Query 023843
Match_columns 276
No_of_seqs 185 out of 1175
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 07:03:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023843.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023843hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2249 3'-5' exonuclease [Rep 100.0 9.4E-41 2E-45 288.9 17.0 169 76-244 101-272 (280)
2 cd06144 REX4_like DEDDh 3'-5' 100.0 2.8E-32 6E-37 225.1 16.5 150 83-232 1-152 (152)
3 cd06149 ISG20 DEDDh 3'-5' exon 100.0 1E-31 2.3E-36 222.8 16.5 150 83-232 1-157 (157)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 8.8E-32 1.9E-36 221.7 15.8 146 83-232 1-150 (150)
5 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 9.8E-32 2.1E-36 223.7 14.6 148 83-232 1-174 (174)
6 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 3.7E-31 8E-36 220.4 12.2 146 83-232 1-161 (161)
7 cd06130 DNA_pol_III_epsilon_li 100.0 2.8E-28 6.2E-33 200.7 16.9 146 82-232 1-155 (156)
8 PRK07740 hypothetical protein; 100.0 5.6E-28 1.2E-32 214.0 19.5 159 77-239 56-227 (244)
9 TIGR01406 dnaQ_proteo DNA poly 100.0 5.9E-28 1.3E-32 211.4 17.1 160 81-242 1-176 (225)
10 PRK05711 DNA polymerase III su 100.0 1.2E-27 2.5E-32 211.0 18.0 157 79-237 3-175 (240)
11 PRK07247 DNA polymerase III su 100.0 1.9E-27 4.2E-32 203.6 18.4 154 79-237 4-168 (195)
12 PRK08517 DNA polymerase III su 100.0 4.9E-27 1.1E-31 209.1 21.3 171 77-253 65-249 (257)
13 PRK06195 DNA polymerase III su 100.0 2E-27 4.3E-32 217.3 18.8 155 80-239 1-165 (309)
14 PRK06807 DNA polymerase III su 100.0 2.3E-27 5.1E-32 216.6 18.8 156 78-238 6-172 (313)
15 PRK09146 DNA polymerase III su 100.0 4.6E-27 1E-31 207.3 19.8 159 76-238 43-227 (239)
16 PRK06063 DNA polymerase III su 100.0 4.4E-27 9.6E-32 215.1 19.9 159 77-240 12-181 (313)
17 cd06131 DNA_pol_III_epsilon_Ec 100.0 3.8E-27 8.2E-32 196.6 16.7 149 82-234 1-166 (167)
18 PRK06310 DNA polymerase III su 99.9 1.1E-26 2.5E-31 206.3 19.4 167 78-250 5-185 (250)
19 TIGR00573 dnaq exonuclease, DN 99.9 5.5E-27 1.2E-31 204.3 16.9 164 77-242 4-181 (217)
20 PRK07748 sporulation inhibitor 99.9 5E-27 1.1E-31 203.2 15.0 156 79-237 3-179 (207)
21 PRK06309 DNA polymerase III su 99.9 2.7E-26 5.8E-31 201.9 19.4 155 80-239 2-167 (232)
22 smart00479 EXOIII exonuclease 99.9 2.2E-26 4.8E-31 191.2 17.7 157 81-239 1-168 (169)
23 PRK07983 exodeoxyribonuclease 99.9 1.8E-26 3.8E-31 201.1 17.1 160 82-251 2-167 (219)
24 PRK09145 DNA polymerase III su 99.9 2.9E-26 6.3E-31 197.6 17.8 154 79-236 28-199 (202)
25 PRK07942 DNA polymerase III su 99.9 2.9E-26 6.2E-31 201.7 18.0 159 78-239 4-181 (232)
26 PRK06722 exonuclease; Provisio 99.9 8.6E-26 1.9E-30 202.5 19.0 158 78-236 3-179 (281)
27 PRK07883 hypothetical protein; 99.9 2.2E-25 4.7E-30 217.9 19.4 158 79-240 14-184 (557)
28 PRK07246 bifunctional ATP-depe 99.9 2.8E-25 6.2E-30 225.6 20.5 158 78-239 5-171 (820)
29 cd06134 RNaseT DEDDh 3'-5' exo 99.9 2.2E-25 4.7E-30 190.3 16.5 155 80-238 5-189 (189)
30 PRK05168 ribonuclease T; Provi 99.9 4.6E-25 1E-29 191.4 17.6 164 72-239 9-202 (211)
31 COG2176 PolC DNA polymerase II 99.9 3.1E-26 6.8E-31 229.4 11.4 177 71-251 412-600 (1444)
32 TIGR01298 RNaseT ribonuclease 99.9 4.8E-25 1E-29 189.8 17.2 160 76-239 4-193 (200)
33 PRK08074 bifunctional ATP-depe 99.9 4.2E-25 9E-30 227.5 19.2 157 79-239 2-170 (928)
34 cd06133 ERI-1_3'hExo_like DEDD 99.9 7.5E-25 1.6E-29 183.6 15.5 152 82-234 1-175 (176)
35 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 5.3E-25 1.2E-29 186.1 13.5 146 82-233 1-176 (177)
36 TIGR01405 polC_Gram_pos DNA po 99.9 1.3E-24 2.8E-29 226.0 19.3 159 78-240 188-357 (1213)
37 TIGR01407 dinG_rel DnaQ family 99.9 2.1E-24 4.6E-29 221.0 18.9 155 81-239 1-166 (850)
38 PRK05601 DNA polymerase III su 99.9 3.2E-24 7E-29 196.7 17.5 155 76-234 42-245 (377)
39 cd06127 DEDDh DEDDh 3'-5' exon 99.9 6.4E-24 1.4E-28 173.1 15.0 148 83-232 1-159 (159)
40 KOG2248 3'-5' exonuclease [Rep 99.9 1.7E-23 3.7E-28 193.8 15.2 156 77-236 213-373 (380)
41 PRK09182 DNA polymerase III su 99.9 3.3E-23 7.2E-28 187.7 16.7 172 75-252 32-216 (294)
42 PF00929 RNase_T: Exonuclease; 99.9 1.8E-25 4E-30 182.7 1.0 148 83-231 1-164 (164)
43 PTZ00315 2'-phosphotransferase 99.9 1.8E-22 3.9E-27 194.7 19.3 157 79-236 55-253 (582)
44 cd06138 ExoI_N N-terminal DEDD 99.9 3E-23 6.5E-28 176.2 12.3 146 83-231 1-182 (183)
45 COG0847 DnaQ DNA polymerase II 99.9 1.8E-22 3.8E-27 178.4 16.6 155 80-237 13-181 (243)
46 PRK11779 sbcB exonuclease I; P 99.9 9.2E-22 2E-26 188.1 17.9 171 78-251 4-211 (476)
47 PRK00448 polC DNA polymerase I 99.9 2.1E-21 4.5E-26 204.4 16.2 160 76-239 415-585 (1437)
48 PRK05359 oligoribonuclease; Pr 99.9 7.4E-21 1.6E-25 161.3 14.3 147 79-238 2-175 (181)
49 cd06135 Orn DEDDh 3'-5' exonuc 99.9 3.8E-21 8.3E-26 161.9 11.1 145 82-237 1-171 (173)
50 KOG0542 Predicted exonuclease 99.6 8.2E-16 1.8E-20 133.0 8.4 158 78-236 54-240 (280)
51 KOG1275 PAB-dependent poly(A) 99.6 7.8E-16 1.7E-20 151.7 8.4 181 74-256 904-1115(1118)
52 COG2925 SbcB Exonuclease I [DN 99.6 1.1E-14 2.4E-19 132.5 12.2 175 77-254 6-217 (475)
53 KOG3242 Oligoribonuclease (3'- 99.6 4.4E-15 9.6E-20 121.7 7.4 150 76-239 22-200 (208)
54 COG5018 KapD Inhibitor of the 99.5 7E-15 1.5E-19 120.1 3.8 157 80-237 4-184 (210)
55 COG1949 Orn Oligoribonuclease 99.5 3E-13 6.4E-18 110.1 10.0 145 79-238 5-178 (184)
56 cd06139 DNA_polA_I_Ecoli_like_ 99.2 1.4E-09 3.1E-14 92.0 15.0 142 80-240 5-172 (193)
57 cd05160 DEDDy_DNA_polB_exo DED 99.0 3.7E-09 8E-14 90.5 12.3 123 82-213 1-163 (199)
58 PF01612 DNA_pol_A_exo1: 3'-5' 99.0 6.8E-09 1.5E-13 86.2 12.8 135 80-239 20-176 (176)
59 PRK05755 DNA polymerase I; Pro 98.9 2E-08 4.4E-13 103.9 13.5 135 79-240 314-471 (880)
60 COG0349 Rnd Ribonuclease D [Tr 98.8 8.8E-08 1.9E-12 88.3 12.2 133 80-240 17-168 (361)
61 cd06129 RNaseD_like DEDDy 3'-5 98.6 1.3E-06 2.8E-11 72.5 12.6 129 79-235 12-160 (161)
62 PRK10829 ribonuclease D; Provi 98.5 2.2E-06 4.8E-11 80.5 14.5 133 79-240 21-172 (373)
63 cd06141 WRN_exo DEDDy 3'-5' ex 98.5 1.8E-06 3.8E-11 72.0 12.4 130 79-235 17-169 (170)
64 cd06146 mut-7_like_exo DEDDy 3 98.5 2.4E-06 5.1E-11 73.2 12.9 136 78-235 20-192 (193)
65 cd00007 35EXOc 3'-5' exonuclea 98.5 5.1E-06 1.1E-10 67.0 13.6 105 81-212 1-110 (155)
66 cd06148 Egl_like_exo DEDDy 3'- 98.5 3.1E-06 6.7E-11 72.7 12.8 138 78-241 8-180 (197)
67 PF04857 CAF1: CAF1 family rib 98.4 1.3E-06 2.8E-11 78.3 9.7 146 81-233 23-262 (262)
68 cd06125 DnaQ_like_exo DnaQ-lik 98.4 2.5E-06 5.3E-11 64.9 9.4 56 83-174 1-60 (96)
69 TIGR01388 rnd ribonuclease D. 98.4 7.2E-06 1.6E-10 77.0 14.0 132 79-240 17-168 (367)
70 PF13482 RNase_H_2: RNase_H su 98.4 2.5E-06 5.4E-11 70.5 9.3 107 83-214 1-117 (164)
71 cd06140 DNA_polA_I_Bacillus_li 98.3 1.4E-05 3E-10 66.9 12.5 133 80-240 3-158 (178)
72 cd05780 DNA_polB_Kod1_like_exo 98.2 1.9E-05 4.1E-10 67.7 12.3 116 80-214 3-157 (195)
73 smart00474 35EXOc 3'-5' exonuc 98.2 4.8E-05 1E-09 62.4 14.2 88 149-238 64-171 (172)
74 cd05781 DNA_polB_B3_exo DEDDy 98.1 0.0001 2.3E-09 62.8 14.1 105 80-212 3-144 (188)
75 cd06142 RNaseD_exo DEDDy 3'-5' 98.1 0.0001 2.2E-09 61.3 13.9 131 81-240 13-162 (178)
76 COG0749 PolA DNA polymerase I 98.0 2.9E-05 6.3E-10 76.1 10.1 133 83-239 25-181 (593)
77 PF10108 DNA_pol_B_exo2: Predi 97.9 0.00085 1.8E-08 58.0 15.2 90 144-235 36-170 (209)
78 KOG0304 mRNA deadenylase subun 97.8 0.00013 2.7E-09 62.8 8.0 154 81-236 25-237 (239)
79 cd05785 DNA_polB_like2_exo Unc 97.7 0.00062 1.3E-08 59.0 12.3 33 142-174 55-91 (207)
80 cd06147 Rrp6p_like_exo DEDDy 3 97.7 0.0005 1.1E-08 58.5 11.5 87 151-241 68-175 (192)
81 cd05779 DNA_polB_epsilon_exo D 97.7 0.00096 2.1E-08 57.7 12.9 90 142-231 70-203 (204)
82 cd05777 DNA_polB_delta_exo DED 97.7 0.0017 3.7E-08 57.0 14.0 72 142-214 68-184 (230)
83 cd09018 DEDDy_polA_RNaseD_like 97.6 0.0018 4E-08 52.0 12.7 60 152-212 45-109 (150)
84 KOG4793 Three prime repair exo 97.6 0.00017 3.7E-09 63.8 6.8 169 75-243 8-223 (318)
85 cd05783 DNA_polB_B1_exo DEDDy 97.6 0.0027 5.8E-08 54.9 14.0 72 142-213 70-171 (204)
86 cd05784 DNA_polB_II_exo DEDDy 97.6 0.0019 4.2E-08 55.3 12.8 117 80-213 3-154 (193)
87 cd05782 DNA_polB_like1_exo Unc 97.4 0.0021 4.5E-08 55.7 11.4 67 145-213 78-170 (208)
88 PTZ00166 DNA polymerase delta 97.3 0.0039 8.4E-08 66.1 13.5 150 77-235 261-483 (1054)
89 TIGR00593 pola DNA polymerase 97.1 0.002 4.3E-08 67.0 8.4 93 145-239 363-478 (887)
90 PHA02528 43 DNA polymerase; Pr 97.0 0.022 4.7E-07 59.3 15.1 162 72-234 98-324 (881)
91 cd05778 DNA_polB_zeta_exo inac 96.9 0.042 9.2E-07 48.3 14.0 85 139-224 75-203 (231)
92 PRK05762 DNA polymerase II; Re 96.7 0.031 6.6E-07 57.8 13.8 140 78-234 153-348 (786)
93 COG3359 Predicted exonuclease 96.6 0.03 6.4E-07 49.3 11.1 113 79-214 97-220 (278)
94 smart00486 POLBc DNA polymeras 96.1 0.15 3.2E-06 48.7 13.7 90 144-234 68-220 (471)
95 PHA02570 dexA exonuclease; Pro 95.9 0.034 7.4E-07 48.3 7.4 93 82-174 3-124 (220)
96 PHA02524 43A DNA polymerase su 95.7 0.19 4.1E-06 49.1 12.3 153 76-232 102-322 (498)
97 KOG1798 DNA polymerase epsilon 95.7 0.13 2.7E-06 55.3 11.7 160 80-245 246-461 (2173)
98 cd05776 DNA_polB_alpha_exo ina 95.5 0.15 3.3E-06 44.8 10.2 71 142-213 79-187 (234)
99 cd06128 DNA_polA_exo DEDDy 3'- 94.9 0.072 1.6E-06 43.1 5.9 60 152-212 45-109 (151)
100 KOG0969 DNA polymerase delta, 94.5 0.021 4.5E-07 57.5 2.0 147 78-235 272-491 (1066)
101 COG0417 PolB DNA polymerase el 94.0 1.1 2.5E-05 46.4 13.7 75 139-213 205-309 (792)
102 PF03104 DNA_pol_B_exo1: DNA p 93.8 0.32 6.9E-06 44.2 8.4 86 78-174 155-255 (325)
103 TIGR03491 RecB family nuclease 93.0 1.7 3.8E-05 42.1 12.4 126 80-234 284-427 (457)
104 KOG3657 Mitochondrial DNA poly 92.6 0.29 6.2E-06 50.0 6.4 35 158-192 241-279 (1075)
105 PF00843 Arena_nucleocap: Aren 91.8 1.4 3E-05 42.0 9.5 143 76-226 368-526 (533)
106 COG5228 POP2 mRNA deadenylase 91.7 0.36 7.7E-06 42.0 5.2 147 81-235 43-250 (299)
107 PRK05761 DNA polymerase I; Rev 90.4 5.3 0.00012 41.5 13.2 89 143-231 208-334 (787)
108 TIGR00592 pol2 DNA polymerase 87.0 26 0.00057 38.2 16.0 102 132-234 571-722 (1172)
109 PHA02563 DNA polymerase; Provi 79.6 5.8 0.00013 40.1 7.0 67 77-174 9-82 (630)
110 PRK14975 bifunctional 3'-5' ex 70.5 8.7 0.00019 38.2 5.6 60 182-241 72-147 (553)
111 KOG4793 Three prime repair exo 69.4 8.6 0.00019 34.7 4.6 48 195-243 249-296 (318)
112 PF09281 Taq-exonuc: Taq polym 66.8 14 0.00031 29.5 5.0 51 182-237 87-137 (138)
113 KOG0970 DNA polymerase alpha, 64.9 31 0.00067 37.1 8.2 155 77-234 526-751 (1429)
114 PHA03036 DNA polymerase; Provi 64.5 61 0.0013 34.7 10.4 97 76-174 156-273 (1004)
115 KOG2206 Exosome 3'-5' exoribon 58.4 18 0.00039 36.1 5.0 93 144-239 249-361 (687)
116 PF13017 Maelstrom: piRNA path 39.6 38 0.00083 29.3 3.7 60 98-157 11-79 (213)
117 PF11074 DUF2779: Domain of un 33.9 1.6E+02 0.0034 23.4 6.1 32 143-174 55-88 (130)
118 KOG2424 Protein involved in tr 22.4 1.2E+02 0.0027 25.7 3.7 45 209-253 137-184 (195)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=9.4e-41 Score=288.93 Aligned_cols=169 Identities=51% Similarity=0.841 Sum_probs=160.1
Q ss_pred CCCCCcEEEEEEeccCCCC-CCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHH
Q 023843 76 DFSLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~~-~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~ 154 (276)
..+.+++||+||||+|.++ |+...+|+|+|+|+.|.++||.||+|+++|+||+|.++||+++++.+|++|..|+.++.+
T Consensus 101 ~~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~k 180 (280)
T KOG2249|consen 101 MGSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLK 180 (280)
T ss_pred ccccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHH
Confidence 3445679999999999996 577899999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCeEEEEchhhHHHHhcccCCCCceeehhhhchhhh--CCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHH
Q 023843 155 LIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLN--RNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYM 232 (276)
Q Consensus 155 ~l~~~~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~--~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~ 232 (276)
||.|+|||||.+++|+++|.+.||+..++||+.+.+++. .....+||+.|+.++||++++.+.|++++||+|||+||.
T Consensus 181 lL~gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~ 260 (280)
T KOG2249|consen 181 LLKGRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYK 260 (280)
T ss_pred HHhCCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999987 467889999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHH
Q 023843 233 KNRKQWEKSVKD 244 (276)
Q Consensus 233 ~l~~~~e~~~~~ 244 (276)
+++.+||+....
T Consensus 261 ~vk~qwe~~~~r 272 (280)
T KOG2249|consen 261 RVKVQWEKIEAR 272 (280)
T ss_pred HHHHHHHHHhhc
Confidence 999999988764
No 2
>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=100.00 E-value=2.8e-32 Score=225.10 Aligned_cols=150 Identities=58% Similarity=0.945 Sum_probs=136.3
Q ss_pred EEEEEeccCCCCC-CeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcCCeE
Q 023843 83 VAMDCEMVGISQG-NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRIL 161 (276)
Q Consensus 83 VaiD~EttG~~~~-~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~~~l 161 (276)
|+|||||||+++. ++++|++|.+++..|.++|+.||+|..+++++++.+||||++++.++++|.+++.+|..|+++.++
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l~~~vl 80 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHhCCCEE
Confidence 6899999999975 578999999999889999999999999999999999999999999999999999999999999999
Q ss_pred EEEchhhHHHHhcccCCCCceeehhhhchhhhCC-CCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHH
Q 023843 162 VGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRN-GRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYM 232 (276)
Q Consensus 162 VgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~~~-~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~ 232 (276)
||||+.||+.||.+..+...++||..+..+..+. ..+++|+.||+.+||+++..++|+|++||++|+.||+
T Consensus 81 VgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred EEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence 9999999999999888877789998876665432 4789999999667899986578999999999999984
No 3
>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=99.98 E-value=1e-31 Score=222.83 Aligned_cols=150 Identities=43% Similarity=0.689 Sum_probs=132.0
Q ss_pred EEEEEeccCCCCC-CeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcCCeE
Q 023843 83 VAMDCEMVGISQG-NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRIL 161 (276)
Q Consensus 83 VaiD~EttG~~~~-~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~~~l 161 (276)
|+|||||||++++ +..+|++|.+++.+|.++|+.||+|..+|+++.+.+||||++++.++++|++++.+|.+|++++++
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l~~~vl 80 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHcCCCEE
Confidence 6899999999965 568999999998889999999999999999999999999999999999999999999999999999
Q ss_pred EEEchhhHHHHhcccCCCCceeehhhhchh----hhCCCCCccHHHHHHHHhCCcCCC--CCCChHHHHHHHHHHHH
Q 023843 162 VGHALHNDLKALLLTHSKKDLRDTSEYQPF----LNRNGRSKALRHLAAEILAVEIQN--GEHCPIDDARAAMLLYM 232 (276)
Q Consensus 162 VgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~----~~~~~~~~sL~~La~~~lgi~~~~--~~H~Al~DA~at~~L~~ 232 (276)
||||+.||+.||++.++...++||..+..+ ..+...+++|+.||++++|..++. .+|+|++||++|++||+
T Consensus 81 V~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred EEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 999999999999998877778999875322 244556799999997776555542 47999999999999985
No 4
>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=99.98 E-value=8.8e-32 Score=221.66 Aligned_cols=146 Identities=41% Similarity=0.615 Sum_probs=130.9
Q ss_pred EEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCC-CHHHHHHHHHHHhc-CCe
Q 023843 83 VAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAK-DFPTVQKKVAELIE-GRI 160 (276)
Q Consensus 83 VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~-~~~ev~~~l~~~l~-~~~ 160 (276)
|++||||||++.+ .+|++|.+++..|+++|+.||+|..+++++++++||||+++|.+++ +|.+++.+|.+|++ +.+
T Consensus 1 ~~iD~E~~g~~~g--~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~~~~v 78 (150)
T cd06145 1 FALDCEMCYTTDG--LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTI 78 (150)
T ss_pred CEEeeeeeeecCC--CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhCCCCE
Confidence 6899999999866 6888888888889999999999999999999999999999999985 99999999999997 899
Q ss_pred EEEEchhhHHHHhcccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCC--CCCCChHHHHHHHHHHHH
Q 023843 161 LVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ--NGEHCPIDDARAAMLLYM 232 (276)
Q Consensus 161 lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~--~~~H~Al~DA~at~~L~~ 232 (276)
|||||+.||+.||...++. ++||..+++.+.+...+++|+.||++++|..++ ..+|+|++||++|++||.
T Consensus 79 lVgHn~~fD~~fL~~~~~~--~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 79 LVGHSLENDLKALKLIHPR--VIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred EEEcChHHHHHHhhccCCC--EEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 9999999999999976654 899999988776666679999999888887765 368999999999999983
No 5
>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=99.98 E-value=9.8e-32 Score=223.73 Aligned_cols=148 Identities=37% Similarity=0.550 Sum_probs=133.2
Q ss_pred EEEEEeccCCCC--------CCe-------eEEEEEEEEe----CCCcEEEEEeecCCcccccccccccCCCHHHhcCCC
Q 023843 83 VAMDCEMVGISQ--------GNK-------SALGRVSLVN----KWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAK 143 (276)
Q Consensus 83 VaiD~EttG~~~--------~~i-------iei~~v~v~~----~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~ 143 (276)
||+|||++|+++ |.. .++|+|+++| ..|+++||.||+|..+|.||+|+++|||+++|..+.
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 578888888875 432 4899999999 689999999999999999999999999999998764
Q ss_pred ------CHHHHHHHHHHHhc-CCeEEEEchhhHHHHhcccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCC
Q 023843 144 ------DFPTVQKKVAELIE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNG 216 (276)
Q Consensus 144 ------~~~ev~~~l~~~l~-~~~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~ 216 (276)
++.+++..+..++. +++||||.+.+|+.+|++.||+..++||+.+++. +....++|+.|++++||.++|.+
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~--~~~r~~sLk~La~~~L~~~IQ~~ 158 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHL--PGQRKLSLRFLAWYLLGEKIQSE 158 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccC--CCCCChhHHHHHHHHcCCcccCC
Confidence 68999999999996 8999999999999999999998889999988654 33457999999999999999988
Q ss_pred CCChHHHHHHHHHHHH
Q 023843 217 EHCPIDDARAAMLLYM 232 (276)
Q Consensus 217 ~H~Al~DA~at~~L~~ 232 (276)
.|++++||+|+|+||+
T Consensus 159 ~HdSvEDArAam~Ly~ 174 (174)
T cd06143 159 THDSIEDARTALKLYR 174 (174)
T ss_pred CcCcHHHHHHHHHHhC
Confidence 9999999999999994
No 6
>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=99.97 E-value=3.7e-31 Score=220.40 Aligned_cols=146 Identities=36% Similarity=0.606 Sum_probs=129.0
Q ss_pred EEEEEeccCCCC--CCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCC-------HHHHHHHHH
Q 023843 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKD-------FPTVQKKVA 153 (276)
Q Consensus 83 VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~-------~~ev~~~l~ 153 (276)
|+|||||||+++ ++|++||+|.+.+ |+++|+.||+|..+|+++.+.+||||++++.++++ |++++.+|.
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~--g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~ 78 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLT--GEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALW 78 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCC--CeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHH
Confidence 689999999985 3788888888854 88889999999999999999999999999998874 459999999
Q ss_pred HHhcC-CeEEEEchhhHHHHhcccCCCCceeehhhhchhhhCCC---CCccHHHHHHHHhCCcCCC--CCCChHHHHHHH
Q 023843 154 ELIEG-RILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNG---RSKALRHLAAEILAVEIQN--GEHCPIDDARAA 227 (276)
Q Consensus 154 ~~l~~-~~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~~~~---~~~sL~~La~~~lgi~~~~--~~H~Al~DA~at 227 (276)
+|+++ .+|||||+.||+.||+..++. ++||..+++.+.+.. .+++|..||+.+||++++. .+|+|++||++|
T Consensus 79 ~~i~~~~vlVgHn~~fD~~fL~~~~~~--~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at 156 (161)
T cd06137 79 KFIDPDTILVGHSLQNDLDALRMIHTR--VVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAA 156 (161)
T ss_pred HhcCCCcEEEeccHHHHHHHHhCcCCC--eeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHH
Confidence 99997 999999999999999976544 899999999887654 6899999998789998863 579999999999
Q ss_pred HHHHH
Q 023843 228 MLLYM 232 (276)
Q Consensus 228 ~~L~~ 232 (276)
++||+
T Consensus 157 ~~l~~ 161 (161)
T cd06137 157 REVVL 161 (161)
T ss_pred HHHhC
Confidence 99984
No 7
>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=99.96 E-value=2.8e-28 Score=200.73 Aligned_cols=146 Identities=25% Similarity=0.404 Sum_probs=132.3
Q ss_pred EEEEEEeccCCCCCCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcCC
Q 023843 82 VVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGR 159 (276)
Q Consensus 82 ~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~~ 159 (276)
||+|||||||..++++++||+|.+.+ |+++ |+.||+|..++++.++.+||||++++.++++|.+++.+|.+|+++.
T Consensus 1 ~v~~D~Ettg~~~~~ii~ig~v~~~~--~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l~~~ 78 (156)
T cd06130 1 FVAIDFETANADRASACSIGLVKVRD--GQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78 (156)
T ss_pred CEEEEEeCCCCCCCceEEEEEEEEEC--CEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHHhCCC
Confidence 69999999998888999999988864 6554 8899999999999999999999999999999999999999999999
Q ss_pred eEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHH
Q 023843 160 ILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYM 232 (276)
Q Consensus 160 ~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~ 232 (276)
++||||+.||+.+|. +..+...++|++.++..+.+...+++|..|+ ++||++.+ +|+|++||++|++||.
T Consensus 79 ~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~-~~~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVA-EHLGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHH-HHcCCCcc--CcCchHHHHHHHHHHh
Confidence 999999999999996 4445567899999888887777889999999 78999987 8999999999999985
No 8
>PRK07740 hypothetical protein; Provisional
Probab=99.96 E-value=5.6e-28 Score=213.97 Aligned_cols=159 Identities=19% Similarity=0.242 Sum_probs=138.8
Q ss_pred CCCCcEEEEEEeccCCCC---CCeeEEEEEEEEeCCCcE-E--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHH
Q 023843 77 FSLTDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGNL-I--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~---~~iiei~~v~v~~~~g~i-i--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~ 150 (276)
....++|+|||||||+++ ++|++||+|.+.+ +.+ . |..+|+|..+++++++.+||||++++.++++|.+++.
T Consensus 56 ~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~--~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~ 133 (244)
T PRK07740 56 LTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKG--GEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLH 133 (244)
T ss_pred ccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHH
Confidence 345689999999999985 4799999999875 444 2 8888999999999999999999999999999999999
Q ss_pred HHHHHhcCCeEEEEchhhHHHHhcc------cC-CCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHH
Q 023843 151 KVAELIEGRILVGHALHNDLKALLL------TH-SKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDD 223 (276)
Q Consensus 151 ~l~~~l~~~~lVgHn~~~D~~~L~~------~~-~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~D 223 (276)
+|.+|+++.++||||+.||+.||.. .. ....++||..+++.+.+...+++|++|| ++||++.. ++|+|++|
T Consensus 134 ~f~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~-~~~gi~~~-~~H~Al~D 211 (244)
T PRK07740 134 RFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDAL-AYYGIPIP-RRHHALGD 211 (244)
T ss_pred HHHHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHH-HHCCcCCC-CCCCcHHH
Confidence 9999999999999999999999961 11 1235899999988887777789999998 88999998 67999999
Q ss_pred HHHHHHHHHHhHHHHH
Q 023843 224 ARAAMLLYMKNRKQWE 239 (276)
Q Consensus 224 A~at~~L~~~l~~~~e 239 (276)
|++|++||.++..+.+
T Consensus 212 a~ata~l~~~ll~~~~ 227 (244)
T PRK07740 212 ALMTAKLWAILLVEAQ 227 (244)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999977754
No 9
>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=99.96 E-value=5.9e-28 Score=211.38 Aligned_cols=160 Identities=20% Similarity=0.208 Sum_probs=136.2
Q ss_pred cEEEEEEeccCCCC---CCeeEEEEEEEEeCCCc-EEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHh
Q 023843 81 DVVAMDCEMVGISQ---GNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (276)
Q Consensus 81 ~~VaiD~EttG~~~---~~iiei~~v~v~~~~g~-ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l 156 (276)
++|+||+||||+++ ++|+|||+|.+.+.... ..|..||+|..++++.++.+||||++++.++|+|.+++.+|.+|+
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~fi 80 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHHh
Confidence 58999999999995 37999999988863111 138999999999999999999999999999999999999999999
Q ss_pred cCCeEEEEchhhHHHHhc-----cc--CC----CCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC-CCCChHHHH
Q 023843 157 EGRILVGHALHNDLKALL-----LT--HS----KKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN-GEHCPIDDA 224 (276)
Q Consensus 157 ~~~~lVgHn~~~D~~~L~-----~~--~~----~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~-~~H~Al~DA 224 (276)
++.++||||+.||+.||. +. .+ ...++||..+++.++++ .+++|+.|| ++||++..+ ..|+|+.||
T Consensus 81 ~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~~L~-~~~gi~~~~r~~H~Al~DA 158 (225)
T TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPG-QRNSLDALC-KRFKVDNSHRTLHGALLDA 158 (225)
T ss_pred CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCC-CCCCHHHHH-HhcCCCCCCCCCcCHHHHH
Confidence 999999999999999997 22 11 14689999998888765 568999999 789998764 369999999
Q ss_pred HHHHHHHHHhHHHHHHHH
Q 023843 225 RAAMLLYMKNRKQWEKSV 242 (276)
Q Consensus 225 ~at~~L~~~l~~~~e~~~ 242 (276)
++++.||..+...+...+
T Consensus 159 ~~~a~v~~~l~~~~~~~~ 176 (225)
T TIGR01406 159 HLLAEVYLALTGGQESLL 176 (225)
T ss_pred HHHHHHHHHHHcCCcchh
Confidence 999999999977655443
No 10
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=1.2e-27 Score=210.98 Aligned_cols=157 Identities=18% Similarity=0.234 Sum_probs=134.1
Q ss_pred CCcEEEEEEeccCCCC---CCeeEEEEEEEEeCCCc-EEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHH
Q 023843 79 LTDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~---~~iiei~~v~v~~~~g~-ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~ 154 (276)
.+++|+||+||||+++ ++|+|||+|.+.+.... ..|..||+|..+|++.++.+||||++++.++|+|.+++.+|.+
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~ 82 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLD 82 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 3689999999999995 38999999998763211 1389999999999999999999999999999999999999999
Q ss_pred HhcCCeEEEEchhhHHHHhc-----c--cCC----CCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC-CCCChHH
Q 023843 155 LIEGRILVGHALHNDLKALL-----L--THS----KKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN-GEHCPID 222 (276)
Q Consensus 155 ~l~~~~lVgHn~~~D~~~L~-----~--~~~----~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~-~~H~Al~ 222 (276)
|+++.++||||+.||+.||. + ..+ ...++||..+++.++++ .+++|+.|| ++||++... ..|+|+.
T Consensus 83 fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~-~~~~L~aL~-~~~gi~~~~r~~H~AL~ 160 (240)
T PRK05711 83 FIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPG-KRNSLDALC-KRYGIDNSHRTLHGALL 160 (240)
T ss_pred HhCCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCC-CCCCHHHHH-HHCCCCCCCCCCCCHHH
Confidence 99999999999999999997 1 122 13589999999888865 467999999 789998753 3699999
Q ss_pred HHHHHHHHHHHhHHH
Q 023843 223 DARAAMLLYMKNRKQ 237 (276)
Q Consensus 223 DA~at~~L~~~l~~~ 237 (276)
||+++++||..+...
T Consensus 161 DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 161 DAEILAEVYLAMTGG 175 (240)
T ss_pred HHHHHHHHHHHHHCc
Confidence 999999999998754
No 11
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.9e-27 Score=203.62 Aligned_cols=154 Identities=18% Similarity=0.203 Sum_probs=128.1
Q ss_pred CCcEEEEEEeccCCC-CCCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHH
Q 023843 79 LTDVVAMDCEMVGIS-QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (276)
Q Consensus 79 ~~~~VaiD~EttG~~-~~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~ 155 (276)
+.+||+|||||||++ .++|+|||+|.+.+ |.++ |+.||+|..+++.+++.+||||+++|.++|+|.+++.+|.+|
T Consensus 4 ~~~~vvlD~EtTGl~~~~eIIeIgaV~v~~--g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f 81 (195)
T PRK07247 4 LETYIAFDLEFNTVNGVSHIIQVSAVKYDD--HKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEF 81 (195)
T ss_pred CCeEEEEEeeCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 568999999999998 45899999999976 5543 999999999999999999999999999999999999999999
Q ss_pred hcCCeEEEEchh-hHHHHhcc---cCCCCceeehhhhchhh----hCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHH
Q 023843 156 IEGRILVGHALH-NDLKALLL---THSKKDLRDTSEYQPFL----NRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAA 227 (276)
Q Consensus 156 l~~~~lVgHn~~-~D~~~L~~---~~~~~~~~Dt~~~~~~~----~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at 227 (276)
+++.++||||+. ||+.||.. .......+|+....... .++..+++|..|| ++||++. .+|+|++||++|
T Consensus 82 ~~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La-~~~gi~~--~~HrAl~DA~~t 158 (195)
T PRK07247 82 VGELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVA-DFLGIKG--RGHNSLEDARMT 158 (195)
T ss_pred HCCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHH-HhcCCCC--CCcCCHHHHHHH
Confidence 999999999996 89999972 22222245665332111 2345689999999 8899985 479999999999
Q ss_pred HHHHHHhHHH
Q 023843 228 MLLYMKNRKQ 237 (276)
Q Consensus 228 ~~L~~~l~~~ 237 (276)
+.||.++...
T Consensus 159 a~v~~~ll~~ 168 (195)
T PRK07247 159 ARVYESFLES 168 (195)
T ss_pred HHHHHHHHhh
Confidence 9999998544
No 12
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=4.9e-27 Score=209.06 Aligned_cols=171 Identities=21% Similarity=0.270 Sum_probs=142.0
Q ss_pred CCCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHH
Q 023843 77 FSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKV 152 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l 152 (276)
.....||+||+||||+++ ++|+|||+|.+.+ |+++ |..||+|. +++++++.+||||++++.++++|.+|+.+|
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~--g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~evl~~f 141 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKN--GEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEF 141 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHHHHHH
Confidence 345689999999999985 3899999999975 6665 88999996 899999999999999999999999999999
Q ss_pred HHHhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHH
Q 023843 153 AELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDAR 225 (276)
Q Consensus 153 ~~~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~ 225 (276)
.+|+++.++||||+.||+.+|. +.......+||..+++.+.+ ..+++|.+|+ +++|++.. .+|+|+.||.
T Consensus 142 ~~fl~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~-~~~~~L~~L~-~~lgi~~~-~~HrAl~DA~ 218 (257)
T PRK08517 142 RLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIE-SPRYGLSFLK-ELLGIEIE-VHHRAYADAL 218 (257)
T ss_pred HHHHCCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHcc-CCCCCHHHHH-HHcCcCCC-CCCChHHHHH
Confidence 9999999999999999999996 22222346899888776553 4678999998 89999987 7899999999
Q ss_pred HHHHHHHHhHHHHHHHH---HHHHHHHHHHh
Q 023843 226 AAMLLYMKNRKQWEKSV---KDQTRLEQKQK 253 (276)
Q Consensus 226 at~~L~~~l~~~~e~~~---~~~~~~~~k~~ 253 (276)
+|++||..+..++...+ .+.+.+.+..+
T Consensus 219 ata~ll~~ll~~~~~~~~t~~~L~~~~k~~~ 249 (257)
T PRK08517 219 AAYEIFKICLLNLPSYIKTTEDLIDFSKTAK 249 (257)
T ss_pred HHHHHHHHHHHHhHHhhcCHHHHHHHhhhcc
Confidence 99999999998876433 34444544333
No 13
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2e-27 Score=217.31 Aligned_cols=155 Identities=19% Similarity=0.328 Sum_probs=137.5
Q ss_pred CcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEE--EEEeecCCc-ccccccccccCCCHHHhcCCCCHHHHHHHHHHHh
Q 023843 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLE-RVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (276)
Q Consensus 80 ~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii--~~~~v~P~~-~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l 156 (276)
+.||+||+||||...++|++||+|.+.+ |+++ |+.||+|.. .+++.++.|||||++++.++++|.+++.+|.+|+
T Consensus 1 ~~~vviD~ETTg~~~d~IieIgav~v~~--g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~fl 78 (309)
T PRK06195 1 MNFVAIDFETANEKRNSPCSIGIVVVKD--GEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYF 78 (309)
T ss_pred CcEEEEEEeCCCCCCCceEEEEEEEEEC--CEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHHHHh
Confidence 3699999999998778999999999975 6665 889999986 5788899999999999999999999999999999
Q ss_pred cCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHH
Q 023843 157 EGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAML 229 (276)
Q Consensus 157 ~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~ 229 (276)
++.++||||+.||+.||. +..+...++||+.+++.+.+...+++|..|+ ++||++. .+|+|++||++|++
T Consensus 79 ~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~-~~~gi~~--~~H~Al~DA~ata~ 155 (309)
T PRK06195 79 NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVN-NFLGYEF--KHHDALADAMACSN 155 (309)
T ss_pred CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHH-HHcCCCC--cccCCHHHHHHHHH
Confidence 999999999999999996 3344456899999988888777889999999 8899985 58999999999999
Q ss_pred HHHHhHHHHH
Q 023843 230 LYMKNRKQWE 239 (276)
Q Consensus 230 L~~~l~~~~e 239 (276)
||..+..++.
T Consensus 156 l~~~l~~~~~ 165 (309)
T PRK06195 156 ILLNISKELN 165 (309)
T ss_pred HHHHHHHHhc
Confidence 9999977654
No 14
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.3e-27 Score=216.58 Aligned_cols=156 Identities=21% Similarity=0.287 Sum_probs=140.1
Q ss_pred CCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
.+.++|+||+||||+++ ++|+|||+|.+.+ |+++ |+.+|+|..++++.++.+||||++++.++++|.+|+..|.
T Consensus 6 ~~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~--g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~ 83 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQVAAVKYRN--HELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFL 83 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHH
Confidence 35789999999999985 5899999999975 6665 8899999999999999999999999999999999999999
Q ss_pred HHhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHH
Q 023843 154 ELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARA 226 (276)
Q Consensus 154 ~~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~a 226 (276)
+|+++.++||||+.||+.+|. +..+...++||..+++.+.+....++|..|+ ++||++. .+|+|+.||++
T Consensus 84 ~fl~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~-~~lgi~~--~~H~Al~DA~~ 160 (313)
T PRK06807 84 AFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLK-RMLGIRL--SSHNAFDDCIT 160 (313)
T ss_pred HHHcCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHH-HHcCCCC--CCcChHHHHHH
Confidence 999999999999999999997 3344556899999988888777789999998 8999998 68999999999
Q ss_pred HHHHHHHhHHHH
Q 023843 227 AMLLYMKNRKQW 238 (276)
Q Consensus 227 t~~L~~~l~~~~ 238 (276)
|+.||.++....
T Consensus 161 ta~l~~~l~~~~ 172 (313)
T PRK06807 161 CAAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHHhh
Confidence 999999997764
No 15
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=4.6e-27 Score=207.32 Aligned_cols=159 Identities=20% Similarity=0.218 Sum_probs=135.4
Q ss_pred CCCCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcE----EEEEeecCCcccccccccccCCCHHHhcCCCCHHHHH
Q 023843 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNL----IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~i----i~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~ 149 (276)
......||+||+||||+++ ++|++||+|.+.+ +.+ .|..+|+|..+|+..++.+||||++++.++++|.+++
T Consensus 43 ~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~--~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~evl 120 (239)
T PRK09146 43 PLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTL--QRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERIL 120 (239)
T ss_pred CcccCCEEEEEeECCCCCCCCCcEEEEEEEEEEC--CeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHHH
Confidence 3445779999999999995 5899999999875 443 3788999999999999999999999999999999999
Q ss_pred HHHHHHhcCCeEEEEchhhHHHHhccc-------CCCCceeehhhhchhhhCCC-------------CCccHHHHHHHHh
Q 023843 150 KKVAELIEGRILVGHALHNDLKALLLT-------HSKKDLRDTSEYQPFLNRNG-------------RSKALRHLAAEIL 209 (276)
Q Consensus 150 ~~l~~~l~~~~lVgHn~~~D~~~L~~~-------~~~~~~~Dt~~~~~~~~~~~-------------~~~sL~~La~~~l 209 (276)
.+|..|+++.++||||+.||+.||... .....++||+.+++.+.+.. .+++|.+++ ++|
T Consensus 121 ~~l~~~~~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~-~~~ 199 (239)
T PRK09146 121 DELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSR-LRY 199 (239)
T ss_pred HHHHHHhCCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHH-HHc
Confidence 999999999999999999999999621 12345899999877654321 567999998 789
Q ss_pred CCcCCCCCCChHHHHHHHHHHHHHhHHHH
Q 023843 210 AVEIQNGEHCPIDDARAAMLLYMKNRKQW 238 (276)
Q Consensus 210 gi~~~~~~H~Al~DA~at~~L~~~l~~~~ 238 (276)
|++.. .+|+|++||.+|++||..+..+.
T Consensus 200 gl~~~-~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 200 GLPAY-SPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred CCCCC-CCCCcHHHHHHHHHHHHHHHHHH
Confidence 99976 78999999999999999987664
No 16
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=4.4e-27 Score=215.06 Aligned_cols=159 Identities=23% Similarity=0.214 Sum_probs=136.9
Q ss_pred CCCCcEEEEEEeccCCCCC--CeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHH
Q 023843 77 FSLTDVVAMDCEMVGISQG--NKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKV 152 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~~--~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l 152 (276)
..+..||+||+||||++++ +|+|||+|.+. .+|++. |..||+|.. .+..+.|||||++++.++++|.+++.+|
T Consensus 12 ~~~~~fvvlD~ETTGl~p~~d~IIeIgav~v~-~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap~f~ev~~~l 88 (313)
T PRK06063 12 HYPRGWAVVDVETSGFRPGQARIISLAVLGLD-ADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQFADIAGEV 88 (313)
T ss_pred CCCCCEEEEEEECCCCCCCCCEEEEEEEEEEE-CCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCCCHHHHHHHH
Confidence 3467899999999999954 89999988885 346664 889999974 4567899999999999999999999999
Q ss_pred HHHhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHH
Q 023843 153 AELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDAR 225 (276)
Q Consensus 153 ~~~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~ 225 (276)
.+|+++.++||||+.||+.||. +..+...++||+.+++.+.+...+++|.+|| ++||++.. .+|+|++||+
T Consensus 89 ~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~-~~~gi~~~-~~H~Al~DA~ 166 (313)
T PRK06063 89 AELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLA-AHWGVPQQ-RPHDALDDAR 166 (313)
T ss_pred HHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHH-HHcCCCCC-CCCCcHHHHH
Confidence 9999999999999999999997 2233345799999988877777899999999 88999976 7899999999
Q ss_pred HHHHHHHHhHHHHHH
Q 023843 226 AAMLLYMKNRKQWEK 240 (276)
Q Consensus 226 at~~L~~~l~~~~e~ 240 (276)
+|++||..+..++..
T Consensus 167 ata~l~~~ll~~~~~ 181 (313)
T PRK06063 167 VLAGILRPSLERARE 181 (313)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999998777654
No 17
>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=99.95 E-value=3.8e-27 Score=196.63 Aligned_cols=149 Identities=19% Similarity=0.264 Sum_probs=128.4
Q ss_pred EEEEEEeccCCCC---CCeeEEEEEEEEeCCCcE---EEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHH
Q 023843 82 VVAMDCEMVGISQ---GNKSALGRVSLVNKWGNL---IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (276)
Q Consensus 82 ~VaiD~EttG~~~---~~iiei~~v~v~~~~g~i---i~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~ 155 (276)
+|+||+||||+++ ++|+|||+|.+.+ +.+ .|+.+|+|..++++.++.+||||++++.++++|.+++.+|.+|
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~--~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~ 78 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELIN--RRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDF 78 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEEC--CcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHH
Confidence 5899999999986 4899999998865 332 3889999999999999999999999999999999999999999
Q ss_pred hcCCeEEEEchhhHHHHhcc-------cC---CCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC-CCCChHHHH
Q 023843 156 IEGRILVGHALHNDLKALLL-------TH---SKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN-GEHCPIDDA 224 (276)
Q Consensus 156 l~~~~lVgHn~~~D~~~L~~-------~~---~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~-~~H~Al~DA 224 (276)
+++.++||||+.||+.||.- .. ....++||+.+++.+.+. ..++|.+++ ++||++.++ .+|+|++||
T Consensus 79 l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~-~~~~L~~l~-~~~~i~~~~~~~H~Al~Da 156 (167)
T cd06131 79 IRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPG-KPNSLDALC-KRFGIDNSHRTLHGALLDA 156 (167)
T ss_pred HCCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCC-CCCCHHHHH-HHCCCCCCCCCCCChHHHH
Confidence 99999999999999999961 11 124579999888777643 568999999 889999863 479999999
Q ss_pred HHHHHHHHHh
Q 023843 225 RAAMLLYMKN 234 (276)
Q Consensus 225 ~at~~L~~~l 234 (276)
++|++||..+
T Consensus 157 ~~~a~l~~~l 166 (167)
T cd06131 157 ELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHh
Confidence 9999999875
No 18
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.1e-26 Score=206.31 Aligned_cols=167 Identities=18% Similarity=0.277 Sum_probs=139.2
Q ss_pred CCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcE--EEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~i--i~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
....+|+|||||||+++ ++|+|||+|.+.. +.+ .|..+|+|..+|+..++.+||||++++.++++|.+++.+|.
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~--~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~ 82 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDRIIEFAAIRFTF--DEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIK 82 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCeEEEEEEEEEEC--CeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHH
Confidence 34789999999999985 5899999998864 333 38899999999999999999999999999999999999999
Q ss_pred HHhcC-CeEEEEchhhHHHHhccc-------C--CCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHH
Q 023843 154 ELIEG-RILVGHALHNDLKALLLT-------H--SKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDD 223 (276)
Q Consensus 154 ~~l~~-~~lVgHn~~~D~~~L~~~-------~--~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~D 223 (276)
+|+++ .++||||+.||+.+|... . ....++||..+++.+. ...+++|..|+ +++|++.. ++|+|++|
T Consensus 83 ~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~-~~~~~~L~~l~-~~~g~~~~-~aH~Al~D 159 (250)
T PRK06310 83 GFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYG-DSPNNSLEALA-VHFNVPYD-GNHRAMKD 159 (250)
T ss_pred HHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcc-cCCCCCHHHHH-HHCCCCCC-CCcChHHH
Confidence 99985 899999999999999721 1 1245899999887653 44578999998 88999987 79999999
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHH
Q 023843 224 ARAAMLLYMKNRKQWEKSVKDQTRLEQ 250 (276)
Q Consensus 224 A~at~~L~~~l~~~~e~~~~~~~~~~~ 250 (276)
|.+|+.||..+..++. .+.+.+....
T Consensus 160 a~at~~vl~~l~~~~~-~~~~l~~~~~ 185 (250)
T PRK06310 160 VEINIKVFKHLCKRFR-TLEQLKQILS 185 (250)
T ss_pred HHHHHHHHHHHHHhcc-cHHHHHHHhh
Confidence 9999999999987653 3344454444
No 19
>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=99.95 E-value=5.5e-27 Score=204.30 Aligned_cols=164 Identities=21% Similarity=0.304 Sum_probs=136.9
Q ss_pred CCCCcEEEEEEeccCCCCC-CeeEEEEEEEEeCCCcE--EEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 77 FSLTDVVAMDCEMVGISQG-NKSALGRVSLVNKWGNL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~~-~iiei~~v~v~~~~g~i--i~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
.....||+||+||||+++. .|+|||+|.+.+. +.+ .|..||+|..++++.++.+||||++++.++++|.+++.+|.
T Consensus 4 l~~~~fvv~D~ETTGl~~~~~IIeIgav~v~~~-~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~ 82 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAGHDIIEIGAVEIINR-RITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFA 82 (217)
T ss_pred EEecCEEEEEecCCCCCCCCCEEEEEEEEEECC-CEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHH
Confidence 3456899999999999853 4999999998764 223 38899999999999999999999999999999999999999
Q ss_pred HHhcCCeEEEEchhhHHHHhccc--------CCCCceeehhhhchhhhCC--CCCccHHHHHHHHhCCcCCC-CCCChHH
Q 023843 154 ELIEGRILVGHALHNDLKALLLT--------HSKKDLRDTSEYQPFLNRN--GRSKALRHLAAEILAVEIQN-GEHCPID 222 (276)
Q Consensus 154 ~~l~~~~lVgHn~~~D~~~L~~~--------~~~~~~~Dt~~~~~~~~~~--~~~~sL~~La~~~lgi~~~~-~~H~Al~ 222 (276)
+|+++.++||||+.||+.||... .....++|+..+++.+.+. ..+++|..|+ ++||++... .+|+|++
T Consensus 83 ~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~-~~~gl~~~~~~~H~Al~ 161 (217)
T TIGR00573 83 DYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALC-KRYEITNSHRALHGALA 161 (217)
T ss_pred HHhCCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHH-HHcCCCCCCcccCCHHH
Confidence 99999999999999999999711 1223578888776666543 3467999998 889998652 5799999
Q ss_pred HHHHHHHHHHHhHHHHHHHH
Q 023843 223 DARAAMLLYMKNRKQWEKSV 242 (276)
Q Consensus 223 DA~at~~L~~~l~~~~e~~~ 242 (276)
||++|++||..+..++....
T Consensus 162 DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 162 DAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred HHHHHHHHHHHHHhcchhhc
Confidence 99999999999988866544
No 20
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.95 E-value=5e-27 Score=203.15 Aligned_cols=156 Identities=20% Similarity=0.220 Sum_probs=130.4
Q ss_pred CCcEEEEEEeccCCCC--------CCeeEEEEEEEEeCCCcEE--EEEeecCCc--ccccccccccCCCHHHhcCCCCHH
Q 023843 79 LTDVVAMDCEMVGISQ--------GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFP 146 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~--------~~iiei~~v~v~~~~g~ii--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~ 146 (276)
..+||+||+||||+++ ++|+|||+|.+.+ |+++ |..||+|.. +++++++.+||||++++.++++|.
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~--~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ 80 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVG--CEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFE 80 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEec--CcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHH
Confidence 4679999999999752 4799999999975 5554 999999987 689999999999999999999999
Q ss_pred HHHHHHHHHhcC-CeEEEEchhhHHHHhc-------ccCCC-CceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCC
Q 023843 147 TVQKKVAELIEG-RILVGHALHNDLKALL-------LTHSK-KDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGE 217 (276)
Q Consensus 147 ev~~~l~~~l~~-~~lVgHn~~~D~~~L~-------~~~~~-~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~ 217 (276)
+++.+|.+|+++ ..+++|++.||+.||. +..+. ..++|+....+.+.+....++|.+++ ++||++..+.+
T Consensus 81 evl~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~-~~~gi~~~~~~ 159 (207)
T PRK07748 81 ELVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAI-EEYGKEGTGKH 159 (207)
T ss_pred HHHHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHH-HHcCCCCCCCC
Confidence 999999999997 4566677899999996 22222 24678877666565555678999988 89999987678
Q ss_pred CChHHHHHHHHHHHHHhHHH
Q 023843 218 HCPIDDARAAMLLYMKNRKQ 237 (276)
Q Consensus 218 H~Al~DA~at~~L~~~l~~~ 237 (276)
|+|++||++|++||.++...
T Consensus 160 H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 160 HCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred cChHHHHHHHHHHHHHHHhC
Confidence 99999999999999998765
No 21
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.7e-26 Score=201.91 Aligned_cols=155 Identities=18% Similarity=0.220 Sum_probs=133.3
Q ss_pred CcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc
Q 023843 80 TDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (276)
Q Consensus 80 ~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~ 157 (276)
.++|+||+||||+++ ++|+|||++ +......|+.+|+|..+|++.++.+||||++++.++++|.+++.+|.+|++
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v---~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~ 78 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAY---NGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG 78 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEE---cCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHc
Confidence 569999999999984 488999974 322334599999999999999999999999999999999999999999998
Q ss_pred -CCeEEEEch-hhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHH
Q 023843 158 -GRILVGHAL-HNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAM 228 (276)
Q Consensus 158 -~~~lVgHn~-~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~ 228 (276)
+.++||||+ .||+.+|. +..+...++||..+++.+.+....++|..|+ ++||++.. .+|+|++||.+|+
T Consensus 79 ~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~-~~~~~~~~-~aH~Al~Da~~t~ 156 (232)
T PRK06309 79 TDNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLR-QVYGFEEN-QAHRALDDVITLH 156 (232)
T ss_pred CCCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHH-HHcCCCCC-CCCCcHHHHHHHH
Confidence 579999995 89999997 2223356899999988877777789999998 88998876 7999999999999
Q ss_pred HHHHHhHHHHH
Q 023843 229 LLYMKNRKQWE 239 (276)
Q Consensus 229 ~L~~~l~~~~e 239 (276)
+||.++..++.
T Consensus 157 ~vl~~l~~~~~ 167 (232)
T PRK06309 157 RVFSALVGDLS 167 (232)
T ss_pred HHHHHHHHHHH
Confidence 99999987764
No 22
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.95 E-value=2.2e-26 Score=191.21 Aligned_cols=157 Identities=30% Similarity=0.467 Sum_probs=133.9
Q ss_pred cEEEEEEeccCCCCC--CeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcC
Q 023843 81 DVVAMDCEMVGISQG--NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (276)
Q Consensus 81 ~~VaiD~EttG~~~~--~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~ 158 (276)
.+|+|||||||++++ +|+|||+|.+.+..-...|+.||+|..+++++++.+||||++++.++++|.+++.+|..|+++
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l~~ 80 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLKG 80 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhcC
Confidence 389999999999854 899999888876321223999999988999999999999999999999999999999999999
Q ss_pred CeEEEEch-hhHHHHhccc-------CCC-CceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHH
Q 023843 159 RILVGHAL-HNDLKALLLT-------HSK-KDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAML 229 (276)
Q Consensus 159 ~~lVgHn~-~~D~~~L~~~-------~~~-~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~ 229 (276)
.++|+||+ .||+.+|... .+. ..++|+..+++.+.+.. .++|.+|+ ++||++..+.+|+|++||++|++
T Consensus 81 ~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~-~~~L~~l~-~~~~~~~~~~~H~A~~Da~~t~~ 158 (169)
T smart00479 81 KILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGR-KYSLKKLA-ERLGLEVIGRAHRALDDARATAK 158 (169)
T ss_pred CEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCC-CCCHHHHH-HHCCCCCCCCCcCcHHHHHHHHH
Confidence 99999999 9999999721 121 23799999888776543 89999999 88999988556999999999999
Q ss_pred HHHHhHHHHH
Q 023843 230 LYMKNRKQWE 239 (276)
Q Consensus 230 L~~~l~~~~e 239 (276)
||.++..+|.
T Consensus 159 l~~~~~~~~~ 168 (169)
T smart00479 159 LFKKLVERLL 168 (169)
T ss_pred HHHHHHHHhh
Confidence 9999988764
No 23
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.95 E-value=1.8e-26 Score=201.06 Aligned_cols=160 Identities=14% Similarity=0.121 Sum_probs=133.5
Q ss_pred EEEEEEeccCCCCCCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcCC
Q 023843 82 VVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGR 159 (276)
Q Consensus 82 ~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~~ 159 (276)
+++||+||||+++ .|+|||+|.|.+ |+++ |..+|+|..+|+..++.+||||++++.++|+|.+++.. |+++.
T Consensus 2 ~~vlD~ETTGl~~-~IieIg~v~v~~--~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~---~~~~~ 75 (219)
T PRK07983 2 LRVIDTETCGLQG-GIVEIASVDVID--GKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPH---YYGSE 75 (219)
T ss_pred eEEEEEECCCCCC-CCEEEEEEEEEC--CEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHH---HcCCC
Confidence 7999999999974 589999999875 6665 89999999999999999999999999999999999876 67899
Q ss_pred eEEEEchhhHHHHhcccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCC----CCCCChHHHHHHHHHHHHHhH
Q 023843 160 ILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ----NGEHCPIDDARAAMLLYMKNR 235 (276)
Q Consensus 160 ~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~----~~~H~Al~DA~at~~L~~~l~ 235 (276)
++||||+.||+.+|.... ..++||..+++.+.+... ++|..|+ +++|++.. ..+|+|++||++|+.||.++.
T Consensus 76 ~lVaHNa~FD~~~L~~~~--~~~idTl~lar~l~p~~~-~~l~~L~-~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~ 151 (219)
T PRK07983 76 WYVAHNASFDRRVLPEMP--GEWICTMKLARRLWPGIK-YSNMALY-KSRKLNVQTPPGLHHHRALYDCYITAALLIDIM 151 (219)
T ss_pred EEEEeCcHhhHHHHhCcC--CCcEeHHHHHHHHccCCC-CCHHHHH-HHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 999999999999997432 348999999998887654 8999999 78998652 368999999999999999998
Q ss_pred HHHHHHHHHHHHHHHH
Q 023843 236 KQWEKSVKDQTRLEQK 251 (276)
Q Consensus 236 ~~~e~~~~~~~~~~~k 251 (276)
....-.+.+.+...++
T Consensus 152 ~~~~~~~~~l~~~~~~ 167 (219)
T PRK07983 152 NTSGWTAEEMADITGR 167 (219)
T ss_pred HHcCCCHHHHHHHhcC
Confidence 5433233444444443
No 24
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2.9e-26 Score=197.62 Aligned_cols=154 Identities=21% Similarity=0.280 Sum_probs=128.5
Q ss_pred CCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcE----EEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHH
Q 023843 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNL----IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKV 152 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~i----i~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l 152 (276)
..++|+||+||||+++ ++|+|||+|.+.+ +.+ .|..||+|..+++++++.+||||++++.+++++.+++.+|
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~--~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~ 105 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRG--NRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQL 105 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEEC--CEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHH
Confidence 3589999999999985 5899999998865 333 2889999999999999999999999999999999999999
Q ss_pred HHHhcCCeEEEEchhhHHHHhccc------C-CCCceeehhhhchhh-----hCCCCCccHHHHHHHHhCCcCCCCCCCh
Q 023843 153 AELIEGRILVGHALHNDLKALLLT------H-SKKDLRDTSEYQPFL-----NRNGRSKALRHLAAEILAVEIQNGEHCP 220 (276)
Q Consensus 153 ~~~l~~~~lVgHn~~~D~~~L~~~------~-~~~~~~Dt~~~~~~~-----~~~~~~~sL~~La~~~lgi~~~~~~H~A 220 (276)
.+|+++.++||||+.||+.||... . ....++|+..+.... .+...+++|.+|+ ++||++.. ++|+|
T Consensus 106 ~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~-~~~gi~~~-~~H~A 183 (202)
T PRK09145 106 LAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAIL-KHLDLPVL-GRHDA 183 (202)
T ss_pred HHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHH-HHcCCCCC-CCCCc
Confidence 999999999999999999999611 1 123478887654211 1123468999998 88999986 78999
Q ss_pred HHHHHHHHHHHHHhHH
Q 023843 221 IDDARAAMLLYMKNRK 236 (276)
Q Consensus 221 l~DA~at~~L~~~l~~ 236 (276)
++||++|+.||.++..
T Consensus 184 l~DA~ata~l~~~l~~ 199 (202)
T PRK09145 184 LNDAIMAALIFLRLRK 199 (202)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999998865
No 25
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=2.9e-26 Score=201.69 Aligned_cols=159 Identities=18% Similarity=0.178 Sum_probs=131.9
Q ss_pred CCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcC-CCCHHHHHHHH
Q 023843 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRK-AKDFPTVQKKV 152 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~-a~~~~ev~~~l 152 (276)
...+||+||+||||+++ ++|++||+|.+. .+|.++ |..||+|..+|+++++.+||||++++.+ ++++.+++.+|
T Consensus 4 ~~~~~vv~D~ETTGl~p~~d~Iieig~v~v~-~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~ 82 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPETARIVTAALVVVD-ADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEI 82 (232)
T ss_pred ccCcEEEEEeccCCCCCCCCeeEEEEEEEEe-CCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHH
Confidence 34679999999999995 479999988775 335554 8889999999999999999999999965 78888888888
Q ss_pred HHHh-----cCCeEEEEchhhHHHHhc-----ccC---CCCceeehhhhchhhhCC-CCCccHHHHHHHHhCCcCCCCCC
Q 023843 153 AELI-----EGRILVGHALHNDLKALL-----LTH---SKKDLRDTSEYQPFLNRN-GRSKALRHLAAEILAVEIQNGEH 218 (276)
Q Consensus 153 ~~~l-----~~~~lVgHn~~~D~~~L~-----~~~---~~~~~~Dt~~~~~~~~~~-~~~~sL~~La~~~lgi~~~~~~H 218 (276)
..+| ++.++||||+.||+.||. ... ....++|+..+.+.+.+. ..+++|.+|| ++||++.. ++|
T Consensus 83 ~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~-~~~gi~~~-~aH 160 (232)
T PRK07942 83 ADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALC-EHYGVRLD-NAH 160 (232)
T ss_pred HHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHH-HHcCCCCC-CCC
Confidence 8876 578999999999999996 111 123478999887766543 3578999999 88999987 799
Q ss_pred ChHHHHHHHHHHHHHhHHHHH
Q 023843 219 CPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 219 ~Al~DA~at~~L~~~l~~~~e 239 (276)
+|++||++|++||..+..++.
T Consensus 161 ~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 161 EATADALAAARVAWALARRFP 181 (232)
T ss_pred ChHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999977665
No 26
>PRK06722 exonuclease; Provisional
Probab=99.94 E-value=8.6e-26 Score=202.52 Aligned_cols=158 Identities=18% Similarity=0.241 Sum_probs=130.6
Q ss_pred CCCcEEEEEEeccCCC-----CCCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHH
Q 023843 78 SLTDVVAMDCEMVGIS-----QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~-----~~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~ 150 (276)
+...||+||+||||.. +++|+|||+|.|.++.+.++ |..||+|..+|+++++.+||||+++|.++|+|.+|+.
T Consensus 3 ~~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~ 82 (281)
T PRK06722 3 NATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIE 82 (281)
T ss_pred CCCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHH
Confidence 3578999999999643 25899999999987544665 9999999999999999999999999999999999999
Q ss_pred HHHHHhcCCeEEEEchhhHHHHhcc-------cCCC---CceeehhhhchhhhCC--CCCccHHHHHHHHhCCcCCCCCC
Q 023843 151 KVAELIEGRILVGHALHNDLKALLL-------THSK---KDLRDTSEYQPFLNRN--GRSKALRHLAAEILAVEIQNGEH 218 (276)
Q Consensus 151 ~l~~~l~~~~lVgHn~~~D~~~L~~-------~~~~---~~~~Dt~~~~~~~~~~--~~~~sL~~La~~~lgi~~~~~~H 218 (276)
+|.+|+++.++|+||+.||+.||.. ..+. ..++|+..+++..++. ...++|..|+ ++||++..+.+|
T Consensus 83 ef~~fig~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~-~~lgL~~~g~~H 161 (281)
T PRK06722 83 KFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAV-EQLGLIWEGKQH 161 (281)
T ss_pred HHHHHHCCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHH-HHCCCCCCCCCc
Confidence 9999999888888888999999972 2221 1246777655433322 2457899998 899999876789
Q ss_pred ChHHHHHHHHHHHHHhHH
Q 023843 219 CPIDDARAAMLLYMKNRK 236 (276)
Q Consensus 219 ~Al~DA~at~~L~~~l~~ 236 (276)
+|++||++|+.||.++..
T Consensus 162 rAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 162 RALADAENTANILLKAYS 179 (281)
T ss_pred CcHHHHHHHHHHHHHHhc
Confidence 999999999999999873
No 27
>PRK07883 hypothetical protein; Validated
Probab=99.94 E-value=2.2e-25 Score=217.93 Aligned_cols=158 Identities=21% Similarity=0.248 Sum_probs=140.3
Q ss_pred CCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHH
Q 023843 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~ 154 (276)
...||+||+||||+++ ++|+|||+|.+.+ |+++ |..+|+|..+++++++.+||||++++.++++|.+++.+|.+
T Consensus 14 ~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~--g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~ 91 (557)
T PRK07883 14 DVTFVVVDLETTGGSPAGDAITEIGAVKVRG--GEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLE 91 (557)
T ss_pred CCCEEEEEEecCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHH
Confidence 4689999999999985 4899999999975 6665 89999999999999999999999999999999999999999
Q ss_pred HhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhC--CCCCccHHHHHHHHhCCcCCCCCCChHHHHH
Q 023843 155 LIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNR--NGRSKALRHLAAEILAVEIQNGEHCPIDDAR 225 (276)
Q Consensus 155 ~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~--~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~ 225 (276)
|+++.++||||+.||+.||. +..+...++||+.+++.+.+ ...+++|.+|+ ++||++.. .+|+|++||.
T Consensus 92 fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~-~~~gi~~~-~~H~Al~DA~ 169 (557)
T PRK07883 92 FARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLA-RLFGATTT-PTHRALDDAR 169 (557)
T ss_pred HhcCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHH-HHCCcccC-CCCCHHHHHH
Confidence 99999999999999999997 33344457999998877665 56789999998 79999987 7899999999
Q ss_pred HHHHHHHHhHHHHHH
Q 023843 226 AAMLLYMKNRKQWEK 240 (276)
Q Consensus 226 at~~L~~~l~~~~e~ 240 (276)
+|++||.++..++..
T Consensus 170 ata~l~~~l~~~~~~ 184 (557)
T PRK07883 170 ATVDVLHGLIERLGN 184 (557)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999888753
No 28
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=2.8e-25 Score=225.64 Aligned_cols=158 Identities=27% Similarity=0.384 Sum_probs=139.9
Q ss_pred CCCcEEEEEEeccCCCC-CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHH
Q 023843 78 SLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~-~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~ 154 (276)
...+||+||+||||+++ ++|+|||+|.+.+ |+++ |..+|+|..+|+++++.+||||++++.++|+|.+|+.+|.+
T Consensus 5 ~~~~~vvvD~ETTGl~~~d~IIeIgaV~v~~--g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~~ 82 (820)
T PRK07246 5 KLRKYAVVDLEATGAGPNASIIQVGIVIIEG--GEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYD 82 (820)
T ss_pred cCCCEEEEEEecCCcCCCCeEEEEEEEEEEC--CEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHHH
Confidence 35789999999999984 5899999999875 6665 88999999999999999999999999999999999999999
Q ss_pred HhcCCeEEEEchhhHHHHhcc-----cC-CCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHH
Q 023843 155 LIEGRILVGHALHNDLKALLL-----TH-SKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAM 228 (276)
Q Consensus 155 ~l~~~~lVgHn~~~D~~~L~~-----~~-~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~ 228 (276)
|+++.++||||+.||+.||.. .. .....+||..+++.+.+...+++|.+|| ++||++.. .+|+|++||++|+
T Consensus 83 ~l~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~-~~lgl~~~-~~H~Al~DA~ata 160 (820)
T PRK07246 83 LIEDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLS-RELNIDLA-DAHTAIADARATA 160 (820)
T ss_pred HhCCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHH-HHcCCCCC-CCCCHHHHHHHHH
Confidence 999999999999999999962 11 1234689999999888877899999999 78999987 7899999999999
Q ss_pred HHHHHhHHHHH
Q 023843 229 LLYMKNRKQWE 239 (276)
Q Consensus 229 ~L~~~l~~~~e 239 (276)
.||..+..++.
T Consensus 161 ~L~~~l~~~l~ 171 (820)
T PRK07246 161 ELFLKLLQKIE 171 (820)
T ss_pred HHHHHHHHHHh
Confidence 99999876654
No 29
>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=99.93 E-value=2.2e-25 Score=190.35 Aligned_cols=155 Identities=23% Similarity=0.286 Sum_probs=124.2
Q ss_pred CcEEEEEEeccCCCC--CCeeEEEEEEEEeC-CCcE----EEEEeecCC--cccccccccccCCCHHH-hcCCCCHHHHH
Q 023843 80 TDVVAMDCEMVGISQ--GNKSALGRVSLVNK-WGNL----IYDEFVRPL--ERVVDFRTRISGIRPRD-LRKAKDFPTVQ 149 (276)
Q Consensus 80 ~~~VaiD~EttG~~~--~~iiei~~v~v~~~-~g~i----i~~~~v~P~--~~i~~~~~~i~GIt~~~-l~~a~~~~ev~ 149 (276)
-..|+||+||||+++ ++|+|||+|.|.+. +|.+ .|+.+|+|. .+|++.++.+||||+++ +..++...+++
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~ 84 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEAL 84 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHH
Confidence 347999999999984 48999999999853 4543 399999994 58999999999999986 56677666666
Q ss_pred HHHHHHhc---------CCeEEEEchhhHHHHhc-----cc---CC--CCceeehhhhchhhhCCCCCccHHHHHHHHhC
Q 023843 150 KKVAELIE---------GRILVGHALHNDLKALL-----LT---HS--KKDLRDTSEYQPFLNRNGRSKALRHLAAEILA 210 (276)
Q Consensus 150 ~~l~~~l~---------~~~lVgHn~~~D~~~L~-----~~---~~--~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lg 210 (276)
.+|.+++. +.++||||+.||+.||. .. .+ ...++||..+++.+.+ .++|.++| +++|
T Consensus 85 ~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~l~-~~~g 160 (189)
T cd06134 85 KEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAKAC-QAAG 160 (189)
T ss_pred HHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHHHH-HHCC
Confidence 66555542 67999999999999997 11 11 2347999999887764 45899998 7899
Q ss_pred CcCC-CCCCChHHHHHHHHHHHHHhHHHH
Q 023843 211 VEIQ-NGEHCPIDDARAAMLLYMKNRKQW 238 (276)
Q Consensus 211 i~~~-~~~H~Al~DA~at~~L~~~l~~~~ 238 (276)
+++. ..+|+|++||++|++||.++..+|
T Consensus 161 i~~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 161 IEFDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred CCCCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 9874 368999999999999999998887
No 30
>PRK05168 ribonuclease T; Provisional
Probab=99.93 E-value=4.6e-25 Score=191.41 Aligned_cols=164 Identities=22% Similarity=0.307 Sum_probs=132.3
Q ss_pred CCCCCCCCCcEEEEEEeccCCCC--CCeeEEEEEEEEe-CCCcE----EEEEeecCC--cccccccccccCCCHHH-hcC
Q 023843 72 PINDDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVN-KWGNL----IYDEFVRPL--ERVVDFRTRISGIRPRD-LRK 141 (276)
Q Consensus 72 ~~~~~~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~-~~g~i----i~~~~v~P~--~~i~~~~~~i~GIt~~~-l~~ 141 (276)
|....+.-..+|+||+||||+++ ++|+|||+|.+.. .+|.+ .|..||+|. .+|++.++.+||||+++ +.+
T Consensus 9 ~~~~~~~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~ 88 (211)
T PRK05168 9 PLKDRFRGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRG 88 (211)
T ss_pred hHHHHhcCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhc
Confidence 33334455678999999999984 4899999999973 23543 389999994 58999999999999986 788
Q ss_pred CCCHHHHHHHHHHHhc---------CCeEEEEchhhHHHHhccc----------CCCCceeehhhhchhhhCCCCCccHH
Q 023843 142 AKDFPTVQKKVAELIE---------GRILVGHALHNDLKALLLT----------HSKKDLRDTSEYQPFLNRNGRSKALR 202 (276)
Q Consensus 142 a~~~~ev~~~l~~~l~---------~~~lVgHn~~~D~~~L~~~----------~~~~~~~Dt~~~~~~~~~~~~~~sL~ 202 (276)
++++.+++.++.+|+. +.++||||+.||+.||... .+.+.++||..+++.+.+ .++|.
T Consensus 89 ~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~---~~~L~ 165 (211)
T PRK05168 89 AVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG---QTVLA 165 (211)
T ss_pred CCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC---CCCHH
Confidence 8999999888888774 6899999999999999711 122347999999887653 35899
Q ss_pred HHHHHHhCCcCCC-CCCChHHHHHHHHHHHHHhHHHHH
Q 023843 203 HLAAEILAVEIQN-GEHCPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 203 ~La~~~lgi~~~~-~~H~Al~DA~at~~L~~~l~~~~e 239 (276)
.+| +++|+++.. .+|+|++||.+|++||.++..++.
T Consensus 166 ~l~-~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 166 KAC-QAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred HHH-HHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 988 789998752 589999999999999999987763
No 31
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.93 E-value=3.1e-26 Score=229.35 Aligned_cols=177 Identities=27% Similarity=0.351 Sum_probs=153.7
Q ss_pred CCCCCCCCCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHH
Q 023843 71 TPINDDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (276)
Q Consensus 71 ~~~~~~~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ 146 (276)
.|...+..-..||+||+||||+++ +.|+|+|++.+.+ |+++ |+.|++|..+++...+++||||.++|.++++..
T Consensus 412 N~~d~~l~datyVVfDiETTGLs~~~d~iIE~aAvKikn--g~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~ 489 (1444)
T COG2176 412 NPDDQKLDDATYVVFDIETTGLSPVYDEIIEIAAVKIKN--GRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIE 489 (1444)
T ss_pred CccccccccccEEEEEeecCCcCcccchhhhheeeeeeC--CcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHH
Confidence 344445566779999999999994 5899999999988 8888 899999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCC
Q 023843 147 TVQKKVAELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHC 219 (276)
Q Consensus 147 ev~~~l~~~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~ 219 (276)
+|+.+|.+|++++++|+||+.||+.||+ +......++||..+++.++|...+|+|..|| +.||+.+. .+|+
T Consensus 490 ~vL~kf~~~~~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~-kk~~v~le-~hHR 567 (1444)
T COG2176 490 EVLEKFREFIGDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLC-KKLGVELE-RHHR 567 (1444)
T ss_pred HHHHHHHHHhcCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHH-HHhCccHH-Hhhh
Confidence 9999999999999999999999999997 2222335899999999999999999999999 78999996 8999
Q ss_pred hHHHHHHHHHHHHHhHHHHH-HHHHHHHHHHHH
Q 023843 220 PIDDARAAMLLYMKNRKQWE-KSVKDQTRLEQK 251 (276)
Q Consensus 220 Al~DA~at~~L~~~l~~~~e-~~~~~~~~~~~k 251 (276)
|..||.+|+.||..+.+.+. .-+...-...++
T Consensus 568 A~yDaeat~~vf~~f~~~~ke~Gi~~l~eln~~ 600 (1444)
T COG2176 568 ADYDAEATAKVFFVFLKDLKEKGITNLSELNDK 600 (1444)
T ss_pred hhhhHHHHHHHHHHHHHHHHHhchhhHHHHhHh
Confidence 99999999999999977655 344444444443
No 32
>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=99.93 E-value=4.8e-25 Score=189.78 Aligned_cols=160 Identities=19% Similarity=0.225 Sum_probs=130.6
Q ss_pred CCCCCcEEEEEEeccCCCC--CCeeEEEEEEEEe-CCCcEE----EEEeecCC--cccccccccccCCCHH-HhcCCCCH
Q 023843 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVN-KWGNLI----YDEFVRPL--ERVVDFRTRISGIRPR-DLRKAKDF 145 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~-~~g~ii----~~~~v~P~--~~i~~~~~~i~GIt~~-~l~~a~~~ 145 (276)
++....+|+||+||||+++ ++|+|||+|.|.. ..|.+. |..+|+|. .+|+..+..+||||++ ++.+++++
T Consensus 4 ~~~~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~ 83 (200)
T TIGR01298 4 RFRGYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSE 83 (200)
T ss_pred hhcCCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcch
Confidence 3455679999999999995 4899999999974 245542 88999984 5899999999999976 58889998
Q ss_pred HHHHHHHHHHh---------cCCeEEEEchhhHHHHhcc-----cC-----CCCceeehhhhchhhhCCCCCccHHHHHH
Q 023843 146 PTVQKKVAELI---------EGRILVGHALHNDLKALLL-----TH-----SKKDLRDTSEYQPFLNRNGRSKALRHLAA 206 (276)
Q Consensus 146 ~ev~~~l~~~l---------~~~~lVgHn~~~D~~~L~~-----~~-----~~~~~~Dt~~~~~~~~~~~~~~sL~~La~ 206 (276)
.+++.++..++ ++.++||||+.||+.||.. .. +...++||..+++.+++ .++|..||
T Consensus 84 ~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~---~~~L~~l~- 159 (200)
T TIGR01298 84 YEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG---QTVLAKAC- 159 (200)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC---cccHHHHH-
Confidence 88888887776 5789999999999999971 11 12347999999887653 45899999
Q ss_pred HHhCCcCC-CCCCChHHHHHHHHHHHHHhHHHHH
Q 023843 207 EILAVEIQ-NGEHCPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 207 ~~lgi~~~-~~~H~Al~DA~at~~L~~~l~~~~e 239 (276)
+++|++.. ..+|+|++||.+|++||..+..++.
T Consensus 160 ~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 160 QAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred HHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 78999864 3689999999999999999988764
No 33
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=4.2e-25 Score=227.50 Aligned_cols=157 Identities=28% Similarity=0.382 Sum_probs=140.2
Q ss_pred CCcEEEEEEeccCCCC---CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 79 LTDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~---~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
.++||+||+||||+++ ++|++||+|.+.+ |+++ |..||+|..+|+++++.+||||++++.++++|.+++..|.
T Consensus 2 ~~~~vvvD~ETTG~~p~~~d~IIeigav~v~~--~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~ 79 (928)
T PRK08074 2 SKRFVVVDLETTGNSPKKGDKIIQIAAVVVED--GEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIV 79 (928)
T ss_pred CCCEEEEEEeCCCCCCCCCCcEEEEEEEEEEC--CEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHH
Confidence 4679999999999873 4799999999965 6775 9999999999999999999999999999999999999999
Q ss_pred HHhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHH
Q 023843 154 ELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARA 226 (276)
Q Consensus 154 ~~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~a 226 (276)
.|+++.++||||+.||+.||. +..+...++||..+++.+.+...+++|.+|+ ++||++.. .+|+|++||++
T Consensus 80 ~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~-~~l~i~~~-~~H~Al~DA~a 157 (928)
T PRK08074 80 ELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLS-EELGLEHD-QPHRADSDAEV 157 (928)
T ss_pred HHhCCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHH-HhCCCCCC-CCCChHHHHHH
Confidence 999999999999999999997 2223345899999999888888899999999 88999886 88999999999
Q ss_pred HHHHHHHhHHHHH
Q 023843 227 AMLLYMKNRKQWE 239 (276)
Q Consensus 227 t~~L~~~l~~~~e 239 (276)
|+.||.++..++.
T Consensus 158 ta~l~~~l~~~~~ 170 (928)
T PRK08074 158 TAELFLQLLNKLE 170 (928)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999966554
No 34
>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=99.93 E-value=7.5e-25 Score=183.64 Aligned_cols=152 Identities=22% Similarity=0.284 Sum_probs=130.1
Q ss_pred EEEEEEeccCCCC-------CCeeEEEEEEEEeCCCcE--EEEEeecCCc--ccccccccccCCCHHHhcCCCCHHHHHH
Q 023843 82 VVAMDCEMVGISQ-------GNKSALGRVSLVNKWGNL--IYDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (276)
Q Consensus 82 ~VaiD~EttG~~~-------~~iiei~~v~v~~~~g~i--i~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~ev~~ 150 (276)
||+||+||||+++ ++|+|||+|.+....+.+ .|+.||+|.. .++++++.+||||++++.++++|.+|+.
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 6999999999985 589999988887543324 3999999998 9999999999999999999999999999
Q ss_pred HHHHHhcCC--eEEEEchhhHHHHhc-------c---cCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCC
Q 023843 151 KVAELIEGR--ILVGHALHNDLKALL-------L---THSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEH 218 (276)
Q Consensus 151 ~l~~~l~~~--~lVgHn~~~D~~~L~-------~---~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H 218 (276)
+|.+|+++. .+++|+..||..+|. . ......++|+..++....+....++|.+|+ ++||++..+..|
T Consensus 81 ~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~-~~~gi~~~~~~H 159 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKAL-EYLGLEFEGRHH 159 (176)
T ss_pred HHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHH-HHCCCCCCCCCc
Confidence 999999986 666667799988765 1 223346899999988887666799999998 899999987799
Q ss_pred ChHHHHHHHHHHHHHh
Q 023843 219 CPIDDARAAMLLYMKN 234 (276)
Q Consensus 219 ~Al~DA~at~~L~~~l 234 (276)
+|++||++|+.||.++
T Consensus 160 ~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 160 RGLDDARNIARILKRL 175 (176)
T ss_pred CcHHHHHHHHHHHHHh
Confidence 9999999999999876
No 35
>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=99.93 E-value=5.3e-25 Score=186.06 Aligned_cols=146 Identities=16% Similarity=0.159 Sum_probs=118.5
Q ss_pred EEEEEEeccCCC-C--CCeeEEEEEEEEeCC---C--------cEE--EEEeecCCcccccccccccCCCHHHhcCCCCH
Q 023843 82 VVAMDCEMVGIS-Q--GNKSALGRVSLVNKW---G--------NLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDF 145 (276)
Q Consensus 82 ~VaiD~EttG~~-~--~~iiei~~v~v~~~~---g--------~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~ 145 (276)
||+||+||||++ + ++|+|||+|.|.... + +++ |+.+|+|..+|++.++.+||||++++.++++|
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~~ 80 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCCc
Confidence 689999999998 3 489999999987531 1 122 78999999999999999999999999999887
Q ss_pred HH-HHHHHHHHhc----CCeEEEEch-hhHHHHhc-------ccCC-CCceeehhhhchhhhCCCCCccHHHHHHHHhCC
Q 023843 146 PT-VQKKVAELIE----GRILVGHAL-HNDLKALL-------LTHS-KKDLRDTSEYQPFLNRNGRSKALRHLAAEILAV 211 (276)
Q Consensus 146 ~e-v~~~l~~~l~----~~~lVgHn~-~~D~~~L~-------~~~~-~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi 211 (276)
.+ +...|.+|++ +.+|||||+ .||+.||. +..+ ...++||+.+++.+.+ +|.+|+..+||+
T Consensus 81 ~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~-----~L~~l~~~~~~~ 155 (177)
T cd06136 81 DSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ-----SLGSLYKRLFGQ 155 (177)
T ss_pred cHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh-----hHHHHHHHHhCC
Confidence 64 6666766764 458999998 89999996 2211 2345899888777653 999999667999
Q ss_pred cCCCCCCChHHHHHHHHHHHHH
Q 023843 212 EIQNGEHCPIDDARAAMLLYMK 233 (276)
Q Consensus 212 ~~~~~~H~Al~DA~at~~L~~~ 233 (276)
+.. .+|+|+.||.+|+++|.+
T Consensus 156 ~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 156 EPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred Ccc-cccchHHHHHHHHHHHhh
Confidence 987 789999999999999875
No 36
>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=99.92 E-value=1.3e-24 Score=225.97 Aligned_cols=159 Identities=27% Similarity=0.373 Sum_probs=143.1
Q ss_pred CCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
...+||+||+||||+++ ++|+|||+|.+.+ |.++ |+.||+|..+|++.++.+||||+++|.+++++.+++.+|.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~--g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~ 265 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKN--GRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFK 265 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEEC--CeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHH
Confidence 56689999999999984 5899999999986 6665 9999999999999999999999999999999999999999
Q ss_pred HHhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHH
Q 023843 154 ELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARA 226 (276)
Q Consensus 154 ~~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~a 226 (276)
+|+++.++||||+.||+.||. +......++||..+++.+.+...+++|..|| ++||++.. .+|+|++||.+
T Consensus 266 ~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~La-k~lgi~~~-~~HrAl~DA~a 343 (1213)
T TIGR01405 266 EFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNIC-KKLGVDLD-DHHRADYDAEA 343 (1213)
T ss_pred HHhCCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHH-HHcCCCCC-CCcCHHHHHHH
Confidence 999999999999999999997 2112345899999999988888899999999 77999998 69999999999
Q ss_pred HHHHHHHhHHHHHH
Q 023843 227 AMLLYMKNRKQWEK 240 (276)
Q Consensus 227 t~~L~~~l~~~~e~ 240 (276)
|++||..+..++++
T Consensus 344 Ta~I~~~ll~~l~~ 357 (1213)
T TIGR01405 344 TAKVFKVMVEQLKE 357 (1213)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999887763
No 37
>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=99.92 E-value=2.1e-24 Score=220.96 Aligned_cols=155 Identities=26% Similarity=0.339 Sum_probs=138.0
Q ss_pred cEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHh
Q 023843 81 DVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (276)
Q Consensus 81 ~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l 156 (276)
+||+||+||||+++ ++|++||+|.+.+ |+++ |..+|+|..+|+++++.+||||++++.++++|.+++..|.+|+
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~--~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVED--GEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLL 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHh
Confidence 48999999999984 5999999999865 6665 9999999999999999999999999999999999999999999
Q ss_pred cCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHH
Q 023843 157 EGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAML 229 (276)
Q Consensus 157 ~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~ 229 (276)
++.++||||+.||+.||. +......++||..+++.+.+...+++|.+|+ ++||++.. ++|+|++||.+|++
T Consensus 79 ~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~-~~~gi~~~-~~H~Al~DA~ata~ 156 (850)
T TIGR01407 79 EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELS-EALGLTHE-NPHRADSDAQATAE 156 (850)
T ss_pred CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHH-HHCCCCCC-CCCChHHHHHHHHH
Confidence 999999999999999997 1212335799999999888877899999999 88999987 79999999999999
Q ss_pred HHHHhHHHHH
Q 023843 230 LYMKNRKQWE 239 (276)
Q Consensus 230 L~~~l~~~~e 239 (276)
||.++..++.
T Consensus 157 l~~~l~~~~~ 166 (850)
T TIGR01407 157 LLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHH
Confidence 9999866543
No 38
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=3.2e-24 Score=196.74 Aligned_cols=155 Identities=17% Similarity=0.236 Sum_probs=129.9
Q ss_pred CCCCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHH
Q 023843 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~ 151 (276)
......||+||+||||+++ ++|++||+|.+.. +|.+. |..||+|...+.. ..|||||+++|.++++|.+++.+
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~-~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTA-DGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEc-CCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHHH
Confidence 4445679999999999995 4899999999973 25554 9999999875443 47999999999999999999999
Q ss_pred HHHHhcCCeEEEEchhhHHHHhccc----------------------------------CCCCceeehhhhchhhhCCCC
Q 023843 152 VAELIEGRILVGHALHNDLKALLLT----------------------------------HSKKDLRDTSEYQPFLNRNGR 197 (276)
Q Consensus 152 l~~~l~~~~lVgHn~~~D~~~L~~~----------------------------------~~~~~~~Dt~~~~~~~~~~~~ 197 (276)
|.+||++.+|||||+.||+.||... .....++||+.+++.+.+...
T Consensus 119 l~~fL~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~ 198 (377)
T PRK05601 119 LDRLIDGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALD 198 (377)
T ss_pred HHHHhCCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCC
Confidence 9999999999999999999998621 011258999999999998888
Q ss_pred CccHHHHHHHHhCCcCCC---------CCCChH--HHHHHHHHHHHHh
Q 023843 198 SKALRHLAAEILAVEIQN---------GEHCPI--DDARAAMLLYMKN 234 (276)
Q Consensus 198 ~~sL~~La~~~lgi~~~~---------~~H~Al--~DA~at~~L~~~l 234 (276)
+++|..|| ++||++... ..|+++ +||+.++.||..+
T Consensus 199 ~~rL~~La-~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 199 DIRIRGVA-HTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred CCCHHHHH-HHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 99999999 789998821 347777 6999999999876
No 39
>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=99.92 E-value=6.4e-24 Score=173.15 Aligned_cols=148 Identities=27% Similarity=0.331 Sum_probs=128.9
Q ss_pred EEEEEeccCCC--CCCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcC
Q 023843 83 VAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (276)
Q Consensus 83 VaiD~EttG~~--~~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~ 158 (276)
|+|||||||++ .++|+|||+|.+... ++++ |+.||+|...+.++++.+|||+++++.+++++.+++.+|.+|+.+
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~-~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l~~ 79 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGG-IEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECC-cChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHHCC
Confidence 68999999999 468999998888653 3443 999999999999999999999999999999999999999999999
Q ss_pred CeEEEEchhhHHHHhccc-------CCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHH
Q 023843 159 RILVGHALHNDLKALLLT-------HSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLY 231 (276)
Q Consensus 159 ~~lVgHn~~~D~~~L~~~-------~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~ 231 (276)
.++||||+.||+.+|... .....++||+.+++.+.+....++|..+..+++|++.. .+|+|++||++|++||
T Consensus 80 ~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE-GAHRALADALATAELL 158 (159)
T ss_pred CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC-CCCCcHHHHHHHHHHh
Confidence 999999999999999721 33456899999988888777889999983478888775 8999999999999998
Q ss_pred H
Q 023843 232 M 232 (276)
Q Consensus 232 ~ 232 (276)
.
T Consensus 159 ~ 159 (159)
T cd06127 159 L 159 (159)
T ss_pred C
Confidence 3
No 40
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.91 E-value=1.7e-23 Score=193.81 Aligned_cols=156 Identities=40% Similarity=0.542 Sum_probs=139.7
Q ss_pred CCCCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCC-CCHHHHHHHHHHH
Q 023843 77 FSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKA-KDFPTVQKKVAEL 155 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a-~~~~ev~~~l~~~ 155 (276)
....+++|+||||+....| .++++|.++|.+++++||.+|+|..+|.||.+.++|||++++.++ .++++++..|..|
T Consensus 213 ~~~~~i~AlDCEm~~te~g--~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~ 290 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVTENG--LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLEL 290 (380)
T ss_pred CCCCCeEEEEeeeeeeccc--eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHhh
Confidence 3457899999999998777 699999999999999999999999999999999999999999755 6999999999999
Q ss_pred hc-CCeEEEEchhhHHHHhcccCCCCceeehhhhchhhhCC-CCCccHHHHHHHHhCCcCC--CCCCChHHHHHHHHHHH
Q 023843 156 IE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRN-GRSKALRHLAAEILAVEIQ--NGEHCPIDDARAAMLLY 231 (276)
Q Consensus 156 l~-~~~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~~~-~~~~sL~~La~~~lgi~~~--~~~H~Al~DA~at~~L~ 231 (276)
+. ++|||||++..|+.+|++.|+. ++||+.++..-.+. ....+|++||..+||..++ ...|++.+||.+|+.|+
T Consensus 291 ~~~~TILVGHSLenDL~aLKl~H~~--ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv 368 (380)
T KOG2248|consen 291 ISKNTILVGHSLENDLKALKLDHPS--VIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHDSVEDALACMKLV 368 (380)
T ss_pred cCcCcEEEeechhhHHHHHhhhCCc--eeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHH
Confidence 97 9999999999999999999998 89999876655542 4567899999999999998 45799999999999999
Q ss_pred HHhHH
Q 023843 232 MKNRK 236 (276)
Q Consensus 232 ~~l~~ 236 (276)
.....
T Consensus 369 ~~k~~ 373 (380)
T KOG2248|consen 369 KLKIK 373 (380)
T ss_pred HHHHh
Confidence 87644
No 41
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=3.3e-23 Score=187.65 Aligned_cols=172 Identities=17% Similarity=0.164 Sum_probs=127.5
Q ss_pred CCCCCCcEEEEEEeccCCCC--CCeeEEEEEEEEe-CCCcE-----EEEEeecCCcccccccccccCCCHHHhcCCCCHH
Q 023843 75 DDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVN-KWGNL-----IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (276)
Q Consensus 75 ~~~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~-~~g~i-----i~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ 146 (276)
....+..+|+||+||||+++ ++|+|||+|.+.. ..|.+ .|+.|++|..+|+..++.+||||++++.+++...
T Consensus 32 ~~~~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 32 RGEFVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CCCCCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH
Confidence 34456789999999999995 5899999999973 24543 2888999999999999999999999999887654
Q ss_pred HHHHHHHHHhc-CCeEEEEchhhHHHHhccc---CCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHH
Q 023843 147 TVQKKVAELIE-GRILVGHALHNDLKALLLT---HSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPID 222 (276)
Q Consensus 147 ev~~~l~~~l~-~~~lVgHn~~~D~~~L~~~---~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~ 222 (276)
+ .|..|++ +.++||||+.||+.||... +....+.|++........+..+++|.+|| .++| ... .+|+|+.
T Consensus 112 ~---~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La-~~~g-~~~-~aHrAl~ 185 (294)
T PRK09182 112 A---AVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLA-GQAG-FFH-EGHRAVD 185 (294)
T ss_pred H---HHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHH-HHcC-CCC-CCcChHH
Confidence 3 4666776 4699999999999999722 22223456664332223345789999999 7888 333 6899999
Q ss_pred HHHHHHHHHHHhHHHHH-HHHHHHHHHHHHH
Q 023843 223 DARAAMLLYMKNRKQWE-KSVKDQTRLEQKQ 252 (276)
Q Consensus 223 DA~at~~L~~~l~~~~e-~~~~~~~~~~~k~ 252 (276)
||.+|+.||..+..... ..+.+.+....+.
T Consensus 186 Da~Ata~ll~~~l~~~~~~~l~~Ll~~~~~~ 216 (294)
T PRK09182 186 DCQALLELLARPLPETGQPPLAELLEASRRS 216 (294)
T ss_pred HHHHHHHHHHHHHhhcCCcCHHHHHHHhccC
Confidence 99999999997754322 3445555554433
No 42
>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=99.90 E-value=1.8e-25 Score=182.70 Aligned_cols=148 Identities=27% Similarity=0.405 Sum_probs=126.1
Q ss_pred EEEEEeccCCCC--CCeeEEEEEEEEeCCC--cEEEEEeecCCcc--cccccccccCCCHHHhcCCCCHHHHHHHHHHHh
Q 023843 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWG--NLIYDEFVRPLER--VVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (276)
Q Consensus 83 VaiD~EttG~~~--~~iiei~~v~v~~~~g--~ii~~~~v~P~~~--i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l 156 (276)
|+|||||||+++ ++++|||+|.+.+... ...|+.||+|... ++++++.+||||++++.+++++.+++..|.+|+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~~ 80 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEEFL 80 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhhhh
Confidence 799999999996 5999999999987653 3359999999997 999999999999999999999999999999999
Q ss_pred c-CCeEEEEchhhHHHHhc--------ccCC-CCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHH
Q 023843 157 E-GRILVGHALHNDLKALL--------LTHS-KKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARA 226 (276)
Q Consensus 157 ~-~~~lVgHn~~~D~~~L~--------~~~~-~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~a 226 (276)
. +.++||||+.||..++. ..++ ...++|+..+.+...+....++|+.|+ ++||++..+.+|+|++||++
T Consensus 81 ~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~~~~H~Al~Da~~ 159 (164)
T PF00929_consen 81 KKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLA-EYFGIPFDGTAHDALDDARA 159 (164)
T ss_dssp HHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHH-HHTTSSSTSTTTSHHHHHHH
T ss_pred hcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHH-HHcCCCCCCCCcChHHHHHH
Confidence 8 89999999999987664 2222 224678888777666555558999999 88999998568999999999
Q ss_pred HHHHH
Q 023843 227 AMLLY 231 (276)
Q Consensus 227 t~~L~ 231 (276)
|++||
T Consensus 160 t~~l~ 164 (164)
T PF00929_consen 160 TAELF 164 (164)
T ss_dssp HHHHH
T ss_pred HhCcC
Confidence 99997
No 43
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.90 E-value=1.8e-22 Score=194.67 Aligned_cols=157 Identities=17% Similarity=0.218 Sum_probs=128.7
Q ss_pred CCcEEEEEEeccCCCC-----CCeeEEEEEEEEeCCCcEE--EEEeecCCc--ccccccccccCCCHHHhcCCCCHHHHH
Q 023843 79 LTDVVAMDCEMVGISQ-----GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~-----~~iiei~~v~v~~~~g~ii--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~ev~ 149 (276)
...||+||+||||+++ ++|||||+|.|...+|+++ |..||+|.. +++++++.+||||+++|.++++|.+|+
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 5789999999999873 5899999999864457775 999999987 799999999999999999999999999
Q ss_pred HHHHHHhcCC----------eEEEEchhhHHH-Hhc--------ccCC--CCceeehh-hhchhhhC-----------CC
Q 023843 150 KKVAELIEGR----------ILVGHALHNDLK-ALL--------LTHS--KKDLRDTS-EYQPFLNR-----------NG 196 (276)
Q Consensus 150 ~~l~~~l~~~----------~lVgHn~~~D~~-~L~--------~~~~--~~~~~Dt~-~~~~~~~~-----------~~ 196 (276)
.+|..||++. ++|+||+.||+. ||. ...+ ...++|+. .++..+++ ..
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~~ 214 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPPL 214 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccccccccc
Confidence 9999999643 689999999995 663 1222 22355653 44444443 34
Q ss_pred CCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhHH
Q 023843 197 RSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRK 236 (276)
Q Consensus 197 ~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~~ 236 (276)
..++|.+++ +++|+++.+.+|+|++||++|++||.++..
T Consensus 215 ~~~~L~~al-~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~ 253 (582)
T PTZ00315 215 GPSDMPDML-QMLGLPLQGRHHSGIDDCRNIAAVLCELLR 253 (582)
T ss_pred CCcCHHHHH-HHCCCCCCCCCcCcHHHHHHHHHHHHHHHH
Confidence 668999988 889999998899999999999999999853
No 44
>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=99.90 E-value=3e-23 Score=176.21 Aligned_cols=146 Identities=20% Similarity=0.182 Sum_probs=116.0
Q ss_pred EEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCc--ccccccccccCCCHHHhcC-CCCHHHHHHHHHHH
Q 023843 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRK-AKDFPTVQKKVAEL 155 (276)
Q Consensus 83 VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~-a~~~~ev~~~l~~~ 155 (276)
++||+||||+++ ++|+|||+|.+.+ .+.++ |+.+|+|.. .++..+..+||||++++.+ ++++.+++.+|..|
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~-~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~ 79 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDE-NFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRL 79 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECC-CCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHH
Confidence 589999999984 4899999887754 33444 889999875 5667789999999999998 89999999999999
Q ss_pred hc--CCeEEEEc-hhhHHHHhcccC-------C------CCceeehhhhchhhh---C----------CCCCccHHHHHH
Q 023843 156 IE--GRILVGHA-LHNDLKALLLTH-------S------KKDLRDTSEYQPFLN---R----------NGRSKALRHLAA 206 (276)
Q Consensus 156 l~--~~~lVgHn-~~~D~~~L~~~~-------~------~~~~~Dt~~~~~~~~---~----------~~~~~sL~~La~ 206 (276)
++ +.++|||| +.||+.||.... . ....+|+..+++... + +..+++|.+||
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~- 158 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLA- 158 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHH-
Confidence 95 67899997 799999997111 0 112357776555432 2 23578999999
Q ss_pred HHhCCcCCCCCCChHHHHHHHHHHH
Q 023843 207 EILAVEIQNGEHCPIDDARAAMLLY 231 (276)
Q Consensus 207 ~~lgi~~~~~~H~Al~DA~at~~L~ 231 (276)
++||++.. .+|+|++||++|++|.
T Consensus 159 ~~~gi~~~-~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 159 QANGIEHS-NAHDALSDVEATIALA 182 (183)
T ss_pred HHCCCCcc-ccccHHHHHHHHHHHh
Confidence 78999986 7899999999999885
No 45
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.89 E-value=1.8e-22 Score=178.41 Aligned_cols=155 Identities=25% Similarity=0.305 Sum_probs=136.9
Q ss_pred CcEEEEEEeccCCC--CCCeeEEEEEEEEeCCCcEE---EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHH
Q 023843 80 TDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (276)
Q Consensus 80 ~~~VaiD~EttG~~--~~~iiei~~v~v~~~~g~ii---~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~ 154 (276)
.++|+||+||||.+ .+++++||+|.+.+ +.++ |..|++|..+|++....+||||.+++.++|.|.++...+.+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~--~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~ 90 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLED--GRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLD 90 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEEC--CeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHH
Confidence 68999999999998 45999999999988 5444 88999998899999999999999999999999999999999
Q ss_pred HhcC-CeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCC-CCCCChHHHHH
Q 023843 155 LIEG-RILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ-NGEHCPIDDAR 225 (276)
Q Consensus 155 ~l~~-~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~-~~~H~Al~DA~ 225 (276)
|+.+ .++|+||+.||+.||. ...+...++||..+.+...++...++|+.|| +++|++.. ...|+|+.||.
T Consensus 91 ~i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~-~~~gi~~~~~~~H~Al~Da~ 169 (243)
T COG0847 91 FIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALA-ERLGIDRNPFHPHRALFDAL 169 (243)
T ss_pred HHCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHH-HHcCCCcCCcCCcchHHHHH
Confidence 9998 9999999999999996 2222334779999999998777899999999 69999943 25699999999
Q ss_pred HHHHHHHHhHHH
Q 023843 226 AAMLLYMKNRKQ 237 (276)
Q Consensus 226 at~~L~~~l~~~ 237 (276)
+++.+|..+...
T Consensus 170 ~~a~~~~~~~~~ 181 (243)
T COG0847 170 ALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHhc
Confidence 999999998874
No 46
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.88 E-value=9.2e-22 Score=188.13 Aligned_cols=171 Identities=17% Similarity=0.164 Sum_probs=131.6
Q ss_pred CCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE---EEEeecCCcc--cccccccccCCCHHHhcC-CCCHHHHH
Q 023843 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI---YDEFVRPLER--VVDFRTRISGIRPRDLRK-AKDFPTVQ 149 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii---~~~~v~P~~~--i~~~~~~i~GIt~~~l~~-a~~~~ev~ 149 (276)
+...||++|+||||+++ ++|+|+|+|.+.+. +.++ +..||+|... +.+.++.+||||++++.+ +.+..+++
T Consensus 4 ~~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~-~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~ 82 (476)
T PRK11779 4 MQPTFLWHDYETFGANPALDRPAQFAGIRTDAD-LNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFA 82 (476)
T ss_pred CCCcEEEEEEECCCCCCCCCeeEEEEEEEEeCC-CceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHH
Confidence 34679999999999995 58999999988652 3332 8899999863 356689999999999854 56899999
Q ss_pred HHHHHHhc--CCeEEEEc-hhhHHHHhcccC----------------CCCceeehhhhchhhhC----------CCCCcc
Q 023843 150 KKVAELIE--GRILVGHA-LHNDLKALLLTH----------------SKKDLRDTSEYQPFLNR----------NGRSKA 200 (276)
Q Consensus 150 ~~l~~~l~--~~~lVgHn-~~~D~~~L~~~~----------------~~~~~~Dt~~~~~~~~~----------~~~~~s 200 (276)
..|.+|+. +.++|||| +.||..||+... .+++++|++.+.+.+.+ +..+++
T Consensus 83 ~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~r 162 (476)
T PRK11779 83 ARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFK 162 (476)
T ss_pred HHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCc
Confidence 99999995 78999997 699999886211 12345566665444322 246799
Q ss_pred HHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 023843 201 LRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQTRLEQK 251 (276)
Q Consensus 201 L~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~~~~e~~~~~~~~~~~k 251 (276)
|.+|+ +++|++.. .+|+|++||++|+.|++.+..+..+.....+..+.|
T Consensus 163 Le~L~-~~~gI~~~-~AHdALsDa~aT~~la~~l~~~qP~l~~~~~~~~~k 211 (476)
T PRK11779 163 LEHLT-KANGIEHE-NAHDAMSDVYATIAMAKLIKQKQPKLFDYLFQLRNK 211 (476)
T ss_pred HHHHH-HHcCCCCC-CCCCcHHHHHHHHHHHHHHHHhChHHHHHHHHhcch
Confidence 99999 78999986 899999999999999999987755554545554443
No 47
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.87 E-value=2.1e-21 Score=204.43 Aligned_cols=160 Identities=29% Similarity=0.395 Sum_probs=142.0
Q ss_pred CCCCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHH
Q 023843 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~ 151 (276)
.+...++|++|+||||+++ ++|+++|++.+.+ |.++ |+.||+|..+++++++.+||||++++.+++++.+++..
T Consensus 415 ~L~~~~~VVfDLETTGL~~~~deIIEIgAV~V~~--G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~ 492 (1437)
T PRK00448 415 DLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKN--GEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPK 492 (1437)
T ss_pred hhccCcEEEEEhhhcCCCCchhhhheeeeEEEeC--CeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHH
Confidence 3445679999999999984 4889999998875 6665 99999999999999999999999999999999999999
Q ss_pred HHHHhcCCeEEEEchhhHHHHhc-------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHH
Q 023843 152 VAELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDA 224 (276)
Q Consensus 152 l~~~l~~~~lVgHn~~~D~~~L~-------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA 224 (276)
|.+|+++.++||||+.||+.+|. +.......+||+.+++.+.+...+++|..|| +.||+... .+|+|++||
T Consensus 493 f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LA-k~lGL~~~-~~HrAl~DA 570 (1437)
T PRK00448 493 FKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLA-KKFGVELE-HHHRADYDA 570 (1437)
T ss_pred HHHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHH-HHcCCCCC-CCcChHHHH
Confidence 99999999999999999999885 3233445899999998888778899999999 78999998 689999999
Q ss_pred HHHHHHHHHhHHHHH
Q 023843 225 RAAMLLYMKNRKQWE 239 (276)
Q Consensus 225 ~at~~L~~~l~~~~e 239 (276)
.+|++||.++..+++
T Consensus 571 ~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 571 EATAYLLIKFLKDLK 585 (1437)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999987765
No 48
>PRK05359 oligoribonuclease; Provisional
Probab=99.86 E-value=7.4e-21 Score=161.26 Aligned_cols=147 Identities=16% Similarity=0.164 Sum_probs=113.4
Q ss_pred CCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE---EEEeecCCcc----ccccccccc---CCCHHHhcCCCCHH
Q 023843 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI---YDEFVRPLER----VVDFRTRIS---GIRPRDLRKAKDFP 146 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii---~~~~v~P~~~----i~~~~~~i~---GIt~~~l~~a~~~~ 146 (276)
..+||+|||||||+++ ++|+|||+|.+.+ .+.++ |..+|+|... ++.+++.+| |||++++.+++++.
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieIgaV~~~~-~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~ 80 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEIATIVTDA-DLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEA 80 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEEEEEEEcC-CceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHH
Confidence 4679999999999995 5899999997643 23333 8888999864 456677777 89999999999999
Q ss_pred HHHHHHHHHhc------CCeEEEEchhhHHHHhcccC------CCCceeehh---hhchhhhCCCCCccHHHHHHHHhCC
Q 023843 147 TVQKKVAELIE------GRILVGHALHNDLKALLLTH------SKKDLRDTS---EYQPFLNRNGRSKALRHLAAEILAV 211 (276)
Q Consensus 147 ev~~~l~~~l~------~~~lVgHn~~~D~~~L~~~~------~~~~~~Dt~---~~~~~~~~~~~~~sL~~La~~~lgi 211 (276)
+++.+|.+|++ +.++||||+.||+.||.-.. ..++++|+. .+++.++|.. ++++
T Consensus 81 e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P~~-----------~~~~ 149 (181)
T PRK05359 81 EAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKPEI-----------LNGF 149 (181)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhChhh-----------hhCC
Confidence 99999999995 57899999999999997221 223466743 3444444321 2456
Q ss_pred cCCCCCCChHHHHHHHHHHHHHhHHHH
Q 023843 212 EIQNGEHCPIDDARAAMLLYMKNRKQW 238 (276)
Q Consensus 212 ~~~~~~H~Al~DA~at~~L~~~l~~~~ 238 (276)
+.. ..|+|++||+++..+|+.++..+
T Consensus 150 ~~~-~~HRal~D~~~s~~~~~~~~~~~ 175 (181)
T PRK05359 150 KKQ-GTHRALADIRESIAELKYYREHF 175 (181)
T ss_pred CCc-CCcccHHHHHHHHHHHHHHHHHh
Confidence 655 67999999999999999997754
No 49
>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=99.85 E-value=3.8e-21 Score=161.93 Aligned_cols=145 Identities=18% Similarity=0.220 Sum_probs=109.1
Q ss_pred EEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE--EEEeecCCcccc----cccccc---cCCCHHHhcCCCCHHHHHH
Q 023843 82 VVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVV----DFRTRI---SGIRPRDLRKAKDFPTVQK 150 (276)
Q Consensus 82 ~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii--~~~~v~P~~~i~----~~~~~i---~GIt~~~l~~a~~~~ev~~ 150 (276)
+|+||+||||+++ ++|+|||+|.+.+..+.+. |+.+|+|..+++ +++..+ |||+++++.+++++.+++.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~ 80 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEA 80 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHH
Confidence 5899999999995 5899999998754333433 999999987554 455566 5999999999999999999
Q ss_pred HHHHHhcC------CeEEEEchhhHHHHhcccC------CCCceeeh---hhhchhhhCCCCCccHHHHHHHHhCCcCCC
Q 023843 151 KVAELIEG------RILVGHALHNDLKALLLTH------SKKDLRDT---SEYQPFLNRNGRSKALRHLAAEILAVEIQN 215 (276)
Q Consensus 151 ~l~~~l~~------~~lVgHn~~~D~~~L~~~~------~~~~~~Dt---~~~~~~~~~~~~~~sL~~La~~~lgi~~~~ 215 (276)
+|.+|+++ .++||||+.||+.||.... ..++.+|+ ..+++.+.+...+ +++...
T Consensus 81 ~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p~~~~----------~~~~~~- 149 (173)
T cd06135 81 ELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYPEIYR----------KAPKKK- 149 (173)
T ss_pred HHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCcHhhh----------cCCCCC-
Confidence 99999974 6899999999999997221 11235676 3344444432111 344443
Q ss_pred CCCChHHHHHHHHHHHHHhHHH
Q 023843 216 GEHCPIDDARAAMLLYMKNRKQ 237 (276)
Q Consensus 216 ~~H~Al~DA~at~~L~~~l~~~ 237 (276)
..|+|++||++++.+|..+...
T Consensus 150 ~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 150 GTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred CCcchHHHHHHHHHHHHHHHHH
Confidence 6799999999999999998653
No 50
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.63 E-value=8.2e-16 Score=133.04 Aligned_cols=158 Identities=20% Similarity=0.282 Sum_probs=124.6
Q ss_pred CCCcEEEEEEeccCCC------CCCeeEEEEEEEEeCCCcEE---EEEeecCCc--ccccccccccCCCHHHhcCCCCHH
Q 023843 78 SLTDVVAMDCEMVGIS------QGNKSALGRVSLVNKWGNLI---YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFP 146 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~------~~~iiei~~v~v~~~~g~ii---~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~ 146 (276)
....+++||+|+|..+ +.+|||+.+|.+.+.+..++ |..||+|.+ .++++++.+|||.++.+..|++|.
T Consensus 54 ~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~ 133 (280)
T KOG0542|consen 54 PFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFP 133 (280)
T ss_pred ccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHH
Confidence 4566999999999776 23899999887876544444 899999997 899999999999999999999999
Q ss_pred HHHHHHHHHhc--------CCeEEEEchhhHHHHh-c-------ccCCC--CceeehhhhchhhhCCCCCccHHHHHHHH
Q 023843 147 TVQKKVAELIE--------GRILVGHALHNDLKAL-L-------LTHSK--KDLRDTSEYQPFLNRNGRSKALRHLAAEI 208 (276)
Q Consensus 147 ev~~~l~~~l~--------~~~lVgHn~~~D~~~L-~-------~~~~~--~~~~Dt~~~~~~~~~~~~~~sL~~La~~~ 208 (276)
+|+.+|..||. +..-..-...-|+... . +..|. ..+||+-..+...+.......+..+. ++
T Consensus 134 ~vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mL-e~ 212 (280)
T KOG0542|consen 134 QVLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGML-EH 212 (280)
T ss_pred HHHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHH-HH
Confidence 99999999993 2333333445666433 2 44442 35788888777666444677888866 99
Q ss_pred hCCcCCCCCCChHHHHHHHHHHHHHhHH
Q 023843 209 LAVEIQNGEHCPIDDARAAMLLYMKNRK 236 (276)
Q Consensus 209 lgi~~~~~~H~Al~DA~at~~L~~~l~~ 236 (276)
+|++++|.+|++++||+.+++|..+|..
T Consensus 213 ~gL~f~Gr~HsGiDDa~Nia~I~~kM~~ 240 (280)
T KOG0542|consen 213 YGLQFEGRAHSGIDDARNIARIAQKMIR 240 (280)
T ss_pred hCCcccCCcccCchhHHHHHHHHHHHHh
Confidence 9999999999999999999999999854
No 51
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.62 E-value=7.8e-16 Score=151.68 Aligned_cols=181 Identities=30% Similarity=0.436 Sum_probs=149.8
Q ss_pred CCCCCCCcEEEEEEeccCCCC--------C-------CeeEEEEEEEEeCCC----cEEEEEeecCCcccccccccccCC
Q 023843 74 NDDFSLTDVVAMDCEMVGISQ--------G-------NKSALGRVSLVNKWG----NLIYDEFVRPLERVVDFRTRISGI 134 (276)
Q Consensus 74 ~~~~~~~~~VaiD~EttG~~~--------~-------~iiei~~v~v~~~~g----~ii~~~~v~P~~~i~~~~~~i~GI 134 (276)
.+...++.+|+||-|++.+.+ | ....+|+|+++++.| -++.|.||...+.|.||-|+++||
T Consensus 904 dEmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI 983 (1118)
T KOG1275|consen 904 DEMPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGI 983 (1118)
T ss_pred cccCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCC
Confidence 445567889999999998862 1 124789999998663 235899999999999999999999
Q ss_pred CHHHhcCCC------CHHHHHHHHHHHhc-CCeEEEEchhhHHHHhcccCCCCceeehhhhchhhhCCCCCccHHHHHHH
Q 023843 135 RPRDLRKAK------DFPTVQKKVAELIE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAE 207 (276)
Q Consensus 135 t~~~l~~a~------~~~ev~~~l~~~l~-~~~lVgHn~~~D~~~L~~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~ 207 (276)
-|.||.-.. ++.-+..++.-+++ |.++|||+++.|++++.+..|.-+++||..++. .+..+..+|..||.+
T Consensus 984 ~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~--~~s~R~LSLrfLa~~ 1061 (1118)
T KOG1275|consen 984 KPGDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFR--LGSQRMLSLRFLAWE 1061 (1118)
T ss_pred CccccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEe--cccccEEEHHHHHHH
Confidence 999985322 56777888888887 999999999999999999999888999999853 334567899999999
Q ss_pred HhCCcCCCCCCChHHHHHHHHHHHHHhH-----HHHHHHHHHHHHHHHHHhhhC
Q 023843 208 ILAVEIQNGEHCPIDDARAAMLLYMKNR-----KQWEKSVKDQTRLEQKQKNRK 256 (276)
Q Consensus 208 ~lgi~~~~~~H~Al~DA~at~~L~~~l~-----~~~e~~~~~~~~~~~k~~~~~ 256 (276)
+||-.+|..+|++++||+.++.||+++. ..+|..++..+......+++-
T Consensus 1062 lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~lkeq~~~~~~l~niye~gr~~q~k~ 1115 (1118)
T KOG1275|consen 1062 LLGETIQMEAHDSIEDARTALKLYKKYLKLKEQGKLESELRNIYECGRPNQFKV 1115 (1118)
T ss_pred HhcchhhccccccHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhhcCccccCCC
Confidence 9999999999999999999999999984 577788887777766655543
No 52
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.59 E-value=1.1e-14 Score=132.50 Aligned_cols=175 Identities=17% Similarity=0.142 Sum_probs=140.7
Q ss_pred CCCCcEEEEEEeccCCCC--CCeeEEEEEEEEeCCCcEE---EEEeecCCccccc--ccccccCCCHHHh-cCCCCHHHH
Q 023843 77 FSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI---YDEFVRPLERVVD--FRTRISGIRPRDL-RKAKDFPTV 148 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii---~~~~v~P~~~i~~--~~~~i~GIt~~~l-~~a~~~~ev 148 (276)
.....|++.|.||.|.+| ++..++|+|.-. .+-+++ ...|++|...+.+ .++-||||||+.. ..+.+..+.
T Consensus 6 ~~~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD-~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F 84 (475)
T COG2925 6 TKQPTFLFYDYETFGVHPALDRPAQFAGIRTD-IEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAF 84 (475)
T ss_pred CCCCcEEEEehhhcCCCcccccchhhheeecc-ccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHH
Confidence 345679999999999995 466789988774 445555 7789999984443 3889999999987 567898998
Q ss_pred HHHHHHHhc--CCeEEEEch-hhHHHHhc----------------ccCCCCceeehhhhchhhhC----------CCCCc
Q 023843 149 QKKVAELIE--GRILVGHAL-HNDLKALL----------------LTHSKKDLRDTSEYQPFLNR----------NGRSK 199 (276)
Q Consensus 149 ~~~l~~~l~--~~~lVgHn~-~~D~~~L~----------------~~~~~~~~~Dt~~~~~~~~~----------~~~~~ 199 (276)
...|...+. +++++|||. +||-.+-+ -...+++++|++...+.++| +..++
T Consensus 85 ~~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSF 164 (475)
T COG2925 85 AARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSF 164 (475)
T ss_pred HHHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcch
Confidence 888888774 899999987 99998876 11234678888888888887 45678
Q ss_pred cHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhh
Q 023843 200 ALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQTRLEQKQKN 254 (276)
Q Consensus 200 sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~~~~e~~~~~~~~~~~k~~~ 254 (276)
+|+.|. ..-|++.. .+|+|++|++||+.+.+.++..-.+..+-.|..+.|.+-
T Consensus 165 kLEhLt-~ANgieH~-nAHdAmsDVyATIamAklvk~~QPrLfdy~f~~R~K~~~ 217 (475)
T COG2925 165 KLEHLT-KANGIEHS-NAHDAMSDVYATIAMAKLVKTAQPRLFDYLFQLRKKHKL 217 (475)
T ss_pred hhHHHh-hccccccc-hhhHHHHHHHHHHHHHHHHHhhCcHHHHHHHHhccHHHH
Confidence 899998 78899887 899999999999999999998878888888887766543
No 53
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.58 E-value=4.4e-15 Score=121.72 Aligned_cols=150 Identities=19% Similarity=0.222 Sum_probs=113.8
Q ss_pred CCCCCcEEEEEEeccCCC--CCCeeEEEEEEEEeCCCcEE---EEEeecCCccc----ccccccc---cCCCHHHhcCCC
Q 023843 76 DFSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLERV----VDFRTRI---SGIRPRDLRKAK 143 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~--~~~iiei~~v~v~~~~g~ii---~~~~v~P~~~i----~~~~~~i---~GIt~~~l~~a~ 143 (276)
+...+++|+|||||||++ .+.|+||| +.|.|++.+++ ++..|+.+.++ .+|+..- +|+|...+.+..
T Consensus 22 ~~l~q~lVWiD~EMTGLdvekd~i~Eia-cIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~ 100 (208)
T KOG3242|consen 22 DKLKQPLVWIDCEMTGLDVEKDRIIEIA-CIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKI 100 (208)
T ss_pred ccccCceEEEeeeccccccccceeEEEE-EEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhc
Confidence 345678999999999999 56889998 77888777766 77888877644 4454433 689999999999
Q ss_pred CHHHHHHHHHHHhc------CCeEEEEchhhHHHHhc------ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCC
Q 023843 144 DFPTVQKKVAELIE------GRILVGHALHNDLKALL------LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAV 211 (276)
Q Consensus 144 ~~~ev~~~l~~~l~------~~~lVgHn~~~D~~~L~------~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi 211 (276)
++.+|-.++.+|+. ..+|.|.+++.|..||. +.|..++++|++.+..+ |++++-.
T Consensus 101 tl~~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL-------------~~Rw~P~ 167 (208)
T KOG3242|consen 101 TLADAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKEL-------------ARRWYPD 167 (208)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHH-------------HHHhCch
Confidence 99999999999993 57889999999999998 33445668887765444 3333321
Q ss_pred -----cCCCCCCChHHHHHHHHHHHHHhHHHHH
Q 023843 212 -----EIQNGEHCPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 212 -----~~~~~~H~Al~DA~at~~L~~~l~~~~e 239 (276)
+-....|+|++|.+..+.-++.++..|-
T Consensus 168 ~~~~aPkK~~~HrAldDI~ESI~ELq~Yr~nif 200 (208)
T KOG3242|consen 168 IKARAPKKKATHRALDDIRESIKELQYYRENIF 200 (208)
T ss_pred hhccCcccccccchHHHHHHHHHHHHHHHHHhc
Confidence 1123579999999999999888876653
No 54
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.52 E-value=7e-15 Score=120.15 Aligned_cols=157 Identities=16% Similarity=0.152 Sum_probs=121.7
Q ss_pred CcEEEEEEeccCCCC------CCeeEEEEEEEEeCCCcEE--EEEeecCCc--ccccccccccCCCHHHhcCCCCHHHHH
Q 023843 80 TDVVAMDCEMVGISQ------GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (276)
Q Consensus 80 ~~~VaiD~EttG~~~------~~iiei~~v~v~~~~g~ii--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~ev~ 149 (276)
..+++||+|+|..+. .+|++|.+..|..-+.+++ |.+||+|.. .++++|..++||++..+.+|+-|..|+
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~ 83 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVF 83 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHH
Confidence 358999999997651 2678888555544445555 999999997 788999999999999999999999999
Q ss_pred HHHHHHhc-----CCeEEEEchhhHHHHhc-------cc-CC-CCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC
Q 023843 150 KKVAELIE-----GRILVGHALHNDLKALL-------LT-HS-KKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN 215 (276)
Q Consensus 150 ~~l~~~l~-----~~~lVgHn~~~D~~~L~-------~~-~~-~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~ 215 (276)
.+|..||. ...-.+-...+|++.|. +. .+ .-.++|+...+.-.+...+..+|...+ +.+|..++|
T Consensus 84 E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~al-e~~G~sf~G 162 (210)
T COG5018 84 EDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKAL-EEYGDSFTG 162 (210)
T ss_pred HHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHH-HHhccccCC
Confidence 99999994 11224455689999986 11 11 124688888777776555557888855 999999999
Q ss_pred CCCChHHHHHHHHHHHHHhHHH
Q 023843 216 GEHCPIDDARAAMLLYMKNRKQ 237 (276)
Q Consensus 216 ~~H~Al~DA~at~~L~~~l~~~ 237 (276)
.+|+|++||+.+++|+..+...
T Consensus 163 ~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 163 THHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred chhhhHHHHHHHHHHHHHHcch
Confidence 9999999999999999987543
No 55
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.47 E-value=3e-13 Score=110.08 Aligned_cols=145 Identities=17% Similarity=0.229 Sum_probs=107.0
Q ss_pred CCcEEEEEEeccCCCCC--CeeEEEEEEEEeCCCcEE---EEEeecCCc----ccccccccc---cCCCHHHhcCCCCHH
Q 023843 79 LTDVVAMDCEMVGISQG--NKSALGRVSLVNKWGNLI---YDEFVRPLE----RVVDFRTRI---SGIRPRDLRKAKDFP 146 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~~--~iiei~~v~v~~~~g~ii---~~~~v~P~~----~i~~~~~~i---~GIt~~~l~~a~~~~ 146 (276)
..++|+|||||||++++ +|+||| ..|.|.+.+++ +..-|..+. ...+++++. +|++.....+..+..
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA-~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIA-TIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEE-EEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccHH
Confidence 46899999999999954 889999 55567777776 444555444 566777766 478888888888999
Q ss_pred HHHHHHHHHh------cCCeEEEEchhhHHHHhcccCCC------CceeehhhhchhhhCCCCCccHHHHHHHHh-----
Q 023843 147 TVQKKVAELI------EGRILVGHALHNDLKALLLTHSK------KDLRDTSEYQPFLNRNGRSKALRHLAAEIL----- 209 (276)
Q Consensus 147 ev~~~l~~~l------~~~~lVgHn~~~D~~~L~~~~~~------~~~~Dt~~~~~~~~~~~~~~sL~~La~~~l----- 209 (276)
++..++.+|| +..++.|.++.-|.+||.-.+|. |+.+|++. |++||+++.
T Consensus 84 ~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVST-------------lKELa~RW~P~i~~ 150 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVST-------------LKELARRWNPEILA 150 (184)
T ss_pred HHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHH-------------HHHHHHhhCcHhhh
Confidence 9988888888 35789999999999999855553 34555554 444444332
Q ss_pred CCcCCCCCCChHHHHHHHHHHHHHhHHHH
Q 023843 210 AVEIQNGEHCPIDDARAAMLLYMKNRKQW 238 (276)
Q Consensus 210 gi~~~~~~H~Al~DA~at~~L~~~l~~~~ 238 (276)
| ...++.|.|++|.+.++.-++.|.+.|
T Consensus 151 ~-~~K~~~H~Al~DI~ESI~EL~~YR~~f 178 (184)
T COG1949 151 G-FKKGGTHRALDDIRESIAELRYYREHF 178 (184)
T ss_pred c-cccccchhHHHHHHHHHHHHHHHHHHh
Confidence 3 333468999999999999888887654
No 56
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=99.15 E-value=1.4e-09 Score=91.97 Aligned_cols=142 Identities=21% Similarity=0.191 Sum_probs=97.9
Q ss_pred CcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcCC
Q 023843 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGR 159 (276)
Q Consensus 80 ~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~~ 159 (276)
..++++|+|++|+++.. ..+..+.+....+..+|-. +.+. .+ .+++++.+++..|..++.+.
T Consensus 5 ~~~~a~d~e~~~~~~~~-~~i~~l~~~~~~~~~~~~~-~~~~--------~~--------~~~~~~~~~~~~l~~~l~~~ 66 (193)
T cd06139 5 AKVFAFDTETTSLDPMQ-AELVGISFAVEPGEAYYIP-LGHD--------YG--------GEQLPREEVLAALKPLLEDP 66 (193)
T ss_pred CCeEEEEeecCCCCcCC-CeEEEEEEEcCCCCEEEEe-cCCC--------cc--------ccCCCHHHHHHHHHHHHhCC
Confidence 56899999999987422 2344455654434343311 1110 00 13456788899999999743
Q ss_pred --eEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCC----------------C---
Q 023843 160 --ILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ----------------N--- 215 (276)
Q Consensus 160 --~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~----------------~--- 215 (276)
.+||||++||+.+|. +..+ ..++||+.+++++.+....++|+.++.+++|.... .
T Consensus 67 ~~~~v~hn~k~d~~~l~~~gi~~~-~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~ 145 (193)
T cd06139 67 SIKKVGQNLKFDLHVLANHGIELR-GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL 145 (193)
T ss_pred CCcEEeeccHHHHHHHHHCCCCCC-CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH
Confidence 789999999999996 2222 23689999999999766457999999888775411 0
Q ss_pred --CCCChHHHHHHHHHHHHHhHHHHHH
Q 023843 216 --GEHCPIDDARAAMLLYMKNRKQWEK 240 (276)
Q Consensus 216 --~~H~Al~DA~at~~L~~~l~~~~e~ 240 (276)
..|.+..||.++.+|+..+..++++
T Consensus 146 ~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 146 EKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0125788899999999999888765
No 57
>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=99.03 E-value=3.7e-09 Score=90.52 Aligned_cols=123 Identities=17% Similarity=0.123 Sum_probs=86.0
Q ss_pred EEEEEEeccCC----C--CCCeeEEEEEEEEeCCCcEE-EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHH
Q 023843 82 VVAMDCEMVGI----S--QGNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (276)
Q Consensus 82 ~VaiD~EttG~----~--~~~iiei~~v~v~~~~g~ii-~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~ 154 (276)
+++||+||+|. + .++|++|+.+...+ |... +.....+..... .||+..++..+++..+++..|.+
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~--g~~~~~~~~~~~~~~~~------~~i~~~~v~~~~~E~~lL~~f~~ 72 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFD--GVKVVFLLKTSTVGDDI------EFIDGIEVEYFADEKELLKRFFD 72 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeC--CceeeEEEeecccCCcC------CCCCCceEEEeCCHHHHHHHHHH
Confidence 47899999998 4 35788888555433 5433 222222221111 17777788888999999999999
Q ss_pred HhcC---CeEEEEch-hhHHHHhc-------ccCC----------------------CCceeehhhhchhhhCCCCCccH
Q 023843 155 LIEG---RILVGHAL-HNDLKALL-------LTHS----------------------KKDLRDTSEYQPFLNRNGRSKAL 201 (276)
Q Consensus 155 ~l~~---~~lVgHn~-~~D~~~L~-------~~~~----------------------~~~~~Dt~~~~~~~~~~~~~~sL 201 (276)
++.. .++||||+ .||+.+|. +... ...++|+..+.+...+ ..+++|
T Consensus 73 ~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~-l~sy~L 151 (199)
T cd05160 73 IIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK-LKSYTL 151 (199)
T ss_pred HHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC-cccCCH
Confidence 9974 59999999 89999996 2220 1236788887766654 788999
Q ss_pred HHHHHHHhCCcC
Q 023843 202 RHLAAEILAVEI 213 (276)
Q Consensus 202 ~~La~~~lgi~~ 213 (276)
+++|..++|...
T Consensus 152 ~~v~~~~l~~~k 163 (199)
T cd05160 152 DAVAEELLGEGK 163 (199)
T ss_pred HHHHHHHhCCCC
Confidence 999988887543
No 58
>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=99.01 E-value=6.8e-09 Score=86.18 Aligned_cols=135 Identities=26% Similarity=0.369 Sum_probs=91.6
Q ss_pred CcEEEEEEeccCCCC-CCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc-
Q 023843 80 TDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE- 157 (276)
Q Consensus 80 ~~~VaiD~EttG~~~-~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~- 157 (276)
.++|+||+|++++.. ..-..++.+.+.+. ...|-. .|.. . ...+ +...|.+++.
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~--~~~~i~--~~~~-----------~-------~~~~--~~~~l~~ll~~ 75 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNPKIALIQLATG--EGCYII--DPID-----------L-------GDNW--ILDALKELLED 75 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSEEEEEEEEEES--CEEEEE--CGTT-----------S-------TTTT--HHHHHHHHHTT
T ss_pred CCeEEEEEEECCCCccccCCeEEEEEEecC--CCceee--eecc-----------c-------cccc--hHHHHHHHHhC
Confidence 459999999999985 22356777888774 222211 1110 0 0000 5667888887
Q ss_pred -CCeEEEEchhhHHHHhcc--cCCCCceeehhhhchhhhCCCCCccHHHHHHHHhC-CcCCCC------C----------
Q 023843 158 -GRILVGHALHNDLKALLL--THSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILA-VEIQNG------E---------- 217 (276)
Q Consensus 158 -~~~lVgHn~~~D~~~L~~--~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lg-i~~~~~------~---------- 217 (276)
+...||||++||+.+|.- ......++||+.+++++.+... ++|++|+.+++| ...... .
T Consensus 76 ~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~-~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~ 154 (176)
T PF01612_consen 76 PNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRS-YSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQI 154 (176)
T ss_dssp TTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTT-SSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHH
T ss_pred CCccEEEEEEechHHHHHHHhccccCCccchhhhhhccccccc-ccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHH
Confidence 567899999999999972 3333458999888888775444 999999999999 333211 1
Q ss_pred CChHHHHHHHHHHHHHhHHHHH
Q 023843 218 HCPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 218 H~Al~DA~at~~L~~~l~~~~e 239 (276)
.-|..||..+.+||..+..++|
T Consensus 155 ~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 155 EYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHHHHHHHTHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHhhC
Confidence 1278899999999999987753
No 59
>PRK05755 DNA polymerase I; Provisional
Probab=98.88 E-value=2e-08 Score=103.91 Aligned_cols=135 Identities=21% Similarity=0.238 Sum_probs=95.7
Q ss_pred CCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcC
Q 023843 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~ 158 (276)
...+++||+||+|+++.. ..++.+.+....|..++ + |. +++. .+++..|.+|+.+
T Consensus 314 ~~~~~a~DtEt~~l~~~~-~~i~~i~ls~~~g~~~~---i-p~----------~~i~----------~~~l~~l~~~L~d 368 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQ-AELVGLSFAVEPGEAAY---I-PL----------DQLD----------REVLAALKPLLED 368 (880)
T ss_pred ccCeEEEEeccCCCCccc-ccEEEEEEEeCCCcEEE---E-ec----------cccc----------HHHHHHHHHHHhC
Confidence 357999999999998542 23444555544454433 2 11 1111 1567778889975
Q ss_pred --CeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC------------------
Q 023843 159 --RILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN------------------ 215 (276)
Q Consensus 159 --~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~------------------ 215 (276)
.++|+||++||+.+|. +..+ ..++||+.+++++.+... ++|++|+.+++|.+...
T Consensus 369 ~~v~kV~HNakfDl~~L~~~gi~~~-~~~~DT~iAa~Ll~~~~~-~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~ 446 (880)
T PRK05755 369 PAIKKVGQNLKYDLHVLARYGIELR-GIAFDTMLASYLLDPGRR-HGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEE 446 (880)
T ss_pred CCCcEEEeccHhHHHHHHhCCCCcC-CCcccHHHHHHHcCCCCC-CCHHHHHHHHhCCCccchHHhcCCCCCccccCHHH
Confidence 4479999999999997 2222 347999999999987654 99999998888876310
Q ss_pred CCCChHHHHHHHHHHHHHhHHHHHH
Q 023843 216 GEHCPIDDARAAMLLYMKNRKQWEK 240 (276)
Q Consensus 216 ~~H~Al~DA~at~~L~~~l~~~~e~ 240 (276)
..|.|..|+..+.+||..+...+.+
T Consensus 447 ~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 447 AAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1257899999999999999877654
No 60
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=98.77 E-value=8.8e-08 Score=88.31 Aligned_cols=133 Identities=22% Similarity=0.285 Sum_probs=95.8
Q ss_pred CcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc--
Q 023843 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE-- 157 (276)
Q Consensus 80 ~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~-- 157 (276)
..+|+||+|+.|..+.. .++|-|.|.+.++.. +|.|... ..+.++| ..++.
T Consensus 17 ~~~iAiDTEf~r~~t~~-p~LcLIQi~~~e~~~----lIdpl~~---------------~~d~~~l-------~~Ll~d~ 69 (361)
T COG0349 17 SKAIAIDTEFMRLRTYY-PRLCLIQISDGEGAS----LIDPLAG---------------ILDLPPL-------VALLADP 69 (361)
T ss_pred CCceEEecccccccccC-CceEEEEEecCCCce----Eeccccc---------------ccccchH-------HHHhcCC
Confidence 56999999999998554 578889998866622 3343211 1122333 33443
Q ss_pred CCeEEEEchhhHHHHhc--ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCC---------------h
Q 023843 158 GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHC---------------P 220 (276)
Q Consensus 158 ~~~lVgHn~~~D~~~L~--~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~---------------A 220 (276)
..+-|-|+++||+.+|. +......++||...+.++..+. +++|++|+.+++|++++.++.+ |
T Consensus 70 ~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~-~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YA 148 (361)
T COG0349 70 NVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-SHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYA 148 (361)
T ss_pred ceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCCcc-cccHHHHHHHHhCCcccccccccccccCCCCHHHHHHH
Confidence 44559999999999997 2222234899999999887555 9999999999999999854321 7
Q ss_pred HHHHHHHHHHHHHhHHHHHH
Q 023843 221 IDDARAAMLLYMKNRKQWEK 240 (276)
Q Consensus 221 l~DA~at~~L~~~l~~~~e~ 240 (276)
..|+.....||.++...+++
T Consensus 149 a~DV~yL~~l~~~L~~~L~~ 168 (361)
T COG0349 149 AADVEYLLPLYDKLTEELAR 168 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999766553
No 61
>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=98.57 E-value=1.3e-06 Score=72.48 Aligned_cols=129 Identities=19% Similarity=0.179 Sum_probs=85.7
Q ss_pred CCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEE-EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc
Q 023843 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii-~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~ 157 (276)
...+|+||+|........ ..++-|.|....+.++ ++.. .. . .....|.+++.
T Consensus 12 ~~~~ig~D~E~~~~~~~~-~~~~liQl~~~~~~~~l~d~~-~~--------------~-----------~~~~~L~~lL~ 64 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYY-GEVALIQLCVSEEKCYLFDPL-SL--------------S-----------VDWQGLKMLLE 64 (161)
T ss_pred CCCEEEEECCccCCCCCC-CceEEEEEEECCCCEEEEecc-cC--------------c-----------cCHHHHHHHhC
Confidence 467999999988765211 2355555555423332 3221 10 0 01233556776
Q ss_pred C--CeEEEEchhhHHHHhc--ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCC---------------C
Q 023843 158 G--RILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGE---------------H 218 (276)
Q Consensus 158 ~--~~lVgHn~~~D~~~L~--~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~---------------H 218 (276)
+ .+.|||+++.|+..|. .......++|++.+++++.+. .+.+|..|+.+++|..++... |
T Consensus 65 d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~-~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~ 143 (161)
T cd06129 65 NPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKL 143 (161)
T ss_pred CCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCC-CCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHH
Confidence 4 3569999999999985 233223478999999988754 456999999899998775321 2
Q ss_pred ChHHHHHHHHHHHHHhH
Q 023843 219 CPIDDARAAMLLYMKNR 235 (276)
Q Consensus 219 ~Al~DA~at~~L~~~l~ 235 (276)
.|..||.++..||.++.
T Consensus 144 YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 144 YAAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 38999999999999874
No 62
>PRK10829 ribonuclease D; Provisional
Probab=98.54 E-value=2.2e-06 Score=80.46 Aligned_cols=133 Identities=22% Similarity=0.220 Sum_probs=90.9
Q ss_pred CCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc-
Q 023843 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE- 157 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~- 157 (276)
...+|+||+|+.+...-. ..++.|.|.+..+ +| +|.|.. ++ + +..|.+++.
T Consensus 21 ~~~~lalDtEf~~~~ty~-~~l~LiQl~~~~~--~~--LiD~l~-----------~~--d----------~~~L~~ll~~ 72 (373)
T PRK10829 21 AFPAIALDTEFVRTRTYY-PQLGLIQLYDGEQ--LS--LIDPLG-----------IT--D----------WSPFKALLRD 72 (373)
T ss_pred cCCeEEEecccccCccCC-CceeEEEEecCCc--eE--EEecCC-----------cc--c----------hHHHHHHHcC
Confidence 456999999998875322 3566676765332 21 233321 10 1 234666775
Q ss_pred -CCeEEEEchhhHHHHhc--ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCC---------------C
Q 023843 158 -GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEH---------------C 219 (276)
Q Consensus 158 -~~~lVgHn~~~D~~~L~--~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H---------------~ 219 (276)
+.+.|+|++.+|+.+|. +......++||+..+.++.. ..+.+|..|+.+++|+.++.... .
T Consensus 73 ~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~-~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~Y 151 (373)
T PRK10829 73 PQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGR-PLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEY 151 (373)
T ss_pred CCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCC-CccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHH
Confidence 33448999999999984 33333458999999887752 23689999999999998874321 2
Q ss_pred hHHHHHHHHHHHHHhHHHHHH
Q 023843 220 PIDDARAAMLLYMKNRKQWEK 240 (276)
Q Consensus 220 Al~DA~at~~L~~~l~~~~e~ 240 (276)
|..|+..+..||..+..++++
T Consensus 152 Aa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 152 AAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 899999999999998776653
No 63
>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=98.53 E-value=1.8e-06 Score=71.97 Aligned_cols=130 Identities=18% Similarity=0.266 Sum_probs=85.9
Q ss_pred CCcEEEEEEeccCCCC-CCeeEEEEEEEEeCCCcEE-EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHh
Q 023843 79 LTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~-~~iiei~~v~v~~~~g~ii-~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l 156 (276)
...+|+||+|.++... +....++-|.+... +.++ |+.. . + ......|.+++
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~-~~~~l~~~~-~--------------~-----------~~~~~~l~~ll 69 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLATE-SRCLLFQLA-H--------------M-----------DKLPPSLKQLL 69 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEecC-CcEEEEEhh-h--------------h-----------hcccHHHHHHh
Confidence 4679999999998653 11123444444432 2332 2111 1 0 11223466677
Q ss_pred c--CCeEEEEchhhHHHHhc--ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCC--CCC-------------
Q 023843 157 E--GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ--NGE------------- 217 (276)
Q Consensus 157 ~--~~~lVgHn~~~D~~~L~--~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~--~~~------------- 217 (276)
. +...|||++++|+.+|. .......++|++.+++++.+.....+|..|+.+++|.... ...
T Consensus 70 ~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~~ 149 (170)
T cd06141 70 EDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKE 149 (170)
T ss_pred cCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCHH
Confidence 6 34569999999999986 2222234799999999998665557999999999998776 211
Q ss_pred --CChHHHHHHHHHHHHHhH
Q 023843 218 --HCPIDDARAAMLLYMKNR 235 (276)
Q Consensus 218 --H~Al~DA~at~~L~~~l~ 235 (276)
|.|..||..+..||..+.
T Consensus 150 qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 150 QILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 238999999999998874
No 64
>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=98.51 E-value=2.4e-06 Score=73.18 Aligned_cols=136 Identities=18% Similarity=0.226 Sum_probs=86.0
Q ss_pred CCCcEEEEEEeccCCCC-CCeeEEEEEEEEeCCCcEE-EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHH
Q 023843 78 SLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~-~~iiei~~v~v~~~~g~ii-~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~ 155 (276)
....+|+||+|.++... +.-..++-+.+... +.++ ++.+--+. ..-......|.++
T Consensus 20 ~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~-~~~~lid~~~~~~---------------------~~~~~~~~~L~~l 77 (193)
T cd06146 20 EAGRVVGIDSEWKPSFLGDSDPRVAILQLATE-DEVFLLDLLALEN---------------------LESEDWDRLLKRL 77 (193)
T ss_pred ccCCEEEEECccCCCccCCCCCCceEEEEecC-CCEEEEEchhccc---------------------cchHHHHHHHHHH
Confidence 34679999999886542 11123444444432 3333 32221110 0012233446777
Q ss_pred hcC--CeEEEEchhhHHHHhcccCC--------CCceeehhhhchhhhCC----------CCCccHHHHHHHHhCCcCCC
Q 023843 156 IEG--RILVGHALHNDLKALLLTHS--------KKDLRDTSEYQPFLNRN----------GRSKALRHLAAEILAVEIQN 215 (276)
Q Consensus 156 l~~--~~lVgHn~~~D~~~L~~~~~--------~~~~~Dt~~~~~~~~~~----------~~~~sL~~La~~~lgi~~~~ 215 (276)
|.+ .+.|||++.+|+.+|.-.+. ...++|+..++..+... ...++|..|+..+||..++.
T Consensus 78 l~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~l~K 157 (193)
T cd06146 78 FEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDK 157 (193)
T ss_pred hCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCCcCc
Confidence 764 45599999999999972221 23589999877765421 35789999999999988764
Q ss_pred CC---------------CChHHHHHHHHHHHHHhH
Q 023843 216 GE---------------HCPIDDARAAMLLYMKNR 235 (276)
Q Consensus 216 ~~---------------H~Al~DA~at~~L~~~l~ 235 (276)
.. +.|..||++++.||.++.
T Consensus 158 ~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 158 SEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 31 238999999999999874
No 65
>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=98.48 E-value=5.1e-06 Score=66.99 Aligned_cols=105 Identities=27% Similarity=0.319 Sum_probs=70.6
Q ss_pred cEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcC--
Q 023843 81 DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG-- 158 (276)
Q Consensus 81 ~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~-- 158 (276)
+.+++|+|+.+..+.. ..+..+.+... ++.+| +.... . ...+...|.+++.+
T Consensus 1 ~~l~~d~e~~~~~~~~-~~i~~~~l~~~-~~~~~---i~~~~----------~-----------~~~~~~~l~~~l~~~~ 54 (155)
T cd00007 1 KEVAFDTETTGLNYHR-GKLVGIQIATA-GEAAY---IPDEL----------E-----------LEEDLEALKELLEDED 54 (155)
T ss_pred CceEEEEecCCCCcCC-CeEEEEEEEEC-CcEEE---EEcCC----------C-----------HHHHHHHHHHHHcCCC
Confidence 3689999987765211 24555666543 33333 11000 0 24566778888874
Q ss_pred CeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCc
Q 023843 159 RILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVE 212 (276)
Q Consensus 159 ~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~ 212 (276)
..+||||+++|+.+|. +..+ ..++||+.+++++.+...+++|+.|+.++++..
T Consensus 55 ~~~v~~~~k~d~~~L~~~~~~~~-~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~ 110 (155)
T cd00007 55 ITKVGHDAKFDLVVLARDGIELP-GNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIE 110 (155)
T ss_pred CcEEeccHHHHHHHHHHCCCCCC-CCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCC
Confidence 4589999999999996 2222 236899999999998663579999998888766
No 66
>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=98.48 E-value=3.1e-06 Score=72.67 Aligned_cols=138 Identities=18% Similarity=0.205 Sum_probs=90.6
Q ss_pred CCCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEE-EEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHh
Q 023843 78 SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii-~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l 156 (276)
....+|+||+|+++.+.. ..++-|.|....+.++ ||.+--+. ......|.+++
T Consensus 8 ~~~~~i~~D~E~~~~~~~--~~~~LiQia~~~~~v~l~D~~~~~~------------------------~~~~~~L~~iL 61 (197)
T cd06148 8 KKQKVIGLDCEGVNLGRK--GKLCLVQIATRTGQIYLFDILKLGS------------------------IVFINGLKDIL 61 (197)
T ss_pred hhCCEEEEEcccccCCCC--CCEEEEEEeeCCCcEEEEEhhhccc------------------------hhHHHHHHHHh
Confidence 346799999999877632 2455555554323342 43321100 11234466677
Q ss_pred c--CCeEEEEchhhHHHHhc--ccCCCCceeehhhhchhhhCCCC-------CccHHHHHHHHhCCcCCC----------
Q 023843 157 E--GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLNRNGR-------SKALRHLAAEILAVEIQN---------- 215 (276)
Q Consensus 157 ~--~~~lVgHn~~~D~~~L~--~~~~~~~~~Dt~~~~~~~~~~~~-------~~sL~~La~~~lgi~~~~---------- 215 (276)
. +...|||++++|+.+|. ....-..++||+.+++++.+... ..+|..++.+++|+++..
T Consensus 62 e~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~ 141 (197)
T cd06148 62 ESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMRE 141 (197)
T ss_pred cCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhc
Confidence 6 34559999999999983 22222247899999988875332 369999999999987631
Q ss_pred ----CC---------CChHHHHHHHHHHHHHhHHHHHHH
Q 023843 216 ----GE---------HCPIDDARAAMLLYMKNRKQWEKS 241 (276)
Q Consensus 216 ----~~---------H~Al~DA~at~~L~~~l~~~~e~~ 241 (276)
.. +.|..||..+..||..+...+.+.
T Consensus 142 ~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 142 DPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred CchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 00 128999999999999998887654
No 67
>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=98.43 E-value=1.3e-06 Score=78.28 Aligned_cols=146 Identities=25% Similarity=0.336 Sum_probs=87.5
Q ss_pred cEEEEEEeccCCCC-----------------------CCeeEEEEEEEE-eCCCcEE-------EEEeecCCcc-ccccc
Q 023843 81 DVVAMDCEMVGISQ-----------------------GNKSALGRVSLV-NKWGNLI-------YDEFVRPLER-VVDFR 128 (276)
Q Consensus 81 ~~VaiD~EttG~~~-----------------------~~iiei~~v~v~-~~~g~ii-------~~~~v~P~~~-i~~~~ 128 (276)
.||+||+|++|+.. -.++++| +++. +.++..- |+.++-|... +. ..
T Consensus 23 ~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~G-lt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~-~~ 100 (262)
T PF04857_consen 23 DFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFG-LTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFS-QA 100 (262)
T ss_dssp SEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEE-EEEETTTTSEEECCEEEEEEEBSTTSTTTCEE-EH
T ss_pred CEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceee-EEEeecccccCCceeEEEEeeeecccccccee-cc
Confidence 49999999999972 1378999 5555 5555532 4555444332 11 11
Q ss_pred c-----cccCCCHHH-hcCCCCHHHHHH-----HHHH---Hh----c-CCeEEEEchhhHHHHhc---------------
Q 023843 129 T-----RISGIRPRD-LRKAKDFPTVQK-----KVAE---LI----E-GRILVGHALHNDLKALL--------------- 174 (276)
Q Consensus 129 ~-----~i~GIt~~~-l~~a~~~~ev~~-----~l~~---~l----~-~~~lVgHn~~~D~~~L~--------------- 174 (276)
. .-+|+.-.. +.+++++....+ ++.. ++ . ..++||||.-+|+.+|-
T Consensus 101 ~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~ 180 (262)
T PF04857_consen 101 SSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFK 180 (262)
T ss_dssp HHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHH
T ss_pred hhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHH
Confidence 1 225666444 355665433331 1111 11 1 48999999999998763
Q ss_pred ----ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcC-----------------------CCC-CCChHHHHHH
Q 023843 175 ----LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEI-----------------------QNG-EHCPIDDARA 226 (276)
Q Consensus 175 ----~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~-----------------------~~~-~H~Al~DA~a 226 (276)
...| .++||..++.... ....+|..|+ +.++... .+. .|.|-.||..
T Consensus 181 ~~~~~~FP--~i~DtK~la~~~~--~~~~~L~~l~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~m 255 (262)
T PF04857_consen 181 ELLRELFP--RIYDTKYLAEECP--GKSTSLQELA-EELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYM 255 (262)
T ss_dssp HHHHHHSS--SEEEHHHHHTSTT--TS-SSHHHHH-HHTTSTT----EEE-TTS-------------SS-TTSHHHHHHH
T ss_pred HHHHHHCc--ccccHHHHHHhcc--ccccCHHHHH-HHhCCCccccccccccccccccccccccccCCCCCCCcchHHHH
Confidence 1123 3899998877654 4567999998 7787654 333 8999999999
Q ss_pred HHHHHHH
Q 023843 227 AMLLYMK 233 (276)
Q Consensus 227 t~~L~~~ 233 (276)
|+.+|.+
T Consensus 256 Tg~~F~~ 262 (262)
T PF04857_consen 256 TGCVFIK 262 (262)
T ss_dssp HHHHHHH
T ss_pred HHHHHcC
Confidence 9999863
No 68
>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=98.41 E-value=2.5e-06 Score=64.86 Aligned_cols=56 Identities=23% Similarity=0.320 Sum_probs=38.4
Q ss_pred EEEEEeccCCCCCCeeEEEEEEEEeCC-CcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcC---
Q 023843 83 VAMDCEMVGISQGNKSALGRVSLVNKW-GNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG--- 158 (276)
Q Consensus 83 VaiD~EttG~~~~~iiei~~v~v~~~~-g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~--- 158 (276)
+++|+||+|+++.. .+|+.+.+.+.. +...+ .. |.+|+++
T Consensus 1 ~~~DiEt~~~~~~~-~~i~~i~~~~~~~~~~~~----~~-------------------------------f~~~l~~~~~ 44 (96)
T cd06125 1 IAIDTEATGLDGAV-HEIIEIALADVNPEDTAV----ID-------------------------------LKDILRDKPL 44 (96)
T ss_pred CEEEEECCCCCCCC-CcEEEEEEEEccCCCEEE----eh-------------------------------HHHHHhhCCC
Confidence 58999999988543 456666666542 33222 10 6667753
Q ss_pred CeEEEEchhhHHHHhc
Q 023843 159 RILVGHALHNDLKALL 174 (276)
Q Consensus 159 ~~lVgHn~~~D~~~L~ 174 (276)
.++||||+.||+.+|.
T Consensus 45 ~v~V~hn~~fD~~fL~ 60 (96)
T cd06125 45 AILVGHNGSFDLPFLN 60 (96)
T ss_pred CEEEEeCcHHhHHHHH
Confidence 5899999999999987
No 69
>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=98.39 E-value=7.2e-06 Score=77.02 Aligned_cols=132 Identities=26% Similarity=0.266 Sum_probs=88.3
Q ss_pred CCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc-
Q 023843 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE- 157 (276)
Q Consensus 79 ~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~- 157 (276)
...+|+||+|++....-. ..++-|.|.+.+ .+| +|.|.. + . .+..|.+++.
T Consensus 17 ~~~~ia~DtE~~~~~~y~-~~l~LiQia~~~--~~~--liD~~~-----------~--------~----~~~~L~~lL~d 68 (367)
T TIGR01388 17 TFPFVALDTEFVRERTFW-PQLGLIQVADGE--QLA--LIDPLV-----------I--------I----DWSPLKELLRD 68 (367)
T ss_pred cCCEEEEeccccCCCCCC-CcceEEEEeeCC--eEE--EEeCCC-----------c--------c----cHHHHHHHHCC
Confidence 457999999998765221 245666665532 222 233321 0 0 0233556675
Q ss_pred -CCeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCC------C---------
Q 023843 158 -GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGE------H--------- 218 (276)
Q Consensus 158 -~~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~------H--------- 218 (276)
+.+.|+|++++|+.+|. ...+ ..++||+..++++.++. +.+|..|+.+++|+.++.+. .
T Consensus 69 ~~i~KV~h~~k~Dl~~L~~~~~~~~-~~~fDtqlAa~lL~~~~-~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~ 146 (367)
T TIGR01388 69 ESVVKVLHAASEDLEVFLNLFGELP-QPLFDTQIAAAFCGFGM-SMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLE 146 (367)
T ss_pred CCceEEEeecHHHHHHHHHHhCCCC-CCcccHHHHHHHhCCCC-CccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHH
Confidence 34569999999999986 2222 24799999999997543 46999999999998775321 1
Q ss_pred ChHHHHHHHHHHHHHhHHHHHH
Q 023843 219 CPIDDARAAMLLYMKNRKQWEK 240 (276)
Q Consensus 219 ~Al~DA~at~~L~~~l~~~~e~ 240 (276)
.|..||.++..||..+..++++
T Consensus 147 YAa~Dv~~L~~L~~~L~~~L~~ 168 (367)
T TIGR01388 147 YAAADVTYLLPLYAKLMERLEE 168 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 2788899999999999777653
No 70
>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=98.37 E-value=2.5e-06 Score=70.55 Aligned_cols=107 Identities=17% Similarity=0.114 Sum_probs=50.9
Q ss_pred EEEEEeccCCCC--CCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHh-cCC
Q 023843 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI-EGR 159 (276)
Q Consensus 83 VaiD~EttG~~~--~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l-~~~ 159 (276)
|+||+||+|+++ +.+.-+| +...+.+....|..+..... .-.+.+.++..++ +..
T Consensus 1 l~~DIET~Gl~~~~~~i~liG-~~~~~~~~~~~~~~~~~~~~---------------------~ee~~~~~~~~~l~~~~ 58 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIG-VADFDDDEIITFIQWFAEDP---------------------DEEEIILEFFELLDEAD 58 (164)
T ss_dssp --EEEEESS-GG-G---EEEE-EEE-ETTTTE-EEEE-GGGH---------------------HHHHHHHH--HHHHTT-
T ss_pred CcEEecCCCCCCCCCCEEEEE-EEEeCCCceEEeeHhhccCc---------------------HHHHHHHHHHHHHhcCC
Confidence 689999999986 4555666 44434433332444433210 0122222222344 578
Q ss_pred eEEEEch-hhHHHHhc-----ccCC-CCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCC
Q 023843 160 ILVGHAL-HNDLKALL-----LTHS-KKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ 214 (276)
Q Consensus 160 ~lVgHn~-~~D~~~L~-----~~~~-~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~ 214 (276)
.+|+||. .||+.+|+ ...+ ....+|+....+... ..+++|+.++ ++||+...
T Consensus 59 ~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~--~~~~~Lk~ve-~~lg~~~~ 117 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHF--LESYSLKNVE-KFLGIERR 117 (164)
T ss_dssp -EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TT--SCCTT--SHH-H-------
T ss_pred eEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhcc--CCCCCHHHHh-hhcccccc
Confidence 8999996 99999997 1112 345789887765433 3778999998 67887765
No 71
>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=98.30 E-value=1.4e-05 Score=66.87 Aligned_cols=133 Identities=23% Similarity=0.148 Sum_probs=89.1
Q ss_pred CcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc--
Q 023843 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE-- 157 (276)
Q Consensus 80 ~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~-- 157 (276)
.+.++||+|++|.++.. ..+.++.+...+ .++| |.+... + .+...|.+++.
T Consensus 3 ~~~~~~~~~~~~~~~~~-~~l~~i~l~~~~-~~~~---i~~~~~---------------~-------~~~~~l~~~l~~~ 55 (178)
T cd06140 3 ADEVALYVELLGENYHT-ADIIGLALANGG-GAYY---IPLELA---------------L-------LDLAALKEWLEDE 55 (178)
T ss_pred CCceEEEEEEcCCCcce-eeEEEEEEEeCC-cEEE---Eeccch---------------H-------HHHHHHHHHHhCC
Confidence 46789999999988543 356667776532 3333 221110 0 13445667776
Q ss_pred CCeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC------C-----C--C---
Q 023843 158 GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN------G-----E--H--- 218 (276)
Q Consensus 158 ~~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~------~-----~--H--- 218 (276)
+...|+||+++|+.+|. +..+. .++||+..++++.+...+++|.+|+.++++.+... . . .
T Consensus 56 ~~~ki~~d~K~~~~~l~~~gi~~~~-~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~ 134 (178)
T cd06140 56 KIPKVGHDAKRAYVALKRHGIELAG-VAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEEVYGKGAKFAVPDEEVL 134 (178)
T ss_pred CCceeccchhHHHHHHHHCCCcCCC-cchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCCcchHHhcCCCCCcccCCHHHH
Confidence 35689999999999995 33332 25899999999998776679999999998876321 0 0 0
Q ss_pred --ChHHHHHHHHHHHHHhHHHHHH
Q 023843 219 --CPIDDARAAMLLYMKNRKQWEK 240 (276)
Q Consensus 219 --~Al~DA~at~~L~~~l~~~~e~ 240 (276)
.+..||.++..|+..+..++++
T Consensus 135 ~~y~~~~a~~l~~l~~~l~~~L~~ 158 (178)
T cd06140 135 AEHLARKAAAIARLAPKLEEELEE 158 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1455577778888888777754
No 72
>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=98.25 E-value=1.9e-05 Score=67.66 Aligned_cols=116 Identities=13% Similarity=0.134 Sum_probs=71.9
Q ss_pred CcEEEEEEecc---CC-C--CCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 80 TDVVAMDCEMV---GI-S--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 80 ~~~VaiD~Ett---G~-~--~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
=++++||+||+ |+ + .+.|+.|+ +....+..++.. .+.. ...+....+..+++..|.
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is---~~~~~~~~~~~~--~~~~-------------~~~v~~~~~E~~lL~~F~ 64 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMIS---FADEGGNKVITW--KKFD-------------LPFVEVVKTEKEMIKRFI 64 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEE---EecCCCceEEEe--cCCC-------------CCeEEEeCCHHHHHHHHH
Confidence 36899999998 43 2 23555555 333334333211 1110 012223355678888888
Q ss_pred HHhc---CCeEEEEch-hhHHHHhc-------ccCC----------------------CCceeehhhhchhhhCCCCCcc
Q 023843 154 ELIE---GRILVGHAL-HNDLKALL-------LTHS----------------------KKDLRDTSEYQPFLNRNGRSKA 200 (276)
Q Consensus 154 ~~l~---~~~lVgHn~-~~D~~~L~-------~~~~----------------------~~~~~Dt~~~~~~~~~~~~~~s 200 (276)
+++. ..++||||+ .||+.+|. +..+ ....+|+..+.+... ...+++
T Consensus 65 ~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~-~l~sy~ 143 (195)
T cd05780 65 EIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL-NLTRYT 143 (195)
T ss_pred HHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC-CCCcCc
Confidence 8886 468999999 79999985 2211 112567776654433 567999
Q ss_pred HHHHHHHHhCCcCC
Q 023843 201 LRHLAAEILAVEIQ 214 (276)
Q Consensus 201 L~~La~~~lgi~~~ 214 (276)
|+++|.++||.+..
T Consensus 144 L~~v~~~~Lg~~k~ 157 (195)
T cd05780 144 LERVYEELFGIEKE 157 (195)
T ss_pred HHHHHHHHhCCCCC
Confidence 99999889997643
No 73
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=98.24 E-value=4.8e-05 Score=62.42 Aligned_cols=88 Identities=27% Similarity=0.298 Sum_probs=63.3
Q ss_pred HHHHHHHhc--CCeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC---C----
Q 023843 149 QKKVAELIE--GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN---G---- 216 (276)
Q Consensus 149 ~~~l~~~l~--~~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~---~---- 216 (276)
...|.+|+. +...||||+++|+.+|. +.... ++||+.+++++.+....++|+.++.+++|..++. .
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~--~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~ 141 (172)
T smart00474 64 LEILKDLLEDETITKVGHNAKFDLHVLARFGIELEN--IFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWG 141 (172)
T ss_pred HHHHHHHhcCCCceEEEechHHHHHHHHHCCCcccc--hhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccc
Confidence 455667776 45689999999999995 33333 5899999999987666579999999988876431 0
Q ss_pred -CC-------ChHHHHHHHHHHHHHhHHHH
Q 023843 217 -EH-------CPIDDARAAMLLYMKNRKQW 238 (276)
Q Consensus 217 -~H-------~Al~DA~at~~L~~~l~~~~ 238 (276)
.. .+..||.++.+|+..+..++
T Consensus 142 ~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 142 ARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 00 25667777788777776553
No 74
>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=98.12 E-value=0.0001 Score=62.81 Aligned_cols=105 Identities=17% Similarity=0.215 Sum_probs=66.2
Q ss_pred CcEEEEEEeccC---C-CC--CCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 80 TDVVAMDCEMVG---I-SQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 80 ~~~VaiD~EttG---~-~~--~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
-++++||+||++ + ++ +.|+.|+ +...+|.+.+-. ....+..+++..|.
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is---~~~~~g~~~~~~-----------------------~~~~~E~~lL~~F~ 56 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVIS---LATSNGDVEFIL-----------------------AEGLDDRKIIREFV 56 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEE---EEeCCCCEEEEE-----------------------ecCCCHHHHHHHHH
Confidence 468999999993 3 22 2445555 444345432211 01245678888898
Q ss_pred HHhc---CCeEEEEch-hhHHHHhc-------ccCC--C------------------CceeehhhhchhhhCCCCCccHH
Q 023843 154 ELIE---GRILVGHAL-HNDLKALL-------LTHS--K------------------KDLRDTSEYQPFLNRNGRSKALR 202 (276)
Q Consensus 154 ~~l~---~~~lVgHn~-~~D~~~L~-------~~~~--~------------------~~~~Dt~~~~~~~~~~~~~~sL~ 202 (276)
+++. ..+|+|||+ .||+.+|. +... + ...+|+..+.+... ...+++|+
T Consensus 57 ~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~-~l~~y~L~ 135 (188)
T cd05781 57 KYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP-EVKVKTLE 135 (188)
T ss_pred HHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC-CCCCCCHH
Confidence 8885 468999998 89999985 1111 0 01566665544333 46789999
Q ss_pred HHHHHHhCCc
Q 023843 203 HLAAEILAVE 212 (276)
Q Consensus 203 ~La~~~lgi~ 212 (276)
++| ++||..
T Consensus 136 ~Va-~~Lg~~ 144 (188)
T cd05781 136 NVA-EYLGVM 144 (188)
T ss_pred HHH-HHHCCC
Confidence 999 579864
No 75
>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=98.12 E-value=0.0001 Score=61.31 Aligned_cols=131 Identities=25% Similarity=0.326 Sum_probs=85.2
Q ss_pred cEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc--C
Q 023843 81 DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE--G 158 (276)
Q Consensus 81 ~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~--~ 158 (276)
..+++|+|+.+..+.. ..+..+.+... +++++ +.+. . . .+...|.+++. +
T Consensus 13 ~~l~~~~e~~~~~~~~-~~~~~i~l~~~-~~~~~---i~~~----------------~------~-~~~~~l~~ll~~~~ 64 (178)
T cd06142 13 GVIAVDTEFMRLNTYY-PRLCLIQISTG-GEVYL---IDPL----------------A------I-GDLSPLKELLADPN 64 (178)
T ss_pred CeEEEECCccCCCcCC-CceEEEEEeeC-CCEEE---EeCC----------------C------c-ccHHHHHHHHcCCC
Confidence 5899999977655211 23445556543 33432 2111 0 0 13344666776 3
Q ss_pred CeEEEEchhhHHHHhcc--cCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCC------C---------CChH
Q 023843 159 RILVGHALHNDLKALLL--THSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNG------E---------HCPI 221 (276)
Q Consensus 159 ~~lVgHn~~~D~~~L~~--~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~------~---------H~Al 221 (276)
...||||+++|+.+|.. ......++|++.+++++.+... .+|++|+.+++|...... . +.+.
T Consensus 65 i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p~~~-~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa 143 (178)
T cd06142 65 IVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDS-VGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAA 143 (178)
T ss_pred ceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCCCcc-ccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHH
Confidence 56799999999999952 2212236899999999987654 599999999988763211 0 1267
Q ss_pred HHHHHHHHHHHHhHHHHHH
Q 023843 222 DDARAAMLLYMKNRKQWEK 240 (276)
Q Consensus 222 ~DA~at~~L~~~l~~~~e~ 240 (276)
.||.++..|+..+..++++
T Consensus 144 ~~a~~l~~L~~~l~~~L~e 162 (178)
T cd06142 144 LDVRYLLPLYEKLKEELEE 162 (178)
T ss_pred HhHHHHHHHHHHHHHHHHH
Confidence 7788899999988877764
No 76
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=98.03 E-value=2.9e-05 Score=76.14 Aligned_cols=133 Identities=23% Similarity=0.214 Sum_probs=93.7
Q ss_pred EEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhcC--Ce
Q 023843 83 VAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG--RI 160 (276)
Q Consensus 83 VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~~--~~ 160 (276)
+++|+||+|+++.. ..+.++++.... +..|...-. + +.. -++...+..|+.+ ..
T Consensus 25 ~a~~~et~~l~~~~-~~lvg~s~~~~~-~~~yi~~~~-------------~--~~~-------~~~~~~l~~~l~~~~~~ 80 (593)
T COG0749 25 IAFDTETDGLDPHG-ADLVGLSVASEE-EAAYIPLLH-------------G--PEQ-------LNVLAALKPLLEDEGIK 80 (593)
T ss_pred ceeeccccccCccc-CCeeEEEeeccc-cceeEeecc-------------c--hhh-------hhhHHHHHHHhhCcccc
Confidence 99999999999643 345556665433 333321111 1 112 2277888999974 45
Q ss_pred EEEEchhhHHHHhcccCC-CCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCC---------------------CC
Q 023843 161 LVGHALHNDLKALLLTHS-KKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNG---------------------EH 218 (276)
Q Consensus 161 lVgHn~~~D~~~L~~~~~-~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~---------------------~H 218 (276)
.||||++||+.+|...-. ..-+.||+.+.+++.++.+.+.+++|+.++++...... .-
T Consensus 81 kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~ 160 (593)
T COG0749 81 KVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATE 160 (593)
T ss_pred hhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHH
Confidence 899999999999983322 13378999999999998889999999999988554321 12
Q ss_pred ChHHHHHHHHHHHHHhHHHHH
Q 023843 219 CPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 219 ~Al~DA~at~~L~~~l~~~~e 239 (276)
.+.+||.++.+|+..+..++.
T Consensus 161 y~a~~a~~~~~L~~~l~~~l~ 181 (593)
T COG0749 161 YAAEDADATLRLESILEPELL 181 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 367899999999999876544
No 77
>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=97.87 E-value=0.00085 Score=58.03 Aligned_cols=90 Identities=20% Similarity=0.248 Sum_probs=66.0
Q ss_pred CHHHHHHHHHHHhc--CCeEEEEch-hhHHHHhc-------ccCCC-----------------CceeehhhhchhhhCCC
Q 023843 144 DFPTVQKKVAELIE--GRILVGHAL-HNDLKALL-------LTHSK-----------------KDLRDTSEYQPFLNRNG 196 (276)
Q Consensus 144 ~~~ev~~~l~~~l~--~~~lVgHn~-~~D~~~L~-------~~~~~-----------------~~~~Dt~~~~~~~~~~~ 196 (276)
+..+++..|.++++ ...||+||. .||+.+|. +..|. .+.+|++.+..... ..
T Consensus 36 ~E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g-~~ 114 (209)
T PF10108_consen 36 DEKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYG-AK 114 (209)
T ss_pred CHHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccC-cc
Confidence 35788899999996 567999998 99999996 22221 13578887643332 45
Q ss_pred CCccHHHHHHHHhCCcCCCCCC------------------ChHHHHHHHHHHHHHhH
Q 023843 197 RSKALRHLAAEILAVEIQNGEH------------------CPIDDARAAMLLYMKNR 235 (276)
Q Consensus 197 ~~~sL~~La~~~lgi~~~~~~H------------------~Al~DA~at~~L~~~l~ 235 (276)
...+|+.|| ..+|++...+-+ -...|+.+|+.||.++.
T Consensus 115 ~~~sLd~la-~~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 115 ARTSLDELA-ALLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred ccCCHHHHH-HHcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999 899988643222 14789999999999984
No 78
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=97.75 E-value=0.00013 Score=62.76 Aligned_cols=154 Identities=19% Similarity=0.178 Sum_probs=98.8
Q ss_pred cEEEEEEeccCCC--C---------------------CCeeEEEEEEEEeCCCcEE--------EEEe-ecCCc-ccccc
Q 023843 81 DVVAMDCEMVGIS--Q---------------------GNKSALGRVSLVNKWGNLI--------YDEF-VRPLE-RVVDF 127 (276)
Q Consensus 81 ~~VaiD~EttG~~--~---------------------~~iiei~~v~v~~~~g~ii--------~~~~-v~P~~-~i~~~ 127 (276)
++|++|+|.-|+- | -.+|++| +++.|..|+.- |+.- ..+.. ...+.
T Consensus 25 ~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlG-lTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~a~~ 103 (239)
T KOG0304|consen 25 PYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLG-LTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMYAQD 103 (239)
T ss_pred CeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhhee-eeeeccCCCCCCCCCceeEEecccCCchhhccchh
Confidence 4888888887762 1 1368888 88888766542 2222 22222 22222
Q ss_pred c---ccccCCCHHHh-cCCCCHHHHHHHHHH---Hh-cCCeEEEEchhhHHHHhc-----ccCC-------------CCc
Q 023843 128 R---TRISGIRPRDL-RKAKDFPTVQKKVAE---LI-EGRILVGHALHNDLKALL-----LTHS-------------KKD 181 (276)
Q Consensus 128 ~---~~i~GIt~~~l-~~a~~~~ev~~~l~~---~l-~~~~lVgHn~~~D~~~L~-----~~~~-------------~~~ 181 (276)
+ .+-+||.-+-. ..++...+....+.. .+ +...+|-+...||+.+|- -..| ...
T Consensus 104 SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~ 183 (239)
T KOG0304|consen 104 SIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPF 183 (239)
T ss_pred hHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcch
Confidence 2 23367765544 445554433333222 11 356778888899998874 1111 123
Q ss_pred eeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhHH
Q 023843 182 LRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRK 236 (276)
Q Consensus 182 ~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~~ 236 (276)
+.|+..+..++.......+|..|| +.|++.-.+.+|.|-+|++.|+..|.+++.
T Consensus 184 vYDiK~l~~~c~~~~l~~GL~~lA-~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 184 VYDVKYLMKFCEGLSLKGGLQRLA-DLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred hhhHHHHHHhhhhhhhhcCHHHHH-HHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 678888887776444578999999 899999988899999999999999999865
No 79
>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=97.73 E-value=0.00062 Score=58.95 Aligned_cols=33 Identities=18% Similarity=0.289 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc
Q 023843 142 AKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL 174 (276)
Q Consensus 142 a~~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~ 174 (276)
..+..+++..|.+++. ..+|||||+ .||+.+|.
T Consensus 55 ~~~E~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~ 91 (207)
T cd05785 55 DAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLR 91 (207)
T ss_pred CCCHHHHHHHHHHHHHHhCCCEEeccCCcccCHHHHH
Confidence 4567889999999986 378899999 99999985
No 80
>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=97.73 E-value=0.0005 Score=58.48 Aligned_cols=87 Identities=21% Similarity=0.213 Sum_probs=61.8
Q ss_pred HHHHHhc--CCeEEEEchhhHHHHhc----ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC-------CC
Q 023843 151 KVAELIE--GRILVGHALHNDLKALL----LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN-------GE 217 (276)
Q Consensus 151 ~l~~~l~--~~~lVgHn~~~D~~~L~----~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~-------~~ 217 (276)
.|.+++. +...|||+++.|+.+|. +.... ++|++..++++.+. . ++|+.|+.++++..+.. ..
T Consensus 68 ~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~--~fD~~laaYLL~p~-~-~~l~~l~~~yl~~~~~k~~~~~~~~~ 143 (192)
T cd06147 68 ILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVN--LFDTGQAARVLNLP-R-HSLAYLLQKYCNVDADKKYQLADWRI 143 (192)
T ss_pred HHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCc--hHHHHHHHHHhCCC-c-ccHHHHHHHHhCCCcchhhhcccccc
Confidence 4666775 46789999999999984 22222 38999999999987 5 59999999998765200 01
Q ss_pred C--------ChHHHHHHHHHHHHHhHHHHHHH
Q 023843 218 H--------CPIDDARAAMLLYMKNRKQWEKS 241 (276)
Q Consensus 218 H--------~Al~DA~at~~L~~~l~~~~e~~ 241 (276)
+ .+..||.++..|+..+..+++++
T Consensus 144 ~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~ 175 (192)
T cd06147 144 RPLPEEMIKYAREDTHYLLYIYDRLRNELLER 175 (192)
T ss_pred CCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHh
Confidence 2 14555777777777777776654
No 81
>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=97.70 E-value=0.00096 Score=57.65 Aligned_cols=90 Identities=19% Similarity=0.100 Sum_probs=58.4
Q ss_pred CCCHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc-------ccCC------C----------Cceeehhhhchhh-h
Q 023843 142 AKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL-------LTHS------K----------KDLRDTSEYQPFL-N 193 (276)
Q Consensus 142 a~~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~-------~~~~------~----------~~~~Dt~~~~~~~-~ 193 (276)
..+..+.+.+|.+++. -.+++|||+ .||+.+|. +... . .-.+|+..+.... .
T Consensus 70 ~~~E~~lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~ 149 (204)
T cd05779 70 EPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSY 149 (204)
T ss_pred CCCHHHHHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhc
Confidence 3567889999999986 358999999 99999985 1111 0 0145655543321 1
Q ss_pred CCCCCccHHHHHHHHhCCcCCCC----------------CCChHHHHHHHHHHH
Q 023843 194 RNGRSKALRHLAAEILAVEIQNG----------------EHCPIDDARAAMLLY 231 (276)
Q Consensus 194 ~~~~~~sL~~La~~~lgi~~~~~----------------~H~Al~DA~at~~L~ 231 (276)
....+++|+.+|..+||..-..- ++-.+.||.+|..||
T Consensus 150 l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 150 LPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLY 203 (204)
T ss_pred CCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCcHHHHhccHHHHHHHHHHh
Confidence 13358999999987899643311 123567777777776
No 82
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=97.65 E-value=0.0017 Score=57.04 Aligned_cols=72 Identities=18% Similarity=0.134 Sum_probs=48.3
Q ss_pred CCCHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc-------ccCC----C---------------------------
Q 023843 142 AKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL-------LTHS----K--------------------------- 179 (276)
Q Consensus 142 a~~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~-------~~~~----~--------------------------- 179 (276)
..+..+.+..|..++. -.+++|||+ .||+.+|. +... +
T Consensus 68 ~~~E~eLL~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~ 147 (230)
T cd05777 68 FETEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEIN 147 (230)
T ss_pred ECCHHHHHHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEE
Confidence 3567888888888885 479999999 89998884 1100 0
Q ss_pred ---CceeehhhhchhhhCCCCCccHHHHHHHHhCCcCC
Q 023843 180 ---KDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQ 214 (276)
Q Consensus 180 ---~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~ 214 (276)
.-++|+..+.+... ...+++|+++|..+||....
T Consensus 148 i~GR~~iD~~~~~~~~~-kl~sy~L~~Va~~~Lg~~k~ 184 (230)
T cd05777 148 IEGRIQFDLLQVIQRDY-KLRSYSLNSVSAHFLGEQKE 184 (230)
T ss_pred EcCEEeeeHHHHHHHhc-CcccCcHHHHHHHHhCCCCC
Confidence 01234444433322 56799999999889985543
No 83
>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=97.61 E-value=0.0018 Score=52.00 Aligned_cols=60 Identities=23% Similarity=0.179 Sum_probs=46.3
Q ss_pred HHHHhc--CCeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCc
Q 023843 152 VAELIE--GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVE 212 (276)
Q Consensus 152 l~~~l~--~~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~ 212 (276)
|.+++. +...||||++.|+.+|. +.... .++|++.+++++.+...+.+|+.|+.++++..
T Consensus 45 l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~-~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKALKVGQNLKYDRGILLNYFIELRG-IAFDTMLEAYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCCceeeecHHHHHHHHHHcCCccCC-cchhHHHHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence 556775 46679999999999996 22222 36899999999998652359999999998876
No 84
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=97.60 E-value=0.00017 Score=63.78 Aligned_cols=169 Identities=14% Similarity=0.134 Sum_probs=104.2
Q ss_pred CCCCCCcEEEEEEeccCCC--CCCeeEEEEEEEE-----------eCCCc------EE---EEEeecCCccccccccccc
Q 023843 75 DDFSLTDVVAMDCEMVGIS--QGNKSALGRVSLV-----------NKWGN------LI---YDEFVRPLERVVDFRTRIS 132 (276)
Q Consensus 75 ~~~~~~~~VaiD~EttG~~--~~~iiei~~v~v~-----------~~~g~------ii---~~~~v~P~~~i~~~~~~i~ 132 (276)
+-.....++++|.|+||+. ..+|.|++...|. +.++. .+ .+.++.|.......+.+|+
T Consensus 8 e~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeit 87 (318)
T KOG4793|consen 8 EVPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEIT 87 (318)
T ss_pred cCCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhc
Confidence 3445788999999999995 1244444432221 11111 11 3444677777777889999
Q ss_pred CCCHHHhcCC--CCHH-HHHHHHHHHhc----CCeEEEEch-hhHHHHhc-------ccCCCC-ceeehhhhchhhhC--
Q 023843 133 GIRPRDLRKA--KDFP-TVQKKVAELIE----GRILVGHAL-HNDLKALL-------LTHSKK-DLRDTSEYQPFLNR-- 194 (276)
Q Consensus 133 GIt~~~l~~a--~~~~-ev~~~l~~~l~----~~~lVgHn~-~~D~~~L~-------~~~~~~-~~~Dt~~~~~~~~~-- 194 (276)
|++..-+.-. .-|+ ++.+-|..|+. ..+||+||. .||+.+|. +..+.- -.+|+......+..
T Consensus 88 gls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~ 167 (318)
T KOG4793|consen 88 GLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRAN 167 (318)
T ss_pred ccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhc
Confidence 9998654322 2343 34444556663 567999999 89998886 333321 12344433322221
Q ss_pred -------CCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHH
Q 023843 195 -------NGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVK 243 (276)
Q Consensus 195 -------~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~~~~e~~~~ 243 (276)
....++|..+..++++-.-..+.|.+..|.....-+|+....++-....
T Consensus 168 s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~d 223 (318)
T KOG4793|consen 168 SMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSD 223 (318)
T ss_pred CcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHh
Confidence 2467899999888888633337899999998888888777655444333
No 85
>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=97.58 E-value=0.0027 Score=54.86 Aligned_cols=72 Identities=15% Similarity=0.075 Sum_probs=48.1
Q ss_pred CCCHHHHHHHHHHHhc-CCeEEEEch-hhHHHHhc-----ccCC----------------CCceeehhhhchh-------
Q 023843 142 AKDFPTVQKKVAELIE-GRILVGHAL-HNDLKALL-----LTHS----------------KKDLRDTSEYQPF------- 191 (276)
Q Consensus 142 a~~~~ev~~~l~~~l~-~~~lVgHn~-~~D~~~L~-----~~~~----------------~~~~~Dt~~~~~~------- 191 (276)
..+..+++.+|.+++. ..++||||+ .||+.+|. +... ....+|.......
T Consensus 70 ~~~E~~lL~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~ 149 (204)
T cd05783 70 FDSEKELIREAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYA 149 (204)
T ss_pred cCCHHHHHHHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhh
Confidence 3567889999999986 568899999 99999985 1111 1124565543221
Q ss_pred hhCCCCCccHHHHHHHHhCCcC
Q 023843 192 LNRNGRSKALRHLAAEILAVEI 213 (276)
Q Consensus 192 ~~~~~~~~sL~~La~~~lgi~~ 213 (276)
+.....+++|+++|..+||..-
T Consensus 150 ~~~~~~~~~L~~Va~~~lg~~K 171 (204)
T cd05783 150 FGNKYREYTLDAVAKALLGEGK 171 (204)
T ss_pred hccccccCcHHHHHHHhcCCCc
Confidence 1113468999999977888543
No 86
>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=97.57 E-value=0.0019 Score=55.28 Aligned_cols=117 Identities=17% Similarity=0.125 Sum_probs=68.2
Q ss_pred CcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc--
Q 023843 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE-- 157 (276)
Q Consensus 80 ~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~-- 157 (276)
=++++||+|++|.+ .|..+| ..+.....++.. -.+. .. .| ..+.-..+..+.+..|.+++.
T Consensus 3 l~~~~fDIE~~~~~--~i~~i~---~~~~~~~~i~~~-~~~~-~~-------~~---~~v~~~~~E~~lL~~f~~~i~~~ 65 (193)
T cd05784 3 LKVVSLDIETSMDG--ELYSIG---LYGEGQERVLMV-GDPE-DD-------AP---DNIEWFADEKSLLLALIAWFAQY 65 (193)
T ss_pred ccEEEEEeecCCCC--CEEEEE---eecCCCCEEEEE-CCCC-CC-------CC---CEEEEECCHHHHHHHHHHHHHhh
Confidence 36899999998753 444444 333322332211 0111 10 01 012223466788888888885
Q ss_pred -CCeEEEEch-hhHHHHhc-------ccCC------------------------CCceeehhhhchhhhCCCCCccHHHH
Q 023843 158 -GRILVGHAL-HNDLKALL-------LTHS------------------------KKDLRDTSEYQPFLNRNGRSKALRHL 204 (276)
Q Consensus 158 -~~~lVgHn~-~~D~~~L~-------~~~~------------------------~~~~~Dt~~~~~~~~~~~~~~sL~~L 204 (276)
-.+++|||+ .||+.+|. +... ..-++|+..+.+.......+++|+++
T Consensus 66 dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~kl~sy~L~~V 145 (193)
T cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENV 145 (193)
T ss_pred CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCCCCcCCHHHH
Confidence 358999999 99999885 2210 00145655443321125689999999
Q ss_pred HHHHhCCcC
Q 023843 205 AAEILAVEI 213 (276)
Q Consensus 205 a~~~lgi~~ 213 (276)
|..+||..-
T Consensus 146 a~~~Lg~~K 154 (193)
T cd05784 146 AQELLGEGK 154 (193)
T ss_pred HHHHhCCCc
Confidence 988998643
No 87
>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=97.43 E-value=0.0021 Score=55.68 Aligned_cols=67 Identities=21% Similarity=0.174 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhc--CCeEEEEch-hhHHHHhc-------ccCCCC----------------ceeehhhhchhhhCCCCC
Q 023843 145 FPTVQKKVAELIE--GRILVGHAL-HNDLKALL-------LTHSKK----------------DLRDTSEYQPFLNRNGRS 198 (276)
Q Consensus 145 ~~ev~~~l~~~l~--~~~lVgHn~-~~D~~~L~-------~~~~~~----------------~~~Dt~~~~~~~~~~~~~ 198 (276)
..+++..|.+++. ..+|||||. .||+.+|. +..+.. +.+|++.+..... ...+
T Consensus 78 E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~-~~~~ 156 (208)
T cd05782 78 EKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYG-ARAR 156 (208)
T ss_pred HHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccC-ccCC
Confidence 4678888888886 568999999 99999996 221210 2677776643322 3478
Q ss_pred ccHHHHHHHHhCCcC
Q 023843 199 KALRHLAAEILAVEI 213 (276)
Q Consensus 199 ~sL~~La~~~lgi~~ 213 (276)
++|+.+| +.||++.
T Consensus 157 ~~L~~va-~~lG~~~ 170 (208)
T cd05782 157 ASLDLLA-KLLGIPG 170 (208)
T ss_pred CCHHHHH-HHhCCCC
Confidence 9999998 7899843
No 88
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.29 E-value=0.0039 Score=66.08 Aligned_cols=150 Identities=15% Similarity=0.079 Sum_probs=86.4
Q ss_pred CCCCcEEEEEEeccCCC----C----CCeeEEEEEEEEeCCCc-EEEEEeecCCcccccccccccCCCHHHhcCCCCHHH
Q 023843 77 FSLTDVVAMDCEMVGIS----Q----GNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPT 147 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~----~----~~iiei~~v~v~~~~g~-ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~e 147 (276)
.++-++++||+||.+.. | +.|++|+.+....+... .+....+.+. .+..+.|. .+....+..+
T Consensus 261 ~pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~-----~c~~i~g~---~V~~f~sE~e 332 (1054)
T PTZ00166 261 IAPLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLK-----ECASIAGA---NVLSFETEKE 332 (1054)
T ss_pred CCCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecC-----ccccCCCc---eEEEeCCHHH
Confidence 35678999999998642 1 36677764433322111 1111111111 11122221 2223356678
Q ss_pred HHHHHHHHhc---CCeEEEEch-hhHHHHhc-------ccC-C---C------------------------------Cce
Q 023843 148 VQKKVAELIE---GRILVGHAL-HNDLKALL-------LTH-S---K------------------------------KDL 182 (276)
Q Consensus 148 v~~~l~~~l~---~~~lVgHn~-~~D~~~L~-------~~~-~---~------------------------------~~~ 182 (276)
.+..|.+|+. -.+|+|||+ .||+.+|. +.. . + .-+
T Consensus 333 LL~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~ 412 (1054)
T PTZ00166 333 LLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQ 412 (1054)
T ss_pred HHHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEEE
Confidence 8888888874 689999999 89998884 110 0 0 013
Q ss_pred eehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCC-------------------ChHHHHHHHHHHHHHhH
Q 023843 183 RDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEH-------------------CPIDDARAAMLLYMKNR 235 (276)
Q Consensus 183 ~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H-------------------~Al~DA~at~~L~~~l~ 235 (276)
+|+..+.+... ...+++|++++..+||.....-.| -.+.||..+++|+.++.
T Consensus 413 iDl~~~~~~~~-kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 413 FDVMDLIRRDY-KLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred EEHHHHHHHhc-CcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34444333222 567899999998899865431111 14789999999888763
No 89
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.06 E-value=0.002 Score=67.04 Aligned_cols=93 Identities=18% Similarity=0.049 Sum_probs=69.8
Q ss_pred HHHHHHHHHHHhcC--CeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCC----
Q 023843 145 FPTVQKKVAELIEG--RILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQN---- 215 (276)
Q Consensus 145 ~~ev~~~l~~~l~~--~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~---- 215 (276)
...+...|.+++.+ ..+||||++||+.+|. +.... .+.||+..++++.+... ++|++|+.+|++.....
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~-~~~Dt~la~yll~~~~~-~~l~~la~~yl~~~~~~~~~~ 440 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGG-VIFDTMLAAYLLDPAQV-STLDTLARRYLVEELILDEKI 440 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCC-cchhHHHHHHHcCCCCC-CCHHHHHHHHcCcccccHHHh
Confidence 45667778888874 4579999999999996 33322 36899999999997654 59999999988744210
Q ss_pred --C-----C-------CChHHHHHHHHHHHHHhHHHHH
Q 023843 216 --G-----E-------HCPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 216 --~-----~-------H~Al~DA~at~~L~~~l~~~~e 239 (276)
. . ..+..||.++.+||..+..+++
T Consensus 441 ~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 441 GGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred ccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0 1367889999999999887765
No 90
>PHA02528 43 DNA polymerase; Provisional
Probab=96.97 E-value=0.022 Score=59.32 Aligned_cols=162 Identities=15% Similarity=0.029 Sum_probs=88.3
Q ss_pred CCCCCCCCCcEEEEEEeccCCC----CC-CeeEEEEEEEEeCCCcEEEEEeecCCcc---cccccccccCCCHHHhcCCC
Q 023843 72 PINDDFSLTDVVAMDCEMVGIS----QG-NKSALGRVSLVNKWGNLIYDEFVRPLER---VVDFRTRISGIRPRDLRKAK 143 (276)
Q Consensus 72 ~~~~~~~~~~~VaiD~EttG~~----~~-~iiei~~v~v~~~~g~ii~~~~v~P~~~---i~~~~~~i~GIt~~~l~~a~ 143 (276)
|..-+.+.-++++||+||+..+ +. ....|..|.+.+..+..++-..+....+ ..+.. .-.....-.+....
T Consensus 98 ~~~~~~p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~-~~~~~~~v~~~~~~ 176 (881)
T PHA02528 98 EIKYDRSKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEV-PQEILDKVVYMPFD 176 (881)
T ss_pred CCCCCCCCccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcc-cccccCCeeEEEcC
Confidence 3333435678999999997522 22 1234555666665555432222211000 00000 00000000111245
Q ss_pred CHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc------ccC------CCC------------------------cee
Q 023843 144 DFPTVQKKVAELIE---GRILVGHAL-HNDLKALL------LTH------SKK------------------------DLR 183 (276)
Q Consensus 144 ~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~------~~~------~~~------------------------~~~ 183 (276)
+..+.+..|.+|+. ..+|+|||+ .||+.+|. +.. ..+ -++
T Consensus 177 sE~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~l 256 (881)
T PHA02528 177 TEREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISIL 256 (881)
T ss_pred CHHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEE
Confidence 67888999999884 579999999 99998884 110 000 012
Q ss_pred ehhhhchhh-hCCCCCccHHHHHHHHhCCcCCCC----------------CCChHHHHHHHHHHHHHh
Q 023843 184 DTSEYQPFL-NRNGRSKALRHLAAEILAVEIQNG----------------EHCPIDDARAAMLLYMKN 234 (276)
Q Consensus 184 Dt~~~~~~~-~~~~~~~sL~~La~~~lgi~~~~~----------------~H~Al~DA~at~~L~~~l 234 (276)
|...+.+.+ .....+++|+++|..+||.....- .+-.+.||..+.+|+.++
T Consensus 257 D~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~kl 324 (881)
T PHA02528 257 DYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDKR 324 (881)
T ss_pred eHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 222222221 114678999999988999655421 012588999999999883
No 91
>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=96.86 E-value=0.042 Score=48.31 Aligned_cols=85 Identities=11% Similarity=0.096 Sum_probs=53.5
Q ss_pred hcCCCCHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc-------ccC-----CC---------------C-------
Q 023843 139 LRKAKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL-------LTH-----SK---------------K------- 180 (276)
Q Consensus 139 l~~a~~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~-------~~~-----~~---------------~------- 180 (276)
+....+..+.+..|..++. -.+++|||+ .||+.+|. +.. .+ +
T Consensus 75 v~~~~~E~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~ 154 (231)
T cd05778 75 VEVVESELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSG 154 (231)
T ss_pred EEEeCCHHHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCc
Confidence 3334567788888888874 689999999 89998874 100 00 0
Q ss_pred ------ceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHH
Q 023843 181 ------DLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDA 224 (276)
Q Consensus 181 ------~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA 224 (276)
-++|+..+.+.- ....+|+|+++|..+||.....-.+..+.+.
T Consensus 155 ~~i~GRi~lD~~~~~r~~-~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~ 203 (231)
T cd05778 155 IKIVGRHILNVWRLMRSE-LALTNYTLENVVYHVLHQRIPLYSNKTLTEW 203 (231)
T ss_pred eEEeeEEEeEhHHHHHHH-cCcccCCHHHHHHHHhCCCCCCCCHHHHHHH
Confidence 022333332221 1567899999999999987663334444443
No 92
>PRK05762 DNA polymerase II; Reviewed
Probab=96.71 E-value=0.031 Score=57.75 Aligned_cols=140 Identities=15% Similarity=0.112 Sum_probs=83.1
Q ss_pred CCCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc
Q 023843 78 SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~ 157 (276)
+.-++++||+||.+- +.+..|+ +.......++. +.+.... ..+.+....+..+.+..|..++.
T Consensus 153 p~lrvlsfDIE~~~~--~~i~sI~---~~~~~~~~vi~--ig~~~~~----------~~~~v~~~~sE~~LL~~F~~~i~ 215 (786)
T PRK05762 153 PPLKVVSLDIETSNK--GELYSIG---LEGCGQRPVIM--LGPPNGE----------ALDFLEYVADEKALLEKFNAWFA 215 (786)
T ss_pred CCCeEEEEEEEEcCC--CceEEee---ecCCCCCeEEE--EECCCCC----------CcceEEEcCCHHHHHHHHHHHHH
Confidence 566899999999873 3444444 32221212211 1211111 00113344677888899888885
Q ss_pred ---CCeEEEEch-hhHHHHhc-------ccC--------------CC-----------CceeehhhhchhhhCCCCCccH
Q 023843 158 ---GRILVGHAL-HNDLKALL-------LTH--------------SK-----------KDLRDTSEYQPFLNRNGRSKAL 201 (276)
Q Consensus 158 ---~~~lVgHn~-~~D~~~L~-------~~~--------------~~-----------~~~~Dt~~~~~~~~~~~~~~sL 201 (276)
..+++|||+ .||+.+|. +.. +. .-++|+..+.+.......+++|
T Consensus 216 ~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL 295 (786)
T PRK05762 216 EHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSL 295 (786)
T ss_pred hcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCH
Confidence 468999998 89999885 111 00 0145555543332224578999
Q ss_pred HHHHHHHhCCcCCC-CCC-------------------ChHHHHHHHHHHHHHh
Q 023843 202 RHLAAEILAVEIQN-GEH-------------------CPIDDARAAMLLYMKN 234 (276)
Q Consensus 202 ~~La~~~lgi~~~~-~~H-------------------~Al~DA~at~~L~~~l 234 (276)
+++|..+||..... ..| -.+.||..+.+|+.++
T Consensus 296 ~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 296 EYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 99998888854321 111 2478999999999854
No 93
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=96.64 E-value=0.03 Score=49.35 Aligned_cols=113 Identities=17% Similarity=0.057 Sum_probs=63.3
Q ss_pred CCcEEEEEEeccCCC-CCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCC-HHHHHHHHHHHh
Q 023843 79 LTDVVAMDCEMVGIS-QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKD-FPTVQKKVAELI 156 (276)
Q Consensus 79 ~~~~VaiD~EttG~~-~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~-~~ev~~~l~~~l 156 (276)
..++++||+||||++ .+.++-+..+.-+ .++....-.+.-|. |. ...++..|....
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~-~~~~~~Vrq~~lp~---------------------p~~E~avle~fl~~~ 154 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARG-VDDTMHVRQHFLPA---------------------PEEEVAVLENFLHDP 154 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEc-cCceEEEEeecCCC---------------------cchhhHHHHHHhcCC
Confidence 567999999999999 3443333322222 11333333333321 11 122334433333
Q ss_pred cCCeEEEEch-hhHHHHhc------ccC-CCCceeehhhhchhhh-CCCCCccHHHHHHHHhCCcCC
Q 023843 157 EGRILVGHAL-HNDLKALL------LTH-SKKDLRDTSEYQPFLN-RNGRSKALRHLAAEILAVEIQ 214 (276)
Q Consensus 157 ~~~~lVgHn~-~~D~~~L~------~~~-~~~~~~Dt~~~~~~~~-~~~~~~sL~~La~~~lgi~~~ 214 (276)
+-..+|.+|. .||..+++ +.. +....+|.+...+-+. ......+|+.+= +.||+.-.
T Consensus 155 ~~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VE-r~LGi~R~ 220 (278)
T COG3359 155 DFNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVE-RILGIRRE 220 (278)
T ss_pred CcceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHH-HHhCcccc
Confidence 4459999999 99999998 111 1223567766544433 233567888866 58887654
No 94
>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=96.09 E-value=0.15 Score=48.70 Aligned_cols=90 Identities=22% Similarity=0.185 Sum_probs=58.5
Q ss_pred CHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc-----ccC------C-----------------------------C
Q 023843 144 DFPTVQKKVAELIE---GRILVGHAL-HNDLKALL-----LTH------S-----------------------------K 179 (276)
Q Consensus 144 ~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~-----~~~------~-----------------------------~ 179 (276)
+..+.+..|..++. ..+++|||+ .||+.+|. +.. . .
T Consensus 68 ~E~~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 147 (471)
T smart00486 68 NEKELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKG 147 (471)
T ss_pred CHHHHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEecc
Confidence 56778888888775 468999999 69998885 100 0 0
Q ss_pred CceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCC-------------------CChHHHHHHHHHHHHHh
Q 023843 180 KDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGE-------------------HCPIDDARAAMLLYMKN 234 (276)
Q Consensus 180 ~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~-------------------H~Al~DA~at~~L~~~l 234 (276)
.-.+|+..+.+... ...+++|+.++..+||.....-. ...+.||..+.+|+.++
T Consensus 148 ~~~~Dl~~~~~~~~-kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 148 RLVIDLYNLYKNKL-KLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEEEhHHHHHHHh-CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12355555544443 46789999999888873332110 01366888888888775
No 95
>PHA02570 dexA exonuclease; Provisional
Probab=95.89 E-value=0.034 Score=48.26 Aligned_cols=93 Identities=20% Similarity=0.178 Sum_probs=55.7
Q ss_pred EEEEEEeccCCCCC-CeeEEEEEEEEeCCCcE-EEEEeecCCcc------------cccccc--cccCCCHHH---hc--
Q 023843 82 VVAMDCEMVGISQG-NKSALGRVSLVNKWGNL-IYDEFVRPLER------------VVDFRT--RISGIRPRD---LR-- 140 (276)
Q Consensus 82 ~VaiD~EttG~~~~-~iiei~~v~v~~~~g~i-i~~~~v~P~~~------------i~~~~~--~i~GIt~~~---l~-- 140 (276)
=+.||+||.|..++ -|++||+|-+....|.. -|..+|..... +.+..| =|-.-+++. |.
T Consensus 3 dlMIDlETmG~~p~AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s 82 (220)
T PHA02570 3 DFIIDFETFGNTPDGAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPS 82 (220)
T ss_pred eEEEEeeccCCCCCceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCC
Confidence 37899999999866 77899988886432321 13333332111 111100 011122222 21
Q ss_pred -CCCCHHHHHHHHHHHhc--C-----CeEEEEchhhHHHHhc
Q 023843 141 -KAKDFPTVQKKVAELIE--G-----RILVGHALHNDLKALL 174 (276)
Q Consensus 141 -~a~~~~ev~~~l~~~l~--~-----~~lVgHn~~~D~~~L~ 174 (276)
+..++.+++.+|.+||. + ..+.|.+..||+.+|.
T Consensus 83 ~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 83 DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred CccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHH
Confidence 23578999999999995 2 3467888899999995
No 96
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=95.67 E-value=0.19 Score=49.08 Aligned_cols=153 Identities=15% Similarity=0.063 Sum_probs=85.9
Q ss_pred CCCCCcEEEEEEeccCCC-CC---CeeEEEEEEEEeCC--CcE--EEEEeecCCccccccccccc----CC-CHHHhcCC
Q 023843 76 DFSLTDVVAMDCEMVGIS-QG---NKSALGRVSLVNKW--GNL--IYDEFVRPLERVVDFRTRIS----GI-RPRDLRKA 142 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~-~~---~iiei~~v~v~~~~--g~i--i~~~~v~P~~~i~~~~~~i~----GI-t~~~l~~a 142 (276)
|...-++..||+|.++.+ |. ...+|-+|+..+.. ... +|..+ +. ...|..... ++ ..-.+...
T Consensus 102 d~~~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~v~v~~f 177 (498)
T PHA02524 102 DRDDVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLV--KD--VGHWDPKKSVLEKYILDNVVYMPF 177 (498)
T ss_pred chhhceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEecc--cc--ccCCCcccccccccccCCeEEEEe
Confidence 555668999999997655 33 22466667776533 111 23322 11 111111100 00 01112334
Q ss_pred CCHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc------ccC---------CCC--------------------cee
Q 023843 143 KDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL------LTH---------SKK--------------------DLR 183 (276)
Q Consensus 143 ~~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~------~~~---------~~~--------------------~~~ 183 (276)
.+..+.+.++.+|+. -.+|+|||+ .||+.+|. +.. .+. -++
T Consensus 178 ~sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~i 257 (498)
T PHA02524 178 EDEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALM 257 (498)
T ss_pred CCHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEe
Confidence 577889999999985 589999999 99997774 111 000 123
Q ss_pred ehhhhchhh-hCCCCCccHHHHHHHHhCCcCCCCCC---------------ChHHHHHHHHHHHH
Q 023843 184 DTSEYQPFL-NRNGRSKALRHLAAEILAVEIQNGEH---------------CPIDDARAAMLLYM 232 (276)
Q Consensus 184 Dt~~~~~~~-~~~~~~~sL~~La~~~lgi~~~~~~H---------------~Al~DA~at~~L~~ 232 (276)
|+..+.... .....+++|++++..++|.......| -.+.||..+.+|+.
T Consensus 258 Dl~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K~d~~~~I~~l~~~d~~rla~YclkDa~L~~~L~~ 322 (498)
T PHA02524 258 DYMDVFKKFSFTPMPDYKLGNVGYREVKADKLDYEGPINKFRKADHQRYVDYCVRDTDIILLIDG 322 (498)
T ss_pred EHHHHHHHhhhccCCCCCHHHHHHHhcCCccccchhhHHHHhcCchHHHHHHHHHHHHHHHHHHH
Confidence 444443332 12568999999997777744331111 25789999877763
No 97
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=95.67 E-value=0.13 Score=55.34 Aligned_cols=160 Identities=19% Similarity=0.204 Sum_probs=91.7
Q ss_pred CcEEEEEEeccCCC---CC-CeeEEEEEEE-EeCCCcEEEEEeecCCcccccccccccCCCHH-------HhcCCCCHHH
Q 023843 80 TDVVAMDCEMVGIS---QG-NKSALGRVSL-VNKWGNLIYDEFVRPLERVVDFRTRISGIRPR-------DLRKAKDFPT 147 (276)
Q Consensus 80 ~~~VaiD~EttG~~---~~-~iiei~~v~v-~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~-------~l~~a~~~~e 147 (276)
-.++|||+|||-+. |+ +-.+|-.|+. +|+.|..+.+.=|-- ..|.++ ..||. .+-+.++...
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs-~DIedf-----EYTPKpE~eG~F~v~Ne~dEv~ 319 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVS-EDIEDF-----EYTPKPEYEGPFCVFNEPDEVG 319 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhc-cchhhc-----ccCCccccccceEEecCCcHHH
Confidence 46999999999887 55 3345655555 355554443322210 011111 00111 1123345566
Q ss_pred HHHHHHHHhc---CCeEEEEch-hhHHHHhc-------------ccCCC-------CceeehhhhchhhhC----CCCCc
Q 023843 148 VQKKVAELIE---GRILVGHAL-HNDLKALL-------------LTHSK-------KDLRDTSEYQPFLNR----NGRSK 199 (276)
Q Consensus 148 v~~~l~~~l~---~~~lVgHn~-~~D~~~L~-------------~~~~~-------~~~~Dt~~~~~~~~~----~~~~~ 199 (276)
++.++.+-+. ..++|-+|. -||+.|+. +.+.+ ..+..-+.+++-... ..++.
T Consensus 320 Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSq 399 (2173)
T KOG1798|consen 320 LLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQ 399 (2173)
T ss_pred HHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCccc
Confidence 7777666663 688999999 78999985 11110 001111112111111 56789
Q ss_pred cHHHHHHHHhCCcCCCC----------------CCChHHHHHHHHHHHHHhHHHHHHHHHHH
Q 023843 200 ALRHLAAEILAVEIQNG----------------EHCPIDDARAAMLLYMKNRKQWEKSVKDQ 245 (276)
Q Consensus 200 sL~~La~~~lgi~~~~~----------------~H~Al~DA~at~~L~~~l~~~~e~~~~~~ 245 (276)
+|+.+.+..||.+...- +..+++||.||.-||.++-..+--.+-..
T Consensus 400 gLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhPFIFsLctI 461 (2173)
T KOG1798|consen 400 GLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHPFIFSLCTI 461 (2173)
T ss_pred chhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhhHHhhhhhc
Confidence 99999999999655321 23589999999999999876655444433
No 98
>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=95.47 E-value=0.15 Score=44.79 Aligned_cols=71 Identities=27% Similarity=0.292 Sum_probs=50.2
Q ss_pred CCCHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc-------ccC------------C---------------CCcee
Q 023843 142 AKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL-------LTH------------S---------------KKDLR 183 (276)
Q Consensus 142 a~~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~-------~~~------------~---------------~~~~~ 183 (276)
..+..+.+..|..++. -.+++|||+ .||+.+|. +.+ + ..-++
T Consensus 79 ~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~ 158 (234)
T cd05776 79 FENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLC 158 (234)
T ss_pred eCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhh
Confidence 4567788888888874 689999999 99998884 110 0 01145
Q ss_pred ehhhhchhhhCCCCCccHHHHHHHHhCCcC
Q 023843 184 DTSEYQPFLNRNGRSKALRHLAAEILAVEI 213 (276)
Q Consensus 184 Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~ 213 (276)
|+....+-+. ...+|+|.++|..+||.+.
T Consensus 159 D~~~~~k~~~-~~~sY~L~~va~~~Lg~~k 187 (234)
T cd05776 159 DTYLSAKELI-RCKSYDLTELSQQVLGIER 187 (234)
T ss_pred ccHHHHHHHh-CCCCCChHHHHHHHhCcCc
Confidence 6665554443 4789999999999999743
No 99
>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=94.89 E-value=0.072 Score=43.09 Aligned_cols=60 Identities=22% Similarity=0.171 Sum_probs=46.5
Q ss_pred HHHHhc--CCeEEEEchhhHHHHhc---ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCc
Q 023843 152 VAELIE--GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVE 212 (276)
Q Consensus 152 l~~~l~--~~~lVgHn~~~D~~~L~---~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~ 212 (276)
|.+|+. +...++||++.++.+|. +.... ..+|++..++++.|..+..+|++|+.++++..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~-~~fD~~LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRG-IAFDTMLEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCC-cchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 666776 35579999999999995 33332 25899999999998775249999998988766
No 100
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=94.47 E-value=0.021 Score=57.48 Aligned_cols=147 Identities=16% Similarity=0.192 Sum_probs=82.6
Q ss_pred CCCcEEEEEEeccCCC---C----CCeeEEEEEEEEeCCCcEEE-EEe-ecCCcccccccccccCCCHHHhcCCCCH---
Q 023843 78 SLTDVVAMDCEMVGIS---Q----GNKSALGRVSLVNKWGNLIY-DEF-VRPLERVVDFRTRISGIRPRDLRKAKDF--- 145 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~---~----~~iiei~~v~v~~~~g~ii~-~~~-v~P~~~i~~~~~~i~GIt~~~l~~a~~~--- 145 (276)
.+-+++.||+|++|.. | +.+++|+-+...-++++.++ +.+ ++|- .+|.-.++....+-
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~c----------apI~G~~V~~~~~e~el 341 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTC----------APIVGSNVHSYETEKEL 341 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCc----------CCCCCceeEEeccHHHH
Confidence 4678999999999876 2 24466664444333333321 111 1222 22222223222222
Q ss_pred HHHHHHHHHHhcCCeEEEEch-hhHHHHhc-------cc---------CCCCcee-------------------------
Q 023843 146 PTVQKKVAELIEGRILVGHAL-HNDLKALL-------LT---------HSKKDLR------------------------- 183 (276)
Q Consensus 146 ~ev~~~l~~~l~~~~lVgHn~-~~D~~~L~-------~~---------~~~~~~~------------------------- 183 (276)
-+.|..|..-++..+|+|||+ .||+..|- +. ..+..+.
T Consensus 342 L~~W~~firevDPDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqf 421 (1066)
T KOG0969|consen 342 LESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQF 421 (1066)
T ss_pred HHHHHHHHHhcCCCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeee
Confidence 345555555557889999999 99996663 11 0011222
Q ss_pred ehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCC-------------------hHHHHHHHHHHHHHhH
Q 023843 184 DTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHC-------------------PIDDARAAMLLYMKNR 235 (276)
Q Consensus 184 Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~-------------------Al~DA~at~~L~~~l~ 235 (276)
|.+..-. .....++|+|..++..|||-.-+.-+|+ .+-||+.=.+|+.++.
T Consensus 422 Dllqvi~-Rd~KLrSytLNaVs~hFL~EQKEDV~~siItdLQng~~~TRRRlA~YCLkDAYLPlRLlekLM 491 (1066)
T KOG0969|consen 422 DLLQVIL-RDYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQTRRRLAVYCLKDAYLPLRLLEKLM 491 (1066)
T ss_pred hHHHHHH-HhhhhhhcchhhhHHHhhhhhcccccccchhhhhcCcHHHHHHHHHHHhhhhcchHHHHHHHH
Confidence 3322211 1114578999999989998766644565 3567877778877763
No 101
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=94.01 E-value=1.1 Score=46.36 Aligned_cols=75 Identities=16% Similarity=0.069 Sum_probs=49.5
Q ss_pred hcCCCCHHHHHHHHHHHhc---CCeEEEEch-hhHHHHhc-------ccCC-------------------CCceeehhhh
Q 023843 139 LRKAKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL-------LTHS-------------------KKDLRDTSEY 188 (276)
Q Consensus 139 l~~a~~~~ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~-------~~~~-------------------~~~~~Dt~~~ 188 (276)
+....+-.+++..|..++. ..+++|||. .||+.+|. +... ....+|+...
T Consensus 205 v~~~~~e~e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~ 284 (792)
T COG0417 205 VEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPA 284 (792)
T ss_pred eEEecCHHHHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHH
Confidence 3344566788888888883 679999999 59999985 1111 1134565554
Q ss_pred chhhhCCCCCccHHHHHHHHhCCcC
Q 023843 189 QPFLNRNGRSKALRHLAAEILAVEI 213 (276)
Q Consensus 189 ~~~~~~~~~~~sL~~La~~~lgi~~ 213 (276)
.........+++|...+..+|+...
T Consensus 285 ~~~~~~~~~~ysl~~v~~~~l~~~k 309 (792)
T COG0417 285 LRRRPLNLKSYSLEAVSEALLGEGK 309 (792)
T ss_pred HhhhhcccccccHHHHHHHhccccc
Confidence 4321225678999999877777444
No 102
>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=93.81 E-value=0.32 Score=44.19 Aligned_cols=86 Identities=10% Similarity=0.072 Sum_probs=49.4
Q ss_pred CCCcEEEEEEeccCCCC-------CCeeEEEEEEEEeC----CCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHH
Q 023843 78 SLTDVVAMDCEMVGISQ-------GNKSALGRVSLVNK----WGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (276)
Q Consensus 78 ~~~~~VaiD~EttG~~~-------~~iiei~~v~v~~~----~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ 146 (276)
++-++++||+||...+. +.|+.|+ +.+.+. .....+..+ .+...+.+ ...+....+..
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is-~~~~~~~~~~~~~~~~~~~-~~~~~~~~---------~~~v~~~~~E~ 223 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMIS-YVVYRNGSSEPYRRKVFTL-GSCDSIED---------NVEVIYFDSEK 223 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEE-EEEEETTEEETTEEEEEEC-SCSCCTTC---------TTEEEEESSHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEE-EEEEeccccCCCceEEEEe-cCCCCCCC---------CcEEEEECCHH
Confidence 57789999999986641 2344444 222211 111112222 22221111 12233345677
Q ss_pred HHHHHHHHHhc---CCeEEEEch-hhHHHHhc
Q 023843 147 TVQKKVAELIE---GRILVGHAL-HNDLKALL 174 (276)
Q Consensus 147 ev~~~l~~~l~---~~~lVgHn~-~~D~~~L~ 174 (276)
+.+..|..++. -.+++|||+ .||+.+|.
T Consensus 224 ~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDPDIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHHHHHS-SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHHHhcCCcEEEEecccCCCHHHHH
Confidence 88888888874 679999999 79999885
No 103
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=93.02 E-value=1.7 Score=42.05 Aligned_cols=126 Identities=15% Similarity=0.123 Sum_probs=71.9
Q ss_pred CcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcE--EEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHhc
Q 023843 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (276)
Q Consensus 80 ~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~i--i~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l~ 157 (276)
...++||+||+. +.+-...+|.+. .+. |.. .|..|..... ....+++.+|.+|+.
T Consensus 284 ~~~~ffDiEt~P-~~~~~yL~G~~~-~~~-~~~~~~~~~fla~~~--------------------~~E~~~~~~f~~~l~ 340 (457)
T TIGR03491 284 PGELIFDIESDP-DENLDYLHGFLV-VDK-GQENEKYRPFLAEDP--------------------NTEELAWQQFLQLLQ 340 (457)
T ss_pred CccEEEEecCCC-CCCCceEEEEEE-ecC-CCCCcceeeeecCCc--------------------hHHHHHHHHHHHHHH
Confidence 568999999983 223335667433 222 322 1444433211 123556777777774
Q ss_pred ---CCeEEEEchhhHHHHhc-----ccCCC-------Cceeehhhhchh-hhCCCCCccHHHHHHHHhCCcCCCCCCChH
Q 023843 158 ---GRILVGHALHNDLKALL-----LTHSK-------KDLRDTSEYQPF-LNRNGRSKALRHLAAEILAVEIQNGEHCPI 221 (276)
Q Consensus 158 ---~~~lVgHn~~~D~~~L~-----~~~~~-------~~~~Dt~~~~~~-~~~~~~~~sL~~La~~~lgi~~~~~~H~Al 221 (276)
+..++.|| .|...+|+ ...+. .+++|+..+.+. +.....++||+.++ .++|.+... ..
T Consensus 341 ~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~-~~lg~~~~~----~~ 414 (457)
T TIGR03491 341 SYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIA-RWLGFEWRQ----KE 414 (457)
T ss_pred HCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHH-HHhCcccCC----CC
Confidence 55788888 78887776 11110 146777754332 22255789999998 889987652 23
Q ss_pred HHHHHHHHHHHHh
Q 023843 222 DDARAAMLLYMKN 234 (276)
Q Consensus 222 ~DA~at~~L~~~l 234 (276)
.|...++..|..+
T Consensus 415 ~~G~~ai~~y~~~ 427 (457)
T TIGR03491 415 ASGAKSLLWYRQW 427 (457)
T ss_pred CCHHHHHHHHHHH
Confidence 3344445556554
No 104
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=92.62 E-value=0.29 Score=49.97 Aligned_cols=35 Identities=23% Similarity=0.310 Sum_probs=27.5
Q ss_pred CCeEEEEchhhHHHHhc----ccCCCCceeehhhhchhh
Q 023843 158 GRILVGHALHNDLKALL----LTHSKKDLRDTSEYQPFL 192 (276)
Q Consensus 158 ~~~lVgHn~~~D~~~L~----~~~~~~~~~Dt~~~~~~~ 192 (276)
+.++||||+.||..-++ +...+.+++|||.+....
T Consensus 241 e~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~ 279 (1075)
T KOG3657|consen 241 EQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAM 279 (1075)
T ss_pred CceEEeccccchHHHHHHHHhccccceeeeechhhhhhh
Confidence 67899999999998887 555566789999764433
No 105
>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=91.78 E-value=1.4 Score=42.01 Aligned_cols=143 Identities=17% Similarity=0.253 Sum_probs=72.1
Q ss_pred CCCCCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCc--ccccccccccCCCHHHhcCCCCHHHHHHHHH
Q 023843 76 DFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~ 153 (276)
...+..-.+||+| |. |+.-+||| |...+..-.+..|-.|.. .+.+.+..-|||--.|+.++.| -....|.
T Consensus 368 ~Ldp~~ttWiDIE--G~-p~DPVElA---iyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aqP--GL~S~vi 439 (533)
T PF00843_consen 368 KLDPNATTWIDIE--GP-PNDPVELA---IYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQP--GLTSAVI 439 (533)
T ss_dssp CS-TTS-EEEEEE--SE-TTSESEEE---EEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB-T--THHHHHH
T ss_pred hCCCCCCeeEecC--CC-CCCCeEEE---EeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhcc--chHHHHH
Confidence 5568889999999 55 34446777 333333344556677876 6677788889999999988754 4555677
Q ss_pred HHhcCCeEEEEchhhHHHHhcccCCCC--ceeehhhhchhhhC--CCCCccHHHHHHHHhCCcCC----------CCCCC
Q 023843 154 ELIEGRILVGHALHNDLKALLLTHSKK--DLRDTSEYQPFLNR--NGRSKALRHLAAEILAVEIQ----------NGEHC 219 (276)
Q Consensus 154 ~~l~~~~lVgHn~~~D~~~L~~~~~~~--~~~Dt~~~~~~~~~--~~~~~sL~~La~~~lgi~~~----------~~~H~ 219 (276)
..|....++---..-|++-|--.|.+. .++|+..-....+. ..---....||..+-|+-+. .+.|+
T Consensus 440 ~~LP~~MVlT~QGsDDIrkLld~hGRrDiKlvDV~lt~eqaR~FEd~VWd~f~~LC~~H~GvVv~KKKkg~~~~~t~PHC 519 (533)
T PF00843_consen 440 ELLPKNMVLTCQGSDDIRKLLDMHGRRDIKLVDVKLTSEQARKFEDQVWDRFGHLCKKHTGVVVKKKKKGKKPESTNPHC 519 (533)
T ss_dssp HHS-TT-EEEESSHHHHHHHHHCTT-TTSEEEE----HHHHTTTHHHHHHHHGGG---B-S-EEE--SSSS-EEE-----
T ss_pred HhCCcCcEEEeeChHHHHHHHHhcCCCcceEEEeecCHHHHHHHHHHHHHHHHHHHHhcCceEEecccCCCCCCCCCchH
Confidence 778755555555566776665444443 36776654332221 01112445677777775432 13799
Q ss_pred hHHHHHH
Q 023843 220 PIDDARA 226 (276)
Q Consensus 220 Al~DA~a 226 (276)
|+-|+..
T Consensus 520 ALlDCiM 526 (533)
T PF00843_consen 520 ALLDCIM 526 (533)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9999875
No 106
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=91.75 E-value=0.36 Score=41.98 Aligned_cols=147 Identities=20% Similarity=0.177 Sum_probs=79.9
Q ss_pred cEEEEEEeccCCC--C---------------------CCeeEEEEEEEEeCCCcEE-------EEEeecCCccccc-ccc
Q 023843 81 DVVAMDCEMVGIS--Q---------------------GNKSALGRVSLVNKWGNLI-------YDEFVRPLERVVD-FRT 129 (276)
Q Consensus 81 ~~VaiD~EttG~~--~---------------------~~iiei~~v~v~~~~g~ii-------~~~~v~P~~~i~~-~~~ 129 (276)
++|.+|+|..|+- | -.|++|| +++.|..|+.- |+.-..|...+-. ...
T Consensus 43 n~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlG-lsLSDe~GN~P~~~sTWQFNF~F~l~~dmya~ESi 121 (299)
T COG5228 43 NHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLG-LSLSDENGNKPNGPSTWQFNFEFDLKKDMYATESI 121 (299)
T ss_pred CceeeccccCceeecccccccccchHHHHHHhcccchhhhhhee-eeeccccCCCCCCCceeEEEEEecchhhhcchHHH
Confidence 5788888888763 1 1468888 88888887641 5555555442211 111
Q ss_pred ---cccCCCHHHh-cCCCCHHHHHHHHHHHh--------cCCeEEEEchhhHHHHhc-----ccCCCC------------
Q 023843 130 ---RISGIRPRDL-RKAKDFPTVQKKVAELI--------EGRILVGHALHNDLKALL-----LTHSKK------------ 180 (276)
Q Consensus 130 ---~i~GIt~~~l-~~a~~~~ev~~~l~~~l--------~~~~lVgHn~~~D~~~L~-----~~~~~~------------ 180 (276)
.-+||.-+.- .-++...| |.+++ +..++|.+...||+.+|- .+.|..
T Consensus 122 eLL~ksgIdFkkHe~~GI~v~e----F~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~yf 197 (299)
T COG5228 122 ELLRKSGIDFKKHENLGIDVFE----FSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQYF 197 (299)
T ss_pred HHHHHcCCChhhHhhcCCCHHH----HHHHHhccCceeccceEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHHC
Confidence 1134443322 11222222 33333 246678888899998874 233321
Q ss_pred -ceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhH
Q 023843 181 -DLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNR 235 (276)
Q Consensus 181 -~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~ 235 (276)
.+.|+..+.... ...+..|.+++ .-|++.-.+..|-|-.||..|+..|..-.
T Consensus 198 P~fYDik~v~ks~--~~~~KglQei~-ndlql~r~g~QhQagsdaLlTa~~ff~~R 250 (299)
T COG5228 198 PNFYDIKLVYKSV--LNNSKGLQEIK-NDLQLQRSGQQHQAGSDALLTADEFFLPR 250 (299)
T ss_pred ccccchHHHHHhh--hhhhhHHHHhc-CcHhhhccchhhhccchhhhhhHHhcchh
Confidence 122222211111 11234566655 44555555567999999999998886543
No 107
>PRK05761 DNA polymerase I; Reviewed
Probab=90.40 E-value=5.3 Score=41.49 Aligned_cols=89 Identities=16% Similarity=0.088 Sum_probs=55.6
Q ss_pred CCHHHHHHHHHHHhc-CCeEEEEch-hhHHHHhc-----ccCCCC---------c-eeehhhhchhh-------hC--CC
Q 023843 143 KDFPTVQKKVAELIE-GRILVGHAL-HNDLKALL-----LTHSKK---------D-LRDTSEYQPFL-------NR--NG 196 (276)
Q Consensus 143 ~~~~ev~~~l~~~l~-~~~lVgHn~-~~D~~~L~-----~~~~~~---------~-~~Dt~~~~~~~-------~~--~~ 196 (276)
.+..+++.+|..|+. -.+.|++|+ .||+.+|. +..... . .+|........ .. ..
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~ 287 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRH 287 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeec
Confidence 345788888999886 566677999 89998885 211100 0 14443322111 01 12
Q ss_pred CCccHHHHHHHHhCCcCCCC------------CCChHHHHHHHHHHH
Q 023843 197 RSKALRHLAAEILAVEIQNG------------EHCPIDDARAAMLLY 231 (276)
Q Consensus 197 ~~~sL~~La~~~lgi~~~~~------------~H~Al~DA~at~~L~ 231 (276)
.+++|+.++..+||..-..- +.-.+.||..+.+|+
T Consensus 288 ~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 288 REARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 37899999988999654210 123789999999984
No 108
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.99 E-value=26 Score=38.18 Aligned_cols=102 Identities=21% Similarity=0.188 Sum_probs=66.0
Q ss_pred cCCCHHHhcCCCCHHHHHHHHHHHh---cCCeEEEEch-hhHHHHhc-----ccCCC-----------------------
Q 023843 132 SGIRPRDLRKAKDFPTVQKKVAELI---EGRILVGHAL-HNDLKALL-----LTHSK----------------------- 179 (276)
Q Consensus 132 ~GIt~~~l~~a~~~~ev~~~l~~~l---~~~~lVgHn~-~~D~~~L~-----~~~~~----------------------- 179 (276)
-|+.+..|..-.+..+.+..+..++ +..+++|||+ .||+.+|. +..+.
T Consensus 571 ~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~G 650 (1172)
T TIGR00592 571 PGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCG 650 (1172)
T ss_pred hccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECC
Confidence 3444445555556677777777766 4678899999 99999885 11111
Q ss_pred CceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCC------------------CChHHHHHHHHHHHHHh
Q 023843 180 KDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGE------------------HCPIDDARAAMLLYMKN 234 (276)
Q Consensus 180 ~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~------------------H~Al~DA~at~~L~~~l 234 (276)
.-++|+....+... ...+|+|..++..+||.+-..-. +..+.||..+++|+.++
T Consensus 651 rl~~D~~~~~k~~~-~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l 722 (1172)
T TIGR00592 651 RMICDVEISAKELI-RCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCEL 722 (1172)
T ss_pred EEEEEHHHHHHHHh-CcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12456665554443 46789999999999985432100 12467888888888765
No 109
>PHA02563 DNA polymerase; Provisional
Probab=79.60 E-value=5.8 Score=40.07 Aligned_cols=67 Identities=16% Similarity=0.073 Sum_probs=41.2
Q ss_pred CCCCcEEEEEEeccCCCCCCeeEEEEEEEEeCCCcEEEEEeecCCcccccccccccCCCHHHhcCCCCHHHHHHHHHHHh
Q 023843 77 FSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~~~iiei~~v~v~~~~g~ii~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~ev~~~l~~~l 156 (276)
..+..+++.|+||++.+... ...+ ..+.+ |...-..++. ....++..|+
T Consensus 9 ~~~~~~~~~DfET~t~~~~~-~~~~-~~~~d--~~~~~s~~~~---------------------------~~~~~f~~~i 57 (630)
T PHA02563 9 HKPRKILACDFETTTINKDC-RRWF-WGEID--VEDFPSYYGG---------------------------NSFDEFLQWI 57 (630)
T ss_pred cccceEEEEEEEecccCCcc-eeee-eeEec--cceeceeecc---------------------------ccHHHHHHHH
Confidence 34577999999999986432 1222 23434 4443222211 1223555566
Q ss_pred c-------CCeEEEEchhhHHHHhc
Q 023843 157 E-------GRILVGHALHNDLKALL 174 (276)
Q Consensus 157 ~-------~~~lVgHn~~~D~~~L~ 174 (276)
. ..++..||+.||..||.
T Consensus 58 ~~~~~k~~~~~vYfHN~~FD~~Fil 82 (630)
T PHA02563 58 EDTTYKETECIIYFHNLKFDGSFIL 82 (630)
T ss_pred hhccccccceEEEEecCCccHHHHH
Confidence 5 66889999999999986
No 110
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=70.55 E-value=8.7 Score=38.20 Aligned_cols=60 Identities=18% Similarity=0.123 Sum_probs=46.9
Q ss_pred eeehhhhchhhhCCCC--CccHHHHHHHHhCCcCCCCC--------------CChHHHHHHHHHHHHHhHHHHHHH
Q 023843 182 LRDTSEYQPFLNRNGR--SKALRHLAAEILAVEIQNGE--------------HCPIDDARAAMLLYMKNRKQWEKS 241 (276)
Q Consensus 182 ~~Dt~~~~~~~~~~~~--~~sL~~La~~~lgi~~~~~~--------------H~Al~DA~at~~L~~~l~~~~e~~ 241 (276)
++||+..++++.++.. +.+|..|+.+++++...... .-|..|+..+..||..+..++++.
T Consensus 72 ~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~ 147 (553)
T PRK14975 72 CHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALSDPPDEEQLLYAAADADVLLELYAVLADQLNRI 147 (553)
T ss_pred CchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhccccccchHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Confidence 7899999999986542 67999999999988865311 136778889999999988887654
No 111
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=69.35 E-value=8.6 Score=34.66 Aligned_cols=48 Identities=15% Similarity=0.094 Sum_probs=38.2
Q ss_pred CCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHH
Q 023843 195 NGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVK 243 (276)
Q Consensus 195 ~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~~~~e~~~~ 243 (276)
....++|..|+ .++......++|+|+.|+..+-.+++++...+-..+.
T Consensus 249 p~~vs~le~La-t~~~~~p~l~ahra~~Dv~~~~k~~q~~~idlla~l~ 296 (318)
T KOG4793|consen 249 PKLVSSLEALA-TYYSLTPELDAHRALSDVLLLSKVFQKLTIDLLASLS 296 (318)
T ss_pred CccchhHHHHH-HHhhcCcccchhhhccccchhhhHHHHhhhhhhhhhh
Confidence 34567899999 6777777779999999999999999998766554443
No 112
>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=66.79 E-value=14 Score=29.50 Aligned_cols=51 Identities=16% Similarity=-0.006 Sum_probs=35.0
Q ss_pred eeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCCChHHHHHHHHHHHHHhHHH
Q 023843 182 LRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQ 237 (276)
Q Consensus 182 ~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H~Al~DA~at~~L~~~l~~~ 237 (276)
--|.+.++|++++.. .....++++|+|-++. .+|...|.++.+|++.+..+
T Consensus 87 GDDPlLlAYLlDPsN--t~p~~varRY~~~~W~---~dA~~RA~~t~~L~~~L~pr 137 (138)
T PF09281_consen 87 GDDPLLLAYLLDPSN--TNPEGVARRYLGGEWP---EDAATRALATARLLRALPPR 137 (138)
T ss_dssp ---HHHHHHHH-TT----SHHHHHHHH-TS------SSHHHHHHHHHHHHHHHHHH
T ss_pred CCCcchhhhhcCccC--CChHHHHHHhcCCCCC---ccHHHHHHHHHHHHHHhhhc
Confidence 469999999998654 4566778888887776 79999999999999988654
No 113
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=64.92 E-value=31 Score=37.12 Aligned_cols=155 Identities=13% Similarity=0.141 Sum_probs=81.7
Q ss_pred CCCCcEEEEEEeccCCCC---CCeeEEEEEEEEeCC-----CcE----EEEEeecCCcccccccccccCCCHHH---hcC
Q 023843 77 FSLTDVVAMDCEMVGISQ---GNKSALGRVSLVNKW-----GNL----IYDEFVRPLERVVDFRTRISGIRPRD---LRK 141 (276)
Q Consensus 77 ~~~~~~VaiD~EttG~~~---~~iiei~~v~v~~~~-----g~i----i~~~~v~P~~~i~~~~~~i~GIt~~~---l~~ 141 (276)
.++-.+.++.++|+--.. .+|+.++..+..+.+ ... .+..+++|...+-+.... .+..+. +.-
T Consensus 526 ~Ppl~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~--ela~~k~~~v~~ 603 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLK--ELAKQKLSKVVL 603 (1429)
T ss_pred CCCeeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHH--HHHHhccCceEE
Confidence 445678888888775442 244444433332211 111 256667777522222100 000000 111
Q ss_pred CCCHHHHHHHHHHHh---cCCeEEEEch-hhHHHHhc-------ccC-----------C----------------CCcee
Q 023843 142 AKDFPTVQKKVAELI---EGRILVGHAL-HNDLKALL-------LTH-----------S----------------KKDLR 183 (276)
Q Consensus 142 a~~~~ev~~~l~~~l---~~~~lVgHn~-~~D~~~L~-------~~~-----------~----------------~~~~~ 183 (276)
..+....+..|..-+ +..++||||+ .|++.+|. +++ + ...+.
T Consensus 604 ~~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~C 683 (1429)
T KOG0970|consen 604 HNSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMC 683 (1429)
T ss_pred ecCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccceEEe
Confidence 123344555555544 4679999994 99998882 110 0 01133
Q ss_pred ehhhhchhhhCCCCCccHHHHHHHHhCCcCCCC------------CC------ChHHHHHHHHHHHHHh
Q 023843 184 DTSEYQPFLNRNGRSKALRHLAAEILAVEIQNG------------EH------CPIDDARAAMLLYMKN 234 (276)
Q Consensus 184 Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~------------~H------~Al~DA~at~~L~~~l 234 (276)
|+...++-+- ...+++|.+|+...++.+-..- .| ....|+..+++|+.++
T Consensus 684 D~~~~a~~li-k~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s~~L~~ll~~~~~d~~~~l~i~~~l 751 (1429)
T KOG0970|consen 684 DLNLAARELI-KAQSYSLSELSQQILKEERKEINANEIPKMYEDSKSLTYLLEHTITDAELILQIMFRL 751 (1429)
T ss_pred ehHHHHHhhh-ccccccHHHHHHHHHhhhcccCCHhHhhhhccChHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 5544444444 3578999999988888632211 01 2466888888888776
No 114
>PHA03036 DNA polymerase; Provisional
Probab=64.50 E-value=61 Score=34.68 Aligned_cols=97 Identities=11% Similarity=-0.096 Sum_probs=50.6
Q ss_pred CCCCCcEEEEEEeccCCC--C----CCeeEEEEEEEEeCCCcEEEEEeecCCc--------ccccccccccCCC---HHH
Q 023843 76 DFSLTDVVAMDCEMVGIS--Q----GNKSALGRVSLVNKWGNLIYDEFVRPLE--------RVVDFRTRISGIR---PRD 138 (276)
Q Consensus 76 ~~~~~~~VaiD~EttG~~--~----~~iiei~~v~v~~~~g~ii~~~~v~P~~--------~i~~~~~~i~GIt---~~~ 138 (276)
-.-+..+++||+|+-.-+ | +-|+.|+- ++++..|...--.+++... ...-....+.-|. ...
T Consensus 156 ~~~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~-~~~~~~~~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (1004)
T PHA03036 156 FDIPRSYLFLDIECHFDKKFPSVFINPVSHISC-CYIDLSGKEKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSK 234 (1004)
T ss_pred ccCcceeEEEEEEeccCCCCCCcccCcceEEEE-EEEecCCCeeEEEEeccccccccccccceeeeeeccccccccCCce
Confidence 334678999999988533 2 24567774 5556556443223333321 1111111222221 111
Q ss_pred hcCCCCHHHHHHHHHHHh---cCCeEEEEch-hhHHHHhc
Q 023843 139 LRKAKDFPTVQKKVAELI---EGRILVGHAL-HNDLKALL 174 (276)
Q Consensus 139 l~~a~~~~ev~~~l~~~l---~~~~lVgHn~-~~D~~~L~ 174 (276)
.....+..+.+ ++..++ +-.+++|+|+ .||+..+.
T Consensus 235 ~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~ 273 (1004)
T PHA03036 235 ELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYIS 273 (1004)
T ss_pred eeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHH
Confidence 11123444433 555555 3678999999 99997774
No 115
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=58.43 E-value=18 Score=36.07 Aligned_cols=93 Identities=18% Similarity=0.140 Sum_probs=62.5
Q ss_pred CHHHHHHHHHHHhc--CCeEEEEchhhHHHHhc--ccCCCCceeehhhhchhhhCCCCCccHHHHHHHHhCCcCCCCCC-
Q 023843 144 DFPTVQKKVAELIE--GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLNRNGRSKALRHLAAEILAVEIQNGEH- 218 (276)
Q Consensus 144 ~~~ev~~~l~~~l~--~~~lVgHn~~~D~~~L~--~~~~~~~~~Dt~~~~~~~~~~~~~~sL~~La~~~lgi~~~~~~H- 218 (276)
.+.+++.-+.+.+. +.+-|-|++..|+-+|+ +......++||....+++ +...+||..|...+-|+... ..|
T Consensus 249 ~l~~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt~~a~r~L--~~~r~sL~~ll~~~~~v~~n-k~yq 325 (687)
T KOG2206|consen 249 KLRDHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDTIQASRLL--GLPRPSLAYLLECVCGVLTN-KKYQ 325 (687)
T ss_pred HHHHHHHHhhhhccCCCeEEEEecCccchhhhhccceEEEEechhhHHHHHHh--CCCcccHHHHHHHHHhhhhh-hhhh
Confidence 44566665566664 55669999999999998 333334578999998888 56789999987666665444 222
Q ss_pred ---------------ChHHHHHHHHHHHHHhHHHHH
Q 023843 219 ---------------CPIDDARAAMLLYMKNRKQWE 239 (276)
Q Consensus 219 ---------------~Al~DA~at~~L~~~l~~~~e 239 (276)
-|-+|+-....||..+..++.
T Consensus 326 ladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~ 361 (687)
T KOG2206|consen 326 LADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELK 361 (687)
T ss_pred hchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHH
Confidence 145566666677766654433
No 116
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=39.65 E-value=38 Score=29.28 Aligned_cols=60 Identities=12% Similarity=0.247 Sum_probs=42.1
Q ss_pred eEEEEEEEEeCCCcE-EEEEeecCCccccccc-------ccccCCCHHHhcCC-CCHHHHHHHHHHHhc
Q 023843 98 SALGRVSLVNKWGNL-IYDEFVRPLERVVDFR-------TRISGIRPRDLRKA-KDFPTVQKKVAELIE 157 (276)
Q Consensus 98 iei~~v~v~~~~g~i-i~~~~v~P~~~i~~~~-------~~i~GIt~~~l~~a-~~~~ev~~~l~~~l~ 157 (276)
+|||.+.+...+|-+ .|..+|+|......++ ..-|+|...-...+ .++..++.+|..||+
T Consensus 11 aEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~ 79 (213)
T PF13017_consen 11 AEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLK 79 (213)
T ss_pred EEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhh
Confidence 688888887777733 3999999986333332 23367665544444 479999999999995
No 117
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=33.92 E-value=1.6e+02 Score=23.45 Aligned_cols=32 Identities=9% Similarity=-0.099 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHhc-C-CeEEEEchhhHHHHhc
Q 023843 143 KDFPTVQKKVAELIE-G-RILVGHALHNDLKALL 174 (276)
Q Consensus 143 ~~~~ev~~~l~~~l~-~-~~lVgHn~~~D~~~L~ 174 (276)
.+..+....|.+.|+ . ..+|.||..|....|+
T Consensus 55 DPr~~~~~~L~~~i~~~~g~ivvyN~sfE~~rL~ 88 (130)
T PF11074_consen 55 DPRRELIEALIKAIGSIYGSIVVYNKSFEKTRLK 88 (130)
T ss_pred CchHHHHHHHHHHhhhhcCeEEEechHHHHHHHH
Confidence 355677778888886 5 7889999999998887
No 118
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=22.35 E-value=1.2e+02 Score=25.67 Aligned_cols=45 Identities=11% Similarity=0.079 Sum_probs=36.0
Q ss_pred hCCcCCCCCCChHHHHHHHHHHHHHhH---HHHHHHHHHHHHHHHHHh
Q 023843 209 LAVEIQNGEHCPIDDARAAMLLYMKNR---KQWEKSVKDQTRLEQKQK 253 (276)
Q Consensus 209 lgi~~~~~~H~Al~DA~at~~L~~~l~---~~~e~~~~~~~~~~~k~~ 253 (276)
.+++++..+.+|.--|.++.+|.+.+. ..||..+.+.+...+.+.
T Consensus 137 iN~DI~Dn~EdA~~Gaf~I~elcq~l~~~s~d~Ed~ideil~~~ee~~ 184 (195)
T KOG2424|consen 137 INVDIKDNHEDATLGAFLILELCQCLQAQSDDLEDNIDEILLEFEEKH 184 (195)
T ss_pred EEeecccCHHhhhhhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhc
Confidence 346676555678888889999999888 689999999998887765
Done!