Query 016210
Match_columns 393
No_of_seqs 285 out of 1128
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 04:48:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016210hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10829 ribonuclease D; Provi 100.0 3.1E-38 6.7E-43 317.9 21.5 247 10-297 2-261 (373)
2 COG0349 Rnd Ribonuclease D [Tr 100.0 2.6E-35 5.6E-40 291.3 17.6 246 19-302 4-262 (361)
3 TIGR01388 rnd ribonuclease D. 100.0 6.8E-34 1.5E-38 286.7 20.8 243 14-297 2-257 (367)
4 cd06146 mut-7_like_exo DEDDy 3 100.0 3E-30 6.4E-35 238.7 20.2 184 11-213 1-192 (193)
5 cd06129 RNaseD_like DEDDy 3'-5 100.0 9E-30 1.9E-34 228.4 17.8 158 22-213 2-160 (161)
6 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 2E-27 4.2E-32 214.0 18.7 163 19-213 4-169 (170)
7 cd06148 Egl_like_exo DEDDy 3'- 100.0 1.2E-27 2.5E-32 221.9 17.2 170 25-220 3-181 (197)
8 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 3.1E-26 6.8E-31 204.5 19.3 174 11-217 1-176 (176)
9 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 4.9E-20 1.1E-24 165.7 18.2 171 22-228 2-175 (178)
10 KOG2206 Exosome 3'-5' exoribon 99.8 5E-21 1.1E-25 196.6 11.6 263 11-315 193-491 (687)
11 smart00474 35EXOc 3'-5' exonuc 99.8 7.2E-18 1.6E-22 149.2 19.7 169 12-216 2-171 (172)
12 cd06147 Rrp6p_like_exo DEDDy 3 99.7 1.8E-16 3.9E-21 145.9 20.3 174 9-220 3-176 (192)
13 cd00007 35EXOc 3'-5' exonuclea 99.7 1.7E-15 3.7E-20 131.6 16.6 149 34-215 2-154 (155)
14 PRK05755 DNA polymerase I; Pro 99.7 1.5E-15 3.2E-20 168.9 20.4 187 8-230 293-488 (880)
15 cd09018 DEDDy_polA_RNaseD_like 99.7 2.1E-15 4.6E-20 131.5 15.6 147 34-213 1-149 (150)
16 KOG2207 Predicted 3'-5' exonuc 99.7 3.6E-18 7.7E-23 176.7 -3.3 252 136-392 155-434 (617)
17 KOG2207 Predicted 3'-5' exonuc 99.7 1.9E-16 4.1E-21 164.0 9.2 192 6-217 387-586 (617)
18 cd06140 DNA_polA_I_Bacillus_li 99.7 2.2E-15 4.7E-20 136.1 15.0 165 32-230 3-174 (178)
19 cd06139 DNA_polA_I_Ecoli_like_ 99.6 8.4E-14 1.8E-18 126.5 16.7 169 30-230 3-189 (193)
20 PRK14975 bifunctional 3'-5' ex 99.5 1.2E-13 2.5E-18 146.7 11.7 158 10-231 2-169 (553)
21 COG0749 PolA DNA polymerase I 99.3 6.2E-12 1.3E-16 132.5 12.1 180 19-231 9-200 (593)
22 TIGR00593 pola DNA polymerase 99.3 7E-11 1.5E-15 131.3 18.0 182 11-231 304-496 (887)
23 KOG4373 Predicted 3'-5' exonuc 98.9 3.4E-09 7.5E-14 103.8 9.9 157 33-220 128-290 (319)
24 cd06128 DNA_polA_exo DEDDy 3'- 98.7 2.7E-07 5.8E-12 81.2 13.7 118 78-213 30-150 (151)
25 PRK06063 DNA polymerase III su 97.4 0.0053 1.1E-07 61.3 15.6 102 91-221 83-184 (313)
26 PRK07740 hypothetical protein; 97.3 0.0099 2.1E-07 57.2 15.2 101 91-221 130-231 (244)
27 cd06149 ISG20 DEDDh 3'-5' exon 97.3 0.0022 4.8E-08 57.5 10.0 88 91-209 66-156 (157)
28 PRK08517 DNA polymerase III su 97.3 0.011 2.4E-07 57.4 15.5 98 91-218 136-233 (257)
29 KOG2249 3'-5' exonuclease [Rep 97.3 0.0022 4.7E-08 62.0 10.3 96 92-219 174-269 (280)
30 PRK07942 DNA polymerase III su 97.2 0.015 3.2E-07 55.5 15.8 90 105-219 94-183 (232)
31 cd06131 DNA_pol_III_epsilon_Ec 97.2 0.016 3.5E-07 51.6 14.6 97 91-212 70-166 (167)
32 PRK06310 DNA polymerase III su 97.0 0.025 5.4E-07 54.6 15.2 149 30-216 5-174 (250)
33 PRK09145 DNA polymerase III su 97.0 0.035 7.6E-07 51.5 15.4 159 22-213 19-198 (202)
34 PRK06807 DNA polymerase III su 97.0 0.027 6E-07 56.2 15.3 97 91-217 77-173 (313)
35 cd06144 REX4_like DEDDh 3'-5' 96.9 0.0036 7.8E-08 55.6 8.1 86 91-210 66-152 (152)
36 smart00479 EXOIII exonuclease 96.9 0.035 7.5E-07 48.9 14.2 99 91-217 69-168 (169)
37 TIGR01405 polC_Gram_pos DNA po 96.9 0.024 5.3E-07 65.8 16.5 103 91-222 259-361 (1213)
38 TIGR01406 dnaQ_proteo DNA poly 96.9 0.031 6.7E-07 53.1 14.7 99 91-214 71-170 (225)
39 PRK06309 DNA polymerase III su 96.9 0.061 1.3E-06 51.2 16.8 145 33-218 3-168 (232)
40 PRK05711 DNA polymerase III su 96.9 0.025 5.4E-07 54.4 13.6 99 91-214 75-174 (240)
41 cd06145 REX1_like DEDDh 3'-5' 96.8 0.0047 1E-07 54.9 7.8 86 91-209 64-149 (150)
42 PRK07883 hypothetical protein; 96.8 0.036 7.8E-07 59.6 15.7 159 27-222 10-188 (557)
43 TIGR01298 RNaseT ribonuclease 96.8 0.091 2E-06 48.9 16.4 91 105-221 106-197 (200)
44 cd06137 DEDDh_RNase DEDDh 3'-5 96.8 0.0056 1.2E-07 54.9 8.0 87 93-209 74-160 (161)
45 PRK07246 bifunctional ATP-depe 96.8 0.02 4.4E-07 64.2 14.0 100 91-220 75-174 (820)
46 PRK05168 ribonuclease T; Provi 96.7 0.13 2.9E-06 48.2 16.9 92 104-221 114-206 (211)
47 TIGR00573 dnaq exonuclease, DN 96.6 0.041 8.9E-07 51.8 13.1 106 91-220 76-181 (217)
48 TIGR01407 dinG_rel DnaQ family 96.6 0.045 9.7E-07 61.7 15.6 98 91-217 69-166 (850)
49 cd06125 DnaQ_like_exo DnaQ-lik 96.6 0.015 3.2E-07 47.8 8.7 82 35-145 1-83 (96)
50 PRK09146 DNA polymerase III su 96.6 0.12 2.6E-06 49.6 16.0 103 92-217 119-228 (239)
51 cd05780 DNA_polB_Kod1_like_exo 96.5 0.075 1.6E-06 49.1 13.8 160 33-212 4-195 (195)
52 PRK08074 bifunctional ATP-depe 96.5 0.061 1.3E-06 61.2 15.8 99 91-218 73-171 (928)
53 cd05160 DEDDy_DNA_polB_exo DED 96.4 0.076 1.6E-06 48.8 13.0 110 91-209 65-198 (199)
54 cd06130 DNA_pol_III_epsilon_li 96.4 0.16 3.6E-06 44.2 14.5 89 91-209 66-154 (156)
55 cd06143 PAN2_exo DEDDh 3'-5' e 96.2 0.015 3.3E-07 53.3 7.1 81 94-209 93-173 (174)
56 COG2176 PolC DNA polymerase II 95.7 0.03 6.6E-07 63.6 8.0 104 90-222 489-592 (1444)
57 PRK05601 DNA polymerase III su 95.5 0.31 6.7E-06 49.8 13.7 161 29-212 43-245 (377)
58 KOG2405 Predicted 3'-5' exonuc 95.0 0.0029 6.4E-08 63.8 -2.3 149 28-204 55-215 (458)
59 PRK07247 DNA polymerase III su 95.0 0.71 1.5E-05 43.0 13.7 106 91-230 73-183 (195)
60 cd05781 DNA_polB_B3_exo DEDDy 94.5 1.2 2.6E-05 41.1 13.8 157 33-212 4-188 (188)
61 cd05784 DNA_polB_II_exo DEDDy 94.2 1.5 3.3E-05 40.7 13.8 110 91-210 53-193 (193)
62 PRK00448 polC DNA polymerase I 94.0 0.9 1.9E-05 54.0 14.4 103 91-222 488-590 (1437)
63 cd06134 RNaseT DEDDh 3'-5' exo 94.0 0.58 1.3E-05 43.1 10.5 84 105-214 103-187 (189)
64 PRK06195 DNA polymerase III su 94.0 0.46 9.9E-06 47.3 10.5 98 91-219 69-167 (309)
65 KOG2405 Predicted 3'-5' exonuc 94.0 0.014 3.1E-07 59.0 -0.3 129 76-216 221-361 (458)
66 cd05785 DNA_polB_like2_exo Unc 93.5 1.4 3E-05 41.4 12.3 155 33-209 10-206 (207)
67 cd06127 DEDDh DEDDh 3'-5' exon 93.1 1 2.2E-05 38.4 10.0 91 91-209 68-158 (159)
68 cd05777 DNA_polB_delta_exo DED 92.4 4.7 0.0001 38.2 14.4 54 160-213 167-224 (230)
69 cd06136 TREX1_2 DEDDh 3'-5' ex 91.8 0.8 1.7E-05 41.7 8.0 88 92-209 84-174 (177)
70 KOG3657 Mitochondrial DNA poly 90.3 1.1 2.3E-05 49.9 8.3 107 103-219 240-386 (1075)
71 PRK11779 sbcB exonuclease I; P 89.7 8.4 0.00018 40.9 14.3 107 91-215 80-197 (476)
72 PF13482 RNase_H_2: RNase_H su 89.7 0.51 1.1E-05 41.7 4.5 148 35-212 1-163 (164)
73 PRK07748 sporulation inhibitor 89.4 3.4 7.3E-05 38.5 10.1 98 91-215 81-179 (207)
74 cd05783 DNA_polB_B1_exo DEDDy 88.8 20 0.00044 33.4 15.1 162 33-210 6-202 (204)
75 cd05779 DNA_polB_epsilon_exo D 88.3 9.1 0.0002 35.9 12.1 110 91-210 75-204 (204)
76 PRK09182 DNA polymerase III su 88.1 16 0.00036 36.2 14.4 87 93-212 111-197 (294)
77 KOG2248 3'-5' exonuclease [Rep 87.9 0.56 1.2E-05 48.2 4.0 92 91-214 282-373 (380)
78 PRK07983 exodeoxyribonuclease 87.5 4.7 0.0001 38.2 9.8 78 105-214 75-152 (219)
79 smart00341 HRDC Helicase and R 86.8 0.3 6.6E-06 38.1 1.1 45 258-302 3-57 (81)
80 PF09281 Taq-exonuc: Taq polym 84.5 5.2 0.00011 35.1 7.5 55 135-216 84-138 (138)
81 COG0847 DnaQ DNA polymerase II 82.3 11 0.00023 35.6 9.7 99 91-215 83-181 (243)
82 cd06138 ExoI_N N-terminal DEDD 82.2 9.1 0.0002 34.8 8.8 100 92-208 72-181 (183)
83 cd05776 DNA_polB_alpha_exo ina 81.7 3.2 6.9E-05 39.5 5.9 54 160-213 171-227 (234)
84 PF00570 HRDC: HRDC domain Blo 81.4 0.29 6.3E-06 37.0 -1.2 44 259-302 1-54 (68)
85 KOG1275 PAB-dependent poly(A) 81.0 0.28 6.2E-06 54.6 -1.8 95 99-229 1009-1104(1118)
86 cd05782 DNA_polB_like1_exo Unc 80.7 22 0.00049 33.2 11.1 109 90-210 79-207 (208)
87 cd06133 ERI-1_3'hExo_like DEDD 80.3 14 0.00031 32.5 9.3 95 91-212 77-175 (176)
88 PRK06722 exonuclease; Provisio 80.1 12 0.00026 36.9 9.4 99 91-214 79-179 (281)
89 PRK05762 DNA polymerase II; Re 75.3 63 0.0014 36.4 14.4 110 91-211 205-347 (786)
90 cd05778 DNA_polB_zeta_exo inac 46.6 30 0.00064 32.9 4.5 50 160-209 176-230 (231)
91 PF10108 DNA_pol_B_exo2: Predi 40.9 3.2E+02 0.007 25.9 10.7 113 90-214 38-171 (209)
92 cd06135 Orn DEDDh 3'-5' exonuc 32.2 1.7E+02 0.0037 26.2 6.9 32 92-123 78-113 (173)
93 TIGR00592 pol2 DNA polymerase 29.7 2.4E+02 0.0052 33.5 9.2 68 137-212 652-722 (1172)
94 PTZ00315 2'-phosphotransferase 26.5 6.5E+02 0.014 27.6 11.1 103 91-213 132-252 (582)
95 PRK05359 oligoribonuclease; Pr 24.4 3.3E+02 0.0072 24.7 7.4 33 91-123 81-117 (181)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=100.00 E-value=3.1e-38 Score=317.86 Aligned_cols=247 Identities=21% Similarity=0.288 Sum_probs=212.9
Q ss_pred cEEEEeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 016210 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (393)
Q Consensus 10 ~i~lV~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~ 89 (393)
.|.+|+| .+++..+++.+.+.++||||+|+..... |.+++|||||++ ++++|+||+..+.
T Consensus 2 ~~~~I~t--~~~L~~~~~~l~~~~~lalDtEf~~~~t---y~~~l~LiQl~~--------------~~~~~LiD~l~~~- 61 (373)
T PRK10829 2 NYQMITT--DDALASVCEAARAFPAIALDTEFVRTRT---YYPQLGLIQLYD--------------GEQLSLIDPLGIT- 61 (373)
T ss_pred CcEEeCC--HHHHHHHHHHHhcCCeEEEecccccCcc---CCCceeEEEEec--------------CCceEEEecCCcc-
Confidence 4788999 9999999999999999999999998764 889999999997 3679999998764
Q ss_pred hhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
.+..|+++|+|++|+||+|++++|+..|.+.+|+ .+.++|| |++|+.+++.+ ..+||+.|++
T Consensus 62 --d~~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~--------~p~~~fD-Tqiaa~~lg~~-------~~~gl~~Lv~ 123 (373)
T PRK10829 62 --DWSPFKALLRDPQVTKFLHAGSEDLEVFLNAFGE--------LPQPLID-TQILAAFCGRP-------LSCGFASMVE 123 (373)
T ss_pred --chHHHHHHHcCCCeEEEEeChHhHHHHHHHHcCC--------CcCCeee-HHHHHHHcCCC-------ccccHHHHHH
Confidence 3788999999999999999999999999877776 2689999 99999999863 3689999999
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccccccccCCcccccccCcccCcc
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSSNLDLGLKGILEKPD 246 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~e~~~l~~~~~~~~~~~~~~~~~ 246 (393)
++||+.++|.++.+||+.||||++|+.|||.||++++.||+.|.++|.+.|++ .+||..+....... .++ .+.|+
T Consensus 124 ~~lgv~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~-~~~-~~~~~ 201 (373)
T PRK10829 124 EYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAALDECRLLCQRRQEV-LAP-EEAYR 201 (373)
T ss_pred HHhCCccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHhccccC-CCh-HHHHH
Confidence 99999999999999999999999999999999999999999999999999988 88888775432111 111 14477
Q ss_pred cCCCccccchhhHHHHHHHHhh------hhcCCCCc-ccccccc---ccCCCCCHHHHHHH
Q 016210 247 IGNKTVRFKLCEALDIIRATSY------YSQCLPEG-VVSRVSY---LNTMPMDESLVKIV 297 (393)
Q Consensus 247 ~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~ 297 (393)
+.++..+.+ +++|+++|+||. +.+|+|++ ||++..+ |...|.+...|..+
T Consensus 202 ~ik~~~~L~-~~~lavl~~L~~WRe~~Ar~~d~p~~~Vl~d~~L~~lA~~~P~~~~~L~~~ 261 (373)
T PRK10829 202 DITNAWQLR-TRQLACLQLLADWRLRKARERDLAVNFVVREEHLWQVARYMPGSLGELDSL 261 (373)
T ss_pred HhccccCCC-HHHHHHHHHHHHHHHHHHHHhCCCcceecChHHHHHHHHhCCCCHHHHHhc
Confidence 888877666 999999999977 45599999 9999887 89999999877554
No 2
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-35 Score=291.30 Aligned_cols=246 Identities=22% Similarity=0.238 Sum_probs=215.0
Q ss_pred hHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHH
Q 016210 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKE 98 (393)
Q Consensus 19 ~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~ 98 (393)
.+.++.++..+.+++.|++|+|+....+ |.+++|||||+.. +++++||+.... .-+..|..
T Consensus 4 ~~~l~~~~~~~~~~~~iAiDTEf~r~~t---~~p~LcLIQi~~~--------------e~~~lIdpl~~~--~d~~~l~~ 64 (361)
T COG0349 4 GDLLAAACALLRGSKAIAIDTEFMRLRT---YYPRLCLIQISDG--------------EGASLIDPLAGI--LDLPPLVA 64 (361)
T ss_pred hhHHHHHHHHhcCCCceEEecccccccc---cCCceEEEEEecC--------------CCceEecccccc--cccchHHH
Confidence 5678889999999999999999998885 8899999999985 348999988632 23788999
Q ss_pred hhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccc
Q 016210 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK 178 (393)
Q Consensus 99 lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K 178 (393)
+|.|++|+||+|.+++|+.+|.+.||+ .+.++|| |++|+.+++.. .++||++||++++|+.++|
T Consensus 65 Ll~d~~v~KIfHaa~~DL~~l~~~~g~--------~p~plfd-TqiAa~l~g~~-------~~~gl~~Lv~~ll~v~ldK 128 (361)
T COG0349 65 LLADPNVVKIFHAARFDLEVLLNLFGL--------LPTPLFD-TQIAAKLAGFG-------TSHGLADLVEELLGVELDK 128 (361)
T ss_pred HhcCCceeeeeccccccHHHHHHhcCC--------CCCchhH-HHHHHHHhCCc-------ccccHHHHHHHHhCCcccc
Confidence 999999999999999999999998775 3789999 99999999975 3899999999999999999
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccccccccCCcccccccCcccCcccCCCccccc
Q 016210 179 ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSSNLDLGLKGILEKPDIGNKTVRFK 255 (393)
Q Consensus 179 ~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 255 (393)
++|.|||+.||||++|++|||.||.||+.||+.|.++|.++|++ .+||.++.+.....- .-...|++.+. ...+
T Consensus 129 ~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ef~~l~~r~~~~~--~~~~~w~~i~~-a~~~ 205 (361)
T COG0349 129 SEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAEDEFRLLPTRRTYKV--LPEDAWREIKI-AHSL 205 (361)
T ss_pred cccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHhhhcccccc--ChHhHHHHhhh-hhcC
Confidence 99999999999999999999999999999999999999999998 888999877621110 12245778877 5678
Q ss_pred hhhHHHHHHHHhh------hhcCCCCc-ccccccc---ccCCCCCHHHHHHHHhhcc
Q 016210 256 LCEALDIIRATSY------YSQCLPEG-VVSRVSY---LNTMPMDESLVKIVRKYGE 302 (393)
Q Consensus 256 ~~~~~~~~~~~~~------~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~~~~~~ 302 (393)
.+++++++|+||. +.||+|++ ||.+..+ +...|.+...+..+..++.
T Consensus 206 ~p~~la~l~~La~wRe~~Ar~rd~~~~~vl~de~i~~~a~~~P~~~~~l~~l~~~~~ 262 (361)
T COG0349 206 DPRELAVLRELAAWREREARERDLARNFVLKDEALWELARYTPKNLKELDALGLIPK 262 (361)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhccccccccchhHHHHHHHhCCCCHHHHHhccCCcc
Confidence 8999999999965 67799999 9999988 8999999999999888765
No 3
>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=100.00 E-value=6.8e-34 Score=286.67 Aligned_cols=243 Identities=22% Similarity=0.310 Sum_probs=205.7
Q ss_pred EeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhH
Q 016210 14 VTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIW 93 (393)
Q Consensus 14 V~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~ 93 (393)
|+| .++++.+++.+...++||||+|+..... |.+++|||||++. +.+|+||+..+. .+
T Consensus 2 I~t--~~~l~~~~~~l~~~~~ia~DtE~~~~~~---y~~~l~LiQia~~--------------~~~~liD~~~~~---~~ 59 (367)
T TIGR01388 2 ITT--DDELATVCEAVRTFPFVALDTEFVRERT---FWPQLGLIQVADG--------------EQLALIDPLVII---DW 59 (367)
T ss_pred cCC--HHHHHHHHHHHhcCCEEEEeccccCCCC---CCCcceEEEEeeC--------------CeEEEEeCCCcc---cH
Confidence 667 8999999999999999999999988764 7899999999983 688999998663 37
Q ss_pred HHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcC
Q 016210 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (393)
Q Consensus 94 ~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg 173 (393)
..|+++|+|+++.||+|++++|+..|.+.+++ .+.++|| |++|+|++++. .++||++|+++|||
T Consensus 60 ~~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~--------~~~~~fD-tqlAa~lL~~~-------~~~~l~~Lv~~~Lg 123 (367)
T TIGR01388 60 SPLKELLRDESVVKVLHAASEDLEVFLNLFGE--------LPQPLFD-TQIAAAFCGFG-------MSMGYAKLVQEVLG 123 (367)
T ss_pred HHHHHHHCCCCceEEEeecHHHHHHHHHHhCC--------CCCCccc-HHHHHHHhCCC-------CCccHHHHHHHHcC
Confidence 88999999999999999999999999885443 2578999 99999999975 35799999999999
Q ss_pred CcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccccccccCCcccccccCcccCcccCCC
Q 016210 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISELDSSNLDLGLKGILEKPDIGNK 250 (393)
Q Consensus 174 ~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~e~~~l~~~~~~~~~~~~~~~~~~~~~ 250 (393)
+.++|+++.+||..|||+.+|+.|||.||++++.||+.|.++|++.|+. .+||..+........ .-...|++.++
T Consensus 124 ~~l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~w~~ee~~~l~~~~~~~~--~~~~~~~~i~~ 201 (367)
T TIGR01388 124 VELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLAWLEEECTLLTDRRTYVV--NPEDAWRDIKN 201 (367)
T ss_pred CCCCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHhccccCCC--ChHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999987 888988765422210 11133667776
Q ss_pred ccccchhhHHHHHHHHhh------hhcCCCCc-ccccccc---ccCCCCCHHHHHHH
Q 016210 251 TVRFKLCEALDIIRATSY------YSQCLPEG-VVSRVSY---LNTMPMDESLVKIV 297 (393)
Q Consensus 251 ~~~~~~~~~~~~~~~~~~------~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~ 297 (393)
..+. .+++|+++|+||. +.+|+|++ ||++..+ |...|.+...|..+
T Consensus 202 ~~~l-~~~~l~~l~~L~~wRe~~A~~~d~p~~~il~d~~l~~lA~~~P~~~~~l~~~ 257 (367)
T TIGR01388 202 AWQL-RPQQLAVLQALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTELASL 257 (367)
T ss_pred cccC-CHHHHHHHHHHHHHHHHHHHHcCCCcceeeCHHHHHHHHHhCCCCHHHHHhc
Confidence 5555 4899999999966 45699999 9999887 99999998887644
No 4
>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=99.97 E-value=3e-30 Score=238.66 Aligned_cols=184 Identities=46% Similarity=0.765 Sum_probs=149.9
Q ss_pred EEEEeCCChHHHHHHHHH--HcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC
Q 016210 11 IHLVTSTESPEFTHLARA--LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP 88 (393)
Q Consensus 11 i~lV~t~~~~el~~ll~~--L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~ 88 (393)
|++|++ ++++++++.. +....+||||+||.+.+..+ ..++++|||||+. +.+|+||+..++
T Consensus 1 ~~~i~~--~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~-~~~~v~LiQiat~--------------~~~~lid~~~~~ 63 (193)
T cd06146 1 IHIVDS--EEELEALLLALSLEAGRVVGIDSEWKPSFLGD-SDPRVAILQLATE--------------DEVFLLDLLALE 63 (193)
T ss_pred CeEecC--HHHHHHHHHHHhhccCCEEEEECccCCCccCC-CCCCceEEEEecC--------------CCEEEEEchhcc
Confidence 588999 9999999999 88999999999999877421 2589999999984 679999988765
Q ss_pred ---chhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCC---CCCCCcc
Q 016210 89 ---LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGR---KLPKETK 162 (393)
Q Consensus 89 ---~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~---~~~~~~~ 162 (393)
.+.+...|+++|+|++|+||||++++|+..|++.||+.+.. +..+.+++|+..++..+.....++ ..+...+
T Consensus 64 ~~~~~~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~--~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~ 141 (193)
T cd06146 64 NLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCM--FERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTK 141 (193)
T ss_pred ccchHHHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccc--cccCCceEEHHHHHHHHhhccccccccccCcccC
Confidence 23466789999999999999999999999999988862110 112579999555555554332111 1112478
Q ss_pred cHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 016210 163 SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 163 sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
||++|++++||.+++|..++|||+.||||++|+.|||.||++++.||+.|.
T Consensus 142 sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 142 GLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred CHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999985
No 5
>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=99.97 E-value=9e-30 Score=228.45 Aligned_cols=158 Identities=34% Similarity=0.576 Sum_probs=140.9
Q ss_pred HHHHHHHHc-CCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhh
Q 016210 22 FTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELF 100 (393)
Q Consensus 22 l~~ll~~L~-~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lL 100 (393)
++++++.+. .+++||||+||.+.+. +.+++++|||++. ++.+|+||+..++. ....|+++|
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~---~~~~~~liQl~~~-------------~~~~~l~d~~~~~~--~~~~L~~lL 63 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRR---YYGEVALIQLCVS-------------EEKCYLFDPLSLSV--DWQGLKMLL 63 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCC---CCCceEEEEEEEC-------------CCCEEEEecccCcc--CHHHHHHHh
Confidence 567888998 9999999999998874 5689999999995 37899999887652 577899999
Q ss_pred CCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccccc
Q 016210 101 VSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKEL 180 (393)
Q Consensus 101 e~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~ 180 (393)
+++++.||||++++|+..|.+.||+ . +.++|| +++++|++++. .+.||+++++++||.+++|..
T Consensus 64 ~d~~i~Kvg~~~k~D~~~L~~~~gi---~-----~~~~~D-~~~aa~ll~~~-------~~~~L~~l~~~~lg~~l~K~~ 127 (161)
T cd06129 64 ENPSIVKALHGIEGDLWKLLRDFGE---K-----LQRLFD-TTIAANLKGLP-------ERWSLASLVEHFLGKTLDKSI 127 (161)
T ss_pred CCCCEEEEEeccHHHHHHHHHHcCC---C-----cccHhH-HHHHHHHhCCC-------CCchHHHHHHHHhCCCCCccc
Confidence 9999999999999999999887776 1 467799 89999999874 357999999999999999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 016210 181 QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 181 q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
++|||+.||||++|+.|||.||++++.||+.|.
T Consensus 128 ~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 128 SCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999985
No 6
>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=99.95 E-value=2e-27 Score=213.95 Aligned_cols=163 Identities=33% Similarity=0.527 Sum_probs=142.9
Q ss_pred hHHHHHHHHHHc-CCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHH
Q 016210 19 SPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLK 97 (393)
Q Consensus 19 ~~el~~ll~~L~-~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~ 97 (393)
.++++.+++.+. ...+||||+||.+.+.. .+.+++++||||+ ++.+|+||+..+. .+...|+
T Consensus 4 ~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~-~~~~~~~liQl~~--------------~~~~~l~~~~~~~--~~~~~l~ 66 (170)
T cd06141 4 AQDAEEAVKELLGKEKVVGFDTEWRPSFRK-GKRNKVALLQLAT--------------ESRCLLFQLAHMD--KLPPSLK 66 (170)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCccCCccCC-CCCCCceEEEEec--------------CCcEEEEEhhhhh--cccHHHH
Confidence 678999999998 99999999999987642 2467999999997 4789999988753 4567899
Q ss_pred HhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccc
Q 016210 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (393)
Q Consensus 98 ~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~ 177 (393)
++|+++++.||||++++|+..|.+.||+ . +.++|| +++++|++++. ....||++|++++||..+.
T Consensus 67 ~ll~~~~i~kv~~~~k~D~~~L~~~~g~---~-----~~~~~D-l~~aa~ll~~~------~~~~~l~~l~~~~l~~~~~ 131 (170)
T cd06141 67 QLLEDPSILKVGVGIKGDARKLARDFGI---E-----VRGVVD-LSHLAKRVGPR------RKLVSLARLVEEVLGLPLS 131 (170)
T ss_pred HHhcCCCeeEEEeeeHHHHHHHHhHcCC---C-----CCCeee-HHHHHHHhCCC------cCCccHHHHHHHHcCcccC
Confidence 9999999999999999999999877876 1 467799 89999999974 1247999999999999998
Q ss_pred --ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 016210 178 --KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 178 --K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
|..++|||..|||+++|++|||.||++++.||+.|.
T Consensus 132 k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 132 KPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 888999999999999999999999999999999885
No 7
>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=99.95 E-value=1.2e-27 Score=221.89 Aligned_cols=170 Identities=25% Similarity=0.327 Sum_probs=143.2
Q ss_pred HHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC
Q 016210 25 LARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD 104 (393)
Q Consensus 25 ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~~~ 104 (393)
+++.|.++.+||||+||.+.+. .++++||||++. .+.+|+||+..++...+...|+++|++++
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~----~~~~~LiQia~~-------------~~~v~l~D~~~~~~~~~~~~L~~iLe~~~ 65 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGR----KGKLCLVQIATR-------------TGQIYLFDILKLGSIVFINGLKDILESKK 65 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCC----CCCEEEEEEeeC-------------CCcEEEEEhhhccchhHHHHHHHHhcCCC
Confidence 4677788999999999987653 468999999984 37999999988754346788999999999
Q ss_pred cEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccC-CCCCCCcccHHHHHHHHcCCcccc-----
Q 016210 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLG-RKLPKETKSLANICKELLDISLSK----- 178 (393)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~-~~~~~~~~sLa~Lve~~Lg~~L~K----- 178 (393)
+.||+|++++|+..|.+.||+ . +.++|| |++|+|++++... ...+....||++++++|||.+++|
T Consensus 66 i~Kv~h~~k~D~~~L~~~~gi---~-----~~~~fD-t~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~ 136 (197)
T cd06148 66 ILKVIHDCRRDSDALYHQYGI---K-----LNNVFD-TQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVK 136 (197)
T ss_pred ccEEEEechhHHHHHHHhcCc---c-----ccceee-HHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHH
Confidence 999999999999999776876 1 467899 8999999987521 112223479999999999999865
Q ss_pred ---cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 016210 179 ---ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (393)
Q Consensus 179 ---~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g 220 (393)
..+++||..|||+++|+.|||.||++++.||+.|...|.+..
T Consensus 137 ~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~~ 181 (197)
T cd06148 137 KLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISKF 181 (197)
T ss_pred HHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhhH
Confidence 467899999999999999999999999999999999998764
No 8
>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=99.95 E-value=3.1e-26 Score=204.55 Aligned_cols=174 Identities=29% Similarity=0.451 Sum_probs=150.7
Q ss_pred EEEEeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 016210 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (393)
Q Consensus 11 i~lV~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~ 90 (393)
|++|++ .+++++++..+...+.+|||+||.+.... .....++++|++.. ..+|+++.......
T Consensus 1 y~~v~~--~~~l~~~~~~l~~~~~~a~D~E~~~~~~~-~~~~~~~~iq~~~~--------------~~~~i~~~~~~~~~ 63 (176)
T PF01612_consen 1 YQIVDT--EEELEEAIKKLKNAKVLAFDTETTGLDPY-SYNPKIALIQLATG--------------EGCYIIDPIDLGDN 63 (176)
T ss_dssp SEEEHS--HHHHHHHHHHHTTTSEEEEEEEEETSTST-TSSEEEEEEEEEES--------------CEEEEECGTTSTTT
T ss_pred CEecCC--HHHHHHHHHHHcCCCeEEEEEEECCCCcc-ccCCeEEEEEEecC--------------CCceeeeecccccc
Confidence 578999 99999999999999999999999987753 24678999999983 78899887765532
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
.+...|+++|+++++.|||||+++|+.+|.+.+|+ .+.+++| ++++++++++. ..+||++|+.+
T Consensus 64 ~~~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i--------~~~~~~D-~~l~~~~l~~~-------~~~~L~~L~~~ 127 (176)
T PF01612_consen 64 WILDALKELLEDPNIIKVGHNAKFDLKWLYRSFGI--------DLKNVFD-TMLAAYLLDPT-------RSYSLKDLAEE 127 (176)
T ss_dssp THHHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS----------SSEEE-HHHHHHHTTTS-------TTSSHHHHHHH
T ss_pred chHHHHHHHHhCCCccEEEEEEechHHHHHHHhcc--------ccCCccc-hhhhhhccccc-------ccccHHHHHHH
Confidence 26889999999999999999999999999987776 2578999 69999999975 23899999999
Q ss_pred HcC-CcccccccccCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLD-ISLSKELQCSDWS-NRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (393)
Q Consensus 171 ~Lg-~~L~K~~q~sdWs-~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (393)
++| ..++|..+.++|. .+||+++|+.|||.||+++++||+.|.++|+
T Consensus 128 ~l~~~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l~ 176 (176)
T PF01612_consen 128 YLGNIDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQLE 176 (176)
T ss_dssp HHSEEE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHHC
T ss_pred HhhhccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999 7788899999999 8999999999999999999999999999874
No 9
>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=99.85 E-value=4.9e-20 Score=165.68 Aligned_cols=171 Identities=30% Similarity=0.484 Sum_probs=138.4
Q ss_pred HHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhC
Q 016210 22 FTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFV 101 (393)
Q Consensus 22 l~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe 101 (393)
+.++++.+...+.+++|+|+.+... ..+.++++|+++. +.+|+||+... ...+.|+++|+
T Consensus 2 ~~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~i~l~~~--------------~~~~~i~~~~~---~~~~~l~~ll~ 61 (178)
T cd06142 2 LEDLCERLASAGVIAVDTEFMRLNT---YYPRLCLIQISTG--------------GEVYLIDPLAI---GDLSPLKELLA 61 (178)
T ss_pred HHHHHHHHhcCCeEEEECCccCCCc---CCCceEEEEEeeC--------------CCEEEEeCCCc---ccHHHHHHHHc
Confidence 3445555555669999998865542 3468899999873 34888885532 25677899999
Q ss_pred CCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccccccc
Q 016210 102 SPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQ 181 (393)
Q Consensus 102 ~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q 181 (393)
++++.||+||+|.|+..|.+.||+ . .+++|| +++++|++++. .+++|++++++|+|..+.+...
T Consensus 62 ~~~i~kv~~d~K~~~~~L~~~~gi-------~-~~~~~D-~~laayLl~p~-------~~~~l~~l~~~~l~~~~~~~~~ 125 (178)
T cd06142 62 DPNIVKVFHAAREDLELLKRDFGI-------L-PQNLFD-TQIAARLLGLG-------DSVGLAALVEELLGVELDKGEQ 125 (178)
T ss_pred CCCceEEEeccHHHHHHHHHHcCC-------C-CCCccc-HHHHHHHhCCC-------ccccHHHHHHHHhCCCCCcccc
Confidence 999999999999999999886676 1 357899 89999999985 2469999999999998766667
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---cccccc
Q 016210 182 CSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS---CSSISE 228 (393)
Q Consensus 182 ~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l---~~e~~~ 228 (393)
+++|..+||+.+|+.|||.||+++++|++.|.++|++.|.. ..||..
T Consensus 126 ~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~~l~~L~~~~~~~ 175 (178)
T cd06142 126 RSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEEGRLEWAEEECEL 175 (178)
T ss_pred cccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence 88999999999999999999999999999999999988765 555543
No 10
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=5e-21 Score=196.63 Aligned_cols=263 Identities=22% Similarity=0.281 Sum_probs=199.5
Q ss_pred EEEEeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 016210 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (393)
Q Consensus 11 i~lV~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~ 90 (393)
..+|.+ ..++.++.+.+.....+|+|.|..+... +.+-.||+||+|. .+-|+||...+.
T Consensus 193 ~~~I~t--~~el~~l~~~l~~~~Efavdlehhsyrs---f~gltclmqISTr--------------~ed~iIDt~~l~-- 251 (687)
T KOG2206|consen 193 KVWICT--LGELEALPEILDSVIEFAVDLEHHSYRS---FLGLTCLMQISTR--------------TEDFIIDTFKLR-- 251 (687)
T ss_pred ceeeec--hHHHHHHHHHHhhhhhhhhhccccchhh---hcCceeEEEeecc--------------chhheehhHHHH--
Confidence 466888 7889999999988889999999987774 7899999999996 567999987664
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+....|+++|.+|.++||+|++..|+.+|+++||| .+.++|| |.-|..+|+.+ +++|+.|.+.
T Consensus 252 ~~i~~l~e~fsdp~ivkvfhgaD~diiwlqrdfgi--------yvvnLfd-t~~a~r~L~~~--------r~sL~~ll~~ 314 (687)
T KOG2206|consen 252 DHIGILNEVFSDPGIVKVFHGADTDIIWLQRDFGI--------YVVNLFD-TIQASRLLGLP--------RPSLAYLLEC 314 (687)
T ss_pred HHHHHhhhhccCCCeEEEEecCccchhhhhccceE--------EEEechh-hHHHHHHhCCC--------cccHHHHHHH
Confidence 45668999999999999999999999999999998 3678999 89999999864 8999999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC----ccc-cccccCCccc--ccccCccc
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS----CSS-ISELDSSNLD--LGLKGILE 243 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l----~~e-~~~l~~~~~~--~~~~~~~~ 243 (393)
|.|+..+|..|..||..|||+++++.||-.|.+|++.||+.|+..|.+-++- -.| .+........ -..+..++
T Consensus 315 ~~~v~~nk~yqladwR~rpLp~~Mv~yar~dthyllyiyD~lr~el~~~a~~~~~~~~~~~d~c~~~~~k~~~~~~sy~~ 394 (687)
T KOG2206|consen 315 VCGVLTNKKYQLADWRIRPLPEEMVRYAREDTHYLLYIYDVLRKELKRLAKGRAVTYSESRDMCTNGYKKKTFCTKSYLE 394 (687)
T ss_pred HHhhhhhhhhhhchhccccCcHHHHHHHhhcchhHHHHHHHHHHHHHHHhcccccccchhhhhhhcceecccCCCcchHh
Confidence 9999999999999999999999999999999999999999999988876643 111 1111111000 01111111
Q ss_pred CcccCCCccccchhhHHHHHHHHhh------hhcCCCCc-ccccccc---ccCCCCCHH-------------------HH
Q 016210 244 KPDIGNKTVRFKLCEALDIIRATSY------YSQCLPEG-VVSRVSY---LNTMPMDES-------------------LV 294 (393)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~-~~~~~~~---~~~~~~~~~-------------------~~ 294 (393)
-.+ +-..=.++++.++|+|-. ++.|=+++ |||+.-. +-.+|.+.. ++
T Consensus 395 v~~----~q~~ln~~q~~~l~~L~~wRd~iARaeDES~~yVlpN~~ll~l~e~~P~~v~gl~~~ln~~~p~vkq~~~~~~ 470 (687)
T KOG2206|consen 395 VED----IQSRLNSSQLDVLRALLRWRDFIARAEDESVHYVLPNDQLLKLAEERPDTVDGLLGGLNRLSPLVKQNVMDFL 470 (687)
T ss_pred HHH----HHhccchhHHHHHHHHHHHHHHHHhhccCCCceecccHHHHHHHHHCCccHHHHHHhccCCCHHHHHHHHHHH
Confidence 111 111134688999999944 44455666 8886554 666666643 45
Q ss_pred HHHHhhcceeeeccccCCCcc
Q 016210 295 KIVRKYGEKILLRECDKAPKT 315 (393)
Q Consensus 295 ~~~~~~~~~~~~~~~~~~~~~ 315 (393)
.+++.=++-+++.+.-..+..
T Consensus 471 ~ii~~a~~~~l~~~~~a~g~~ 491 (687)
T KOG2206|consen 471 YIIRSAGRGFLLQNLTASGRK 491 (687)
T ss_pred HHHHHHhhhhhhhchhhccCC
Confidence 667777777777766544433
No 11
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.80 E-value=7.2e-18 Score=149.21 Aligned_cols=169 Identities=32% Similarity=0.441 Sum_probs=132.9
Q ss_pred EEEeCCChHHHHHHHHHHc-CCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCch
Q 016210 12 HLVTSTESPEFTHLARALS-QSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLP 90 (393)
Q Consensus 12 ~lV~t~~~~el~~ll~~L~-~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~ 90 (393)
.+|++ .+++..+++.+. ....+++|+|+.+... +.+.++++|++.. ++.+|+++.... .
T Consensus 2 ~~i~~--~~~~~~~~~~~~~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~-------------~~~~~i~~~~~~--~ 61 (172)
T smart00474 2 RVVTD--SETLEELLEKLRAAGGEVALDTETTGLNS---YSGKLVLIQISVT-------------GEGAFIIDPLAL--G 61 (172)
T ss_pred EEecC--HHHHHHHHHHHHhcCCeEEEeccccCCcc---CCCCEEEEEEeEc-------------CCceEEEEeccc--h
Confidence 56777 677777666665 5669999999876553 3568889999863 235666554322 2
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
.....|+++|+++++.||+||+|.|+..|.+ +|+ . +.++|| +++++|++++. ...++|++++++
T Consensus 62 ~~~~~l~~~l~~~~~~kv~~d~k~~~~~L~~-~gi---~-----~~~~~D-~~laayll~p~------~~~~~l~~l~~~ 125 (172)
T smart00474 62 DDLEILKDLLEDETITKVGHNAKFDLHVLAR-FGI---E-----LENIFD-TMLAAYLLLGG------PSKHGLATLLKE 125 (172)
T ss_pred hhHHHHHHHhcCCCceEEEechHHHHHHHHH-CCC---c-----ccchhH-HHHHHHHHcCC------CCcCCHHHHHHH
Confidence 3466789999999999999999999999987 776 1 345699 89999999875 223699999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L 216 (393)
|+|..+.+..+.++|..+|+..+|+.||+.||+++++|++.|.++|
T Consensus 126 ~l~~~~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 126 YLGVELDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred HhCCCCCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9998876555556897788999999999999999999999998876
No 12
>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=99.74 E-value=1.8e-16 Score=145.86 Aligned_cols=174 Identities=25% Similarity=0.400 Sum_probs=133.4
Q ss_pred ccEEEEeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC
Q 016210 9 LKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP 88 (393)
Q Consensus 9 ~~i~lV~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~ 88 (393)
.+|.+|++ .+++..+++.+...+.+++++|+.+..+ +.+.+..+|++.. +++|+|++. .
T Consensus 3 ~~~~~i~~--~~~l~~~~~~l~~~~~l~~~~e~~~~~~---~~~~~~~l~l~~~--------------~~~~~i~~l--~ 61 (192)
T cd06147 3 TPLTFVDT--EEKLEELVEKLKNCKEIAVDLEHHSYRS---YLGFTCLMQISTR--------------EEDYIVDTL--K 61 (192)
T ss_pred CCcEEECC--HHHHHHHHHHHhcCCeEEEEeEecCCcc---CCCceEEEEEecC--------------CCcEEEEec--c
Confidence 35677866 5667776666655568999998654432 2457778888874 237787742 2
Q ss_pred chhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHH
Q 016210 89 LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANIC 168 (393)
Q Consensus 89 ~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lv 168 (393)
.......|+++|+++++.||+||+|.++..|.+.+|+ . ..++|| ++|++||+++. +++|+.++
T Consensus 62 ~~~~~~~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi---~-----~~~~fD-~~laaYLL~p~--------~~~l~~l~ 124 (192)
T cd06147 62 LRDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGL---Y-----VVNLFD-TGQAARVLNLP--------RHSLAYLL 124 (192)
T ss_pred cccchHHHHHHhcCCCceEEEechHHHHHHHHHHhCC---C-----cCchHH-HHHHHHHhCCC--------cccHHHHH
Confidence 2234566899999999999999999999999733665 1 233499 89999999984 35999999
Q ss_pred HHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 016210 169 KELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (393)
Q Consensus 169 e~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g 220 (393)
++||+..+.|..+.++|+.+||+.+|..|++.+|.++++|++.|.++|+++.
T Consensus 125 ~~yl~~~~~k~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 125 QKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176 (192)
T ss_pred HHHhCCCcchhhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhc
Confidence 9999887545456677987888999999999999999999999999998764
No 13
>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=99.68 E-value=1.7e-15 Score=131.57 Aligned_cols=149 Identities=28% Similarity=0.310 Sum_probs=114.0
Q ss_pred eEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEehH
Q 016210 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (393)
Q Consensus 34 ~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k 113 (393)
.+++|+|+.+... +.++++++|+++. +++++|+... ....+.+.|+++|+++.+.||+||++
T Consensus 2 ~l~~d~e~~~~~~---~~~~i~~~~l~~~--------------~~~~~i~~~~-~~~~~~~~l~~~l~~~~~~~v~~~~k 63 (155)
T cd00007 2 EVAFDTETTGLNY---HRGKLVGIQIATA--------------GEAAYIPDEL-ELEEDLEALKELLEDEDITKVGHDAK 63 (155)
T ss_pred ceEEEEecCCCCc---CCCeEEEEEEEEC--------------CcEEEEEcCC-CHHHHHHHHHHHHcCCCCcEEeccHH
Confidence 5799999866552 3568899999973 2244443221 11346777999999999999999999
Q ss_pred hHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccccccccCCC----CCC
Q 016210 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS----NRP 189 (393)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~sdWs----~RP 189 (393)
+|+..|.+. ++ ....++|| +++++|++++. ...++|++++++|++..+.+..+..+|. .++
T Consensus 64 ~d~~~L~~~-~~-------~~~~~~~D-~~~~ayll~~~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 128 (155)
T cd00007 64 FDLVVLARD-GI-------ELPGNIFD-TMLAAYLLNPG------EGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARP 128 (155)
T ss_pred HHHHHHHHC-CC-------CCCCCccc-HHHHHHHhCCC------CCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccC
Confidence 999999874 32 12567899 89999999985 2147999999999998865533455553 478
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 190 LTEEQKNYAAIDAHCLIEIFNIFQVK 215 (393)
Q Consensus 190 Ls~~Ql~YAA~DA~~Ll~L~~~L~~~ 215 (393)
++.+|..||+.||.++++|++.|.++
T Consensus 129 ~~~~~~~y~~~da~~~~~l~~~l~~~ 154 (155)
T cd00007 129 LSEELLEYAAEDADALLRLYEKLLEE 154 (155)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHHhh
Confidence 89999999999999999999999765
No 14
>PRK05755 DNA polymerase I; Provisional
Probab=99.68 E-value=1.5e-15 Score=168.95 Aligned_cols=187 Identities=18% Similarity=0.205 Sum_probs=149.0
Q ss_pred CccEEEEeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCC
Q 016210 8 PLKIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSI 87 (393)
Q Consensus 8 ~~~i~lV~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l 87 (393)
.+.|.+|++ .+++..+++.+.....++||+|+.+..+ +.++++++|++.. ++.+|+|++..+
T Consensus 293 ~~~~~~I~~--~~~L~~~l~~l~~~~~~a~DtEt~~l~~---~~~~i~~i~ls~~-------------~g~~~~ip~~~i 354 (880)
T PRK05755 293 EEDYETILD--EEELEAWLAKLKAAGLFAFDTETTSLDP---MQAELVGLSFAVE-------------PGEAAYIPLDQL 354 (880)
T ss_pred CCceEEeCC--HHHHHHHHHHhhccCeEEEEeccCCCCc---ccccEEEEEEEeC-------------CCcEEEEecccc
Confidence 456778887 8899999999888899999999988764 6788999999875 345888887544
Q ss_pred CchhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHH
Q 016210 88 PLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (393)
Q Consensus 88 ~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~L 167 (393)
+. ..+..|.++|+++.+.||+||+++|+..|.+ +|+ . ...++|| |++|+|++++. . .++|+++
T Consensus 355 ~~-~~l~~l~~~L~d~~v~kV~HNakfDl~~L~~-~gi---~----~~~~~~D-T~iAa~Ll~~~------~-~~~L~~L 417 (880)
T PRK05755 355 DR-EVLAALKPLLEDPAIKKVGQNLKYDLHVLAR-YGI---E----LRGIAFD-TMLASYLLDPG------R-RHGLDSL 417 (880)
T ss_pred cH-HHHHHHHHHHhCCCCcEEEeccHhHHHHHHh-CCC---C----cCCCccc-HHHHHHHcCCC------C-CCCHHHH
Confidence 32 4678899999999999999999999999987 565 1 2467999 99999999985 2 3899999
Q ss_pred HHHHcCCcccccc----cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-----cccccccc
Q 016210 168 CKELLDISLSKEL----QCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS-----CSSISELD 230 (393)
Q Consensus 168 ve~~Lg~~L~K~~----q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l-----~~e~~~l~ 230 (393)
+++|+|.++.... ...+|+..|+ +.|..||+.||.+++.||+.|.++|.+.+.+ ..||++..
T Consensus 418 ~~~ylg~~~~~~~~~~gk~~~~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~L~~~~~l~~l~~eiE~p~~~ 488 (880)
T PRK05755 418 AERYLGHKTISFEEVAGKQLTFAQVDL-EEAAEYAAEDADVTLRLHEVLKPKLLEEPGLLELYEEIELPLVP 488 (880)
T ss_pred HHHHhCCCccchHHhcCCCCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhhchHHH
Confidence 9999998752211 1223444566 5789999999999999999999999887444 77787764
No 15
>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=99.67 E-value=2.1e-15 Score=131.46 Aligned_cols=147 Identities=27% Similarity=0.281 Sum_probs=112.5
Q ss_pred eEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEehH
Q 016210 34 LVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFK 113 (393)
Q Consensus 34 ~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k 113 (393)
++++|+|+.+..+ ...+++.+|++.. ++.+|+|++.... -....|+++|+++++.||+||+|
T Consensus 1 ~~~~~~e~~~~~~---~~~~~~~l~l~~~-------------~~~~~~i~~~~~~--~~~~~l~~~l~~~~~~kv~~d~K 62 (150)
T cd09018 1 VFAFDTETDSLDN---ISANLVLIQLAIE-------------PGVAALIPVAHDY--LALELLKPLLEDEKALKVGQNLK 62 (150)
T ss_pred CEEEEeecCCCCC---CCceEEEEEEEcC-------------CCcEEEEEcCCcc--cCHHHHHHHhcCCCCceeeecHH
Confidence 4789998766553 3468899999974 2347888754321 12566899999999999999999
Q ss_pred hHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccc-cc-cccCCCCCCCC
Q 016210 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK-EL-QCSDWSNRPLT 191 (393)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K-~~-q~sdWs~RPLs 191 (393)
.|+..|.+ +|+ ...+++|| +++|+||+++. ..+++|++++++||+..+.+ .. ..++|..++++
T Consensus 63 ~~~~~L~~-~~~-------~~~~~~~D-~~laayLl~p~------~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 127 (150)
T cd09018 63 YDRGILLN-YFI-------ELRGIAFD-TMLEAYILNSV------AGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLT 127 (150)
T ss_pred HHHHHHHH-cCC-------ccCCcchh-HHHHHHHhCCC------CCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCH
Confidence 99999987 454 12467899 89999999985 21469999999999988544 21 12248557889
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 016210 192 EEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 192 ~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
.+|+.||+.||.++++|++.|.
T Consensus 128 ~~~~~ya~~~a~~l~~L~~~l~ 149 (150)
T cd09018 128 EEQGRYAAEDADVTLQIHLKLW 149 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999874
No 16
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.66 E-value=3.6e-18 Score=176.67 Aligned_cols=252 Identities=29% Similarity=0.333 Sum_probs=185.2
Q ss_pred CceeeHHH--HHHHHhccccCCCCCCC-cc---cHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHH--
Q 016210 136 EPYLDITS--IYNHLHHKQLGRKLPKE-TK---SLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIE-- 207 (393)
Q Consensus 136 ~~~fDlt~--LA~yLl~~~~~~~~~~~-~~---sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~-- 207 (393)
..++|++. +..||-+..++...+.. .+ +--++.+..+..-+.+..++++|..+++++.|..|+..++..+..
T Consensus 155 ~~~~Di~l~~i~e~lq~~~f~e~a~~~ik~~l~~~~~~e~~~ldlIls~k~q~a~~ll~~~~~~q~p~v~fld~~v~~~~ 234 (617)
T KOG2207|consen 155 KQTLDITLCKIDEYLQNQRFGEAAPKAIKSLLLSDNAFEQLMLDLILSKKLQIADELLRHLTELQKPYVEFLDQMVLDNF 234 (617)
T ss_pred hhhHhHhcchhHHHHHhHHHHHHHHHHHHhhhhhhhhHHHHhccHhhccchhHHHHHHhhhhhhhhhHHHHHHHHHHHHH
Confidence 35778776 67777665433222211 11 122345566666778889999999999999999999999999998
Q ss_pred HHHHHHHHHHhcC-----CCccccccccCCcccccccCcccCc-ccCCCccccchhhHHHHHHHHhhhhcCCCCcccccc
Q 016210 208 IFNIFQVKVAQKG-----NSCSSISELDSSNLDLGLKGILEKP-DIGNKTVRFKLCEALDIIRATSYYSQCLPEGVVSRV 281 (393)
Q Consensus 208 L~~~L~~~L~~~g-----~l~~e~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 (393)
..+.+.+.+.+.- .+..-|+...+ |...-+.-. +.+.++.+...|+++...+...++.+....+..++.
T Consensus 235 ~v~e~~~~~~e~~~~~~~tl~~~v~~i~~-----rn~~~~~f~~~~~~n~v~~~~~kal~~~~~~~e~~~~~~~~f~~~~ 309 (617)
T KOG2207|consen 235 IVDERCAHLLERTINLPKTLTILVQEIIN-----RNQKKYTFSDEYAKNYVQNKNCKALHYIRSEREKGQMADKGFVQHV 309 (617)
T ss_pred HHHHHHHHHHhhccCCCchhhhhHHHHHh-----ccchhhhhhhhhhhhHhhcccHHHHHHHHHHhhhhhhHHHhhchhh
Confidence 7777776666541 01222222211 111111111 467788889999999999999888888778888888
Q ss_pred ccccCCCCCHHHHHHHHhhc---ceeeeccccCCC-----cccccccccccch-----hhhhhhcccCCCCCCCCCCCCC
Q 016210 282 SYLNTMPMDESLVKIVRKYG---EKILLRECDKAP-----KTSKKKGRKRSSV-----IVDSREKRLDDIGDWQGPPPWD 348 (393)
Q Consensus 282 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~-----~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~ 348 (393)
..-.|+|+++++++++..+| |+|.+...|.-+ +..+++-.++... ..+..+..+.++..|+++|||+
T Consensus 310 ~~~~t~~~d~~~lkyLw~~~~~iEai~~~~~~~i~~~d~~~el~~~~s~~~~~k~~~~~~~~~~~pl~~~~~~~~~~~~~ 389 (617)
T KOG2207|consen 310 VETKTKPDDENLLKYLWSFGEHIEAIYLATYDNIDPKDDAKELEKRTSRRGAGKTLFNQRMTTNVPLVCEDLFLFEPPWV 389 (617)
T ss_pred eeecccccchhHHHHHHHHHHhhhhhhhhhhhcCCCchhHHHHhchhhhcccChhhhhcccccccCccchhhhccCCCcc
Confidence 89999999999999999999 999999888553 2222222222222 2256778899999999999999
Q ss_pred CCCCCCCCcchhHHHHHHhHhhhhhhcccccCCCCC-CCCCCCCC
Q 016210 349 LSLGGDGYPKFLCDVMVEGLAKHLRCVGIDAATPRS-KKPEPRSN 392 (393)
Q Consensus 349 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 392 (393)
-++|+.|++|++=|+|+|+|++++||||||++.++| ++|++|..
T Consensus 390 ~~i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~ 434 (617)
T KOG2207|consen 390 ESIGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLA 434 (617)
T ss_pred cceeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHH
Confidence 999999999999999999999999999999999999 66777753
No 17
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.66 E-value=1.9e-16 Score=163.98 Aligned_cols=192 Identities=31% Similarity=0.502 Sum_probs=146.3
Q ss_pred CCCccEEEEeCCChHHHHHHH-HHHcCC-CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEe
Q 016210 6 RKPLKIHLVTSTESPEFTHLA-RALSQS-SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLD 83 (393)
Q Consensus 6 ~~~~~i~lV~t~~~~el~~ll-~~L~~~-~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID 83 (393)
+....+++|++ +.++..++ +.+... -.||+|+||.+... ....+++++|++. ++.+||||
T Consensus 387 ~~~~~i~~V~~--e~El~~l~l~~l~~e~~yVGiDsEwkps~~--v~dsk~~IlQif~--------------~~~v~Lid 448 (617)
T KOG2207|consen 387 PWVESIGMVGN--EKELRDLLLESLSEELRYVGIDSEWKPSKK--VSDSKLAILQIFF--------------KDCVYLID 448 (617)
T ss_pred CcccceeeeCC--HHHHHHHHHHHhhhcCEEEEEccccCcccC--CChhHHHHHHHHh--------------cCeEEEee
Confidence 44456888998 88988876 466655 78999999998722 2467999999998 48999999
Q ss_pred CCCCCc--hhhHH-HHHHhhCCCCcEEEEEehHhHHHHHHhhcccC--CCcCCcCCCCceeeHHHHHHHHhcccc-CCCC
Q 016210 84 LSSIPL--PSIWE-LLKELFVSPDILKLGFKFKQDLIYLSSTFCSQ--GCDIGFDRVEPYLDITSIYNHLHHKQL-GRKL 157 (393)
Q Consensus 84 ~~~l~~--~~~~~-~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~--g~~~~~~~~~~~fDlt~LA~yLl~~~~-~~~~ 157 (393)
+.++.. .+++. .+..+|+++++.|||+++.+|++.|++..+.+ .|. +..+.+++++..++..+.+-.. ...+
T Consensus 449 c~~l~~~~se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~k--i~~~~l~~~~~kl~e~~~~~~~~i~n~ 526 (617)
T KOG2207|consen 449 CVKLENLASEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMK--IEGLQLVSCVLKLAENVIDLPLSIENL 526 (617)
T ss_pred hHHhhhchHHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhccc--ccchHHHHHHHHHHHHHhcccchhhhh
Confidence 876432 34444 45679999999999999999999998532210 111 1223455665677766655321 1123
Q ss_pred CCCcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 158 PKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (393)
Q Consensus 158 ~~~~~sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (393)
+....+|+.|....||.+++|..||+||..|||+..|+.|||.||.++..++..+....+
T Consensus 527 ~~~~~~L~~Lt~~llg~~lnKteqcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~ 586 (617)
T KOG2207|consen 527 NEATKGLADLTDCLLGKKLNKTEQCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVE 586 (617)
T ss_pred cchhhhhhhhhHHHhhhhcccccccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcc
Confidence 345789999999999999999999999999999999999999999999999999987665
No 18
>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=99.66 E-value=2.2e-15 Score=136.13 Aligned_cols=165 Identities=16% Similarity=0.121 Sum_probs=125.2
Q ss_pred CCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEe
Q 016210 32 SSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFK 111 (393)
Q Consensus 32 ~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~~~i~KVgh~ 111 (393)
.+.+++|+|.....+ ...++..++++.. +++|+|++... ......|+++|+++++.|++||
T Consensus 3 ~~~~~~~~~~~~~~~---~~~~l~~i~l~~~--------------~~~~~i~~~~~--~~~~~~l~~~l~~~~~~ki~~d 63 (178)
T cd06140 3 ADEVALYVELLGENY---HTADIIGLALANG--------------GGAYYIPLELA--LLDLAALKEWLEDEKIPKVGHD 63 (178)
T ss_pred CCceEEEEEEcCCCc---ceeeEEEEEEEeC--------------CcEEEEeccch--HHHHHHHHHHHhCCCCceeccc
Confidence 356788998876553 3456777777763 35777874321 0235668899999999999999
Q ss_pred hHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccccccccCCC---CC
Q 016210 112 FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWS---NR 188 (393)
Q Consensus 112 ~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~sdWs---~R 188 (393)
+|.|++.|.+ +|+ ...+++|| |+||+||+++. ...+++.+++.+|++..+.+..+...|. .+
T Consensus 64 ~K~~~~~l~~-~gi-------~~~~~~fD-t~laaYLL~p~------~~~~~l~~l~~~yl~~~~~~~~~~~~~~~~~~~ 128 (178)
T cd06140 64 AKRAYVALKR-HGI-------ELAGVAFD-TMLAAYLLDPT------RSSYDLADLAKRYLGRELPSDEEVYGKGAKFAV 128 (178)
T ss_pred hhHHHHHHHH-CCC-------cCCCcchh-HHHHHHHcCCC------CCCCCHHHHHHHHcCCCCcchHHhcCCCCCccc
Confidence 9999999987 665 22457899 99999999986 2247999999999999875533344452 23
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC----cccccccc
Q 016210 189 PLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS----CSSISELD 230 (393)
Q Consensus 189 PLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l----~~e~~~l~ 230 (393)
+....+..|++.||.+++.|++.|.++|++++.. +.|||++.
T Consensus 129 ~~~~~~~~y~~~~a~~l~~l~~~l~~~L~~~~l~~L~~~iE~PL~~ 174 (178)
T cd06140 129 PDEEVLAEHLARKAAAIARLAPKLEEELEENEQLELYYEVELPLAE 174 (178)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhHHH
Confidence 4457788999999999999999999999988765 88998763
No 19
>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=99.57 E-value=8.4e-14 Score=126.52 Aligned_cols=169 Identities=20% Similarity=0.303 Sum_probs=123.3
Q ss_pred cCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC------CCchhhHHHHHHhhCCC
Q 016210 30 SQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS------IPLPSIWELLKELFVSP 103 (393)
Q Consensus 30 ~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~------l~~~~~~~~L~~lLe~~ 103 (393)
.+...+++|+|..+..+ +..++..++++.. .+.+|+|+... .........|+++|++.
T Consensus 3 ~~~~~~a~d~e~~~~~~---~~~~i~~l~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~ 66 (193)
T cd06139 3 EKAKVFAFDTETTSLDP---MQAELVGISFAVE-------------PGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDP 66 (193)
T ss_pred ccCCeEEEEeecCCCCc---CCCeEEEEEEEcC-------------CCCEEEEecCCCccccCCCHHHHHHHHHHHHhCC
Confidence 35678999998766553 3456677777763 23366665432 12234566789999998
Q ss_pred CcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccc------
Q 016210 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS------ 177 (393)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~------ 177 (393)
.+.+|+||+++|+..|.+ +|+ . ....++| |++++|++++. ...++|.+++++|++....
T Consensus 67 ~~~~v~hn~k~d~~~l~~-~gi---~----~~~~~~D-t~l~a~ll~p~------~~~~~l~~l~~~~l~~~~~~~~~~~ 131 (193)
T cd06139 67 SIKKVGQNLKFDLHVLAN-HGI---E----LRGPAFD-TMLASYLLNPG------RRRHGLDDLAERYLGHKTISFEDLV 131 (193)
T ss_pred CCcEEeeccHHHHHHHHH-CCC---C----CCCCccc-HHHHHHHhCCC------CCCCCHHHHHHHHhCCCCccHHHHc
Confidence 888999999999999987 565 1 2457899 99999999985 2157999999999987621
Q ss_pred -ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCC----cccccccc
Q 016210 178 -KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ-KGNS----CSSISELD 230 (393)
Q Consensus 178 -K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~-~g~l----~~e~~~l~ 230 (393)
|..+..+|...|+ ..+.+||+.|+.++++|++.|.++|++ .+.. ..|||++.
T Consensus 132 ~k~~~~~~~~~~~~-~~~~~ya~~d~~~~~~l~~~l~~~l~~~~~~~~l~~~iE~Pl~~ 189 (193)
T cd06139 132 GKGKKQITFDQVPL-EKAAEYAAEDADITLRLYELLKPKLKEEPGLLELYEEIEMPLIP 189 (193)
T ss_pred CCCcCcCCccccCH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhccHHH
Confidence 2223344543344 668999999999999999999999987 5543 88888753
No 20
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.49 E-value=1.2e-13 Score=146.73 Aligned_cols=158 Identities=21% Similarity=0.201 Sum_probs=127.7
Q ss_pred cEEEEeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc
Q 016210 10 KIHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL 89 (393)
Q Consensus 10 ~i~lV~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~ 89 (393)
.+.+|++ .+++..++..+...+.+++|+|+..... .++++|++. ++.+|+||+...
T Consensus 2 ~~~~I~~--~~~l~~~~~~l~~~~~~a~DtEf~r~~t------~l~liQ~~~--------------~~~~~liDpl~~-- 57 (553)
T PRK14975 2 DMKVILA--PEELGAALERLSPAGVVAGDTETTGDDA------AAAAAQEGE--------------EEPRWVWASTAA-- 57 (553)
T ss_pred CceEEec--cchhHHHHHHhccCCceeCCccccCCcc------hhheeeecC--------------CCceEEECchHH--
Confidence 3567888 7889999999999999999999876542 789999986 467899986531
Q ss_pred hhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
+. ++ |.+ +|+ . +.++|| |+||+|++++..+ ...++++.+++
T Consensus 58 ---l~---~~-------------------L~~-~Gv---~-----~~~~fD-T~LAa~lL~~~~~----~~~~~l~~la~ 98 (553)
T PRK14975 58 ---LY---PR-------------------LLA-AGV---R-----VERCHD-LMLASQLLLGSEG----RAGSSLSAAAA 98 (553)
T ss_pred ---hH---HH-------------------HHH-CCC---c-----cCCCch-HHHHHHHcCCCCC----cCCCCHHHHHH
Confidence 22 11 444 454 2 466999 9999999997511 01589999999
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCC----ccccccccC
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK------GNS----CSSISELDS 231 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~------g~l----~~e~~~l~~ 231 (393)
++|++.++|..+.+||. ||++++|+.||+.||.+++.||+.|.++|++. |.+ ..||+.+..
T Consensus 99 ~~l~~~l~k~~~~sdw~-rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~~~~~~~~g~l~ll~~~E~~~~~~ 169 (553)
T PRK14975 99 RALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRIAAAAHPGRLRLLAAAESAGALA 169 (553)
T ss_pred HHhCCCCCChhhhcccc-ccchHHHHHHHHHHhHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHhhHHHH
Confidence 99999999988889997 99999999999999999999999999999976 444 788887643
No 21
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.34 E-value=6.2e-12 Score=132.48 Aligned_cols=180 Identities=16% Similarity=0.167 Sum_probs=133.3
Q ss_pred hHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCC-chhhHHHHH
Q 016210 19 SPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIP-LPSIWELLK 97 (393)
Q Consensus 19 ~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~-~~~~~~~L~ 97 (393)
...+..+...+...+.+++|+|+.+..+ ...++++++... +..+++|....-+ .-.....|+
T Consensus 9 ~~~~~~~~~~~~~~~~~a~~~et~~l~~-----~~~~lvg~s~~~------------~~~~~yi~~~~~~~~~~~~~~l~ 71 (593)
T COG0749 9 LAVLNAWLTKLNAAANIAFDTETDGLDP-----HGADLVGLSVAS------------EEEAAYIPLLHGPEQLNVLAALK 71 (593)
T ss_pred HHHHHHHHHHHhhcccceeeccccccCc-----ccCCeeEEEeec------------cccceeEeeccchhhhhhHHHHH
Confidence 5556666666665555999999988874 356678777652 2255555544311 113678999
Q ss_pred HhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccc
Q 016210 98 ELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (393)
Q Consensus 98 ~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~ 177 (393)
++|+++...|+|||+|.|.+.|++ +|+ . .+..|| |||++|++++. ...+++.++++++++.+..
T Consensus 72 ~~l~~~~~~kv~~~~K~d~~~l~~-~Gi-------~-~~~~~D-tmlasYll~~~------~~~~~~~~l~~r~l~~~~~ 135 (593)
T COG0749 72 PLLEDEGIKKVGQNLKYDYKVLAN-LGI-------E-PGVAFD-TMLASYLLNPG------AGAHNLDDLAKRYLGLETI 135 (593)
T ss_pred HHhhCcccchhccccchhHHHHHH-cCC-------c-ccchHH-HHHHHhccCcC------cCcCCHHHHHHHhcCCccc
Confidence 999999999999999999999999 554 1 367899 99999999986 3469999999999998765
Q ss_pred ccccccCCCC-----CCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-----ccccccccC
Q 016210 178 KELQCSDWSN-----RPLT-EEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS-----CSSISELDS 231 (393)
Q Consensus 178 K~~q~sdWs~-----RPLs-~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l-----~~e~~~l~~ 231 (393)
......+-.. ..++ +....|+|.||.++++|+..|.+++.+...+ ..|||++..
T Consensus 136 ~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~~~L~~l~~~iE~Pl~~V 200 (593)
T COG0749 136 TFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKTPVLLELYEEIEMPLVRV 200 (593)
T ss_pred hhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHhccHHHH
Confidence 4333322211 1122 4558999999999999999999999887763 889998753
No 22
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.30 E-value=7e-11 Score=131.26 Aligned_cols=182 Identities=12% Similarity=0.024 Sum_probs=123.5
Q ss_pred EEEEeCCChHHHHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCC-CEEEEEeCC---C
Q 016210 11 IHLVTSTESPEFTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNA-SVVFLLDLS---S 86 (393)
Q Consensus 11 i~lV~t~~~~el~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~-~~v~LID~~---~ 86 (393)
+..|++ .+++..+++. ...+.+++ .+..+ ....+..+.+++. . +.+|+++.. .
T Consensus 304 ~~~~~~--~~~~~~~~~~-~~~~~~~~----~~~~~---~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~ 360 (887)
T TIGR00593 304 AKESEE--AAPLANPAEK-AEVGGFVL----ERLLD---QLKKALALAFATE-------------NQSYVAYASEADGIP 360 (887)
T ss_pred ceEeCC--HHHHHHHHHh-CcCCeEEE----cCccc---ccCceeEEEEEec-------------CCCceEEEecccchh
Confidence 445655 5667776655 44456777 12221 1123333344442 2 336666533 1
Q ss_pred CCchhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHH
Q 016210 87 IPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (393)
Q Consensus 87 l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~ 166 (393)
+........|+++|+++.+.||+||+|+|+.+|.+ +|+ . ..+.+|| ||||+||+++. ..++|++
T Consensus 361 ~~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~-~gi---~----~~~~~~D-t~la~yll~~~-------~~~~l~~ 424 (887)
T TIGR00593 361 LLTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKR-EGI---E----LGGVIFD-TMLAAYLLDPA-------QVSTLDT 424 (887)
T ss_pred hhhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHh-CCC---C----CCCcchh-HHHHHHHcCCC-------CCCCHHH
Confidence 12234566799999999999999999999999987 665 2 2356899 99999999985 2469999
Q ss_pred HHHHHcCCcccccccccCCC--CCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC----ccccccccC
Q 016210 167 ICKELLDISLSKELQCSDWS--NRPLT-EEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS----CSSISELDS 231 (393)
Q Consensus 167 Lve~~Lg~~L~K~~q~sdWs--~RPLs-~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l----~~e~~~l~~ 231 (393)
++.+||+..+.+..+...+. ...++ +.+..||+.||.++++|+..|.++|.+++.. ..|||++..
T Consensus 425 la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~~~~l~~l~~~iE~pl~~v 496 (887)
T TIGR00593 425 LARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELDENKLLSLYREIELPLSKV 496 (887)
T ss_pred HHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHH
Confidence 99999997754422222221 12444 4567899999999999999999999887644 788888753
No 23
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=98.94 E-value=3.4e-09 Score=103.82 Aligned_cols=157 Identities=22% Similarity=0.238 Sum_probs=118.0
Q ss_pred CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEeh
Q 016210 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKF 112 (393)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~~~i~KVgh~~ 112 (393)
..+..+.|+.+...+++..+.+..+||+.. ++.++|+.+.... .+...|+.+|+|++.++||.+.
T Consensus 128 ~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~-------------en~C~I~ql~~~~--~IP~~LR~fl~D~~~~~vgv~~ 192 (319)
T KOG4373|consen 128 PFVCYRREAQPYLDMGRSDPPPDTLQLCVG-------------ENRCLIIQLIHCK--RIPHELRSFLEDPDHTFVGVWN 192 (319)
T ss_pred cceeecccccccccccccCCCcchhhhhhc-------------ccceeeEEeeccc--cchHHHHHhhcCCCceEEeccc
Confidence 455666777776655556677999999984 5788888766544 3678888999999999999999
Q ss_pred HhHHHHHHh-hcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcC-----CcccccccccCCC
Q 016210 113 KQDLIYLSS-TFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD-----ISLSKELQCSDWS 186 (393)
Q Consensus 113 k~Dl~~L~~-~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg-----~~L~K~~q~sdWs 186 (393)
++|...|.+ .|++ . +..+.||..++.-.++.. ..+.+...|++..+| +.+++..+++||+
T Consensus 193 d~D~~KL~r~~hql---~-----I~~~~dlr~~~~d~~g~~------~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~ 258 (319)
T KOG4373|consen 193 DQDAGKLERKEHQL---E-----IGELEDLRLLVNDSLGGS------MPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWS 258 (319)
T ss_pred cccHHHHhhhhhcc---c-----HHhhhhHHhhcchhhccC------ccCccHHHHHHHHhhccccccccChhcccccce
Confidence 999999987 4544 1 456778766666665542 234566666666654 4567888999999
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 016210 187 NRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (393)
Q Consensus 187 ~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g 220 (393)
..+|+.+|+.||+.||++...|+ ....+.+..
T Consensus 259 ~~~Ls~~Ql~~asidvy~c~~lg--~~~~~w~~~ 290 (319)
T KOG4373|consen 259 VYPLSDDQLLQASIDVYVCHKLG--VLERLWEVK 290 (319)
T ss_pred eeeccHHHHHHHHhHHHHHHHHH--HHHHHHHHh
Confidence 99999999999999999999999 334444443
No 24
>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=98.73 E-value=2.7e-07 Score=81.23 Aligned_cols=118 Identities=19% Similarity=0.189 Sum_probs=79.7
Q ss_pred EEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCC
Q 016210 78 VVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKL 157 (393)
Q Consensus 78 ~v~LID~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~ 157 (393)
++|+|++.. .. ....|+++|++.++.|++||+|.+++.|.+ +|+ . ..+.+|| ++||+||++|.
T Consensus 30 ~~~yi~~~~-~~--~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~-~gi-~------l~~~~fD-~~LAaYLL~p~----- 92 (151)
T cd06128 30 VAAYIPVAH-DY--ALELLKPLLEDEKALKVGQNLKYDRVILAN-YGI-E------LRGIAFD-TMLEAYLLDPV----- 92 (151)
T ss_pred CeEEEeCCC-Cc--CHHHHHHHHcCCCCCEEeeehHHHHHHHHH-CCC-C------CCCcchh-HHHHHHHcCCC-----
Confidence 467775321 00 245588999999999999999999999977 565 1 2356799 89999999986
Q ss_pred CCCcccHHHHHHHHcCCcccccccccCCCC--CCC-CHHHHHHHHHHHHHHHHHHHHHH
Q 016210 158 PKETKSLANICKELLDISLSKELQCSDWSN--RPL-TEEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 158 ~~~~~sLa~Lve~~Lg~~L~K~~q~sdWs~--RPL-s~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
....++++++++||+..+....+...+.. ..+ ..+...|++..+.++.+|++.|.
T Consensus 93 -~~~~~l~~la~~yl~~~~~~~~~~~gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 93 -AGRHDMDSLAERWLKEKTITFEEIAGKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred -CCCCCHHHHHHHHcCCCCccHHHHcCCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 22159999999999877221011111110 012 12223488888888999988874
No 25
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=97.41 E-value=0.0053 Score=61.26 Aligned_cols=102 Identities=14% Similarity=0.107 Sum_probs=68.8
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..|.+++.+. ..|+||+.+|+..|.+.+.-.|.. + ....++| |+..+..+.+. ...++|.++++.
T Consensus 83 ev~~~l~~~l~~~--~lVaHNa~FD~~fL~~~~~r~g~~--~-~~~~~ld-Tl~lar~~~~~------~~~~kL~~l~~~ 150 (313)
T PRK06063 83 DIAGEVAELLRGR--TLVAHNVAFDYSFLAAEAERAGAE--L-PVDQVMC-TVELARRLGLG------LPNLRLETLAAH 150 (313)
T ss_pred HHHHHHHHHcCCC--EEEEeCHHHHHHHHHHHHHHcCCC--C-CCCCEEe-hHHHHHHhccC------CCCCCHHHHHHH
Confidence 4566777777764 459999999999987654221211 0 0245889 55444444432 237889999976
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (393)
+|++....|. |..||.++.+|+..+..++.+.+.
T Consensus 151 -~gi~~~~~H~----------------Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 151 -WGVPQQRPHD----------------ALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred -cCCCCCCCCC----------------cHHHHHHHHHHHHHHHHHHHhcCC
Confidence 5776433332 789999999999999998887764
No 26
>PRK07740 hypothetical protein; Provisional
Probab=97.27 E-value=0.0099 Score=57.20 Aligned_cols=101 Identities=13% Similarity=0.169 Sum_probs=66.8
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhc-ccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTF-CSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~-gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
+++..|.+++.+. ..|+||+..|...|.+.+ ...+. .....++|+..++ ..+.+. ...++|+++++
T Consensus 130 evl~~f~~fi~~~--~lVahna~fD~~fL~~~~~~~~~~----~~~~~~iDt~~l~-r~l~~~------~~~~sL~~l~~ 196 (244)
T PRK07740 130 EVLHRFYAFIGAG--VLVAHHAGHDKAFLRHALWRTYRQ----PFTHRLIDTMFLT-KLLAHE------RDFPTLDDALA 196 (244)
T ss_pred HHHHHHHHHhCCC--EEEEeCHHHHHHHHHHHHHHhcCC----CcCCCeechHHHH-HHHcCC------CCCCCHHHHHH
Confidence 3455566666553 459999999999886532 11011 1235789954444 444432 23789999996
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (393)
. +|++....+. |..||..+.+|+..+..++.+.|.
T Consensus 197 ~-~gi~~~~~H~----------------Al~Da~ata~l~~~ll~~~~~~~~ 231 (244)
T PRK07740 197 Y-YGIPIPRRHH----------------ALGDALMTAKLWAILLVEAQQRGI 231 (244)
T ss_pred H-CCcCCCCCCC----------------cHHHHHHHHHHHHHHHHHHHHcCC
Confidence 5 6877643332 788999999999999999887653
No 27
>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=97.27 E-value=0.0022 Score=57.46 Aligned_cols=88 Identities=17% Similarity=0.172 Sum_probs=56.4
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHH--HHHH-hccccCCCCCCCcccHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSI--YNHL-HHKQLGRKLPKETKSLANI 167 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~L--A~yL-l~~~~~~~~~~~~~sLa~L 167 (393)
++...|.+++.+. +.||||+++|+..|...+. ...+.|+..+ +... ..+. ...++|..|
T Consensus 66 ~v~~~l~~~l~~~--vlV~Hn~~~D~~~l~~~~~----------~~~~~Dt~~l~~~~~~~~~p~------~~~~~L~~L 127 (157)
T cd06149 66 VAQKEILKILKGK--VVVGHAIHNDFKALKYFHP----------KHMTRDTSTIPLLNRKAGFPE------NCRVSLKVL 127 (157)
T ss_pred HHHHHHHHHcCCC--EEEEeCcHHHHHHhcccCC----------CcCEEECcccccchhhcCCcc------cCChhHHHH
Confidence 4667777788653 4599999999999865311 2356783222 1111 1221 246899999
Q ss_pred HHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 168 CKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 168 ve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
++++++..+....+..+ |..||.++.+||
T Consensus 128 ~~~~~~~~i~~~~~~H~-------------Al~DA~at~~l~ 156 (157)
T cd06149 128 AKRLLHRDIQVGRQGHS-------------SVEDARATMELY 156 (157)
T ss_pred HHHHcChhhcCCCCCcC-------------cHHHHHHHHHHh
Confidence 99999776654222122 678999988876
No 28
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=97.26 E-value=0.011 Score=57.41 Aligned_cols=98 Identities=16% Similarity=0.192 Sum_probs=65.7
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..+.+++.+. ..|+||+.+|...|.+.+.-.|..+ .....+|+..++..+... ..++|+++++
T Consensus 136 evl~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~---~~~~~ldtl~la~~~~~~--------~~~~L~~L~~- 201 (257)
T PRK08517 136 EVLEEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGP---LLNRKLCTIDLAKRTIES--------PRYGLSFLKE- 201 (257)
T ss_pred HHHHHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCC---CCCCcEehHHHHHHHccC--------CCCCHHHHHH-
Confidence 4566777777764 4599999999998865322112111 134578855566555432 3689999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~ 218 (393)
++|++....|. |..||.++.+|+..+..++..
T Consensus 202 ~lgi~~~~~Hr----------------Al~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 202 LLGIEIEVHHR----------------AYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred HcCcCCCCCCC----------------hHHHHHHHHHHHHHHHHHhHH
Confidence 46876543332 788999999999999877753
No 29
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=97.26 E-value=0.0022 Score=61.98 Aligned_cols=96 Identities=22% Similarity=0.217 Sum_probs=65.2
Q ss_pred hHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHH
Q 016210 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (393)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~ 171 (393)
+-..+.++|.+. +.|||++++|+.+|.-.|.- .-+-| |.-+.-|... .....+.||..|++.+
T Consensus 174 aQ~ev~klL~gR--IlVGHaLhnDl~~L~l~hp~----------s~iRD-Ts~~~pl~k~----~~~~~tpSLK~Lt~~~ 236 (280)
T KOG2249|consen 174 AQKEVLKLLKGR--ILVGHALHNDLQALKLEHPR----------SMIRD-TSKYPPLMKL----LSKKATPSLKKLTEAL 236 (280)
T ss_pred HHHHHHHHHhCC--EEeccccccHHHHHhhhCch----------hhhcc-cccCchHHHH----hhccCCccHHHHHHHH
Confidence 345667788874 34999999999999754321 23557 4322222210 0012478999999999
Q ss_pred cCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 016210 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (393)
Q Consensus 172 Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (393)
||+.+--++..| .+||.+..+||.....+-++.
T Consensus 237 Lg~~IQ~GeHsS---------------vEDA~AtM~LY~~vk~qwe~~ 269 (280)
T KOG2249|consen 237 LGKDIQVGEHSS---------------VEDARATMELYKRVKVQWEKI 269 (280)
T ss_pred hchhhhccccCc---------------HHHHHHHHHHHHHHHHHHHHH
Confidence 999886555333 589999999999998877754
No 30
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.23 E-value=0.015 Score=55.50 Aligned_cols=90 Identities=17% Similarity=0.273 Sum_probs=57.6
Q ss_pred cEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccccccccC
Q 016210 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSD 184 (393)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~sd 184 (393)
...|+||+.+|+..|.+.+.-.|... + ...+++| +......+.+. + ..+++|.++++. +|++....+.
T Consensus 94 ~~lVahNa~FD~~fL~~~~~r~~~~~-~-~~~~~iD-t~~l~~~~~~~--~---~~~~~L~~l~~~-~gi~~~~aH~--- 161 (232)
T PRK07942 94 VPVVVFNAPYDLTVLDRELRRHGLPS-L-VPGPVID-PYVIDKAVDRY--R---KGKRTLTALCEH-YGVRLDNAHE--- 161 (232)
T ss_pred CEEEEeCcHhhHHHHHHHHHHcCCCC-c-cCCcEee-HHHHHhhhhcc--c---CCCCCHHHHHHH-cCCCCCCCCC---
Confidence 34599999999988865432112110 0 1246889 65544433321 0 125789999977 5876643332
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 016210 185 WSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (393)
Q Consensus 185 Ws~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (393)
|..||.++.+|+..|..+..+-
T Consensus 162 -------------Al~Da~ata~l~~~l~~~~~~l 183 (232)
T PRK07942 162 -------------ATADALAAARVAWALARRFPEL 183 (232)
T ss_pred -------------hHHHHHHHHHHHHHHHHHHHHh
Confidence 8899999999999998776643
No 31
>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=97.18 E-value=0.016 Score=51.57 Aligned_cols=97 Identities=18% Similarity=0.193 Sum_probs=58.5
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..|.+++.+.. .|+||+.+|+..|.+.+.-.|....+.....++| |+..+..+.+. ..++|+++++.
T Consensus 70 ~v~~~l~~~l~~~~--lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~id-t~~~~~~~~~~-------~~~~L~~l~~~ 139 (167)
T cd06131 70 EIADEFLDFIRGAE--LVIHNASFDVGFLNAELSLLGLGKKIIDFCRVID-TLALARKKFPG-------KPNSLDALCKR 139 (167)
T ss_pred HHHHHHHHHHCCCe--EEEeChHHhHHHHHHHHHHhCCCcccccCCCceE-hHHHHHHHcCC-------CCCCHHHHHHH
Confidence 34566777777643 4999999999888654221111110111246799 55433333332 25799999988
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
+ |++..... ..-|..||..+.+|+..|
T Consensus 140 ~-~i~~~~~~--------------~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 140 F-GIDNSHRT--------------LHGALLDAELLAEVYLEL 166 (167)
T ss_pred C-CCCCCCCC--------------CCChHHHHHHHHHHHHHh
Confidence 6 65542111 122889999999888765
No 32
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.02 E-value=0.025 Score=54.62 Aligned_cols=149 Identities=17% Similarity=0.188 Sum_probs=85.7
Q ss_pred cCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-CC----------c---------
Q 016210 30 SQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-IP----------L--------- 89 (393)
Q Consensus 30 ~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~-l~----------~--------- 89 (393)
.....|.||+|+++..+ .+-.+|||+.-. .+ ++.. .+.-..+|.+.. ++ .
T Consensus 5 ~~~~~v~~D~ETTGl~~-----~~d~IIEIa~v~-v~--~~~~--~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~ 74 (250)
T PRK06310 5 KDTEFVCLDCETTGLDV-----KKDRIIEFAAIR-FT--FDEV--IDSVEFLINPERVVSAESQRIHHISDAMLRDKPKI 74 (250)
T ss_pred cCCcEEEEEEeCCCCCC-----CCCeEEEEEEEE-EE--CCeE--EEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCH
Confidence 45678999999988764 234577775421 00 0000 011223444321 11 0
Q ss_pred hhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCC-CCceeeHHHHHHHHhccccCCCCCCCcccHHHHH
Q 016210 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDR-VEPYLDITSIYNHLHHKQLGRKLPKETKSLANIC 168 (393)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~-~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lv 168 (393)
.++...+.+++.+.. ..||||+.+|...|.+.+--.|.. +.. ...++|+..++ ..... ...++|++++
T Consensus 75 ~ev~~~~~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~--~~~~~~~~iDtl~la-r~~~~-------~~~~~L~~l~ 143 (250)
T PRK06310 75 AEVFPQIKGFFKEGD-YIVGHSVGFDLQVLSQESERIGET--FLSKHYYIIDTLRLA-KEYGD-------SPNNSLEALA 143 (250)
T ss_pred HHHHHHHHHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCC--ccccCCcEEehHHHH-Hhccc-------CCCCCHHHHH
Confidence 234556677776544 459999999999986543111211 110 14689944444 33332 1368999998
Q ss_pred HHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 169 KELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (393)
Q Consensus 169 e~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L 216 (393)
+.+ |++....++ |..||.++..|+..+..++
T Consensus 144 ~~~-g~~~~~aH~----------------Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 144 VHF-NVPYDGNHR----------------AMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred HHC-CCCCCCCcC----------------hHHHHHHHHHHHHHHHHhc
Confidence 775 776543332 8899999999999887654
No 33
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=96.98 E-value=0.035 Score=51.51 Aligned_cols=159 Identities=17% Similarity=0.197 Sum_probs=87.1
Q ss_pred HHHHHHHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CC--
Q 016210 22 FTHLARALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IP-- 88 (393)
Q Consensus 22 l~~ll~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~-----------l~-- 88 (393)
+..+.+.......|.||+|+++..+ . .-.+++|+.-. .+.+... ....-.++|.+.. +.
T Consensus 19 ~~~~~~~~~~~~~vviD~ETTGl~~---~--~d~IieIgaV~-~~~~~~~--~~~~f~~~i~p~~~i~~~~~~ihGIt~~ 90 (202)
T PRK09145 19 YAFLFEPPPPDEWVALDCETTGLDP---R--RAEIVSIAAVK-IRGNRIL--TSERLELLVRPPQSLSAESIKIHRLRHQ 90 (202)
T ss_pred HHHHhcCCCCCCEEEEEeECCCCCC---C--CCceEEEEEEE-EECCEEe--ecCceEEEECCCCCCCHhHhhhcCcCHH
Confidence 3334443445688999999997764 2 23467775421 0000000 0001112344321 11
Q ss_pred -------chhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhccc-CCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCC
Q 016210 89 -------LPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKE 160 (393)
Q Consensus 89 -------~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~ 160 (393)
..+++..+.+++.+.- .||||+.+|...|.+.+.- .|. ......+|+..++......... ....
T Consensus 91 ~l~~~~~~~~vl~~~~~~i~~~~--lv~hn~~fD~~fL~~~~~~~~~~----~~~~~~id~~~l~~~~~~~~~~--~~~~ 162 (202)
T PRK09145 91 DLEDGLSEEEALRQLLAFIGNRP--LVGYYLEFDVAMLNRYVRPLLGI----PLPNPLIEVSALYYDKKERHLP--DAYI 162 (202)
T ss_pred HHhcCCCHHHHHHHHHHHHcCCe--EEEeCHHHHHHHHHHHHHHhcCC----CCCCCeeeHHHHHHHHhhccCC--Cccc
Confidence 1245667777777643 4999999999988654210 111 1235678965555432221100 0113
Q ss_pred cccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 016210 161 TKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 161 ~~sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
.++|+++++.+ |++....+. |..||.++..|+..|.
T Consensus 163 ~~~L~~l~~~~-gi~~~~~H~----------------Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 163 DLRFDAILKHL-DLPVLGRHD----------------ALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCHHHHHHHc-CCCCCCCCC----------------cHHHHHHHHHHHHHHH
Confidence 58999999764 776533332 7889999999998774
No 34
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.95 E-value=0.027 Score=56.21 Aligned_cols=97 Identities=13% Similarity=0.154 Sum_probs=64.9
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..|.+++.+..+ |+||+.+|+..|.+.+.-.|+. .....++|+..++..+.. . ...++|.++++.
T Consensus 77 evl~~f~~fl~~~~l--VaHNa~FD~~fL~~~~~~~gl~---~~~~~~iDtl~la~~~~~-~------~~~~kL~~L~~~ 144 (313)
T PRK06807 77 EVLPLFLAFLHTNVI--VAHNASFDMRFLKSNVNMLGLP---EPKNKVIDTVFLAKKYMK-H------APNHKLETLKRM 144 (313)
T ss_pred HHHHHHHHHHcCCeE--EEEcHHHHHHHHHHHHHHcCCC---CCCCCEeeHHHHHHHHhC-C------CCCCCHHHHHHH
Confidence 455666667765433 9999999999997654322321 013468996566555543 2 136799999865
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (393)
+|++. +.|. |-.||.++..|+..+.....
T Consensus 145 -lgi~~-~~H~----------------Al~DA~~ta~l~~~l~~~~~ 173 (313)
T PRK06807 145 -LGIRL-SSHN----------------AFDDCITCAAVYQKCASIEE 173 (313)
T ss_pred -cCCCC-CCcC----------------hHHHHHHHHHHHHHHHHhhh
Confidence 57765 3332 77899999999998887764
No 35
>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=96.95 E-value=0.0036 Score=55.60 Aligned_cols=86 Identities=24% Similarity=0.362 Sum_probs=57.2
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..|..++.+ .+ -||||+.+|+..|... . + ...++| |.......... +..+++|++++++
T Consensus 66 ~~~~~l~~~l~~-~v-lVgHn~~fD~~~L~~~--~----~----~~~~~d-t~~l~~~~~~~-----~~~~~sL~~l~~~ 127 (152)
T cd06144 66 EVQKKVAELLKG-RI-LVGHALKNDLKVLKLD--H----P----KKLIRD-TSKYKPLRKTA-----KGKSPSLKKLAKQ 127 (152)
T ss_pred HHHHHHHHHhCC-CE-EEEcCcHHHHHHhcCc--C----C----CccEEE-eEEeecccccc-----CCCChhHHHHHHH
Confidence 466778888876 33 4999999999999642 1 0 235778 43322222211 0247999999999
Q ss_pred HcCCcccc-cccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSK-ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (393)
Q Consensus 171 ~Lg~~L~K-~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~ 210 (393)
+||+.+.. .++ |..||.++.+||+
T Consensus 128 ~lgi~~~~~~H~----------------Al~DA~at~~l~~ 152 (152)
T cd06144 128 LLGLDIQEGEHS----------------SVEDARAAMRLYR 152 (152)
T ss_pred HcCcccCCCCcC----------------cHHHHHHHHHHhC
Confidence 99987642 222 7789999988873
No 36
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=96.92 E-value=0.035 Score=48.92 Aligned_cols=99 Identities=17% Similarity=0.179 Sum_probs=63.1
Q ss_pred hhHHHHHHhhCCCCcEEEEEeh-HhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
++...|..++.+.. .|+||. ++|+..|...+.-.|.. +......+|+..++..+. +. ..++|.++++
T Consensus 69 ~~~~~~~~~l~~~~--~v~~n~~~fD~~~L~~~~~~~~~~--~~~~~~~iD~~~~~~~~~-~~-------~~~~L~~l~~ 136 (169)
T smart00479 69 EVLEELLEFLKGKI--LVAGNALNFDLRFLKLEHPRLGIK--DPPKNPVIDTLKLARALN-PG-------RKYSLKKLAE 136 (169)
T ss_pred HHHHHHHHHhcCCE--EEEeCCHHHhHHHHHHHHHHhCCC--CCcCCCeeEHHHHHHHHC-CC-------CCCCHHHHHH
Confidence 45677778887653 377888 99999987653322211 011234799545444333 22 2789999997
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (393)
.+ |++.... ...|..||..+.+|+..+.+++.
T Consensus 137 ~~-~~~~~~~---------------~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 137 RL-GLEVIGR---------------AHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred HC-CCCCCCC---------------CcCcHHHHHHHHHHHHHHHHHhh
Confidence 76 4443211 13488999999999999877653
No 37
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.92 E-value=0.024 Score=65.78 Aligned_cols=103 Identities=22% Similarity=0.415 Sum_probs=71.6
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..+.+++.+. ..|+||+.+|+..|.+.+.-.|..+ ....++|+..++ +.+.+. ...++|++++++
T Consensus 259 evl~~f~~fl~~~--iLVaHNa~FD~~fL~~~~~r~g~~~---~~~~~IDTl~la-r~l~p~------~k~~kL~~Lak~ 326 (1213)
T TIGR01405 259 EVLEKFKEFFKDS--ILVAHNASFDIGFLNTNFEKVGLEP---LENPVIDTLELA-RALNPE------YKSHRLGNICKK 326 (1213)
T ss_pred HHHHHHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCc---cCCCEeEHHHHH-HHHhcc------CCCCCHHHHHHH
Confidence 4667777788763 4599999999999875422112221 135789944444 444443 247899999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (393)
+|+++... +.|..||.++.+|+..+..++.+.|..
T Consensus 327 -lgi~~~~~----------------HrAl~DA~aTa~I~~~ll~~l~~~~i~ 361 (1213)
T TIGR01405 327 -LGVDLDDH----------------HRADYDAEATAKVFKVMVEQLKEKGIT 361 (1213)
T ss_pred -cCCCCCCC----------------cCHHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 48776432 338899999999999999999887654
No 38
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=96.92 E-value=0.031 Score=53.15 Aligned_cols=99 Identities=17% Similarity=0.208 Sum_probs=61.3
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCc-CCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
+++..|.+++.+..+ |+||+.+|+.+|...+.-.|.. +.+.....++| |...+..+.+. .+++|.++++
T Consensus 71 ev~~~f~~fi~~~~l--VaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iD-Tl~lar~~~p~-------~~~~L~~L~~ 140 (225)
T TIGR01406 71 EIADEFLDFIGGSEL--VIHNAAFDVGFLNYELERLGPTIKKIGEFCRVID-TLAMARERFPG-------QRNSLDALCK 140 (225)
T ss_pred HHHHHHHHHhCCCEE--EEEecHHHHHHHHHHHHHhCCCCcccccCCCEEE-HHHHHHHHcCC-------CCCCHHHHHH
Confidence 455667777776443 9999999999986543221210 00111246899 54444444442 3689999999
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
+| |+...... . .=|..||..+.+||..|..
T Consensus 141 ~~-gi~~~~r~-~-------------H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 141 RF-KVDNSHRT-L-------------HGALLDAHLLAEVYLALTG 170 (225)
T ss_pred hc-CCCCCCCC-C-------------cCHHHHHHHHHHHHHHHHc
Confidence 86 65542111 1 1188999999999988754
No 39
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.92 E-value=0.061 Score=51.21 Aligned_cols=145 Identities=13% Similarity=0.134 Sum_probs=85.4
Q ss_pred CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-CC----------c---------hhh
Q 016210 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-IP----------L---------PSI 92 (393)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~-l~----------~---------~~~ 92 (393)
..+.||+|+++... .+-.+|||+.-. ... ...-..++++.. ++ . .++
T Consensus 3 ~~vv~D~ETTGl~~-----~~d~IIeig~v~--~~~------~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev 69 (232)
T PRK06309 3 ALIFYDTETTGTQI-----DKDRIIEIAAYN--GVT------SESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEA 69 (232)
T ss_pred cEEEEEeeCCCCCC-----CCCEEEEEEEEc--Ccc------ccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHH
Confidence 46889999988764 233588887531 000 012223444321 11 1 134
Q ss_pred HHHHHHhhCCCCcEEEEEe-hHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHH
Q 016210 93 WELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (393)
Q Consensus 93 ~~~L~~lLe~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~ 171 (393)
...+.+++.+. ...|+|| ..+|+..|.+.+.-.|+.. .....+|+..++..+ .+. ...++|..+++.|
T Consensus 70 ~~~~~~fi~~~-~~lVaHN~~~FD~~~L~~e~~r~g~~~---~~~~~iDt~~l~~~~-~~~------~~~~~L~~l~~~~ 138 (232)
T PRK06309 70 YQKFIEFCGTD-NILVAHNNDAFDFPLLRKECRRHGLEP---PTLRTIDSLKWAQKY-RPD------LPKHNLQYLRQVY 138 (232)
T ss_pred HHHHHHHHcCC-CEEEEeCCHHHHHHHHHHHHHHcCCCC---CCCcEEeHHHHHHHH-cCC------CCCCCHHHHHHHc
Confidence 44566666543 3459999 5899999875432112221 124689955555443 332 1368899998776
Q ss_pred cCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 016210 172 LDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (393)
Q Consensus 172 Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~ 218 (393)
|++....+. |..||.++.+|+..+..++..
T Consensus 139 -~~~~~~aH~----------------Al~Da~~t~~vl~~l~~~~~~ 168 (232)
T PRK06309 139 -GFEENQAHR----------------ALDDVITLHRVFSALVGDLSP 168 (232)
T ss_pred -CCCCCCCCC----------------cHHHHHHHHHHHHHHHHHHHH
Confidence 665433332 889999999999998877753
No 40
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=96.86 E-value=0.025 Score=54.45 Aligned_cols=99 Identities=17% Similarity=0.188 Sum_probs=60.0
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCc-CCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
++...+.+++.+.. .|+||+.+|+..|.+.+.-.|.. +.+.....++| |...+..+.+. ..++|.++|+
T Consensus 75 ev~~~f~~fi~~~~--lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iD-Tl~lar~~~p~-------~~~~L~aL~~ 144 (240)
T PRK05711 75 EVADEFLDFIRGAE--LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTD-TLAMARRMFPG-------KRNSLDALCK 144 (240)
T ss_pred HHHHHHHHHhCCCE--EEEEccHHhHHHHHHHHHHhCCCCCcccccCceee-HHHHHHHHcCC-------CCCCHHHHHH
Confidence 34556667776644 49999999999886543211210 00101135899 54444444443 3579999998
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
+| |+..... +. .=|-.||..+.++|..|..
T Consensus 145 ~~-gi~~~~r-~~-------------H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 145 RY-GIDNSHR-TL-------------HGALLDAEILAEVYLAMTG 174 (240)
T ss_pred HC-CCCCCCC-CC-------------CCHHHHHHHHHHHHHHHHC
Confidence 75 6543211 11 1288999999999988753
No 41
>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=96.82 E-value=0.0047 Score=54.86 Aligned_cols=86 Identities=21% Similarity=0.284 Sum_probs=55.4
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..+.+++.+ +.+.||||+.+|+..|... ...++|+..++..+... ..+++|..|+++
T Consensus 64 ~v~~~~~~fl~~-~~vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~r~~~~~-------~~~~~L~~L~~~ 123 (150)
T cd06145 64 DVQKKLLSLISP-DTILVGHSLENDLKALKLI------------HPRVIDTAILFPHPRGP-------PYKPSLKNLAKK 123 (150)
T ss_pred HHHHHHHHHhCC-CCEEEEcChHHHHHHhhcc------------CCCEEEcHHhccccCCC-------CCChhHHHHHHH
Confidence 455667777753 2345999999999999752 23578943333322222 236899999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
|++..+....+..+ |..||.++.+||
T Consensus 124 ~~~~~i~~~~~~H~-------------Al~DA~~t~~l~ 149 (150)
T cd06145 124 YLGRDIQQGEGGHD-------------SVEDARAALELV 149 (150)
T ss_pred HCCcceeCCCCCCC-------------cHHHHHHHHHHh
Confidence 99865532111111 778999888876
No 42
>PRK07883 hypothetical protein; Validated
Probab=96.80 E-value=0.036 Score=59.58 Aligned_cols=159 Identities=13% Similarity=0.163 Sum_probs=95.0
Q ss_pred HHHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC-----------CCc------
Q 016210 27 RALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS-----------IPL------ 89 (393)
Q Consensus 27 ~~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~-----------l~~------ 89 (393)
..+.+...|.||+|+++..+ ....++||+.-. .+ ++.. ...-..+|++.. +..
T Consensus 10 ~~~~~~~~Vv~D~ETTGl~p-----~~~~IIEIgaV~-v~-~g~i---v~~f~~lV~P~~~i~~~~~~itGIt~e~l~~a 79 (557)
T PRK07883 10 TPLRDVTFVVVDLETTGGSP-----AGDAITEIGAVK-VR-GGEV---LGEFATLVNPGRPIPPFITVLTGITTAMVAGA 79 (557)
T ss_pred CCCcCCCEEEEEEecCCCCC-----CCCeEEEEEEEE-EE-CCEE---EEEEEEEECCCCCCChhHHhhcCCCHHHHhCC
Confidence 44556789999999998764 134577775421 00 0000 001112343321 110
Q ss_pred ---hhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHH
Q 016210 90 ---PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLAN 166 (393)
Q Consensus 90 ---~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~ 166 (393)
.+++..+.+++.+ -..|+||+.+|+..|.+.+.-.|.. +. ....+|+..++..+..+. ....++|++
T Consensus 80 p~~~evl~~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~--~~-~~~~iDTl~lar~l~~~~-----~~~~~~L~~ 149 (557)
T PRK07883 80 PPIEEVLPAFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYP--WP-GPPVLCTVRLARRVLPRD-----EAPNVRLST 149 (557)
T ss_pred CCHHHHHHHHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCC--CC-CCCcEecHHHHHHhcccC-----CCCCCCHHH
Confidence 2345566777765 3459999999999987543222222 10 235789555555555321 024789999
Q ss_pred HHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 016210 167 ICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (393)
Q Consensus 167 Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (393)
+++ ++|++....|. |..||.++..|+..+..++.+.|..
T Consensus 150 L~~-~~gi~~~~~H~----------------Al~DA~ata~l~~~l~~~~~~~~~~ 188 (557)
T PRK07883 150 LAR-LFGATTTPTHR----------------ALDDARATVDVLHGLIERLGNLGVH 188 (557)
T ss_pred HHH-HCCcccCCCCC----------------HHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 987 56877543332 8899999999999999999876653
No 43
>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=96.78 E-value=0.091 Score=48.94 Aligned_cols=91 Identities=16% Similarity=0.163 Sum_probs=57.7
Q ss_pred cEEEEEehHhHHHHHHhhcccCCCcCCcCC-CCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccccccccc
Q 016210 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDR-VEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (393)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~-~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~s 183 (393)
...|+||+.+|+..|.+.+.-.|... ... ...++|+-.++. .+.+ ..+|+.+++.+ |++...
T Consensus 106 ~~lVaHNa~FD~~fL~~~~~r~~~~~-~~~~~~~~lDTl~lar-~~~~---------~~~L~~l~~~~-gi~~~~----- 168 (200)
T TIGR01298 106 AILVGHNANFDLGFLNAAVERTSLKR-NPFHPFSTFDTATLAG-LAYG---------QTVLAKACQAA-GXDFDS----- 168 (200)
T ss_pred CEEEEECchhhHHHHHHHHHHhCCCC-CCCCCCcEEEHHHHHH-HHcC---------cccHHHHHHHc-CCCccc-----
Confidence 45699999999999875421111100 000 124799444444 3333 35799999864 765421
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 016210 184 DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (393)
Q Consensus 184 dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (393)
.+..-|..||..+.+|+..+..++.+.+.
T Consensus 169 ---------~~~H~Al~Da~ata~lf~~l~~~~~~~~~ 197 (200)
T TIGR01298 169 ---------TQAHSALYDTEKTAELFCEIVNRWKRLGG 197 (200)
T ss_pred ---------cchhhhHHhHHHHHHHHHHHHHHHHHccC
Confidence 12233889999999999999999987764
No 44
>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=96.78 E-value=0.0056 Score=54.92 Aligned_cols=87 Identities=20% Similarity=0.236 Sum_probs=56.2
Q ss_pred HHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHc
Q 016210 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (393)
Q Consensus 93 ~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~L 172 (393)
...|.+++.+. .+.||||+.+|+..|... ...++|+..++..+. +.. ....+++|.+|+++++
T Consensus 74 ~~~~~~~i~~~-~vlVgHn~~fD~~fL~~~------------~~~~iDT~~l~~~~~-~~~---~~~~~~~L~~L~~~~~ 136 (161)
T cd06137 74 RAALWKFIDPD-TILVGHSLQNDLDALRMI------------HTRVVDTAILTREAV-KGP---LAKRQWSLRTLCRDFL 136 (161)
T ss_pred HHHHHHhcCCC-cEEEeccHHHHHHHHhCc------------CCCeeEehhhhhhcc-CCC---cCCCCccHHHHHHHHC
Confidence 34566666653 345999999999999752 235789555554443 320 0013699999999999
Q ss_pred CCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 173 g~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
|+++.......+ |..||.++.+||
T Consensus 137 ~~~~~~~~~~H~-------------A~~DA~at~~l~ 160 (161)
T cd06137 137 GLKIQGGGEGHD-------------SLEDALAAREVV 160 (161)
T ss_pred CchhcCCCCCCC-------------cHHHHHHHHHHh
Confidence 987743111122 678888887776
No 45
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.77 E-value=0.02 Score=64.19 Aligned_cols=100 Identities=20% Similarity=0.268 Sum_probs=67.4
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..+.+++.+. ..|+||+.+|+..|.+.+...|.. ...+.+|+-.++. .+.+. ..+++|.++++.
T Consensus 75 ev~~~~~~~l~~~--~lVaHN~~FD~~fL~~~~~~~g~~----~~~~~iDT~~la~-~~~p~------~~~~~L~~L~~~ 141 (820)
T PRK07246 75 QVARHIYDLIEDC--IFVAHNVKFDANLLAEALFLEGYE----LRTPRVDTVELAQ-VFFPT------LEKYSLSHLSRE 141 (820)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHcCCC----CCCCceeHHHHHH-HHhCC------CCCCCHHHHHHH
Confidence 4566777777763 459999999999997643211222 2356789444444 44443 247899999986
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g 220 (393)
+|++....|+ |..||.++..|+..|..++.+.+
T Consensus 142 -lgl~~~~~H~----------------Al~DA~ata~L~~~l~~~l~~l~ 174 (820)
T PRK07246 142 -LNIDLADAHT----------------AIADARATAELFLKLLQKIESLP 174 (820)
T ss_pred -cCCCCCCCCC----------------HHHHHHHHHHHHHHHHHHHhhcC
Confidence 6876543332 88899999999998888876543
No 46
>PRK05168 ribonuclease T; Provisional
Probab=96.69 E-value=0.13 Score=48.23 Aligned_cols=92 Identities=15% Similarity=0.137 Sum_probs=58.5
Q ss_pred CcEEEEEehHhHHHHHHhhcccCCCcCCcCC-CCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccccccc
Q 016210 104 DILKLGFKFKQDLIYLSSTFCSQGCDIGFDR-VEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQC 182 (393)
Q Consensus 104 ~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~-~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~ 182 (393)
+...|+||+.+|+..|.+.+.-.|+.. ... ...++|+-.++..+ .+ ..+|..+++. +|+++.....
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~-~~~~~~~~iDt~~lar~~-~~---------~~~L~~l~~~-~gl~~~~~~~- 180 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKR-NPFHPFSTFDTATLSGLA-LG---------QTVLAKACQA-AGIEFDNKEA- 180 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCC-CCCCCCcEeeHHHHHHHH-cC---------CCCHHHHHHH-CCCCCCCCCC-
Confidence 456699999999998865421112110 000 12479954555444 32 3579999987 4766532111
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 016210 183 SDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGN 221 (393)
Q Consensus 183 sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~ 221 (393)
.-|..||..+.+|+..+..++.+.|.
T Consensus 181 -------------H~Al~DA~ata~l~~~l~~~~~~~~~ 206 (211)
T PRK05168 181 -------------HSALYDTEKTAELFCEIVNRWKRLGG 206 (211)
T ss_pred -------------CChHHHHHHHHHHHHHHHHHHHHccC
Confidence 11889999999999999999987664
No 47
>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=96.63 E-value=0.041 Score=51.78 Aligned_cols=106 Identities=18% Similarity=0.218 Sum_probs=65.1
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..|..++.+. ..|+||+.+|+..|.+.+.-.+.. ......++|+..++.++. +. .+..+++|.++++.
T Consensus 76 ev~~~~~~~~~~~--~lVaHNa~FD~~fL~~~~~r~~~~--~~~~~~~~dtl~l~~~~~-~~----~~~~~~~L~~l~~~ 146 (217)
T TIGR00573 76 EIAEDFADYIRGA--ELVIHNASFDVGFLNYEFSKLYKV--EPKTNDVIDTTDTLQYAR-PE----FPGKRNTLDALCKR 146 (217)
T ss_pred HHHHHHHHHhCCC--EEEEeccHHHHHHHHHHHHHhcCC--CCCccceecHHHHHHHHH-Hh----CCCCCCCHHHHHHH
Confidence 4556677777653 349999999999997654311100 011246789444454443 22 11236789999977
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKG 220 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g 220 (393)
+ |++.... ...+ |..||.++.+|+..+..+..+.+
T Consensus 147 ~-gl~~~~~-~~H~-------------Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 147 Y-EITNSHR-ALHG-------------ALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred c-CCCCCCc-ccCC-------------HHHHHHHHHHHHHHHHhcchhhc
Confidence 5 6543210 1112 88999999999999987766544
No 48
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.63 E-value=0.045 Score=61.66 Aligned_cols=98 Identities=15% Similarity=0.257 Sum_probs=60.7
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
++...|.+++.+. ..|+||+.+|+..|.+.+.-.|..+ .....+|+..++..+ .+. ...++|.++++.
T Consensus 69 ev~~~l~~~l~~~--~~VahN~~fD~~fL~~~~~~~g~~~---~~~~~iDt~~l~~~~-~p~------~~~~~L~~l~~~ 136 (850)
T TIGR01407 69 QVAQEIYDLLEDG--IFVAHNVHFDLNFLAKALKDCGYEP---LPKPRIDTVELAQIF-FPT------EESYQLSELSEA 136 (850)
T ss_pred HHHHHHHHHhCCC--EEEEeCcHHHHHHHHHHHHHcCCCC---CCCCeEeHHHHHHHh-cCC------CCCCCHHHHHHH
Confidence 4566677777653 4599999999999875432212221 135789944455444 332 247899999887
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (393)
+|++....|+ |..||.++.+|+..+..++.
T Consensus 137 -~gi~~~~~H~----------------Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 137 -LGLTHENPHR----------------ADSDAQATAELLLLLFEKME 166 (850)
T ss_pred -CCCCCCCCCC----------------hHHHHHHHHHHHHHHHHHHH
Confidence 5776643332 55666666666666655554
No 49
>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=96.60 E-value=0.015 Score=47.80 Aligned_cols=82 Identities=17% Similarity=0.203 Sum_probs=54.8
Q ss_pred EEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCC-cEEEEEehH
Q 016210 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPD-ILKLGFKFK 113 (393)
Q Consensus 35 Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~~~-i~KVgh~~k 113 (393)
+++|+|+.+..+ +...+.++|++... ++..|++| +.+++.+.. ...|+||+.
T Consensus 1 ~~~DiEt~~~~~---~~~~i~~i~~~~~~------------~~~~~~~~------------f~~~l~~~~~~v~V~hn~~ 53 (96)
T cd06125 1 IAIDTEATGLDG---AVHEIIEIALADVN------------PEDTAVID------------LKDILRDKPLAILVGHNGS 53 (96)
T ss_pred CEEEEECCCCCC---CCCcEEEEEEEEcc------------CCCEEEeh------------HHHHHhhCCCCEEEEeCcH
Confidence 479999988764 67889999997641 25567765 556777765 678999999
Q ss_pred hHHHHHHhhcccCCCcCCcCCCCceeeHHHHH
Q 016210 114 QDLIYLSSTFCSQGCDIGFDRVEPYLDITSIY 145 (393)
Q Consensus 114 ~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA 145 (393)
.|+..|.+.+...|.... ....+.+| |+.+
T Consensus 54 fD~~fL~~~~~~~~~~~p-~~~~~~lD-T~~l 83 (96)
T cd06125 54 FDLPFLNNRCAELGLKYP-LLAGSWID-TIKL 83 (96)
T ss_pred HhHHHHHHHHHHcCCCCC-CcCCcEEE-ehHH
Confidence 999888765432222100 01356889 6544
No 50
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.56 E-value=0.12 Score=49.61 Aligned_cols=103 Identities=17% Similarity=0.124 Sum_probs=62.1
Q ss_pred hHHHHHHhhCCCCcEEEEEehHhHHHHHHhhccc-CCCcCCcCCCCceeeHHHHHHHHhccccCCC------CCCCcccH
Q 016210 92 IWELLKELFVSPDILKLGFKFKQDLIYLSSTFCS-QGCDIGFDRVEPYLDITSIYNHLHHKQLGRK------LPKETKSL 164 (393)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi-~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~------~~~~~~sL 164 (393)
++..|.+++.+. ..|+||+..|...|.+.+.- .+.. ....++|+..++..+.....+.. .....++|
T Consensus 119 vl~~l~~~~~~~--~lVaHna~FD~~fL~~~l~~~~~~~----~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L 192 (239)
T PRK09146 119 ILDELLEALAGK--VVVVHYRRIERDFLDQALRNRIGEG----IEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRL 192 (239)
T ss_pred HHHHHHHHhCCC--EEEEECHHHHHHHHHHHHHHhcCCC----CCCceechHHHHHHHcccccccccchhccCCCCCCCH
Confidence 455555666553 45999999999988654210 0111 13568995566665543210000 00135789
Q ss_pred HHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 165 ANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVA 217 (393)
Q Consensus 165 a~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~ 217 (393)
.+++++ +|++....+. |..||.++..|+..+..+.-
T Consensus 193 ~~l~~~-~gl~~~~~H~----------------Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 193 ADSRLR-YGLPAYSPHH----------------ALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred HHHHHH-cCCCCCCCCC----------------cHHHHHHHHHHHHHHHHHHc
Confidence 999987 4765432222 88999999999888877664
No 51
>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=96.52 E-value=0.075 Score=49.14 Aligned_cols=160 Identities=16% Similarity=0.214 Sum_probs=89.1
Q ss_pred CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC------CC-chhhHHHHHHhhCC--C
Q 016210 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS------IP-LPSIWELLKELFVS--P 103 (393)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~------l~-~~~~~~~L~~lLe~--~ 103 (393)
.+++||.|..+.... .....-.++||+... . .++.++...... .. ..+++..+..++.. |
T Consensus 4 ~i~~fDIEt~~~~g~-p~~~~d~Ii~Is~~~---~-------~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dp 72 (195)
T cd05780 4 KILSFDIEVLNHEGE-PNPEKDPIIMISFAD---E-------GGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDP 72 (195)
T ss_pred eEEEEEEEecCCCCC-CCCCCCcEEEEEEec---C-------CCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCC
Confidence 578999999743211 012334567777642 0 122333221110 11 13456666666665 7
Q ss_pred CcEEEEEehH-hHHHHHHhhcccCCCcCCcCC------------------C-CceeeHHHHHHHHhccccCCCCCCCccc
Q 016210 104 DILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR------------------V-EPYLDITSIYNHLHHKQLGRKLPKETKS 163 (393)
Q Consensus 104 ~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~------------------~-~~~fDlt~LA~yLl~~~~~~~~~~~~~s 163 (393)
++ .+|||.. +|+..|......+|+...+.. . ...+|+-.++..... ..+++
T Consensus 73 di-ivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~--------l~sy~ 143 (195)
T cd05780 73 DV-IYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN--------LTRYT 143 (195)
T ss_pred CE-EEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC--------CCcCc
Confidence 75 4999976 799998543211222211100 0 136785444433222 24799
Q ss_pred HHHHHHHHcCCcccc--cccccC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 164 LANICKELLDISLSK--ELQCSD-WSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 164 La~Lve~~Lg~~L~K--~~q~sd-Ws~RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
|.++++++||.+... ..+... |...+-...-++|+-.||..+++|.+.|
T Consensus 144 L~~v~~~~Lg~~k~d~~~~~i~~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 144 LERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred HHHHHHHHhCCCCCcCCHHHHHHHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 999999999986321 122222 4433334667899999999999998753
No 52
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.52 E-value=0.061 Score=61.19 Aligned_cols=99 Identities=20% Similarity=0.237 Sum_probs=63.5
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
++...|..++.+. ..|+||+.+|+..|.+.+.-.|..+ .....+|+..++..+ .+. ...++|.+|++.
T Consensus 73 ev~~~l~~~l~~~--~~VaHN~~FD~~fL~~~~~~~g~~~---~~~~~iDt~~la~~~-~p~------~~~~~L~~l~~~ 140 (928)
T PRK08074 73 DVAPEIVELLEGA--YFVAHNVHFDLNFLNEELERAGYTE---IHCPKLDTVELARIL-LPT------AESYKLRDLSEE 140 (928)
T ss_pred HHHHHHHHHhCCC--eEEEEChHHHHHHHHHHHHHcCCCC---CCCCeeeHHHHHHHh-cCC------CCCCCHHHHHHh
Confidence 4566777788754 4599999999999976432223221 124689955555544 343 247899999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQ 218 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~ 218 (393)
+|+.....|+ |-.||.++..|+..|.+++.+
T Consensus 141 -l~i~~~~~H~----------------Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 141 -LGLEHDQPHR----------------ADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCCCCCCCC----------------hHHHHHHHHHHHHHHHHHHHh
Confidence 5776543332 666777777777777666654
No 53
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=96.39 E-value=0.076 Score=48.76 Aligned_cols=110 Identities=22% Similarity=0.282 Sum_probs=64.0
Q ss_pred hhHHHHHHhhCC--CCcEEEEEeh-HhHHHHHHhhcccCCCcC--CcCC-----------------CCceeeHHHHHHHH
Q 016210 91 SIWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDI--GFDR-----------------VEPYLDITSIYNHL 148 (393)
Q Consensus 91 ~~~~~L~~lLe~--~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~--~~~~-----------------~~~~fDlt~LA~yL 148 (393)
+++..+.+++.+ |++ .||||. .+|+..|.+....+|+.. ++.. -..++|+-.++...
T Consensus 65 ~lL~~f~~~i~~~dpdi-ivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~ 143 (199)
T cd05160 65 ELLKRFFDIIREYDPDI-LTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRD 143 (199)
T ss_pred HHHHHHHHHHHhcCCCE-EEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHh
Confidence 456666666654 554 499999 789999854322122221 0000 02468854444333
Q ss_pred hccccCCCCCCCcccHHHHHHHHcCCcccc--cccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 149 HHKQLGRKLPKETKSLANICKELLDISLSK--ELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 149 l~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K--~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
.. ..+++|.++++++|+..-.. .....+|....-...-++|.-.||..++.|+
T Consensus 144 ~~--------l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 144 FK--------LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred cC--------cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 22 24799999999999864322 1223332111223566899999999999886
No 54
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=96.36 E-value=0.16 Score=44.24 Aligned_cols=89 Identities=19% Similarity=0.242 Sum_probs=57.0
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..|..++.+. ..||||+.+|+..|.+.+.-.|... .....+|+..++..+. +. ...++|..+++.
T Consensus 66 ~v~~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~g~~~---~~~~~idt~~~~~~~~-~~------~~~~~L~~l~~~ 133 (156)
T cd06130 66 EVWPEIKPFLGGS--LVVAHNASFDRSVLRAALEAYGLPP---PPYQYLCTVRLARRVW-PL------LPNHKLNTVAEH 133 (156)
T ss_pred HHHHHHHHHhCCC--EEEEeChHHhHHHHHHHHHHcCCCC---CCCCEEEHHHHHHHHh-cc------CCCCCHHHHHHH
Confidence 4566777888763 4599999999999865432112111 1346889444444443 32 236899999986
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
+|+... .|. |..||..+.+|+
T Consensus 134 -~g~~~~-~H~----------------Al~Da~~ta~l~ 154 (156)
T cd06130 134 -LGIELN-HHD----------------ALEDARACAEIL 154 (156)
T ss_pred -cCCCcc-CcC----------------chHHHHHHHHHH
Confidence 577654 332 678888887776
No 55
>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=96.20 E-value=0.015 Score=53.28 Aligned_cols=81 Identities=20% Similarity=0.203 Sum_probs=54.3
Q ss_pred HHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcC
Q 016210 94 ELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLD 173 (393)
Q Consensus 94 ~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg 173 (393)
..|..++ +++.+.|||++.+|+.+|.-.+. -..+.| |.+... .+. ....||..|+.++||
T Consensus 93 ~~l~~li-~~~tILVGHsL~nDL~aL~l~hp----------~~~viD-Ta~l~~--~~~------~r~~sLk~La~~~L~ 152 (174)
T cd06143 93 LKLRLLV-DLGCIFVGHGLAKDFRVINIQVP----------KEQVID-TVELFH--LPG------QRKLSLRFLAWYLLG 152 (174)
T ss_pred HHHHHHc-CCCCEEEeccchhHHHHhcCcCC----------CcceEE-cHHhcc--CCC------CCChhHHHHHHHHcC
Confidence 3455555 44556699999999999865311 146889 543321 121 136899999999999
Q ss_pred CcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 174 ISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 174 ~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
..+..+. .| ..+||.+.++||
T Consensus 153 ~~IQ~~~--Hd-------------SvEDArAam~Ly 173 (174)
T cd06143 153 EKIQSET--HD-------------SIEDARTALKLY 173 (174)
T ss_pred CcccCCC--cC-------------cHHHHHHHHHHh
Confidence 8875421 11 468999999988
No 56
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=95.70 E-value=0.03 Score=63.61 Aligned_cols=104 Identities=20% Similarity=0.374 Sum_probs=75.5
Q ss_pred hhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 90 PSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
.+++..+++++.+. +-|.||+.+|+..|...|--.|..+ .-.+++| |.-.++-++|. -.+|+|..||.
T Consensus 489 ~~vL~kf~~~~~d~--IlVAHNasFD~gFl~~~~~k~~~~~---~~~pvID-TL~lar~L~P~------~ksh~Lg~l~k 556 (1444)
T COG2176 489 EEVLEKFREFIGDS--ILVAHNASFDMGFLNTNYEKYGLEP---LTNPVID-TLELARALNPE------FKSHRLGTLCK 556 (1444)
T ss_pred HHHHHHHHHHhcCc--EEEeccCccchhHHHHHHHHhCCcc---ccCchhh-HHHHHHHhChh------hhhcchHHHHH
Confidence 35677888888774 4499999999999865433112221 2368999 54455555665 25899999998
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (393)
++ |+.+ ++.+-|-.|+.++-.++-.+.+.+.+.|..
T Consensus 557 k~-~v~l----------------e~hHRA~yDaeat~~vf~~f~~~~ke~Gi~ 592 (1444)
T COG2176 557 KL-GVEL----------------ERHHRADYDAEATAKVFFVFLKDLKEKGIT 592 (1444)
T ss_pred Hh-CccH----------------HHhhhhhhhHHHHHHHHHHHHHHHHHhchh
Confidence 86 5544 344557889999999999999999999865
No 57
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=95.50 E-value=0.31 Score=49.81 Aligned_cols=161 Identities=8% Similarity=0.050 Sum_probs=85.2
Q ss_pred HcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCC---------CC---------ch
Q 016210 29 LSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSS---------IP---------LP 90 (393)
Q Consensus 29 L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~---------l~---------~~ 90 (393)
+.....++||+|+.+..+ . ...+|+|+.-. -..++.. .+.-..+|++.. +. ..
T Consensus 43 ~~~~~fVvlDiETTGLdp---~--~drIIeIgAV~-i~~~g~i---ve~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~ 113 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHP---S--TSRLITIDAVT-LTADGEE---VEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFS 113 (377)
T ss_pred CCCCCEEEEEEECCCCCC---C--CCeEEEEEEEE-EEcCCEE---EEEEEEEECcCCCCCCccccCCCHHHHhcCCCHH
Confidence 445789999999998875 2 33566663210 0000000 011222343321 11 13
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCc------------------------CCcCCCCceeeHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD------------------------IGFDRVEPYLDITSIYN 146 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~------------------------~~~~~~~~~fDlt~LA~ 146 (393)
+++..|.+++.+. +.|+||+.+|+.+|.+.+.-.+.. .+......++| |.-.+
T Consensus 114 eVl~el~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iD-TL~LA 190 (377)
T PRK05601 114 QILKPLDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVD-TLATA 190 (377)
T ss_pred HHHHHHHHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEE-hHHHH
Confidence 5677788888865 349999999999886542110000 00112346899 54444
Q ss_pred HHhccccCCCCCCCcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 147 HLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 147 yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
..+.+. ..+++|..|+++ +|+..+... .|. .++.-+..++ +-.|+.++..|+..+
T Consensus 191 Rrl~p~------l~~~rL~~La~~-lGi~~p~~~-A~~-~Ra~~p~~~l--~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 191 RRQGVA------LDDIRIRGVAHT-LGLDAPAAE-ASV-ERAQVPHRQL--CREETLLVARLYFAL 245 (377)
T ss_pred HHHcCC------CCCCCHHHHHHH-hCCCCCchh-hhh-hhhcCChhhh--hhHHHHHHHHHHHHh
Confidence 444443 247999999987 477653211 110 0111222222 225888888888776
No 58
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=95.04 E-value=0.0029 Score=63.81 Aligned_cols=149 Identities=19% Similarity=0.229 Sum_probs=98.8
Q ss_pred HHcCCCeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCCCCcEE
Q 016210 28 ALSQSSLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVSPDILK 107 (393)
Q Consensus 28 ~L~~~~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~~~i~K 107 (393)
++....+. +-.|.+..-. .+++|.+|.++. ..+|++|+..++...+...++.++++.+|.|
T Consensus 55 ~ik~qn~~-~~~e~a~~~~----~~~l~~~q~~~~--------------~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~ 115 (458)
T KOG2405|consen 55 HIKKQNVL-VAAEGANVCR----HGKLCWLQVATN--------------CRVYLFDIFLLGSRAFHNGLQMILEDKRILK 115 (458)
T ss_pred hhHhhcCc-ccccCccccc----cCcchhHHHHHH--------------HHHHHHHHHHhhhHHHHHHHHHHhhhhhHhh
Confidence 33333433 4556555443 358999999884 6789999877766667788899999999999
Q ss_pred EEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhcc-ccCCCCCCCcccHHHHHHHHcCCcc------cc--
Q 016210 108 LGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHK-QLGRKLPKETKSLANICKELLDISL------SK-- 178 (393)
Q Consensus 108 Vgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~-~~~~~~~~~~~sLa~Lve~~Lg~~L------~K-- 178 (393)
+.|+++.-+.+++++||| +.+++|| |+++.-+-.. +.|..+|..-..+.+-.-+.|.+-+ .|
T Consensus 116 ~~~d~~~~~~~~~~~~~i--------~~n~v~~-~q~~d~~q~~~e~g~~~~n~~~~~q~sl~kh~~~a~k~~~~l~~r~ 186 (458)
T KOG2405|consen 116 VIHDCRWLSDCLSHQYGI--------LLNNVFD-TQVADVLQFSMETGGYLPNCITTLQESLIKHLQVAPKYLSFLEKRQ 186 (458)
T ss_pred hHHHHHHHHHHhccccee--------eecchhh-hhhhhhhhhcccccccCCccccchHHHHHHHHHhcccHHHHHHHHH
Confidence 999999999999999998 2688999 8888776543 2344444332333322222333221 11
Q ss_pred ---cccccCCCCCCCCHHHHHHHHHHHHH
Q 016210 179 ---ELQCSDWSNRPLTEEQKNYAAIDAHC 204 (393)
Q Consensus 179 ---~~q~sdWs~RPLs~~Ql~YAA~DA~~ 204 (393)
.+...-|-.||.++.-+.--|..+-+
T Consensus 187 ~~~~~n~e~~~i~~~~~s~~~~~~~e~~~ 215 (458)
T KOG2405|consen 187 KLIQENPEVWFIRPVSPSLLKILALEATY 215 (458)
T ss_pred HHHhhCcceeEeecCchhHHHhhhhhhhh
Confidence 12334588899888876666655555
No 59
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.03 E-value=0.71 Score=42.98 Aligned_cols=106 Identities=14% Similarity=0.092 Sum_probs=62.7
Q ss_pred hhHHHHHHhhCCCCcEEEEEehH-hHHHHHHhhcccCCCcCCcCCCC-ceeeHHHHH--HHHh-ccccCCCCCCCcccHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDRVE-PYLDITSIY--NHLH-HKQLGRKLPKETKSLA 165 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~~~-~~fDlt~LA--~yLl-~~~~~~~~~~~~~sLa 165 (393)
+++..+.+++.+.. .||||+. .|+..|.+ +|. . ... ..+|+-..+ .... .+. ...++|.
T Consensus 73 evl~~f~~f~~~~~--lVaHNa~~fD~~fL~~-~g~---~----~~~~~~idt~~~~~~~~~~~~~~------~~~~~L~ 136 (195)
T PRK07247 73 EVLAAFKEFVGELP--LIGYNAQKSDLPILAE-NGL---D----LSDQYQVDLYDEAFERRSSDLNG------IANLKLQ 136 (195)
T ss_pred HHHHHHHHHHCCCe--EEEEeCcHhHHHHHHH-cCC---C----cCCCceeehHHHHHHhhccccCC------CCCCCHH
Confidence 45667777887654 4999995 79999987 443 1 112 234521111 1111 111 2368999
Q ss_pred HHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc
Q 016210 166 NICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISELD 230 (393)
Q Consensus 166 ~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l~~e~~~l~ 230 (393)
+|++. +|++. ..|+ |..||.++..|+..|...-+...-+.+|=++.+
T Consensus 137 ~La~~-~gi~~-~~Hr----------------Al~DA~~ta~v~~~ll~~~~~~~~~~~~~~~~~ 183 (195)
T PRK07247 137 TVADF-LGIKG-RGHN----------------SLEDARMTARVYESFLESDQNKEYLEQQEEVTS 183 (195)
T ss_pred HHHHh-cCCCC-CCcC----------------CHHHHHHHHHHHHHHHhhccchhhhhcchhhcc
Confidence 99986 57653 1221 778999999999888665543333344434433
No 60
>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=94.52 E-value=1.2 Score=41.07 Aligned_cols=157 Identities=15% Similarity=0.212 Sum_probs=82.7
Q ss_pred CeEEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCC--CCcEEEEE
Q 016210 33 SLVGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVS--PDILKLGF 110 (393)
Q Consensus 33 ~~Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~--~~i~KVgh 110 (393)
..++||.|+.+.... .....-.+++|+... . .+...++-.......+++..+..++.. |+++ +||
T Consensus 4 ~~l~fDIEt~~~~gf-p~~~~d~Ii~Is~~~---------~--~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~i-~gy 70 (188)
T cd05781 4 KTLAFDIEVYSKYGT-PNPRRDPIIVISLAT---------S--NGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGY 70 (188)
T ss_pred eEEEEEEEecCCCCC-CCCCCCCEEEEEEEe---------C--CCCEEEEEecCCCHHHHHHHHHHHHHHcCCCEE-Eec
Confidence 468999999743210 012234566666541 0 122233321112223556666666554 5543 799
Q ss_pred ehH-hHHHHHHh---hcccCCCcCCcCC---C------------CceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHH
Q 016210 111 KFK-QDLIYLSS---TFCSQGCDIGFDR---V------------EPYLDITSIYNHLHHKQLGRKLPKETKSLANICKEL 171 (393)
Q Consensus 111 ~~k-~Dl~~L~~---~~gi~g~~~~~~~---~------------~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~ 171 (393)
|.. +|+.+|.. .+|+ .+..|... + ...+|+-.+...... ..+++|.++++ +
T Consensus 71 N~~~FDlpyl~~Ra~~~gi-~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~--------l~~y~L~~Va~-~ 140 (188)
T cd05781 71 NSNAFDWPYLVERARVLGV-KLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE--------VKVKTLENVAE-Y 140 (188)
T ss_pred CCCcCcHHHHHHHHHHhCC-CcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC--------CCCCCHHHHHH-H
Confidence 954 89988742 2444 11100000 0 026774333332221 24799999997 5
Q ss_pred cCCc--cccc----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 172 LDIS--LSKE----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 172 Lg~~--L~K~----~q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
||.. ..|. .+.. -|...--...-..|...|+..++.|++.+
T Consensus 141 Lg~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 141 LGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred HCCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 8863 1221 1222 24331134677899999999999998753
No 61
>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=94.22 E-value=1.5 Score=40.72 Aligned_cols=110 Identities=23% Similarity=0.254 Sum_probs=61.2
Q ss_pred hhHHHHHHhhCC--CCcEEEEEehH-hHHHHHHhhcccCCCcCCcCC--------------------CC-ceeeHHHHHH
Q 016210 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSSTFCSQGCDIGFDR--------------------VE-PYLDITSIYN 146 (393)
Q Consensus 91 ~~~~~L~~lLe~--~~i~KVgh~~k-~Dl~~L~~~~gi~g~~~~~~~--------------------~~-~~fDlt~LA~ 146 (393)
+.+..+..++.+ |+++ +|||.. +|+.+|.+....+|+.+.+.+ .+ .++|+-.++.
T Consensus 53 ~lL~~f~~~i~~~dPDvi-~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k 131 (193)
T cd05784 53 SLLLALIAWFAQYDPDII-IGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALK 131 (193)
T ss_pred HHHHHHHHHHHhhCCCEE-EECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHH
Confidence 455555555544 4544 999977 599887532211222211110 11 2678433332
Q ss_pred HHhccccCCCCCCCcccHHHHHHHHcCCccccc------cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 016210 147 HLHHKQLGRKLPKETKSLANICKELLDISLSKE------LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (393)
Q Consensus 147 yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~------~q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~ 210 (393)
.- .. ...+++|.++++++||..-... .+.. -|...+ ..-++|+..||..+++|++
T Consensus 132 ~~-~~------kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 132 TA-TY------HFESFSLENVAQELLGEGKLIHDVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred Hc-cC------CCCcCCHHHHHHHHhCCCccccCcccCHHHHHHHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 20 00 1248999999999999642211 1122 244333 4668999999999999873
No 62
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=94.01 E-value=0.9 Score=54.01 Aligned_cols=103 Identities=16% Similarity=0.236 Sum_probs=68.4
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..+.+++.+ ...|+||+.+|...|...+.-+|..+ .....+| |.-.++.+.+. ...++|.+++++
T Consensus 488 EaL~~f~~figg--~vLVAHNa~FD~~fL~~~l~rlgl~~---l~~~~ID-TLelar~l~p~------~k~~kL~~LAk~ 555 (1437)
T PRK00448 488 EVLPKFKEFCGD--SILVAHNASFDVGFINTNYEKLGLEK---IKNPVID-TLELSRFLYPE------LKSHRLNTLAKK 555 (1437)
T ss_pred HHHHHHHHHhCC--CEEEEeCccccHHHHHHHHHHcCCcc---cccccee-HHHHHHHHcCc------cccccHHHHHHH
Confidence 344555555544 56699999999987754322222221 1346789 44444444443 247899999987
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNS 222 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l 222 (393)
+|+.....| -|-.||.++.+|+..+..++.+.|..
T Consensus 556 -lGL~~~~~H----------------rAl~DA~aTa~lf~~ll~~l~~~gi~ 590 (1437)
T PRK00448 556 -FGVELEHHH----------------RADYDAEATAYLLIKFLKDLKEKGIT 590 (1437)
T ss_pred -cCCCCCCCc----------------ChHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 577664332 38899999999999999999877654
No 63
>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=94.00 E-value=0.58 Score=43.07 Aligned_cols=84 Identities=17% Similarity=0.185 Sum_probs=51.5
Q ss_pred cEEEEEehHhHHHHHHhhcccCCC-cCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccccccccc
Q 016210 105 ILKLGFKFKQDLIYLSSTFCSQGC-DIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCS 183 (393)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~-~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~s 183 (393)
...|+||+..|+..|.+.+.-.|+ ...+ ....++|+..++..+ .+ ..+|++++++ +|+++.....
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~-~~~~~lDt~~la~~~-~~---------~~~L~~l~~~-~gi~~~~~~~-- 168 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPF-HPFSTFDTATLAGLA-YG---------QTVLAKACQA-AGIEFDNKEA-- 168 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCC-CCCcEEEHHHHHHHH-hC---------CCcHHHHHHH-CCCCCCCCCC--
Confidence 456999999999988754321121 0000 012479955555444 33 3579999986 4776421111
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 184 DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 184 dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
.=|..||..+.+|+..|.+
T Consensus 169 ------------H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 169 ------------HSALYDTQKTAELFCKIVN 187 (189)
T ss_pred ------------cChHHHHHHHHHHHHHHHH
Confidence 1288999999999888764
No 64
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=93.99 E-value=0.46 Score=47.28 Aligned_cols=98 Identities=18% Similarity=0.197 Sum_probs=63.6
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCC-CceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRV-EPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~-~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
+++..|.+++.+ -..|+||+.+|+..|.+.+.-.|.. .+ ..++|+-.++..+.. . ...++|.+|++
T Consensus 69 ev~~~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~----~~~~~~idT~~lar~l~~-~------~~~~~L~~L~~ 135 (309)
T PRK06195 69 KIWEKIKHYFNN--NLVIAHNASFDISVLRKTLELYNIP----MPSFEYICTMKLAKNFYS-N------IDNARLNTVNN 135 (309)
T ss_pred HHHHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCC----CCCCCEEEHHHHHHHHcC-C------CCcCCHHHHHH
Confidence 456677777765 3459999999999886542211211 12 368894455555543 2 13689999998
Q ss_pred HHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 016210 170 ELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQK 219 (393)
Q Consensus 170 ~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (393)
.+ |++. .. +-|..||.++.+|+..|..++...
T Consensus 136 ~~-gi~~-~~----------------H~Al~DA~ata~l~~~l~~~~~~~ 167 (309)
T PRK06195 136 FL-GYEF-KH----------------HDALADAMACSNILLNISKELNSK 167 (309)
T ss_pred Hc-CCCC-cc----------------cCCHHHHHHHHHHHHHHHHHhccC
Confidence 85 6543 11 228899999999998888776543
No 65
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=93.96 E-value=0.014 Score=58.99 Aligned_cols=129 Identities=22% Similarity=0.234 Sum_probs=81.4
Q ss_pred CCEEEEEeCCCCCchhhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhcccc-C
Q 016210 76 ASVVFLLDLSSIPLPSIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQL-G 154 (393)
Q Consensus 76 ~~~v~LID~~~l~~~~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~-~ 154 (393)
++..|++|...-+.--...-.+..|++..+ +. |.+.+...|...|++ ...+++| |++++.|..+.. |
T Consensus 221 ~n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~--------~L~nVkD-tQia~sLve~~e~g 288 (458)
T KOG2405|consen 221 GNEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHS--------ALKNVKD-TQIASSLVEPSEYG 288 (458)
T ss_pred cchhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHH--------HHHhhHH-HHHHHHHhhhHHhc
Confidence 477888887643321122334556776555 44 999999999888876 2678999 999999988753 5
Q ss_pred CCCCCCc-ccHHHHHH--HHcCCcc------cccc-ccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 155 RKLPKET-KSLANICK--ELLDISL------SKEL-QCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKV 216 (393)
Q Consensus 155 ~~~~~~~-~sLa~Lve--~~Lg~~L------~K~~-q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L 216 (393)
+..|... .++..+-. .|.+.+. .+.. ++- +|..||.++...+-++.||.+|+.....+.+..
T Consensus 289 rr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~~ 361 (458)
T KOG2405|consen 289 RRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVAVC 361 (458)
T ss_pred ccCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhhhC
Confidence 4433211 11111111 1111111 1111 233 699999999999999999999999777766543
No 66
>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=93.53 E-value=1.4 Score=41.36 Aligned_cols=155 Identities=15% Similarity=0.172 Sum_probs=80.2
Q ss_pred CeEEEEEEEeCCCCCC---CCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCchhhHHHHHHhhCC--CCcEE
Q 016210 33 SLVGLDAEWKPQRSHQ---SNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPLPSIWELLKELFVS--PDILK 107 (393)
Q Consensus 33 ~~Va~D~E~~~~~~~~---~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~~~~~~~L~~lLe~--~~i~K 107 (393)
.+++||.|..+..... .....-.++||+... . .+...++........+++..+.+++.. |+++
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~---------~--~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPdii- 77 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRD---------N--RGWEEVLHAEDAAEKELLEELVAIIRERDPDVI- 77 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEeccc---------C--CCceeeeccCCCCHHHHHHHHHHHHHHhCCCEE-
Confidence 6789999986543210 112345688898752 0 111112221112223456666665555 5653
Q ss_pred EEEeh-HhHHHHHHhh---cccCCCcCCcCC--------------------------CC-ceeeHHHHHHHHhccccCCC
Q 016210 108 LGFKF-KQDLIYLSST---FCSQGCDIGFDR--------------------------VE-PYLDITSIYNHLHHKQLGRK 156 (393)
Q Consensus 108 Vgh~~-k~Dl~~L~~~---~gi~g~~~~~~~--------------------------~~-~~fDlt~LA~yLl~~~~~~~ 156 (393)
+|||. .+|+.+|.+. +|+ ...+.+ .+ .++|+-.++....... +.
T Consensus 78 ~g~N~~~FD~pyl~~R~~~~~~---~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~--~~ 152 (207)
T cd05785 78 EGHNIFRFDLPYLRRRCRRHGV---PLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSS--RD 152 (207)
T ss_pred eccCCcccCHHHHHHHHHHhCC---CcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccc--cC
Confidence 79998 6899987432 443 110000 11 2368322222110000 11
Q ss_pred CCCCcccHHHHHHHHcCCccc-c----ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 157 LPKETKSLANICKELLDISLS-K----ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 157 ~~~~~~sLa~Lve~~Lg~~L~-K----~~q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
..+++|.++++.+ |..-. | ..+.. -|... .+.-++|+..||..++.|.
T Consensus 153 --l~sysL~~Va~~~-g~~~~~k~d~~~~~I~~l~~~~--~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 153 --LPSYGLKAVAKHF-GLASPDRTYIDGRQIAEVWRSD--PARLLAYALDDVRETEGLA 206 (207)
T ss_pred --CCCCCHHHHHHHh-cccCCCcCCCCHHHHHHHHhcC--HHHHHHHHHHHHHHHHHhh
Confidence 1368999999986 33111 1 11111 24433 2667899999999998875
No 67
>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=93.12 E-value=1 Score=38.38 Aligned_cols=91 Identities=18% Similarity=0.195 Sum_probs=57.5
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+....+..++.+ -..|+||...|...|.+.+.-.|.. ......+|+..++..+.... ..+++..+...
T Consensus 68 ~~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~---~~~~~~iDt~~~~~~~~~~~-------~~~~l~~~~~~ 135 (159)
T cd06127 68 EVLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPGL-------RSHRLGLLLAE 135 (159)
T ss_pred HHHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCC---CCCCCeeEHHHHHHHHcCCC-------CcCchHHHHHH
Confidence 456677778877 4569999999999987654321101 01356899555555554432 35778877555
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
++|....+.| -|..||..+.+|+
T Consensus 136 ~~~~~~~~~H----------------~Al~Da~~t~~l~ 158 (159)
T cd06127 136 RYGIPLEGAH----------------RALADALATAELL 158 (159)
T ss_pred HcCCCCCCCC----------------CcHHHHHHHHHHh
Confidence 5665433223 2788999888876
No 68
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=92.44 E-value=4.7 Score=38.15 Aligned_cols=54 Identities=17% Similarity=0.177 Sum_probs=38.5
Q ss_pred CcccHHHHHHHHcCCcccc--cccccC-CCCCCCC-HHHHHHHHHHHHHHHHHHHHHH
Q 016210 160 ETKSLANICKELLDISLSK--ELQCSD-WSNRPLT-EEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 160 ~~~sLa~Lve~~Lg~~L~K--~~q~sd-Ws~RPLs-~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
.+++|.++++++||..... ...... |...|-. ..-++|...||...++|.+.|.
T Consensus 167 ~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~ 224 (230)
T cd05777 167 RSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKLM 224 (230)
T ss_pred ccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHHh
Confidence 4799999999999965321 122333 4333322 4568999999999999999885
No 69
>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=91.82 E-value=0.8 Score=41.66 Aligned_cols=88 Identities=17% Similarity=0.091 Sum_probs=54.0
Q ss_pred hHHHHHHhhCC--CCcEEEEEeh-HhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHH
Q 016210 92 IWELLKELFVS--PDILKLGFKF-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANIC 168 (393)
Q Consensus 92 ~~~~L~~lLe~--~~i~KVgh~~-k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lv 168 (393)
+.+.|.+++.. ...+.|+||+ .+|+..|.+.+.-.|.. +.....++| |.-....+. . +|++++
T Consensus 84 ~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~--~~~~~~~iD-tl~l~r~~~----------~-~L~~l~ 149 (177)
T cd06136 84 TANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTK--LPDDILCVD-SLPAFRELD----------Q-SLGSLY 149 (177)
T ss_pred HHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCC--CCCCCEEEE-eHHHHhhhH----------h-hHHHHH
Confidence 34556666653 2346799998 89999986543211222 111134579 543333221 2 899999
Q ss_pred HHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 016210 169 KELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 169 e~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~ 209 (393)
++++|++....+. |..||.++.+++
T Consensus 150 ~~~~~~~~~~~H~----------------A~~Da~at~~v~ 174 (177)
T cd06136 150 KRLFGQEPKNSHT----------------AEGDVLALLKCA 174 (177)
T ss_pred HHHhCCCcccccc----------------hHHHHHHHHHHH
Confidence 9988887654442 888999887765
No 70
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=90.34 E-value=1.1 Score=49.89 Aligned_cols=107 Identities=22% Similarity=0.181 Sum_probs=69.5
Q ss_pred CCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhc-cc-cCC-----------------CCC-----
Q 016210 103 PDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHH-KQ-LGR-----------------KLP----- 158 (393)
Q Consensus 103 ~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~-~~-~~~-----------------~~~----- 158 (393)
.+-+.||||..+|..-+++.|.|.|. -..++| ||-.+--.. -. ..+ ..+
T Consensus 240 ke~liVGHNVsfDRaRirEeY~i~~S------k~rFlD-TMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~ 312 (1075)
T KOG3657|consen 240 KEQLIVGHNVSFDRARIREEYNINGS------KIRFLD-TMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDY 312 (1075)
T ss_pred CCceEEeccccchHHHHHHHHhcccc------ceeeee-chhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhh
Confidence 45667999999999999888988442 235789 765443211 00 000 000
Q ss_pred -------CCcccHHHHHHHHcCCc-ccccccccCCCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHhc
Q 016210 159 -------KETKSLANICKELLDIS-LSKELQCSDWSNRPLTEEQ--------KNYAAIDAHCLIEIFNIFQVKVAQK 219 (393)
Q Consensus 159 -------~~~~sLa~Lve~~Lg~~-L~K~~q~sdWs~RPLs~~Q--------l~YAA~DA~~Ll~L~~~L~~~L~~~ 219 (393)
....||.++...++|+. ++|.....-- ..+.+| ++|.|.|++++.+++..+.+..-+.
T Consensus 313 ~~pWL~~SS~NSL~dVhk~~c~~~~LdKt~Rd~Fv---s~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP~Fler 386 (1075)
T KOG3657|consen 313 DNPWLGRSSLNSLVDVHKFHCGIDALDKTPRDSFV---SGTKEQIRENFQPLMNYCARDVIATHQVFFRLFPLFLER 386 (1075)
T ss_pred hhhhhhhhhhHHHHHHHHhhCCCCccccchHHhhh---cCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhHHHHHh
Confidence 01246888888888888 8776543311 123333 7899999999999999998877654
No 71
>PRK11779 sbcB exonuclease I; Provisional
Probab=89.70 E-value=8.4 Score=40.86 Aligned_cols=107 Identities=15% Similarity=0.117 Sum_probs=57.7
Q ss_pred hhHHHHHHhhCCCCcEEEEEe-hHhHHHHHHhhcccCCCcCC---cCCCC---ceeeHHHHHHHHhccc---cCCC-CCC
Q 016210 91 SIWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDIG---FDRVE---PYLDITSIYNHLHHKQ---LGRK-LPK 159 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~~---~~~~~---~~fDlt~LA~yLl~~~---~~~~-~~~ 159 (393)
++...+..+|..+..+.|||| +.+|...|+..+.-....+. +.... .++|+..++ +.+.+. ++.. ...
T Consensus 80 e~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~-~~lrp~~i~~P~~~~g~ 158 (476)
T PRK11779 80 EFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRAC-YALRPEGINWPENEDGL 158 (476)
T ss_pred HHHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHH-HHhccccccCcccccCC
Confidence 345566777764555679997 78999887664311000000 00001 234532222 222221 0000 002
Q ss_pred CcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 160 ETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (393)
Q Consensus 160 ~~~sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~ 215 (393)
.++.|++|++.+ |++....|. |-.||.++.+|+..+..+
T Consensus 159 ~s~rLe~L~~~~-gI~~~~AHd----------------ALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 159 PSFKLEHLTKAN-GIEHENAHD----------------AMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCcHHHHHHHc-CCCCCCCCC----------------cHHHHHHHHHHHHHHHHh
Confidence 368999999875 665432222 778999999988888866
No 72
>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=89.67 E-value=0.51 Score=41.69 Aligned_cols=148 Identities=17% Similarity=0.179 Sum_probs=66.9
Q ss_pred EEEEEEEeCCCCCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCCCCCc---hhhHHHHHHhhCCCCcEEEEEe
Q 016210 35 VGLDAEWKPQRSHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLSSIPL---PSIWELLKELFVSPDILKLGFK 111 (393)
Q Consensus 35 Va~D~E~~~~~~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~~l~~---~~~~~~L~~lLe~~~i~KVgh~ 111 (393)
+.||+|+.+..+ ..+.+.+++++... .++..++.....-.. ..+.+.+ ..+.+...+ |+||
T Consensus 1 l~~DIET~Gl~~---~~~~i~liG~~~~~-----------~~~~~~~~~~~~~~~~ee~~~~~~~-~~l~~~~~i-v~yn 64 (164)
T PF13482_consen 1 LFFDIETTGLSP---DNDTIYLIGVADFD-----------DDEIITFIQWFAEDPDEEEIILEFF-ELLDEADNI-VTYN 64 (164)
T ss_dssp --EEEEESS-GG----G---EEEEEEE-E-----------TTTTE-EEEE-GGGHHHHHHHHH---HHHHTT--E-EESS
T ss_pred CcEEecCCCCCC---CCCCEEEEEEEEeC-----------CCceEEeeHhhccCcHHHHHHHHHH-HHHhcCCeE-EEEe
Confidence 468999997764 34568888887531 122222222111111 1123333 344444333 7787
Q ss_pred h-HhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccc-cc---cccc---
Q 016210 112 F-KQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS-KE---LQCS--- 183 (393)
Q Consensus 112 ~-k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~-K~---~q~s--- 183 (393)
. .+|..+|.+.+.-.++. .....+||-.++..... .+++|..+... ||+.-. +. .+..
T Consensus 65 g~~FD~p~L~~~~~~~~~~----~~~~~iDl~~~~~~~~~---------~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~ 130 (164)
T PF13482_consen 65 GKNFDIPFLKRRAKRYGLP----PPFNHIDLLKIIKKHFL---------ESYSLKNVEKF-LGIERRDDDISGSESVKLY 130 (164)
T ss_dssp TTTTHHHHHHHHH-HHHH------GGGEEEHHHHHT-TTS---------CCTT--SHHH------------HHHHHHHHH
T ss_pred CcccCHHHHHHHHHHcCCC----cccchhhHHHHHHhccC---------CCCCHHHHhhh-cccccccCCCCHHHHHHHH
Confidence 5 57999987654111211 14578896444321111 36788888776 676543 11 1111
Q ss_pred -CCCC---CCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 184 -DWSN---RPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 184 -dWs~---RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
.|.. ....+..+.|.-.|+..+..|++.|
T Consensus 131 ~~~~~~~~~~~~~~i~~yN~~Dv~~~~~L~~~l 163 (164)
T PF13482_consen 131 KEYLETGDPEALEEILEYNEDDVRATRRLYEWL 163 (164)
T ss_dssp H---TTGGTS--HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1211 2345777999999999999999876
No 73
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=89.44 E-value=3.4 Score=38.49 Aligned_cols=98 Identities=17% Similarity=0.103 Sum_probs=59.7
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
+++..|.+++.+.... +.|+...|+..|.+.+...|.. +.....++|+..++..+... ...++|.+++++
T Consensus 81 evl~~f~~~~~~~~~~-iv~~~~fD~~fL~~~~~~~~~~--~~~~~~~~dl~~~~~~~~~~-------~~~~~L~~~~~~ 150 (207)
T PRK07748 81 ELVEKLAEYDKRCKPT-IVTWGNMDMKVLKHNCEKAGVP--FPFKGQCRDLSLEYKKFFGE-------RNQTGLWKAIEE 150 (207)
T ss_pred HHHHHHHHHhCcCCeE-EEEECHHHHHHHHHHHHHcCCC--CcccccceeHHHHHHHHhCc-------CCCCCHHHHHHH
Confidence 4667788888763333 5566799999986543211221 11134577855444333322 136899998887
Q ss_pred HcCCccc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (393)
Q Consensus 171 ~Lg~~L~-K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~ 215 (393)
+ |++.. ..+ -|..||..+.+|+..|...
T Consensus 151 ~-gi~~~~~~H----------------~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 151 Y-GKEGTGKHH----------------CALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred c-CCCCCCCCc----------------ChHHHHHHHHHHHHHHHhC
Confidence 4 66532 112 2889999999998887654
No 74
>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=88.80 E-value=20 Score=33.44 Aligned_cols=162 Identities=14% Similarity=0.097 Sum_probs=83.5
Q ss_pred CeEEEEEEEeCCC----CCCCCCCceeEEEEeccCCCCCCCCCCCCCCCEEEEEeCC----------------CC-Cchh
Q 016210 33 SLVGLDAEWKPQR----SHQSNFPRVSLLQLACQPGPRFNPESDESNASVVFLLDLS----------------SI-PLPS 91 (393)
Q Consensus 33 ~~Va~D~E~~~~~----~~~~~~~~v~LlQIa~~~~~~~~~~~~~~~~~~v~LID~~----------------~l-~~~~ 91 (393)
.+++||.|..+.. +. .......++||+.... ++...++++... .. ...+
T Consensus 6 rilsfDIE~~~~~~~~fP~-~~~~~d~IisI~~~~~---------~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~ 75 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPD-PKTAEYPVISVALAGS---------DGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKE 75 (204)
T ss_pred eEEEEEEEECCCCCCCCcC-CCCCCCeEEEEEEcCC---------CCCcEEEEEecCCcccccccCCCCCeEEecCCHHH
Confidence 5789999997532 21 0111236889988520 012344544310 01 1135
Q ss_pred hHHHHHHhhCCCCcEEEEEehH-hHHHHHHhh---cccCC--CcCCc-----CC-CCceeeHHHHHHH-Hhc-cccCCCC
Q 016210 92 IWELLKELFVSPDILKLGFKFK-QDLIYLSST---FCSQG--CDIGF-----DR-VEPYLDITSIYNH-LHH-KQLGRKL 157 (393)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~---~gi~g--~~~~~-----~~-~~~~fDlt~LA~y-Ll~-~~~~~~~ 157 (393)
++..+.+++.+.. ..||+|.. +|+.+|... +|+.. ....+ .. -...+|+-..... .+. ..++.
T Consensus 76 lL~~F~~~i~~~~-~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~-- 152 (204)
T cd05783 76 LIREAFKIISEYP-IVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGN-- 152 (204)
T ss_pred HHHHHHHHHhcCC-EEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcc--
Confidence 6666777777664 45899966 899987532 44310 00000 00 1235674332221 110 00000
Q ss_pred CCCcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 016210 158 PKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (393)
Q Consensus 158 ~~~~~sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~ 210 (393)
+..+++|.++++.+||..-... .-.-|.. =.+.-+.|+..||..++.|..
T Consensus 153 ~~~~~~L~~Va~~~lg~~K~~~-~~~i~~~--~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 153 KYREYTLDAVAKALLGEGKVEL-EKNISEL--NLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccccCcHHHHHHHhcCCCcccC-Cchhhhh--cHHHHHHhhHHHHHHHHHHhc
Confidence 1247899999999999642111 1011211 125568999999999988864
No 75
>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=88.26 E-value=9.1 Score=35.87 Aligned_cols=110 Identities=15% Similarity=0.197 Sum_probs=61.3
Q ss_pred hhHHHHHHhhCC--CCcEEEEEehH-hHHHHHHhh---cccCCCc--CCcCC--------C-CceeeHHHHHHHHhcccc
Q 016210 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSST---FCSQGCD--IGFDR--------V-EPYLDITSIYNHLHHKQL 153 (393)
Q Consensus 91 ~~~~~L~~lLe~--~~i~KVgh~~k-~Dl~~L~~~---~gi~g~~--~~~~~--------~-~~~fDlt~LA~yLl~~~~ 153 (393)
+++..+.+++.+ |+++ +|+|.. +|+..|... +|+ ... .|+.. . ...+|+-.++..-..
T Consensus 75 ~lL~~f~~~i~~~~Pd~i-~gyN~~~FD~pyl~~R~~~~~~-~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~--- 149 (204)
T cd05779 75 ALLQRFFEHIREVKPHII-VTYNGDFFDWPFVEARAAIHGL-SMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSY--- 149 (204)
T ss_pred HHHHHHHHHHHHhCCCEE-EecCccccCHHHHHHHHHHhCC-CchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhc---
Confidence 455566665554 5553 899865 899887432 443 100 11110 0 114674333221101
Q ss_pred CCCCCCCcccHHHHHHHHcCCccccc--ccc-cCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 016210 154 GRKLPKETKSLANICKELLDISLSKE--LQC-SDWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (393)
Q Consensus 154 ~~~~~~~~~sLa~Lve~~Lg~~L~K~--~q~-sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~ 210 (393)
++...++|..+++.+||.+-... ... .-|...+ +.-++|.-.||..++.||.
T Consensus 150 ---l~~~sysLd~Va~~~Lg~~K~~~~~~~I~~~~~~~~--~~l~~Y~~~D~~~T~~l~~ 204 (204)
T cd05779 150 ---LPQGSQGLKAVTKAKLGYDPVELDPEDMVPLAREDP--QTLASYSVSDAVATYYLYM 204 (204)
T ss_pred ---CCCCCccHHHHHHHHhCCCcCcCCHHHHHHHHhCCc--HHHHhccHHHHHHHHHHhC
Confidence 11237899999999999742211 111 1355443 5678999999999999873
No 76
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=88.11 E-value=16 Score=36.18 Aligned_cols=87 Identities=15% Similarity=0.133 Sum_probs=50.3
Q ss_pred HHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHc
Q 016210 93 WELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELL 172 (393)
Q Consensus 93 ~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~L 172 (393)
.+.+..++.... +.|+||+.+|...|.+.+.- +. .....+ ++.......+. ..+++|.+|+..+
T Consensus 111 ~~~l~~fl~~~~-vlVAHNA~FD~~fL~~~~~~------~~-~~~~~c-t~~~i~~~~~~------~~~~kL~~La~~~- 174 (294)
T PRK09182 111 PAAVDALIAPAD-LIIAHNAGFDRPFLERFSPV------FA-TKPWAC-SVSEIDWSARG------FEGTKLGYLAGQA- 174 (294)
T ss_pred HHHHHHHhcCCC-EEEEeCHHHHHHHHHHHHHh------cc-CCcccc-cHHHHhhcccc------CCCCCHHHHHHHc-
Confidence 456777777643 45999999999999763211 10 112333 33211111111 1368999999875
Q ss_pred CCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 173 DISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 173 g~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
|. ....| =|..||.++.+|+...
T Consensus 175 g~-~~~aH----------------rAl~Da~Ata~ll~~~ 197 (294)
T PRK09182 175 GF-FHEGH----------------RAVDDCQALLELLARP 197 (294)
T ss_pred CC-CCCCc----------------ChHHHHHHHHHHHHHH
Confidence 52 11111 2889999998777744
No 77
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=87.95 E-value=0.56 Score=48.18 Aligned_cols=92 Identities=20% Similarity=0.264 Sum_probs=59.6
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
++-..|..++ +.+-+-|||+...||.+|+-.| ..+.|+..+..+-.++ . ....+|..|++.
T Consensus 282 dvq~~l~~~~-~~~TILVGHSLenDL~aLKl~H------------~~ViDTa~lf~~~~g~-----~-~~k~sLk~L~~~ 342 (380)
T KOG2248|consen 282 DVQKELLELI-SKNTILVGHSLENDLKALKLDH------------PSVIDTAVLFKHPTGP-----Y-PFKSSLKNLAKS 342 (380)
T ss_pred HHHHHHHhhc-CcCcEEEeechhhHHHHHhhhC------------CceeeeeEEEecCCCC-----c-cchHHHHHHHHH
Confidence 4556777755 4555569999999999998753 3467833233332221 0 136789999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
|||..+.-+..-.| ..+||..+++|......
T Consensus 343 ~L~~~Iq~~~~~Hd-------------S~eDA~acm~Lv~~k~~ 373 (380)
T KOG2248|consen 343 YLGKLIQEGVGGHD-------------SVEDALACMKLVKLKIK 373 (380)
T ss_pred HHHHHHhccCCCCc-------------cHHHHHHHHHHHHHHHh
Confidence 99977751111111 67899999888776543
No 78
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=87.51 E-value=4.7 Score=38.19 Aligned_cols=78 Identities=9% Similarity=-0.061 Sum_probs=49.5
Q ss_pred cEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccccccccC
Q 016210 105 ILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSD 184 (393)
Q Consensus 105 i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~sd 184 (393)
-.-||||+.+|...|.. + ....+| |.-.+..+.++ ..+++..|+.. +|+...... ..
T Consensus 75 ~~lVaHNa~FD~~~L~~-~-----------~~~~id-Tl~lar~l~p~-------~~~~l~~L~~~-~~l~~~~~~-~~- 131 (219)
T PRK07983 75 EWYVAHNASFDRRVLPE-M-----------PGEWIC-TMKLARRLWPG-------IKYSNMALYKS-RKLNVQTPP-GL- 131 (219)
T ss_pred CEEEEeCcHhhHHHHhC-c-----------CCCcEe-HHHHHHHHccC-------CCCCHHHHHHH-cCCCCCCCC-CC-
Confidence 34599999999999865 2 245789 54444444443 24889888865 465431100 00
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 185 WSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 185 Ws~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
...-|..||.++..|+..+..
T Consensus 132 ---------~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 132 ---------HHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred ---------CCCcHHHHHHHHHHHHHHHHH
Confidence 112388999999888888753
No 79
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=86.80 E-value=0.3 Score=38.11 Aligned_cols=45 Identities=18% Similarity=0.261 Sum_probs=34.6
Q ss_pred hHHHHHHHHhh------hhcCCCCc-ccccccc---ccCCCCCHHHHHHHHhhcc
Q 016210 258 EALDIIRATSY------YSQCLPEG-VVSRVSY---LNTMPMDESLVKIVRKYGE 302 (393)
Q Consensus 258 ~~~~~~~~~~~------~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~~~~~~ 302 (393)
++++++++||. +..++||. |+++..+ +...|.+...|..+.+++.
T Consensus 3 ~~~~~~~~L~~wR~~~A~~~~~~~~~I~~~~~L~~ia~~~P~~~~~L~~i~g~~~ 57 (81)
T smart00341 3 RQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGE 57 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCeEEECHHHHHHHHHHCCCCHHHHhcCCCCCH
Confidence 56777777765 55689998 9998887 9999999998766655543
No 80
>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=84.49 E-value=5.2 Score=35.09 Aligned_cols=55 Identities=18% Similarity=0.319 Sum_probs=35.3
Q ss_pred CCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 135 VEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 135 ~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
+.+--| -+|.+||+++. +.+...++++|+| .+|... |+..|...-+|+..|..
T Consensus 84 v~PGDD-PlLlAYLlDPs--------Nt~p~~varRY~~---------~~W~~d---------A~~RA~~t~~L~~~L~p 136 (138)
T PF09281_consen 84 VEPGDD-PLLLAYLLDPS--------NTNPEGVARRYLG---------GEWPED---------AATRALATARLLRALPP 136 (138)
T ss_dssp --B----HHHHHHHH-TT----------SHHHHHHHH-T---------S---SS---------HHHHHHHHHHHHHHHHH
T ss_pred cCCCCC-cchhhhhcCcc--------CCChHHHHHHhcC---------CCCCcc---------HHHHHHHHHHHHHHhhh
Confidence 455568 99999999985 6788999999987 345432 77888888888888877
Q ss_pred HH
Q 016210 215 KV 216 (393)
Q Consensus 215 ~L 216 (393)
+|
T Consensus 137 rL 138 (138)
T PF09281_consen 137 RL 138 (138)
T ss_dssp HT
T ss_pred cC
Confidence 64
No 81
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=82.31 E-value=11 Score=35.58 Aligned_cols=99 Identities=19% Similarity=0.195 Sum_probs=61.6
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICKE 170 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~ 170 (393)
++...+.+++.+. -.-|+||+..|...|...+...+..+ ....+.|.-.++.... +. ...++|..+++
T Consensus 83 ~v~~~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~---~~~~~~~t~~~~r~~~-~~------~~~~~L~~l~~- 150 (243)
T COG0847 83 EVLPEFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEI---PGDPVLDTLALARRHF-PG------FDRSSLDALAE- 150 (243)
T ss_pred HHHHHHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCc---ccCceehHHHHHHHHc-CC------CccchHHHHHH-
Confidence 3455566667663 34499999999999875433322111 1246778334443333 32 14789999999
Q ss_pred HcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 171 LLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVK 215 (393)
Q Consensus 171 ~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~ 215 (393)
.+|+....... .=|..||.++..++..+...
T Consensus 151 ~~gi~~~~~~~--------------H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 151 RLGIDRNPFHP--------------HRALFDALALAELFLLLQTG 181 (243)
T ss_pred HcCCCcCCcCC--------------cchHHHHHHHHHHHHHHHhc
Confidence 66776431111 12889999999999888764
No 82
>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=82.19 E-value=9.1 Score=34.79 Aligned_cols=100 Identities=16% Similarity=0.205 Sum_probs=51.9
Q ss_pred hHHHHHHhhCCCCcEEEEEe-hHhHHHHHHhhcccCCCcC-CcCC--CCceeeHHHHHHHHh--ccc---cCCCC-CCCc
Q 016210 92 IWELLKELFVSPDILKLGFK-FKQDLIYLSSTFCSQGCDI-GFDR--VEPYLDITSIYNHLH--HKQ---LGRKL-PKET 161 (393)
Q Consensus 92 ~~~~L~~lLe~~~i~KVgh~-~k~Dl~~L~~~~gi~g~~~-~~~~--~~~~fDlt~LA~yLl--~~~---~~~~~-~~~~ 161 (393)
++..+..++..+....|+|| +.+|+..|.+.+.-.|..+ .+.. ....+|+..++..+. .+. +.... ...+
T Consensus 72 ~l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~ 151 (183)
T cd06138 72 FIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPS 151 (183)
T ss_pred HHHHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcc
Confidence 45566667764444458997 7999999876432111110 0000 112357444444322 121 00000 0136
Q ss_pred ccHHHHHHHHcCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHH
Q 016210 162 KSLANICKELLDISLSKELQCSDWSNRPLTEEQKNYAAIDAHCLIEI 208 (393)
Q Consensus 162 ~sLa~Lve~~Lg~~L~K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L 208 (393)
++|++++++ +|++....+ -|..||..+.+|
T Consensus 152 ~~L~~l~~~-~gi~~~~~H----------------~Al~Da~~ta~l 181 (183)
T cd06138 152 FKLEDLAQA-NGIEHSNAH----------------DALSDVEATIAL 181 (183)
T ss_pred hhHHHHHHH-CCCCccccc----------------cHHHHHHHHHHH
Confidence 889999986 576653222 377888887665
No 83
>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=81.73 E-value=3.2 Score=39.53 Aligned_cols=54 Identities=9% Similarity=0.132 Sum_probs=35.3
Q ss_pred CcccHHHHHHHHcCCcccc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 016210 160 ETKSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 160 ~~~sLa~Lve~~Lg~~L~K--~~q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
.+++|.++++.+||..-.. ..... -|....--..-++|...||+..++|...|.
T Consensus 171 ~sY~L~~va~~~Lg~~k~di~~~~i~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~ 227 (234)
T cd05776 171 KSYDLTELSQQVLGIERQDIDPEEILNMYNDSESLLKLLEHTEKDAYLILQLMFKLN 227 (234)
T ss_pred CCCChHHHHHHHhCcCcccCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 4899999999999973211 11122 243201113348999999999999988763
No 84
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=81.36 E-value=0.29 Score=37.05 Aligned_cols=44 Identities=14% Similarity=0.221 Sum_probs=29.8
Q ss_pred HHHHHHHHhh------hhcCCCCc-ccccccc---ccCCCCCHHHHHHHHhhcc
Q 016210 259 ALDIIRATSY------YSQCLPEG-VVSRVSY---LNTMPMDESLVKIVRKYGE 302 (393)
Q Consensus 259 ~~~~~~~~~~------~~~~~~~~-~~~~~~~---~~~~~~~~~~~~~~~~~~~ 302 (393)
+++++++||. +..+++|. |+++..+ +...|.|...|..+.+++.
T Consensus 1 q~~~~~~L~~~R~~~A~~~~~~~~~Il~~~~L~~ia~~~P~s~~~L~~i~g~~~ 54 (68)
T PF00570_consen 1 QLALLKALKEWREELAREEDVPPYRILSDEALLEIAKRLPTSIEELLQIPGMGK 54 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH--SSHHHHHTSTTCGH
T ss_pred CHHHHHHHHHHHHHHHHHcCcCcccccCHHHHHHHHHhCCCCHHHHHHccCCCH
Confidence 3566666644 55688888 9999888 8999999999988755543
No 85
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=81.00 E-value=0.28 Score=54.63 Aligned_cols=95 Identities=20% Similarity=0.310 Sum_probs=66.7
Q ss_pred hhCCCCcEEEEEehHhHHHHHHhhcccCCCcCCcCCC-CceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCccc
Q 016210 99 LFVSPDILKLGFKFKQDLIYLSSTFCSQGCDIGFDRV-EPYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLS 177 (393)
Q Consensus 99 lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~~~~~~~-~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~ 177 (393)
+|-+-.++.|||++++|..++- + . ++ +.++| |... ++++.. +..+|..|+-++||..+.
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvIN----i---~----Vp~~QiiD-Tv~l-f~~~s~-------R~LSLrfLa~~lLg~~IQ 1068 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVIN----I---H----VPEEQIID-TVTL-FRLGSQ-------RMLSLRFLAWELLGETIQ 1068 (1118)
T ss_pred HHHHcCcEEEcccccccceEEE----E---e----cChhhhee-eeEE-Eecccc-------cEEEHHHHHHHHhcchhh
Confidence 5777889999999999987652 2 0 13 35889 5332 233322 478999999999997763
Q ss_pred ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccccc
Q 016210 178 KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQVKVAQKGNSCSSISEL 229 (393)
Q Consensus 178 K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~~L~~~g~l~~e~~~l 229 (393)
-+. .| ..+||...+.||+... +|+++|+++.|+..+
T Consensus 1069 ~~~--HD-------------SIeDA~taLkLYk~Yl-~lkeq~~~~~~l~ni 1104 (1118)
T KOG1275|consen 1069 MEA--HD-------------SIEDARTALKLYKKYL-KLKEQGKLESELRNI 1104 (1118)
T ss_pred ccc--cc-------------cHHHHHHHHHHHHHHH-HHHHhhHHHHHHHHH
Confidence 221 22 4689999999999985 688888886666643
No 86
>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=80.67 E-value=22 Score=33.21 Aligned_cols=109 Identities=20% Similarity=0.179 Sum_probs=61.3
Q ss_pred hhhHHHHHHhhCCCCcEEEEEehH-hHHHHHHhh---cccCCCcCCcCC-----------CCceeeHHHHHHHHhccccC
Q 016210 90 PSIWELLKELFVSPDILKLGFKFK-QDLIYLSST---FCSQGCDIGFDR-----------VEPYLDITSIYNHLHHKQLG 154 (393)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~---~gi~g~~~~~~~-----------~~~~fDlt~LA~yLl~~~~~ 154 (393)
.+++..+..++.+.....||||.+ +|+++|... +|+ .+...+.. ....+|+-.+. ....
T Consensus 79 ~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi-~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~---~~~~-- 152 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGV-SAPAYFDLGNKDWNYRNRYSERHLDLMDLL---AFYG-- 152 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCC-CCccccCcccchhhccCcCCCCcccHHHHH---hccC--
Confidence 356666666666533356999984 999998543 333 10100000 01256743332 2211
Q ss_pred CCCCCCcccHHHHHHHHcCCccccc----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 016210 155 RKLPKETKSLANICKELLDISLSKE----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFN 210 (393)
Q Consensus 155 ~~~~~~~~sLa~Lve~~Lg~~L~K~----~q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~ 210 (393)
+ ..+.+|..+++ +||++ .|. .+.. -|.... -..-.+|...||..+..||.
T Consensus 153 ~---~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~t~~l~l 207 (208)
T cd05782 153 A---RARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGK-LDEIAEYCETDVLNTYLLYL 207 (208)
T ss_pred c---cCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHHHHHHHh
Confidence 1 24789999986 67763 221 1111 244333 46668999999999988874
No 87
>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=80.33 E-value=14 Score=32.48 Aligned_cols=95 Identities=11% Similarity=0.080 Sum_probs=57.6
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhh---cccCCCcCCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSST---FCSQGCDIGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANI 167 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~---~gi~g~~~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~L 167 (393)
+++..+.+++.+..-..+.|+...|...+... ++..... ......+|+..++..+.+.. ..++|.++
T Consensus 77 ~vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~---~~~~~~~D~~~~~~~~~~~~-------~~~~L~~l 146 (176)
T cd06133 77 EVLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLP---PFFRQWIDLKKEFAKFYGLK-------KRTGLSKA 146 (176)
T ss_pred HHHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCc---ccccceEEHHHHHHHHhCCC-------CCCCHHHH
Confidence 45667777887741123555668887655432 2210000 12357899777777665431 37899999
Q ss_pred HHHHcCCccc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 168 CKELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 168 ve~~Lg~~L~-K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
++. +|++.. ..| -|-.||..+.+++..|
T Consensus 147 ~~~-~gi~~~~~~H----------------~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 147 LEY-LGLEFEGRHH----------------RGLDDARNIARILKRL 175 (176)
T ss_pred HHH-CCCCCCCCCc----------------CcHHHHHHHHHHHHHh
Confidence 866 477654 222 2778999998887765
No 88
>PRK06722 exonuclease; Provisional
Probab=80.10 E-value=12 Score=36.93 Aligned_cols=99 Identities=18% Similarity=0.132 Sum_probs=57.6
Q ss_pred hhHHHHHHhhCCCCcEEEEEehHhHHHHHHhhcccCCCc-CCcCCCCceeeHHHHHHHHhccccCCCCCCCcccHHHHHH
Q 016210 91 SIWELLKELFVSPDILKLGFKFKQDLIYLSSTFCSQGCD-IGFDRVEPYLDITSIYNHLHHKQLGRKLPKETKSLANICK 169 (393)
Q Consensus 91 ~~~~~L~~lLe~~~i~KVgh~~k~Dl~~L~~~~gi~g~~-~~~~~~~~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve 169 (393)
+++..+.+++.+..+ |+|++..|...|.+.+...|+. |.+. ....+|+..++..+.... ....++|.++++
T Consensus 79 eVl~ef~~fig~~~l--vahna~FD~~FL~~~l~~~gi~~p~~~-~~~~idl~~la~~~~~~l-----~~~~~sL~~l~~ 150 (281)
T PRK06722 79 QIIEKFIQFIGEDSI--FVTWGKEDYRFLSHDCTLHSVECPCME-KERRIDLQKFVFQAYEEL-----FEHTPSLQSAVE 150 (281)
T ss_pred HHHHHHHHHHCCCcE--EEEEeHHHHHHHHHHHHHcCCCCCccc-ccchhHHHHHHHHHhhhh-----ccCCCCHHHHHH
Confidence 456677777776444 7788899999987653322211 0000 012467554443322110 012468999998
Q ss_pred HHcCCccc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 170 ELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 170 ~~Lg~~L~-K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
.+ |++.. ..|+ |-.||..+..|+..|..
T Consensus 151 ~l-gL~~~g~~Hr----------------AL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 151 QL-GLIWEGKQHR----------------ALADAENTANILLKAYS 179 (281)
T ss_pred HC-CCCCCCCCcC----------------cHHHHHHHHHHHHHHhc
Confidence 75 66542 1232 77899999988888863
No 89
>PRK05762 DNA polymerase II; Reviewed
Probab=75.27 E-value=63 Score=36.44 Aligned_cols=110 Identities=17% Similarity=0.257 Sum_probs=61.8
Q ss_pred hhHHHHHHhhCC--CCcEEEEEehH-hHHHHHHhh---cccCCCcCC-------c-----C-------CCC-ceeeHHHH
Q 016210 91 SIWELLKELFVS--PDILKLGFKFK-QDLIYLSST---FCSQGCDIG-------F-----D-------RVE-PYLDITSI 144 (393)
Q Consensus 91 ~~~~~L~~lLe~--~~i~KVgh~~k-~Dl~~L~~~---~gi~g~~~~-------~-----~-------~~~-~~fDlt~L 144 (393)
+++..+..++.. |+++ +|||.. +|+..|.+. +|+ .+..| + . ..+ .++|+=.+
T Consensus 205 ~LL~~F~~~i~~~DPDII-vGyNi~~FDlpyL~~Ra~~lgi-~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~ 282 (786)
T PRK05762 205 ALLEKFNAWFAEHDPDVI-IGWNVVQFDLRLLQERAERYGI-PLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDA 282 (786)
T ss_pred HHHHHHHHHHHhcCCCEE-EEeCCCCCcHHHHHHHHHHhCC-CcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHH
Confidence 455555555544 6754 999965 799987432 444 11000 0 0 001 25674333
Q ss_pred HHHHhccccCCCCCCCcccHHHHHHHHcCCcccc--c----cccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 016210 145 YNHLHHKQLGRKLPKETKSLANICKELLDISLSK--E----LQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNI 211 (393)
Q Consensus 145 A~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K--~----~q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~ 211 (393)
+...... ..+++|..+++++||..... . .+.. -|... ....++|...||..++.|+..
T Consensus 283 ~k~~~~~-------l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~--~~~l~~Y~l~Da~lt~~L~~k 347 (786)
T PRK05762 283 LKSATWV-------FDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAED--KPALARYNLKDCELVTRIFEK 347 (786)
T ss_pred HHHhhcc-------CCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHH
Confidence 3322211 24789999999999864321 0 1111 23211 245689999999999999983
No 90
>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=46.63 E-value=30 Score=32.91 Aligned_cols=50 Identities=14% Similarity=0.215 Sum_probs=36.2
Q ss_pred CcccHHHHHHHHcCCcccc--cccccCC-CC-CC-CCHHHHHHHHHHHHHHHHHH
Q 016210 160 ETKSLANICKELLDISLSK--ELQCSDW-SN-RP-LTEEQKNYAAIDAHCLIEIF 209 (393)
Q Consensus 160 ~~~sLa~Lve~~Lg~~L~K--~~q~sdW-s~-RP-Ls~~Ql~YAA~DA~~Ll~L~ 209 (393)
.+++|.+++.++||...+. ..+.+.| .. .+ -...-++|...||...++|.
T Consensus 176 ~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 176 TNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred ccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 4899999999999987553 2345555 22 22 23556899999999998875
No 91
>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=40.90 E-value=3.2e+02 Score=25.87 Aligned_cols=113 Identities=19% Similarity=0.196 Sum_probs=64.2
Q ss_pred hhhHHHHHHhhCCCCcEEEEEehH-hHHHHHHhh---cccCCCcCCcCCC------------CceeeHHHHHHHHhcccc
Q 016210 90 PSIWELLKELFVSPDILKLGFKFK-QDLIYLSST---FCSQGCDIGFDRV------------EPYLDITSIYNHLHHKQL 153 (393)
Q Consensus 90 ~~~~~~L~~lLe~~~i~KVgh~~k-~Dl~~L~~~---~gi~g~~~~~~~~------------~~~fDlt~LA~yLl~~~~ 153 (393)
.+++..+...++......|+||.+ +|+++|... +|+ -+..-+... ..-+|| +..+.+.+
T Consensus 38 ~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi-~~p~~~~~~~k~WenY~~Ry~~~H~DL---md~l~~~g- 112 (209)
T PF10108_consen 38 KELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGI-SAPRYLDIGNKPWENYRNRYSERHLDL---MDLLSFYG- 112 (209)
T ss_pred HHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCC-CCchhhhcCCCCccccccccCcccccH---HHHHhccC-
Confidence 456777777887766667999977 899987422 444 100000000 113563 22333321
Q ss_pred CCCCCCCcccHHHHHHHHcCCcccccc----ccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 016210 154 GRKLPKETKSLANICKELLDISLSKEL----QCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIFQV 214 (393)
Q Consensus 154 ~~~~~~~~~sLa~Lve~~Lg~~L~K~~----q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~~ 214 (393)
.+...+|..||. .||++- |.. +.. -|....+ ++-..|.-.||..+..||-.+.-
T Consensus 113 ----~~~~~sLd~la~-~lgiPg-K~~idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 113 ----AKARTSLDELAA-LLGIPG-KDDIDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred ----ccccCCHHHHHH-HcCCCC-CCCCCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 124688988875 568764 421 111 1322111 44578999999999999988753
No 92
>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=32.23 E-value=1.7e+02 Score=26.22 Aligned_cols=32 Identities=19% Similarity=0.075 Sum_probs=22.2
Q ss_pred hHHHHHHhhCC----CCcEEEEEehHhHHHHHHhhc
Q 016210 92 IWELLKELFVS----PDILKLGFKFKQDLIYLSSTF 123 (393)
Q Consensus 92 ~~~~L~~lLe~----~~i~KVgh~~k~Dl~~L~~~~ 123 (393)
++..|..++.+ ....-+|||+.+|+..|.+.+
T Consensus 78 vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~ 113 (173)
T cd06135 78 AEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYM 113 (173)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHH
Confidence 44556666653 245668999999999987653
No 93
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.74 E-value=2.4e+02 Score=33.52 Aligned_cols=68 Identities=12% Similarity=0.059 Sum_probs=42.6
Q ss_pred ceeeHHHHHHHHhccccCCCCCCCcccHHHHHHHHcCCcccc--ccccc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 016210 137 PYLDITSIYNHLHHKQLGRKLPKETKSLANICKELLDISLSK--ELQCS-DWSNRPLTEEQKNYAAIDAHCLIEIFNIF 212 (393)
Q Consensus 137 ~~fDlt~LA~yLl~~~~~~~~~~~~~sLa~Lve~~Lg~~L~K--~~q~s-dWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L 212 (393)
.++|+-.++...+.. .+++|.+++.++||..-.. ..... -|....--..-+.|...||.++++|...+
T Consensus 652 l~~D~~~~~k~~~~~--------~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l 722 (1172)
T TIGR00592 652 MICDVEISAKELIRC--------KSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCEL 722 (1172)
T ss_pred EEEEHHHHHHHHhCc--------CCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468866665555443 3799999999999853211 11111 13321112445899999999998888754
No 94
>PTZ00315 2'-phosphotransferase; Provisional
Probab=26.49 E-value=6.5e+02 Score=27.64 Aligned_cols=103 Identities=12% Similarity=0.153 Sum_probs=57.5
Q ss_pred hhHHHHHHhhCCCC--------cEEEEEehHhHHH-HHHhhcc---cCCCcCCcCCCCceeeHHHHHHHHhcccc-----
Q 016210 91 SIWELLKELFVSPD--------ILKLGFKFKQDLI-YLSSTFC---SQGCDIGFDRVEPYLDITSIYNHLHHKQL----- 153 (393)
Q Consensus 91 ~~~~~L~~lLe~~~--------i~KVgh~~k~Dl~-~L~~~~g---i~g~~~~~~~~~~~fDlt~LA~yLl~~~~----- 153 (393)
+++..+..+|.+.. -..|+|+...|+. .|...+. ..|+.. ....++|++...+.++.+..
T Consensus 132 eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~---~f~~widLk~~lar~l~p~~~~~~~ 208 (582)
T PTZ00315 132 VVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPL---SFQRWCNLKKYMSQLGFGNGSGCGG 208 (582)
T ss_pred HHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCc---ccceEEEhHHHHHHHhCcccccccc
Confidence 46777777877643 1358999999985 5643221 112111 12346676434333333210
Q ss_pred CCCCCCCcccHHHHHHHHcCCccc-ccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 016210 154 GRKLPKETKSLANICKELLDISLS-KELQCSDWSNRPLTEEQKNYAAIDAHCLIEIFNIFQ 213 (393)
Q Consensus 154 ~~~~~~~~~sLa~Lve~~Lg~~L~-K~~q~sdWs~RPLs~~Ql~YAA~DA~~Ll~L~~~L~ 213 (393)
+..-....++|.++++. +|++.. +.++ |-.||..+.+|+..|.
T Consensus 209 ~~~~~~~~~~L~~al~~-lgL~~eGr~Hr----------------AlDDA~ntA~L~~~Ll 252 (582)
T PTZ00315 209 GATPPLGPSDMPDMLQM-LGLPLQGRHHS----------------GIDDCRNIAAVLCELL 252 (582)
T ss_pred ccccccCCcCHHHHHHH-CCCCCCCCCcC----------------cHHHHHHHHHHHHHHH
Confidence 00111236899999986 576653 2232 6678888877777764
No 95
>PRK05359 oligoribonuclease; Provisional
Probab=24.41 E-value=3.3e+02 Score=24.70 Aligned_cols=33 Identities=15% Similarity=0.037 Sum_probs=20.8
Q ss_pred hhHHHHHHhhCC----CCcEEEEEehHhHHHHHHhhc
Q 016210 91 SIWELLKELFVS----PDILKLGFKFKQDLIYLSSTF 123 (393)
Q Consensus 91 ~~~~~L~~lLe~----~~i~KVgh~~k~Dl~~L~~~~ 123 (393)
+++..|.+++.. ....-+||++.+|...|.+.+
T Consensus 81 e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~ 117 (181)
T PRK05359 81 EAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYM 117 (181)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHH
Confidence 344555555542 122348999999999887754
Done!