777777743 589999999999987654
No 118
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=22.18 E-value=1.4e+02 Score=21.97 Aligned_cols=47 Identities=15% Similarity=0.181 Sum_probs=35.6
Q ss_pred hhhhcCCCHHHHhCCCCHHHHHHHHHHHhCCCEEEEeCCchhHHHHHHHHHHHhCCCC
Q 023805 69 SSRCDGITREAVESAPEFEEVADKIFSILNGRVWAGHNIRRFDCARIKEAFAEIGKPA 126 (277)
Q Consensus 69 ~~~~~GIt~e~l~~a~~f~ev~~~l~~~l~~~~lv~hn~~~fD~~~L~~~~~~~g~~~ 126 (277)
-...||+++++|..+-.-.+.+..+.+|+ -.|-.++...+...|+++
T Consensus 27 FLa~TG~~p~~LR~~a~dp~FL~~VLdFl-----------~~de~~l~af~~a~~~~p 73 (88)
T PF12096_consen 27 FLALTGLSPDDLRAAAGDPAFLAAVLDFL-----------LMDEAWLLAFCDAAGIPP 73 (88)
T ss_pred HHHHhCCCHHHHHHHccChHHHHHHHHHH-----------HcchHHHHHHHHHcCcCh
Confidence 34578999999987766677888888886 455567777788888775
No 119
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=20.96 E-value=1.5e+02 Score=28.52 Aligned_cols=91 Identities=12% Similarity=0.161 Sum_probs=52.9
Q ss_pred HHHHHHHHHHhCCC--EEEEeCCchhHHHHHHHHHHHhCCCCC----CCCceeehHHHHHHHhCCCCCCCCHHHHHHHhC
Q 023805 87 EEVADKIFSILNGR--VWAGHNIRRFDCARIKEAFAEIGKPAP----VPVGMIDSLGVLTEKFGRRAGNMKMATLASYFG 160 (277)
Q Consensus 87 ~ev~~~l~~~l~~~--~lv~hn~~~fD~~~L~~~~~~~g~~~p----~~~~~iDt~~l~~~~~~~~~~~~~L~~La~~~g 160 (277)
..++.+|.+++... .-..++.-.++.. +...+.+|.... ....++|...+.+..+--...+++|+.|+.++|
T Consensus 339 ~~~~~efl~~v~~~yp~~~~YH~~~ye~~--~rL~klyg~~~~~v~~~l~~~vDi~~lvr~~v~~p~es~sLK~la~~lG 416 (474)
T COG2251 339 RKALQEFLGIVVRQYPEATIYHYAPYEKT--RRLVKLYGVPQNQVSPVLDSLVDIYALVRSSVVVPVESYSLKALAPYLG 416 (474)
T ss_pred HHHHHHHHhhhheecCCCCccccCchhhh--chhheeeccCcchhhHHHHHHhHHHHHHHhccccCccchhHHHhhhhhC
Confidence 35888888877632 1222233266663 222345566543 122466777766665544457899999999999
Q ss_pred CC-CCCCChHHHHHHHHHHH
Q 023805 161 LG-QQKHRSLDDVRMNLEVL 179 (277)
Q Consensus 161 i~-~~~H~Al~DA~~t~~l~ 179 (277)
.+ ....-|.++.+.....+
T Consensus 417 ~~wrD~~~ag~~~~~~Y~~~ 436 (474)
T COG2251 417 FQWRDVEAAGDESLEMYERW 436 (474)
T ss_pred CCccccccchHHHHHHHHHH
Confidence 97 33444555555444433
Done!