Query 022027
Match_columns 304
No_of_seqs 204 out of 1303
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 07:27:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022027.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022027hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06146 mut-7_like_exo DEDDy 3 100.0 2.2E-30 4.8E-35 227.2 19.2 170 97-280 1-193 (193)
2 cd06129 RNaseD_like DEDDy 3'-5 100.0 4.3E-30 9.4E-35 219.0 19.2 158 106-280 2-161 (161)
3 cd06141 WRN_exo DEDDy 3'-5' ex 100.0 1.2E-29 2.7E-34 217.3 19.5 166 101-279 2-169 (170)
4 PRK10829 ribonuclease D; Provi 99.9 4.8E-25 1E-29 210.5 20.2 166 97-280 3-168 (373)
5 PF01612 DNA_pol_A_exo1: 3'-5' 99.9 4.4E-25 9.5E-30 188.3 17.4 169 97-280 1-173 (176)
6 cd06148 Egl_like_exo DEDDy 3'- 99.9 2.5E-25 5.3E-30 195.8 13.5 150 126-280 10-175 (197)
7 TIGR01388 rnd ribonuclease D. 99.9 4.2E-23 9.1E-28 197.6 19.9 164 99-280 1-164 (367)
8 COG0349 Rnd Ribonuclease D [Tr 99.9 1.9E-22 4.2E-27 188.9 16.2 164 101-282 2-166 (361)
9 smart00474 35EXOc 3'-5' exonuc 99.8 4.7E-18 1E-22 143.8 19.6 166 98-280 2-169 (172)
10 cd06142 RNaseD_exo DEDDy 3'-5' 99.8 3.8E-18 8.2E-23 146.3 19.0 147 126-280 12-158 (178)
11 cd09018 DEDDy_polA_RNaseD_like 99.7 8.2E-17 1.8E-21 134.0 16.2 148 128-280 1-150 (150)
12 cd06147 Rrp6p_like_exo DEDDy 3 99.7 5E-16 1.1E-20 135.8 20.3 168 94-280 2-170 (192)
13 KOG4373 Predicted 3'-5' exonuc 99.7 2.9E-17 6.3E-22 150.9 8.4 152 124-275 125-281 (319)
14 cd00007 35EXOc 3'-5' exonuclea 99.7 1.9E-15 4.2E-20 125.4 15.5 145 128-280 2-153 (155)
15 KOG2207 Predicted 3'-5' exonuc 99.6 8.7E-15 1.9E-19 143.4 9.5 177 94-284 389-587 (617)
16 PRK05755 DNA polymerase I; Pro 99.5 5.5E-13 1.2E-17 140.9 18.4 169 96-281 295-468 (880)
17 cd06140 DNA_polA_I_Bacillus_li 99.5 1.5E-12 3.3E-17 111.9 14.8 146 127-280 4-154 (178)
18 KOG2206 Exosome 3'-5' exoribon 99.4 4.6E-13 1E-17 130.8 9.2 164 97-279 193-357 (687)
19 cd06139 DNA_polA_I_Ecoli_like_ 99.4 5.4E-11 1.2E-15 103.0 17.6 150 126-281 5-169 (193)
20 COG0749 PolA DNA polymerase I 99.2 2.5E-10 5.4E-15 113.9 14.3 152 127-285 23-184 (593)
21 PRK14975 bifunctional 3'-5' ex 99.1 5.4E-10 1.2E-14 112.7 11.4 138 97-280 3-142 (553)
22 TIGR00593 pola DNA polymerase 99.1 2.7E-09 5.8E-14 112.5 16.5 132 146-280 335-475 (887)
23 cd06128 DNA_polA_exo DEDDy 3'- 99.0 1.1E-08 2.5E-13 85.5 15.2 130 146-279 18-150 (151)
24 cd06143 PAN2_exo DEDDh 3'-5' e 96.5 0.0051 1.1E-07 53.1 5.7 80 174-276 95-174 (174)
25 cd06149 ISG20 DEDDh 3'-5' exon 96.4 0.04 8.7E-07 46.6 10.4 86 172-276 69-157 (157)
26 cd06144 REX4_like DEDDh 3'-5' 96.3 0.016 3.5E-07 48.6 7.5 83 172-276 69-152 (152)
27 cd06145 REX1_like DEDDh 3'-5' 96.1 0.021 4.6E-07 47.9 7.1 82 173-275 68-149 (150)
28 cd06137 DEDDh_RNase DEDDh 3'-5 96.1 0.023 4.9E-07 48.2 7.4 82 173-275 76-160 (161)
29 cd05780 DNA_polB_Kod1_like_exo 96.1 0.1 2.3E-06 45.6 11.7 149 126-278 3-195 (195)
30 cd06125 DnaQ_like_exo DnaQ-lik 96.0 0.034 7.3E-07 43.1 7.4 74 129-214 1-83 (96)
31 PRK06063 DNA polymerase III su 96.0 0.17 3.8E-06 47.7 13.5 86 172-279 86-176 (313)
32 KOG2249 3'-5' exonuclease [Rep 96.0 0.057 1.2E-06 49.3 9.6 86 173-280 177-264 (280)
33 cd05160 DEDDy_DNA_polB_exo DED 96.0 0.18 4E-06 43.8 12.7 101 172-275 68-198 (199)
34 PRK06310 DNA polymerase III su 95.9 0.18 4E-06 45.9 13.0 85 173-279 80-171 (250)
35 PRK08517 DNA polymerase III su 95.8 0.29 6.3E-06 44.9 13.6 86 172-280 139-229 (257)
36 PRK05711 DNA polymerase III su 95.6 0.33 7.2E-06 44.1 13.1 88 173-281 79-175 (240)
37 PRK07740 hypothetical protein; 95.5 0.58 1.3E-05 42.5 14.3 86 174-281 135-225 (244)
38 PRK07883 hypothetical protein; 95.3 0.47 1E-05 48.3 14.6 87 173-280 88-180 (557)
39 PRK09146 DNA polymerase III su 95.3 0.62 1.3E-05 42.3 13.8 85 174-279 123-224 (239)
40 PRK07246 bifunctional ATP-depe 95.2 0.34 7.4E-06 51.6 13.7 86 172-279 78-167 (820)
41 PRK06807 DNA polymerase III su 95.1 0.47 1E-05 44.8 12.8 87 173-282 81-172 (313)
42 PRK09145 DNA polymerase III su 95.0 0.89 1.9E-05 39.8 13.6 87 173-280 104-199 (202)
43 PRK06309 DNA polymerase III su 94.9 1.5 3.2E-05 39.4 15.0 87 173-280 72-164 (232)
44 TIGR01407 dinG_rel DnaQ family 94.1 0.91 2E-05 48.6 13.6 65 172-240 72-141 (850)
45 KOG3657 Mitochondrial DNA poly 93.6 0.28 6.2E-06 51.2 8.3 99 182-280 241-381 (1075)
46 cd06127 DEDDh DEDDh 3'-5' exon 93.2 0.79 1.7E-05 37.2 9.1 83 172-275 71-158 (159)
47 PRK07942 DNA polymerase III su 93.1 0.54 1.2E-05 42.4 8.5 80 182-280 93-178 (232)
48 PRK08074 bifunctional ATP-depe 92.7 2.8 6E-05 45.5 14.5 84 173-278 77-165 (928)
49 cd05784 DNA_polB_II_exo DEDDy 92.2 1.3 2.8E-05 38.8 9.5 102 170-276 54-193 (193)
50 cd06130 DNA_pol_III_epsilon_li 92.2 1.6 3.4E-05 36.0 9.7 81 172-275 69-154 (156)
51 TIGR01405 polC_Gram_pos DNA po 92.1 3.4 7.4E-05 45.9 14.5 87 172-280 262-353 (1213)
52 cd06134 RNaseT DEDDh 3'-5' exo 91.9 1.3 2.9E-05 38.4 9.2 77 182-279 102-186 (189)
53 KOG2248 3'-5' exonuclease [Rep 91.9 0.16 3.6E-06 49.1 3.7 89 173-281 286-374 (380)
54 PRK06195 DNA polymerase III su 91.5 1.4 3E-05 41.4 9.5 85 173-280 73-162 (309)
55 cd06131 DNA_pol_III_epsilon_Ec 91.4 1.7 3.7E-05 36.4 9.2 86 172-278 73-166 (167)
56 TIGR01406 dnaQ_proteo DNA poly 91.0 1.6 3.5E-05 39.1 9.0 89 173-282 75-172 (225)
57 cd05781 DNA_polB_B3_exo DEDDy 90.8 7.6 0.00016 33.7 12.8 148 126-278 3-188 (188)
58 cd05783 DNA_polB_B1_exo DEDDy 90.8 7.4 0.00016 34.3 12.9 100 170-276 76-202 (204)
59 smart00479 EXOIII exonuclease 90.1 3.7 8E-05 34.0 10.0 87 172-280 72-165 (169)
60 PF09281 Taq-exonuc: Taq polym 89.4 2.1 4.5E-05 35.1 7.4 65 192-279 71-135 (138)
61 cd06136 TREX1_2 DEDDh 3'-5' ex 89.3 1.9 4E-05 37.0 7.6 81 172-276 86-175 (177)
62 TIGR00573 dnaq exonuclease, DN 88.8 3.3 7.1E-05 36.7 9.1 93 173-284 80-179 (217)
63 cd05779 DNA_polB_epsilon_exo D 88.7 5.8 0.00013 35.0 10.5 99 173-275 79-203 (204)
64 PRK09182 DNA polymerase III su 88.6 16 0.00035 34.2 13.9 86 171-279 111-198 (294)
65 PRK05601 DNA polymerase III su 88.5 4.9 0.00011 38.8 10.5 97 171-278 116-245 (377)
66 cd05785 DNA_polB_like2_exo Unc 88.4 5.4 0.00012 35.2 10.2 146 126-275 9-206 (207)
67 TIGR01298 RNaseT ribonuclease 87.5 3.7 7.9E-05 36.0 8.5 77 182-279 105-189 (200)
68 PRK05168 ribonuclease T; Provi 87.4 5.1 0.00011 35.4 9.4 78 182-280 114-199 (211)
69 PRK07247 DNA polymerase III su 87.1 6.2 0.00013 34.6 9.7 91 172-285 76-172 (195)
70 PRK11779 sbcB exonuclease I; P 85.6 15 0.00033 36.8 12.5 88 173-280 84-196 (476)
71 KOG1275 PAB-dependent poly(A) 85.4 0.22 4.9E-06 52.4 -0.4 85 177-285 1009-1095(1118)
72 PRK07983 exodeoxyribonuclease 82.7 9.6 0.00021 34.0 8.9 86 173-280 67-152 (219)
73 PRK07748 sporulation inhibitor 82.5 13 0.00028 32.6 9.6 92 172-283 84-181 (207)
74 cd05782 DNA_polB_like1_exo Unc 80.0 20 0.00043 31.6 9.9 126 146-276 51-207 (208)
75 PF13482 RNase_H_2: RNase_H su 77.2 7.6 0.00017 32.2 6.2 142 129-278 1-163 (164)
76 cd06133 ERI-1_3'hExo_like DEDD 74.6 29 0.00063 28.8 9.1 87 172-278 80-175 (176)
77 COG2176 PolC DNA polymerase II 74.1 11 0.00023 41.7 7.4 90 170-281 491-585 (1444)
78 PRK06722 exonuclease; Provisio 73.2 80 0.0017 29.4 13.0 88 173-280 83-179 (281)
79 PF10108 DNA_pol_B_exo2: Predi 72.1 38 0.00083 30.1 9.4 110 170-285 40-176 (209)
80 KOG2405 Predicted 3'-5' exonuc 69.2 0.15 3.1E-06 48.9 -6.8 69 146-216 74-145 (458)
81 cd06138 ExoI_N N-terminal DEDD 68.4 16 0.00034 31.3 6.2 84 173-275 75-182 (183)
82 cd05776 DNA_polB_alpha_exo ina 66.1 9.2 0.0002 34.4 4.4 74 209-285 158-233 (234)
83 KOG2405 Predicted 3'-5' exonuc 63.0 8.9 0.00019 37.1 3.7 130 149-283 214-362 (458)
84 cd05777 DNA_polB_delta_exo DED 62.9 11 0.00024 33.6 4.3 71 209-282 154-227 (230)
85 PRK00448 polC DNA polymerase I 62.2 42 0.00091 38.3 9.4 81 182-282 499-584 (1437)
86 cd05778 DNA_polB_zeta_exo inac 61.1 12 0.00025 33.7 4.1 71 203-275 155-230 (231)
87 COG0847 DnaQ DNA polymerase II 61.1 91 0.002 27.6 9.9 89 173-280 87-180 (243)
88 TIGR00592 pol2 DNA polymerase 50.9 38 0.00082 37.9 6.7 103 180-286 599-730 (1172)
89 COG3359 Predicted exonuclease 43.3 2.7E+02 0.0058 25.7 10.3 109 127-239 99-218 (278)
90 PRK05762 DNA polymerase II; Re 40.8 2.1E+02 0.0045 30.6 10.1 111 170-285 206-355 (786)
91 cd06135 Orn DEDDh 3'-5' exonuc 23.4 2.6E+02 0.0057 23.5 6.2 28 173-200 81-112 (173)
92 PF04857 CAF1: CAF1 family rib 23.4 1.7E+02 0.0036 26.6 5.2 54 180-236 147-215 (262)
93 COG2925 SbcB Exonuclease I [DN 22.5 2.9E+02 0.0062 27.2 6.6 101 170-280 84-199 (475)
No 1
>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=2.2e-30 Score=227.21 Aligned_cols=170 Identities=30% Similarity=0.486 Sum_probs=144.9
Q ss_pred EEEecCHHHHHHHHHH--HHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCC------
Q 022027 97 ILYSRTSTEVEMAAIE--LRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHS------ 168 (304)
Q Consensus 97 i~~i~t~~~l~~~~~~--l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~------ 168 (304)
|.+|++++++++++.+ +.. ..+||||+||.+.+..|. .+++++||||+. +.||+||+...
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~----------~~vig~D~Ew~~~~~~~~-~~~v~LiQiat~-~~~~lid~~~~~~~~~~ 68 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEA----------GRVVGIDSEWKPSFLGDS-DPRVAILQLATE-DEVFLLDLLALENLESE 68 (193)
T ss_pred CeEecCHHHHHHHHHHHhhcc----------CCEEEEECccCCCccCCC-CCCceEEEEecC-CCEEEEEchhccccchH
Confidence 5688999999999998 544 799999999998765442 368999999987 68999998643
Q ss_pred CCcHHHHHhHcCCCceEEEecchHHHHHHHHhcCC------ccCCcchHHHHHHHHhCC---------CCCCCCHHHHHH
Q 022027 169 GIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNV------SVKASEDLSYLAKHKIGG---------DSQKWGLASLTE 233 (304)
Q Consensus 169 ~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi------~l~~~~Dl~~LA~ylL~~---------~~~~~sL~~La~ 233 (304)
.+++.|+++|+|++|+||||++++|+.+|++.||+ .+.|++|++.++..+... ....+||+.|++
T Consensus 69 ~~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~ 148 (193)
T cd06146 69 DWDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQ 148 (193)
T ss_pred HHHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHH
Confidence 25678999999999999999999999999989987 367899998777654321 124789999999
Q ss_pred HHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 234 MLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 234 ~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
++||..++|. .++|||..+||+++|+.|||.||++++.||+.|.+
T Consensus 149 ~~lg~~l~K~--~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~~ 193 (193)
T cd06146 149 EVLGKPLDKS--EQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193 (193)
T ss_pred HHhCCCcCcc--cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 9999999885 58999999999999999999999999999999863
No 2
>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=4.3e-30 Score=218.99 Aligned_cols=158 Identities=32% Similarity=0.522 Sum_probs=137.8
Q ss_pred HHHHHHHHH-HHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCC-CcHHHHHhHcCCCc
Q 022027 106 VEMAAIELR-RILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSG-IPPSLQLLLEDSTI 183 (304)
Q Consensus 106 l~~~~~~l~-~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~-~~~~L~~lL~d~~i 183 (304)
++++++++. . ..+||||+||.+.+.. .+++++||||+.++.||+||+.... .++.|+++|+++.|
T Consensus 2 l~~~~~~l~~~----------~~~ig~D~E~~~~~~~---~~~~~liQl~~~~~~~~l~d~~~~~~~~~~L~~lL~d~~i 68 (161)
T cd06129 2 LSSLCEDLSMD----------GDVIAFDMEWPPGRRY---YGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSI 68 (161)
T ss_pred HHHHHHHHhcC----------CCEEEEECCccCCCCC---CCceEEEEEEECCCCEEEEecccCccCHHHHHHHhCCCCE
Confidence 455666665 4 8999999999986543 3689999999986789999987544 78899999999999
Q ss_pred eEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCHHHHHH
Q 022027 184 LKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSKDQLLY 263 (304)
Q Consensus 184 ~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~Y 263 (304)
+||||+++.|+..|.+.+|+.+.+++|+ ++++|+++++ .++||+.|+++|+|..++| ..++|||..+|||++|+.|
T Consensus 69 ~Kvg~~~k~D~~~L~~~~gi~~~~~~D~-~~aa~ll~~~-~~~~L~~l~~~~lg~~l~K--~~~~s~W~~rpLt~~qi~Y 144 (161)
T cd06129 69 VKALHGIEGDLWKLLRDFGEKLQRLFDT-TIAANLKGLP-ERWSLASLVEHFLGKTLDK--SISCADWSYRPLTEDQKLY 144 (161)
T ss_pred EEEEeccHHHHHHHHHHcCCCcccHhHH-HHHHHHhCCC-CCchHHHHHHHHhCCCCCc--cceeccCCCCCCCHHHHHH
Confidence 9999999999999977799999999999 6777889865 4679999999999999976 5689999999999999999
Q ss_pred HHHHHHHHHHHHHHHhC
Q 022027 264 AATDAFASWHLYQVLKS 280 (304)
Q Consensus 264 AA~DA~a~~~L~~~L~~ 280 (304)
||.||++++.||+.|.+
T Consensus 145 Aa~Da~~l~~l~~~l~~ 161 (161)
T cd06129 145 AAADVYALLIIYTKLRN 161 (161)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999999999863
No 3
>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=99.97 E-value=1.2e-29 Score=217.32 Aligned_cols=166 Identities=45% Similarity=0.756 Sum_probs=145.8
Q ss_pred cCHHHHHHHHHHHH-HHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCC-CCCcHHHHHhH
Q 022027 101 RTSTEVEMAAIELR-RILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIH-SGIPPSLQLLL 178 (304)
Q Consensus 101 ~t~~~l~~~~~~l~-~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~-~~~~~~L~~lL 178 (304)
.++.+++.+++.+. . ...||||+||.+.+..+. .+++++||||+. +.||+|++.. ..+++.|+++|
T Consensus 2 ~~~~~~~~~~~~~~~~----------~~~ig~D~E~~~~~~~~~-~~~~~liQl~~~-~~~~l~~~~~~~~~~~~l~~ll 69 (170)
T cd06141 2 DSAQDAEEAVKELLGK----------EKVVGFDTEWRPSFRKGK-RNKVALLQLATE-SRCLLFQLAHMDKLPPSLKQLL 69 (170)
T ss_pred CCHHHHHHHHHHHhcC----------CCEEEEeCccCCccCCCC-CCCceEEEEecC-CcEEEEEhhhhhcccHHHHHHh
Confidence 46677888888876 4 799999999998654322 368999999987 7899999976 57888999999
Q ss_pred cCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCH
Q 022027 179 EDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSK 258 (304)
Q Consensus 179 ~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~ 258 (304)
+++.+.||||+++.|+..|.+.+|+.+.+++|+ ++++|++++.....||+.|++.++|..+.|.+.+++|||..+||++
T Consensus 70 ~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl-~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt~ 148 (170)
T cd06141 70 EDPSILKVGVGIKGDARKLARDFGIEVRGVVDL-SHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSK 148 (170)
T ss_pred cCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeH-HHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCCH
Confidence 999999999999999999977999999999999 6777889865345799999999999999987788999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 022027 259 DQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 259 ~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
+|++|||.||++++.||..|.
T Consensus 149 ~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 149 EQILYAATDAYASLELYRKLL 169 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999886
No 4
>PRK10829 ribonuclease D; Provisional
Probab=99.93 E-value=4.8e-25 Score=210.51 Aligned_cols=166 Identities=18% Similarity=0.150 Sum_probs=145.3
Q ss_pred EEEecCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCCCcHHHHH
Q 022027 97 ILYSRTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSGIPPSLQL 176 (304)
Q Consensus 97 i~~i~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~~~~~L~~ 176 (304)
+.+|++.+++..+++.+.. ...+|+|+|+...+.. ..++++|||+++ +.+|+||.........|++
T Consensus 3 ~~~I~t~~~L~~~~~~l~~----------~~~lalDtEf~~~~ty---~~~l~LiQl~~~-~~~~LiD~l~~~d~~~L~~ 68 (373)
T PRK10829 3 YQMITTDDALASVCEAARA----------FPAIALDTEFVRTRTY---YPQLGLIQLYDG-EQLSLIDPLGITDWSPFKA 68 (373)
T ss_pred cEEeCCHHHHHHHHHHHhc----------CCeEEEecccccCccC---CCceeEEEEecC-CceEEEecCCccchHHHHH
Confidence 5689999999999998765 8999999998764321 257999999987 5789999765445678999
Q ss_pred hHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCC
Q 022027 177 LLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVL 256 (304)
Q Consensus 177 lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pL 256 (304)
+|+|+.|+||+|++++|+..|.+.+|+.+.++||| ++|+.++|.+ ..+||+.|+++++|+.++|.. +.+||..|||
T Consensus 69 ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDT-qiaa~~lg~~-~~~gl~~Lv~~~lgv~ldK~~--~~sDW~~RPL 144 (373)
T PRK10829 69 LLRDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDT-QILAAFCGRP-LSCGFASMVEEYTGVTLDKSE--SRTDWLARPL 144 (373)
T ss_pred HHcCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeH-HHHHHHcCCC-ccccHHHHHHHHhCCccCccc--ccCCCCCCCC
Confidence 99999999999999999999988999999999999 7777788753 478999999999999998864 7899999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 257 SKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 257 t~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
|++|+.|||.|+++++.||..|..
T Consensus 145 s~~ql~YAa~Dv~~L~~l~~~L~~ 168 (373)
T PRK10829 145 SERQCEYAAADVFYLLPIAAKLMA 168 (373)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999875
No 5
>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=99.93 E-value=4.4e-25 Score=188.31 Aligned_cols=169 Identities=30% Similarity=0.442 Sum_probs=141.1
Q ss_pred EEEecCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCC---CcHH
Q 022027 97 ILYSRTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSG---IPPS 173 (304)
Q Consensus 97 i~~i~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~---~~~~ 173 (304)
+.+|++.+++++++..+.. ...+|||+||.+...... ..++++||+|+. ..+|+++..... ++..
T Consensus 1 y~~v~~~~~l~~~~~~l~~----------~~~~a~D~E~~~~~~~~~-~~~~~~iq~~~~-~~~~i~~~~~~~~~~~~~~ 68 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKN----------AKVLAFDTETTGLDPYSY-NPKIALIQLATG-EGCYIIDPIDLGDNWILDA 68 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTT----------TSEEEEEEEEETSTSTTS-SEEEEEEEEEES-CEEEEECGTTSTTTTHHHH
T ss_pred CEecCCHHHHHHHHHHHcC----------CCeEEEEEEECCCCcccc-CCeEEEEEEecC-CCceeeeeccccccchHHH
Confidence 3678999999999998876 679999999998644222 367999999998 677887665433 3689
Q ss_pred HHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCC-
Q 022027 174 LQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWE- 252 (304)
Q Consensus 174 L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~- 252 (304)
|+++|+++.|+||||+++.|+.+|.+.+|+.+.+++|+ +++.|++++. ..+||++|+..++| ...+.++.++++|.
T Consensus 69 l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~-~~~~L~~L~~~~l~-~~~~~~~~~~~~~~~ 145 (176)
T PF01612_consen 69 LKELLEDPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPT-RSYSLKDLAEEYLG-NIDLDKKEQMSDWRK 145 (176)
T ss_dssp HHHHHTTTTSEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTS-TTSSHHHHHHHHHS-EEE-GHCCTTSSTTT
T ss_pred HHHHHhCCCccEEEEEEechHHHHHHHhccccCCccch-hhhhhccccc-ccccHHHHHHHHhh-hccCcHHHhhccCCc
Confidence 99999999999999999999999987899999999999 9999999865 34999999999999 44444456899999
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 253 ADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 253 ~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.++|+++|++|||.||+++++||+.|.+
T Consensus 146 ~~~l~~~~~~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 146 ARPLSEEQIEYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp SSS-HHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999875
No 6
>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=99.93 E-value=2.5e-25 Score=195.82 Aligned_cols=150 Identities=24% Similarity=0.329 Sum_probs=129.1
Q ss_pred CceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCC---CcHHHHHhHcCCCceEEEecchHHHHHHHHhcC
Q 022027 126 QVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSG---IPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYN 202 (304)
Q Consensus 126 ~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~---~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~g 202 (304)
..+||||+||....+ .+++++||+|+..+.+|+||+...+ +...|+++|+++.|.||||+++.|+..|++.+|
T Consensus 10 ~~~i~~D~E~~~~~~----~~~~~LiQia~~~~~v~l~D~~~~~~~~~~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~g 85 (197)
T cd06148 10 QKVIGLDCEGVNLGR----KGKLCLVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHDCRRDSDALYHQYG 85 (197)
T ss_pred CCEEEEEcccccCCC----CCCEEEEEEeeCCCcEEEEEhhhccchhHHHHHHHHhcCCCccEEEEechhHHHHHHHhcC
Confidence 789999999975432 3689999999985689999997543 568899999999999999999999999988899
Q ss_pred CccCCcchHHHHHHHHhCCCCC-------CCCHHHHHHHHcCcccCCCC------ccccCCCCCCCCCHHHHHHHHHHHH
Q 022027 203 VSVKASEDLSYLAKHKIGGDSQ-------KWGLASLTEMLVCKELKKPN------RIRLGNWEADVLSKDQLLYAATDAF 269 (304)
Q Consensus 203 i~l~~~~Dl~~LA~ylL~~~~~-------~~sL~~La~~~Lg~~l~K~~------~i~~s~W~~~pLt~~Qi~YAA~DA~ 269 (304)
+.+.+++|+ ++|+|++++... ..||+.++++||+..+.|.. ..++++|..||||++|+.|||.||+
T Consensus 86 i~~~~~fDt-~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~ 164 (197)
T cd06148 86 IKLNNVFDT-QVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVL 164 (197)
T ss_pred ccccceeeH-HHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHH
Confidence 999999999 788898875321 36999999999999886421 2467999999999999999999999
Q ss_pred HHHHHHHHHhC
Q 022027 270 ASWHLYQVLKS 280 (304)
Q Consensus 270 a~~~L~~~L~~ 280 (304)
+++.||..|..
T Consensus 165 ~Ll~l~~~l~~ 175 (197)
T cd06148 165 CLLPLYYAMLD 175 (197)
T ss_pred hHHHHHHHHHH
Confidence 99999999976
No 7
>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=99.91 E-value=4.2e-23 Score=197.57 Aligned_cols=164 Identities=21% Similarity=0.199 Sum_probs=141.1
Q ss_pred EecCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCCCcHHHHHhH
Q 022027 99 YSRTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSGIPPSLQLLL 178 (304)
Q Consensus 99 ~i~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~~~~~L~~lL 178 (304)
+|++.++++.+++.+.. ..+||||+||..... ...++++|||+++ +.+|+||+......+.|+++|
T Consensus 1 ~I~t~~~l~~~~~~l~~----------~~~ia~DtE~~~~~~---y~~~l~LiQia~~-~~~~liD~~~~~~~~~L~~lL 66 (367)
T TIGR01388 1 WITTDDELATVCEAVRT----------FPFVALDTEFVRERT---FWPQLGLIQVADG-EQLALIDPLVIIDWSPLKELL 66 (367)
T ss_pred CcCCHHHHHHHHHHHhc----------CCEEEEeccccCCCC---CCCcceEEEEeeC-CeEEEEeCCCcccHHHHHHHH
Confidence 46788999999999876 789999999976422 1357999999987 689999986544577899999
Q ss_pred cCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCH
Q 022027 179 EDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSK 258 (304)
Q Consensus 179 ~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~ 258 (304)
+|+.++||+|++|.|+..|.+.+++...++||+ ++|+|+++++ ...||+.|++.|||..++|. .+.++|..+||+.
T Consensus 67 ~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDt-qlAa~lL~~~-~~~~l~~Lv~~~Lg~~l~K~--~~~sdW~~rPL~~ 142 (367)
T TIGR01388 67 RDESVVKVLHAASEDLEVFLNLFGELPQPLFDT-QIAAAFCGFG-MSMGYAKLVQEVLGVELDKS--ESRTDWLARPLTD 142 (367)
T ss_pred CCCCceEEEeecHHHHHHHHHHhCCCCCCcccH-HHHHHHhCCC-CCccHHHHHHHHcCCCCCcc--cccccCCCCCCCH
Confidence 999999999999999999977667766777999 8888999975 45799999999999999875 4689999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhC
Q 022027 259 DQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 259 ~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
+|+.|||.||++++.||..|..
T Consensus 143 ~q~~YAa~Dv~~L~~L~~~L~~ 164 (367)
T TIGR01388 143 AQLEYAAADVTYLLPLYAKLME 164 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999864
No 8
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=1.9e-22 Score=188.85 Aligned_cols=164 Identities=24% Similarity=0.237 Sum_probs=139.6
Q ss_pred cCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCC-CCCcHHHHHhHc
Q 022027 101 RTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIH-SGIPPSLQLLLE 179 (304)
Q Consensus 101 ~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~-~~~~~~L~~lL~ 179 (304)
++.+.++.++..+.+ ...|++|+|+...+.. ..++++||++.+++ +++|+... ..-.+.|..+|.
T Consensus 2 ~~~~~l~~~~~~~~~----------~~~iAiDTEf~r~~t~---~p~LcLIQi~~~e~-~~lIdpl~~~~d~~~l~~Ll~ 67 (361)
T COG0349 2 TTGDLLAAACALLRG----------SKAIAIDTEFMRLRTY---YPRLCLIQISDGEG-ASLIDPLAGILDLPPLVALLA 67 (361)
T ss_pred CchhHHHHHHHHhcC----------CCceEEeccccccccc---CCceEEEEEecCCC-ceEecccccccccchHHHHhc
Confidence 345566677766654 7899999999764322 36899999999866 89998865 345678999999
Q ss_pred CCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCHH
Q 022027 180 DSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSKD 259 (304)
Q Consensus 180 d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~ 259 (304)
|++|+||.|....|+..|.+.||+.+.++||+ .+|+.++|-+ .++||+.||++++|++++|+. +.|||..+|||++
T Consensus 68 d~~v~KIfHaa~~DL~~l~~~~g~~p~plfdT-qiAa~l~g~~-~~~gl~~Lv~~ll~v~ldK~~--q~SDW~~RPLs~~ 143 (361)
T COG0349 68 DPNVVKIFHAARFDLEVLLNLFGLLPTPLFDT-QIAAKLAGFG-TSHGLADLVEELLGVELDKSE--QRSDWLARPLSEA 143 (361)
T ss_pred CCceeeeeccccccHHHHHHhcCCCCCchhHH-HHHHHHhCCc-ccccHHHHHHHHhCCcccccc--cccccccCCCCHH
Confidence 99999999999999999999999999999999 6666667755 499999999999999999864 8999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCC
Q 022027 260 QLLYAATDAFASWHLYQVLKSLP 282 (304)
Q Consensus 260 Qi~YAA~DA~a~~~L~~~L~~l~ 282 (304)
|++|||.|+.+++.||..|...-
T Consensus 144 Ql~YAa~DV~yL~~l~~~L~~~L 166 (361)
T COG0349 144 QLEYAAADVEYLLPLYDKLTEEL 166 (361)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999997643
No 9
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.81 E-value=4.7e-18 Score=143.76 Aligned_cols=166 Identities=29% Similarity=0.297 Sum_probs=127.9
Q ss_pred EEecCHHHHHHHHHHHH-HHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCC-CCCcHHHH
Q 022027 98 LYSRTSTEVEMAAIELR-RILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIH-SGIPPSLQ 175 (304)
Q Consensus 98 ~~i~t~~~l~~~~~~l~-~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~-~~~~~~L~ 175 (304)
.++++.+++..+++.+. . ...+++|+||.+... . ..+++++|+|...+.+|+++... ...+..|+
T Consensus 2 ~~i~~~~~~~~~~~~~~~~----------~~~l~~~~e~~~~~~-~--~~~~~~l~l~~~~~~~~i~~~~~~~~~~~~l~ 68 (172)
T smart00474 2 RVVTDSETLEELLEKLRAA----------GGEVALDTETTGLNS-Y--SGKLVLIQISVTGEGAFIIDPLALGDDLEILK 68 (172)
T ss_pred EEecCHHHHHHHHHHHHhc----------CCeEEEeccccCCcc-C--CCCEEEEEEeEcCCceEEEEeccchhhHHHHH
Confidence 46677777777665553 2 468999999865421 1 25789999997533566544321 22355699
Q ss_pred HhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCC
Q 022027 176 LLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADV 255 (304)
Q Consensus 176 ~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~p 255 (304)
++|+++.+.|||||+|.|.+.|. .+|+.+.+++|+ ++++|++++....++|+.++..|++..+.+ ....++|..++
T Consensus 69 ~~l~~~~~~kv~~d~k~~~~~L~-~~gi~~~~~~D~-~laayll~p~~~~~~l~~l~~~~l~~~~~~--~~~~~~~~~~~ 144 (172)
T smart00474 69 DLLEDETITKVGHNAKFDLHVLA-RFGIELENIFDT-MLAAYLLLGGPSKHGLATLLKEYLGVELDK--EEQKSDWGARP 144 (172)
T ss_pred HHhcCCCceEEEechHHHHHHHH-HCCCcccchhHH-HHHHHHHcCCCCcCCHHHHHHHHhCCCCCc--ccCccccccCC
Confidence 99999999999999999999995 599999988899 889899987644479999999999987643 23456896678
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 256 LSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 256 Lt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
+..+|+.||+.||++++.|++.|.+
T Consensus 145 l~~~~~~ya~~~a~~~~~L~~~l~~ 169 (172)
T smart00474 145 LSEEQLQYAAEDADALLRLYEKLEK 169 (172)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999998875
No 10
>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=99.80 E-value=3.8e-18 Score=146.29 Aligned_cols=147 Identities=28% Similarity=0.330 Sum_probs=120.8
Q ss_pred CceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCCCcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCcc
Q 022027 126 QVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSGIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSV 205 (304)
Q Consensus 126 ~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l 205 (304)
...++||+||.+.. .. ..++.++|+|+. +.+|+|++.....++.|+++|+++.+.|||||+|.|.+.|.+.+|+..
T Consensus 12 ~~~l~~~~e~~~~~-~~--~~~~~~i~l~~~-~~~~~i~~~~~~~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~ 87 (178)
T cd06142 12 AGVIAVDTEFMRLN-TY--YPRLCLIQISTG-GEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLKRDFGILP 87 (178)
T ss_pred CCeEEEECCccCCC-cC--CCceEEEEEeeC-CCEEEEeCCCcccHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCC
Confidence 45899999886432 11 257899999987 568998765324566799999999999999999999999976669984
Q ss_pred CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 206 KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 206 ~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.+++|+ ++|+|++++. .+++|+.+++.|++..+.+. ...++|..++++.+|+.||+.||++++.|+..|.+
T Consensus 88 ~~~~D~-~laayLl~p~-~~~~l~~l~~~~l~~~~~~~--~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~ 158 (178)
T cd06142 88 QNLFDT-QIAARLLGLG-DSVGLAALVEELLGVELDKG--EQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKE 158 (178)
T ss_pred CCcccH-HHHHHHhCCC-ccccHHHHHHHHhCCCCCcc--cccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHH
Confidence 455899 8999999976 34699999999999886553 26789998999999999999999999999999875
No 11
>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=99.74 E-value=8.2e-17 Score=133.96 Aligned_cols=148 Identities=24% Similarity=0.286 Sum_probs=114.0
Q ss_pred eEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCC-CcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCccC
Q 022027 128 VVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSG-IPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVK 206 (304)
Q Consensus 128 ~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~-~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~ 206 (304)
++++|+||.+.. +- ..+++++|+|++++.++++++.+.. ....|+++|+++.+.|+||++|.|++.| ...|+...
T Consensus 1 ~~~~~~e~~~~~-~~--~~~~~~l~l~~~~~~~~~i~~~~~~~~~~~l~~~l~~~~~~kv~~d~K~~~~~L-~~~~~~~~ 76 (150)
T cd09018 1 VFAFDTETDSLD-NI--SANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGIL-LNYFIELR 76 (150)
T ss_pred CEEEEeecCCCC-CC--CceEEEEEEEcCCCcEEEEEcCCcccCHHHHHHHhcCCCCceeeecHHHHHHHH-HHcCCccC
Confidence 368899876532 10 2579999999874558888865422 3567999999999999999999999999 56777666
Q ss_pred Cc-chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 207 AS-EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 207 ~~-~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
+. +|+ ++|+|+|++...+++|+.|+++|++..+.+.+++..++|..++++.+|+.||+.||+++++|++.|.+
T Consensus 77 ~~~~D~-~laayLl~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~~a~~l~~L~~~l~~ 150 (150)
T cd09018 77 GIAFDT-MLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLWP 150 (150)
T ss_pred CcchhH-HHHHHHhCCCCCCCCHHHHHHHHhCCCcccHHHhcCCCCcccCCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 55 798 89999999763146999999999998755422233335855677888999999999999999998863
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=99.73 E-value=5e-16 Score=135.82 Aligned_cols=168 Identities=21% Similarity=0.241 Sum_probs=129.1
Q ss_pred CCcEEEecCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEec-CCCCCcH
Q 022027 94 GGQILYSRTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQI-IHSGIPP 172 (304)
Q Consensus 94 ~g~i~~i~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l-~~~~~~~ 172 (304)
.|+|.++.+.+++..+++.+.. ...+++++|+.+. .+. ..++.++|++.+++ +|+|++ .......
T Consensus 2 ~~~~~~i~~~~~l~~~~~~l~~----------~~~l~~~~e~~~~-~~~--~~~~~~l~l~~~~~-~~~i~~l~~~~~~~ 67 (192)
T cd06147 2 ETPLTFVDTEEKLEELVEKLKN----------CKEIAVDLEHHSY-RSY--LGFTCLMQISTREE-DYIVDTLKLRDDMH 67 (192)
T ss_pred CCCcEEECCHHHHHHHHHHHhc----------CCeEEEEeEecCC-ccC--CCceEEEEEecCCC-cEEEEecccccchH
Confidence 4678888666767766554422 4589999976432 111 24688899998754 777763 2223445
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWE 252 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~ 252 (304)
.|+++|+++.+.|+||++|.+++.|.+.+|+.+.+.+|+ ++|+|+|+++ . ++|+.|+++||+..+.| +.+.++|.
T Consensus 68 ~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~-~laaYLL~p~-~-~~l~~l~~~yl~~~~~k--~~~~~~~~ 142 (192)
T cd06147 68 ILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDT-GQAARVLNLP-R-HSLAYLLQKYCNVDADK--KYQLADWR 142 (192)
T ss_pred HHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCchHHH-HHHHHHhCCC-c-ccHHHHHHHHhCCCcch--hhhccccc
Confidence 689999999999999999999999944889998888898 9999999986 4 59999999999876533 24566787
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 253 ADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 253 ~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
..+|..+|..|++.+|.+++.|+..|..
T Consensus 143 ~~~l~~~~~~y~a~~a~~l~~L~~~L~~ 170 (192)
T cd06147 143 IRPLPEEMIKYAREDTHYLLYIYDRLRN 170 (192)
T ss_pred cCCCCHHHHHHHHhhHHHHHHHHHHHHH
Confidence 7777889999999999999999999876
No 13
>KOG4373 consensus Predicted 3'-5' exonuclease [General function prediction only]
Probab=99.70 E-value=2.9e-17 Score=150.86 Aligned_cols=152 Identities=29% Similarity=0.467 Sum_probs=126.5
Q ss_pred cCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCC-CCcHHHHHhHcCCCceEEEecchHHHHHHHH-hc
Q 022027 124 AGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHS-GIPPSLQLLLEDSTILKVGVGIGSDAGKVYR-DY 201 (304)
Q Consensus 124 ~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~-~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~-~~ 201 (304)
+....++.+.||.+.+..|....++..+|||++++.|+|+++.+. .+|..|+.||+|+..++||.++++|..+|.+ .|
T Consensus 125 s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~~~~~IP~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~h 204 (319)
T KOG4373|consen 125 SDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLIHCKRIPHELRSFLEDPDHTFVGVWNDQDAGKLERKEH 204 (319)
T ss_pred cCCcceeecccccccccccccCCCcchhhhhhcccceeeEEeeccccchHHHHHhhcCCCceEEeccccccHHHHhhhhh
Confidence 345667788888876444444456889999999999999999875 5999999999999999999999999999988 79
Q ss_pred CCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHc---CcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 202 NVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLV---CKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 202 gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~L---g~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
++.+....|+..+++..+++...+.+...|+...+ |..+.+++.++++||...+|+.+|+.||+.|||+++.++
T Consensus 205 ql~I~~~~dlr~~~~d~~g~~~~~~s~e~i~~~~~~~~~~~v~l~~~i~msdw~~~~Ls~~Ql~~asidvy~c~~lg 281 (319)
T KOG4373|consen 205 QLEIGELEDLRLLVNDSLGGSMPNDSFEEIVSETLGYYGKDVRLDKEIRMSDWSVYPLSDDQLLQASIDVYVCHKLG 281 (319)
T ss_pred cccHHhhhhHHhhcchhhccCccCccHHHHHHHHhhccccccccChhcccccceeeeccHHHHHHHHhHHHHHHHHH
Confidence 99998889999999888886433445555555544 555677788999999999999999999999999999988
No 14
>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=99.67 E-value=1.9e-15 Score=125.38 Aligned_cols=145 Identities=27% Similarity=0.178 Sum_probs=108.4
Q ss_pred eEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCC--CCCcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCcc
Q 022027 128 VVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIH--SGIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSV 205 (304)
Q Consensus 128 ~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~--~~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l 205 (304)
.+++|+|+.+.. . ...++.++|+|+. +.++++++.. ..+++.|+++|+++.+.||||++|.|++.|.+ .++..
T Consensus 2 ~l~~d~e~~~~~-~--~~~~i~~~~l~~~-~~~~~i~~~~~~~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~-~~~~~ 76 (155)
T cd00007 2 EVAFDTETTGLN-Y--HRGKLVGIQIATA-GEAAYIPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLAR-DGIEL 76 (155)
T ss_pred ceEEEEecCCCC-c--CCCeEEEEEEEEC-CcEEEEEcCCCHHHHHHHHHHHHcCCCCcEEeccHHHHHHHHHH-CCCCC
Confidence 478999886532 1 1257899999987 4466665442 13455689999999999999999999999954 45444
Q ss_pred -CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCC----CCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 206 -KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNW----EADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 206 -~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W----~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.+++|+ ++++|++++...+++|+.|+++|++..+.+..+ ..+| ..++++.+|+.||+.||++++.|+..|.+
T Consensus 77 ~~~~~D~-~~~ayll~~~~~~~~l~~l~~~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~y~~~da~~~~~l~~~l~~ 153 (155)
T cd00007 77 PGNIFDT-MLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQ--IYGKGAKTFARPLSEELLEYAAEDADALLRLYEKLLE 153 (155)
T ss_pred CCCcccH-HHHHHHhCCCCCcCCHHHHHHHHcCCCCccHHH--HhcCCCCccccCCHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 455798 888899997642579999999999987544221 2233 24677888999999999999999999875
No 15
>KOG2207 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.56 E-value=8.7e-15 Score=143.39 Aligned_cols=177 Identities=27% Similarity=0.375 Sum_probs=135.2
Q ss_pred CCcEEEecCHHHHHHHH-HHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCC---
Q 022027 94 GGQILYSRTSTEVEMAA-IELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSG--- 169 (304)
Q Consensus 94 ~g~i~~i~t~~~l~~~~-~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~--- 169 (304)
...|+.++++.++..++ +.+.. +...||+|.||.+. .+....+++++|++.. +.+|++++....
T Consensus 389 ~~~i~~V~~e~El~~l~l~~l~~---------e~~yVGiDsEwkps--~~v~dsk~~IlQif~~-~~v~Lidc~~l~~~~ 456 (617)
T KOG2207|consen 389 VESIGMVGNEKELRDLLLESLSE---------ELRYVGIDSEWKPS--KKVSDSKLAILQIFFK-DCVYLIDCVKLENLA 456 (617)
T ss_pred ccceeeeCCHHHHHHHHHHHhhh---------cCEEEEEccccCcc--cCCChhHHHHHHHHhc-CeEEEeehHHhhhch
Confidence 45789999999998887 22322 13789999999874 2223578999999988 689999975321
Q ss_pred ---CcHHHHHhHcCCCceEEEecchHHHHHHHH-----hcCCccC---CcchHHHHHHHHh-------CCCCCCCCHHHH
Q 022027 170 ---IPPSLQLLLEDSTILKVGVGIGSDAGKVYR-----DYNVSVK---ASEDLSYLAKHKI-------GGDSQKWGLASL 231 (304)
Q Consensus 170 ---~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~-----~~gi~l~---~~~Dl~~LA~ylL-------~~~~~~~sL~~L 231 (304)
..-.+..+|+++.+.|||+++..|+..+.+ .+.+.+. +.+++..++..+. +......+|++|
T Consensus 457 se~w~~~~s~if~s~~i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~~~~~~~i~n~~~~~~~L~~L 536 (617)
T KOG2207|consen 457 SEIWHLLLSQIFESKSILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENVIDLPLSIENLNEATKGLADL 536 (617)
T ss_pred HHHHHHHHHHHccCCceeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHhcccchhhhhcchhhhhhhh
Confidence 123466699999999999999999999964 2233332 3344445554332 222347799999
Q ss_pred HHHHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCc
Q 022027 232 TEMLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPEP 284 (304)
Q Consensus 232 a~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~ 284 (304)
....+|..++|.+ ++|||..|||+..|+.|||+||.++..+|..+.+.+.+
T Consensus 537 t~~llg~~lnKte--qcsnWqcrpLr~nQi~yaalDa~~~~~ifkkv~~vv~~ 587 (617)
T KOG2207|consen 537 TDCLLGKKLNKTE--QCSNWQCRPLRRNQIYYAALDAVVLVEIFKKVCSVVEH 587 (617)
T ss_pred hHHHhhhhccccc--ccchhhcCCchhhHHHHHHhcchhhHHHHHHHHhhcch
Confidence 9999999999864 89999999999999999999999999999999998874
No 16
>PRK05755 DNA polymerase I; Provisional
Probab=99.51 E-value=5.5e-13 Score=140.95 Aligned_cols=169 Identities=21% Similarity=0.211 Sum_probs=129.6
Q ss_pred cEEEecCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCC--CCcHH
Q 022027 96 QILYSRTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHS--GIPPS 173 (304)
Q Consensus 96 ~i~~i~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~--~~~~~ 173 (304)
.+.+|.+.+++..+++.+.. ...++||+|+.+.... ..+++++|++..++.++++++.+. ...+.
T Consensus 295 ~~~~I~~~~~L~~~l~~l~~----------~~~~a~DtEt~~l~~~---~~~i~~i~ls~~~g~~~~ip~~~i~~~~l~~ 361 (880)
T PRK05755 295 DYETILDEEELEAWLAKLKA----------AGLFAFDTETTSLDPM---QAELVGLSFAVEPGEAAYIPLDQLDREVLAA 361 (880)
T ss_pred ceEEeCCHHHHHHHHHHhhc----------cCeEEEEeccCCCCcc---cccEEEEEEEeCCCcEEEEecccccHHHHHH
Confidence 35678888889888877754 6889999998764211 367999999998776888887542 34567
Q ss_pred HHHhHcCCCceEEEecchHHHHHHHHhcCCccCC-cchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcc--ccCC
Q 022027 174 LQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKA-SEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRI--RLGN 250 (304)
Q Consensus 174 L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~-~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i--~~s~ 250 (304)
|.++|+++.+.||+||+++|+..|. .+|+.+.+ ++|+ ++|+|+++++. .++|+.|+++|+|..+....++ ...+
T Consensus 362 l~~~L~d~~v~kV~HNakfDl~~L~-~~gi~~~~~~~DT-~iAa~Ll~~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~ 438 (880)
T PRK05755 362 LKPLLEDPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDT-MLASYLLDPGR-RHGLDSLAERYLGHKTISFEEVAGKQLT 438 (880)
T ss_pred HHHHHhCCCCcEEEeccHhHHHHHH-hCCCCcCCCcccH-HHHHHHcCCCC-CCCHHHHHHHHhCCCccchHHhcCCCCC
Confidence 8999999999999999999999994 57988755 5798 88989998764 4999999999998875321111 1122
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC
Q 022027 251 WEADVLSKDQLLYAATDAFASWHLYQVLKSL 281 (304)
Q Consensus 251 W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l 281 (304)
|...|+ +.+..||+.|+.+++.||..|...
T Consensus 439 ~~~~pl-e~~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 439 FAQVDL-EEAAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred ccccCH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333345 468999999999999999999863
No 17
>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=99.47 E-value=1.5e-12 Score=111.90 Aligned_cols=146 Identities=17% Similarity=0.072 Sum_probs=108.4
Q ss_pred ceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCC-CCcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCcc
Q 022027 127 VVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHS-GIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSV 205 (304)
Q Consensus 127 ~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~-~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l 205 (304)
..+++++|..... .. ..++.++++|..+ .++++++.+. ...+.|+++|+++.+.|++|++|.+++.| ..+|+.+
T Consensus 4 ~~~~~~~~~~~~~-~~--~~~l~~i~l~~~~-~~~~i~~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~~ 78 (178)
T cd06140 4 DEVALYVELLGEN-YH--TADIIGLALANGG-GAYYIPLELALLDLAALKEWLEDEKIPKVGHDAKRAYVAL-KRHGIEL 78 (178)
T ss_pred CceEEEEEEcCCC-cc--eeeEEEEEEEeCC-cEEEEeccchHHHHHHHHHHHhCCCCceeccchhHHHHHH-HHCCCcC
Confidence 4567777765431 11 2568889999874 6777775432 12345889999999999999999999998 6689988
Q ss_pred CCc-chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCC---CCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 206 KAS-EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWE---ADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 206 ~~~-~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~---~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.+. +|+ ++|+|+|+++..++++++++.+|++..+.+... ...|. ..+....+..|++.+|.++++|+..|.+
T Consensus 79 ~~~~fDt-~laaYLL~p~~~~~~l~~l~~~yl~~~~~~~~~--~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~ 154 (178)
T cd06140 79 AGVAFDT-MLAAYLLDPTRSSYDLADLAKRYLGRELPSDEE--VYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEE 154 (178)
T ss_pred CCcchhH-HHHHHHcCCCCCCCCHHHHHHHHcCCCCcchHH--hcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 776 788 999999998644579999999999987654211 22231 1233455889999999999999999876
No 18
>KOG2206 consensus Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]
Probab=99.42 E-value=4.6e-13 Score=130.85 Aligned_cols=164 Identities=23% Similarity=0.266 Sum_probs=136.3
Q ss_pred EEEecCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCC-CCcHHHH
Q 022027 97 ILYSRTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHS-GIPPSLQ 175 (304)
Q Consensus 97 i~~i~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~-~~~~~L~ 175 (304)
.++|.+..++.++.+.+.. ...+++|.|... |+.- .+-.++||+++.+ .-|+||.... .....|+
T Consensus 193 ~~~I~t~~el~~l~~~l~~----------~~Efavdlehhs-yrsf--~gltclmqISTr~-ed~iIDt~~l~~~i~~l~ 258 (687)
T KOG2206|consen 193 KVWICTLGELEALPEILDS----------VIEFAVDLEHHS-YRSF--LGLTCLMQISTRT-EDFIIDTFKLRDHIGILN 258 (687)
T ss_pred ceeeechHHHHHHHHHHhh----------hhhhhhhccccc-hhhh--cCceeEEEeeccc-hhheehhHHHHHHHHHhh
Confidence 4667788888888877765 567889999764 3332 3678999999984 5677775421 2334888
Q ss_pred HhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCC
Q 022027 176 LLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADV 255 (304)
Q Consensus 176 ~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~p 255 (304)
+.|.+|+++||.|+...|+.+|.++|||.+.|.+|+ .-|..+|+. ..++|+.|.+.|.|...+| +.|..+|..+|
T Consensus 259 e~fsdp~ivkvfhgaD~diiwlqrdfgiyvvnLfdt-~~a~r~L~~--~r~sL~~ll~~~~~v~~nk--~yqladwR~rp 333 (687)
T KOG2206|consen 259 EVFSDPGIVKVFHGADTDIIWLQRDFGIYVVNLFDT-IQASRLLGL--PRPSLAYLLECVCGVLTNK--KYQLADWRIRP 333 (687)
T ss_pred hhccCCCeEEEEecCccchhhhhccceEEEEechhh-HHHHHHhCC--CcccHHHHHHHHHhhhhhh--hhhhchhcccc
Confidence 999999999999999999999999999999999999 777778886 4899999999999876554 57899999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 256 LSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 256 Lt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
|+++.+.||-.|.++++.||..|.
T Consensus 334 Lp~~Mv~yar~dthyllyiyD~lr 357 (687)
T KOG2206|consen 334 LPEEMVRYAREDTHYLLYIYDVLR 357 (687)
T ss_pred CcHHHHHHHhhcchhHHHHHHHHH
Confidence 999999999999999999999987
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=99.36 E-value=5.4e-11 Score=103.02 Aligned_cols=150 Identities=22% Similarity=0.278 Sum_probs=108.1
Q ss_pred CceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCC---------CCcHHHHHhHcCCCceEEEecchHHHHH
Q 022027 126 QVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHS---------GIPPSLQLLLEDSTILKVGVGIGSDAGK 196 (304)
Q Consensus 126 ~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~---------~~~~~L~~lL~d~~i~KVG~~ik~Dl~~ 196 (304)
...++||+|..+. ... ..++..+++|...+..+++++.+. .....|+.+|++..+.+||||+|.|+..
T Consensus 5 ~~~~a~d~e~~~~-~~~--~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~ 81 (193)
T cd06139 5 AKVFAFDTETTSL-DPM--QAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHV 81 (193)
T ss_pred CCeEEEEeecCCC-CcC--CCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHHHHHHHHHhCCCCcEEeeccHHHHHH
Confidence 5779999986542 111 256888999977554677765431 1223488899998889999999999999
Q ss_pred HHHhcCCccCCc-chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCC-----CCccccCCCCCCCCCHHHHHHHHHHHHH
Q 022027 197 VYRDYNVSVKAS-EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKK-----PNRIRLGNWEADVLSKDQLLYAATDAFA 270 (304)
Q Consensus 197 L~~~~gi~l~~~-~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K-----~~~i~~s~W~~~pLt~~Qi~YAA~DA~a 270 (304)
| ..+|+.+.+. +|+ ++++|+++++..+++|+.++++|++..+.+ .+.....+|...++ ..+..||+.||.+
T Consensus 82 l-~~~gi~~~~~~~Dt-~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~-~~~~~ya~~d~~~ 158 (193)
T cd06139 82 L-ANHGIELRGPAFDT-MLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL-EKAAEYAAEDADI 158 (193)
T ss_pred H-HHCCCCCCCCcccH-HHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH-HHHHHHHHHHHHH
Confidence 9 6689887765 688 888899997642679999999999865321 11112233433233 5588999999999
Q ss_pred HHHHHHHHhCC
Q 022027 271 SWHLYQVLKSL 281 (304)
Q Consensus 271 ~~~L~~~L~~l 281 (304)
++.|+..|.+.
T Consensus 159 ~~~l~~~l~~~ 169 (193)
T cd06139 159 TLRLYELLKPK 169 (193)
T ss_pred HHHHHHHHHHH
Confidence 99999999863
No 20
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=99.20 E-value=2.5e-10 Score=113.88 Aligned_cols=152 Identities=20% Similarity=0.198 Sum_probs=111.9
Q ss_pred ceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCC--C--CCcHHHHHhHcCCCceEEEecchHHHHHHHHhcC
Q 022027 127 VVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIH--S--GIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYN 202 (304)
Q Consensus 127 ~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~--~--~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~g 202 (304)
..++||+|..+.... ...+.++.+|..+ .++++++.+ . .....|++||+++.+.|+||+.|.|.+.| ..+|
T Consensus 23 ~~~a~~~et~~l~~~---~~~lvg~s~~~~~-~~~yi~~~~~~~~~~~~~~l~~~l~~~~~~kv~~~~K~d~~~l-~~~G 97 (593)
T COG0749 23 ANIAFDTETDGLDPH---GADLVGLSVASEE-EAAYIPLLHGPEQLNVLAALKPLLEDEGIKKVGQNLKYDYKVL-ANLG 97 (593)
T ss_pred ccceeeccccccCcc---cCCeeEEEeeccc-cceeEeeccchhhhhhHHHHHHHhhCcccchhccccchhHHHH-HHcC
Confidence 339999998765322 2456677777775 667777765 2 35678999999999999999999999999 6788
Q ss_pred CccCCc-chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCC---CCCC-HHHHHHHHHHHHHHHHHHHH
Q 022027 203 VSVKAS-EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEA---DVLS-KDQLLYAATDAFASWHLYQV 277 (304)
Q Consensus 203 i~l~~~-~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~---~pLt-~~Qi~YAA~DA~a~~~L~~~ 277 (304)
+. .+. +|+ |+|+|+++++...++++.|+++|++......+.+....-.. ..+. +....|+|.||.++++|+..
T Consensus 98 i~-~~~~~Dt-mlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~ 175 (593)
T COG0749 98 IE-PGVAFDT-MLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESI 175 (593)
T ss_pred Cc-ccchHHH-HHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 66 455 687 99999999876789999999999987765433322111111 1112 34569999999999999999
Q ss_pred HhC-CCCcc
Q 022027 278 LKS-LPEPV 285 (304)
Q Consensus 278 L~~-l~~~~ 285 (304)
|.. +++..
T Consensus 176 l~~~l~~~~ 184 (593)
T COG0749 176 LEPELLKTP 184 (593)
T ss_pred HHHHhhhhh
Confidence 985 55433
No 21
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=99.09 E-value=5.4e-10 Score=112.75 Aligned_cols=138 Identities=26% Similarity=0.228 Sum_probs=110.0
Q ss_pred EEEecCHHHHHHHHHHHHHHHhhcccccCCceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCCCcHHHHH
Q 022027 97 ILYSRTSTEVEMAAIELRRILEANKSEAGQVVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSGIPPSLQL 176 (304)
Q Consensus 97 i~~i~t~~~l~~~~~~l~~~~~~~~~~~~~~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~~~~~L~~ 176 (304)
..+|.+.+++..++..+.. .+.+++|+|+.... ..++++|++.. +.++++|.. ..+-
T Consensus 3 ~~~I~~~~~l~~~~~~l~~----------~~~~a~DtEf~r~~------t~l~liQ~~~~-~~~~liDpl-----~~l~- 59 (553)
T PRK14975 3 MKVILAPEELGAALERLSP----------AGVVAGDTETTGDD------AAAAAAQEGEE-EPRWVWAST-----AALY- 59 (553)
T ss_pred ceEEeccchhHHHHHHhcc----------CCceeCCccccCCc------chhheeeecCC-CceEEECch-----HHhH-
Confidence 3577788888888888876 78999999986531 26889999976 577887632 1111
Q ss_pred hHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCC--CCCHHHHHHHHcCcccCCCCccccCCCCCC
Q 022027 177 LLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQ--KWGLASLTEMLVCKELKKPNRIRLGNWEAD 254 (304)
Q Consensus 177 lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~--~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~ 254 (304)
..| ..+|+.+.+++|+ ++|+|+|+.+.. .++++.++..+++..++|.. +.++|. +
T Consensus 60 ------------------~~L-~~~Gv~~~~~fDT-~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~--~~sdw~-r 116 (553)
T PRK14975 60 ------------------PRL-LAAGVRVERCHDL-MLASQLLLGSEGRAGSSLSAAAARALGEGLDKPP--QTSALS-D 116 (553)
T ss_pred ------------------HHH-HHCCCccCCCchH-HHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChh--hhcccc-c
Confidence 114 4569988889999 999999997531 78999999999999998854 468896 8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 255 VLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 255 pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
|++++|+.||+.|+.+++.||..|..
T Consensus 117 pls~~q~~YAa~Dv~~l~~L~~~L~~ 142 (553)
T PRK14975 117 PPDEEQLLYAAADADVLLELYAVLAD 142 (553)
T ss_pred cchHHHHHHHHHHhHHHHHHHHHHHH
Confidence 99999999999999999999999876
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=99.08 E-value=2.7e-09 Score=112.50 Aligned_cols=132 Identities=16% Similarity=0.050 Sum_probs=97.1
Q ss_pred CcEEEEEEEecC-CeEEEEecCC------CCCcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCc-chHHHHHHH
Q 022027 146 RKAAVMQICGDS-NHCYVMQIIH------SGIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKAS-EDLSYLAKH 217 (304)
Q Consensus 146 ~~valiQL~~~~-~~~~l~~l~~------~~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~-~Dl~~LA~y 217 (304)
..+.++.+|+.. +..|++++.. ......|+++|+++.+.|+|||+|+|++.| ..+|+.+.+. +|+ ++|+|
T Consensus 335 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l-~~~gi~~~~~~~Dt-~la~y 412 (887)
T TIGR00593 335 KKALALAFATENQSYVAYASEADGIPLLTILTDDKFARWLLNEQIKKIGHDAKFLMHLL-KREGIELGGVIFDT-MLAAY 412 (887)
T ss_pred CceeEEEEEecCCCceEEEecccchhhhhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHH-HhCCCCCCCcchhH-HHHHH
Confidence 457778888864 4466666431 122345899999999999999999999999 6799998776 688 99999
Q ss_pred HhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHhC
Q 022027 218 KIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSK-DQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 218 lL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~-~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
+|+++ ..++|+.++.+|++..+.+...+...++....++. ....||+.||.++++||..|.+
T Consensus 413 ll~~~-~~~~l~~la~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~ 475 (887)
T TIGR00593 413 LLDPA-QVSTLDTLARRYLVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLK 475 (887)
T ss_pred HcCCC-CCCCHHHHHHHHcCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99976 45699999999999765432221111111113433 3668999999999999999876
No 23
>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=99.03 E-value=1.1e-08 Score=85.51 Aligned_cols=130 Identities=19% Similarity=0.186 Sum_probs=90.1
Q ss_pred CcEEEEEEEecCCeEEEEecCCCCCcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCc-chHHHHHHHHhCCCCC
Q 022027 146 RKAAVMQICGDSNHCYVMQIIHSGIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKAS-EDLSYLAKHKIGGDSQ 224 (304)
Q Consensus 146 ~~valiQL~~~~~~~~l~~l~~~~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~-~Dl~~LA~ylL~~~~~ 224 (304)
.++..+.++..+ .++++++........|+++|+++.+.|+|||+|.+++.| +.+|+.+.+. +|+ +||+|+|++...
T Consensus 18 ~~~~glal~~~~-~~~yi~~~~~~~~~~l~~~l~~~~~~ki~~d~K~~~~~l-~~~gi~l~~~~fD~-~LAaYLL~p~~~ 94 (151)
T cd06128 18 ANLVGLAFAIEG-VAAYIPVAHDYALELLKPLLEDEKALKVGQNLKYDRVIL-ANYGIELRGIAFDT-MLEAYLLDPVAG 94 (151)
T ss_pred CcEEEEEEEcCC-CeEEEeCCCCcCHHHHHHHHcCCCCCEEeeehHHHHHHH-HHCCCCCCCcchhH-HHHHHHcCCCCC
Confidence 356667788764 467766432102456889999999999999999999998 7789998877 688 999999998654
Q ss_pred CCCHHHHHHHHcCcccCCCCccccCCCCC-CCC-CHHHHHHHHHHHHHHHHHHHHHh
Q 022027 225 KWGLASLTEMLVCKELKKPNRIRLGNWEA-DVL-SKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 225 ~~sL~~La~~~Lg~~l~K~~~i~~s~W~~-~pL-t~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
..++++|+++||+..+....++. +.... ..+ ..+...|++..|.++++|++.|.
T Consensus 95 ~~~l~~la~~yl~~~~~~~~~~~-gkg~~~~~~~~~~~~~~~~~~a~~l~~L~~~l~ 150 (151)
T cd06128 95 RHDMDSLAERWLKEKTITFEEIA-GKGLTFNQIALEEAGEYAAEDAAVTLQLHLKMW 150 (151)
T ss_pred CCCHHHHHHHHcCCCCccHHHHc-CCCCChhhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 24999999999987632100111 10000 012 11133488888999999998875
No 24
>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=96.54 E-value=0.0051 Score=53.08 Aligned_cols=80 Identities=24% Similarity=0.290 Sum_probs=54.5
Q ss_pred HHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCC
Q 022027 174 LQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEA 253 (304)
Q Consensus 174 L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~ 253 (304)
|..++ ++..+.|||++.+|+.+| + +-..-..++|++.+.. +. ..+.++|..|++.+||+.+..+.
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL-~-l~hp~~~viDTa~l~~--~~-~~r~~sLk~La~~~L~~~IQ~~~--------- 159 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVI-N-IQVPKEQVIDTVELFH--LP-GQRKLSLRFLAWYLLGEKIQSET--------- 159 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHh-c-CcCCCcceEEcHHhcc--CC-CCCChhHHHHHHHHcCCcccCCC---------
Confidence 44444 455678999999999998 2 1111235679965542 22 23579999999999998774321
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q 022027 254 DVLSKDQLLYAATDAFASWHLYQ 276 (304)
Q Consensus 254 ~pLt~~Qi~YAA~DA~a~~~L~~ 276 (304)
.-..+||.+++.||+
T Consensus 160 --------HdSvEDArAam~Ly~ 174 (174)
T cd06143 160 --------HDSIEDARTALKLYR 174 (174)
T ss_pred --------cCcHHHHHHHHHHhC
Confidence 115689999999983
No 25
>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=96.42 E-value=0.04 Score=46.59 Aligned_cols=86 Identities=19% Similarity=0.167 Sum_probs=53.4
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHH--HHHH-hCCCCCCCCHHHHHHHHcCcccCCCCcccc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYL--AKHK-IGGDSQKWGLASLTEMLVCKELKKPNRIRL 248 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~L--A~yl-L~~~~~~~sL~~La~~~Lg~~l~K~~~i~~ 248 (304)
+.|.+++.+ -+.|||+++.|+..|... ......+|+..+ ++.. +-+...+++|..|++++++..+....+ .
T Consensus 69 ~~l~~~l~~--~vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~--~ 142 (157)
T cd06149 69 KEILKILKG--KVVVGHAIHNDFKALKYF--HPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQ--G 142 (157)
T ss_pred HHHHHHcCC--CEEEEeCcHHHHHHhccc--CCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCC--C
Confidence 345566654 468999999999988322 111234576433 2222 123335799999999998876643211 1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 022027 249 GNWEADVLSKDQLLYAATDAFASWHLYQ 276 (304)
Q Consensus 249 s~W~~~pLt~~Qi~YAA~DA~a~~~L~~ 276 (304)
.-|..||.++..||+
T Consensus 143 -------------H~Al~DA~at~~l~~ 157 (157)
T cd06149 143 -------------HSSVEDARATMELYK 157 (157)
T ss_pred -------------cCcHHHHHHHHHHhC
Confidence 127789999988873
No 26
>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=96.32 E-value=0.016 Score=48.57 Aligned_cols=83 Identities=19% Similarity=0.178 Sum_probs=53.8
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCC-CCCCCHHHHHHHHcCcccCCCCccccCC
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGD-SQKWGLASLTEMLVCKELKKPNRIRLGN 250 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~-~~~~sL~~La~~~Lg~~l~K~~~i~~s~ 250 (304)
+.|..++.+ . +.|||++..|+..|. .+......+|+..+..+ .... ..+++|+.|+++++|+.+... .
T Consensus 69 ~~l~~~l~~-~-vlVgHn~~fD~~~L~--~~~~~~~~~dt~~l~~~-~~~~~~~~~sL~~l~~~~lgi~~~~~----~-- 137 (152)
T cd06144 69 KKVAELLKG-R-ILVGHALKNDLKVLK--LDHPKKLIRDTSKYKPL-RKTAKGKSPSLKKLAKQLLGLDIQEG----E-- 137 (152)
T ss_pred HHHHHHhCC-C-EEEEcCcHHHHHHhc--CcCCCccEEEeEEeecc-ccccCCCChhHHHHHHHHcCcccCCC----C--
Confidence 356677775 4 459999999999983 22222234576443322 2211 257999999999999765321 1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHH
Q 022027 251 WEADVLSKDQLLYAATDAFASWHLYQ 276 (304)
Q Consensus 251 W~~~pLt~~Qi~YAA~DA~a~~~L~~ 276 (304)
.-|..||.++..||+
T Consensus 138 -----------H~Al~DA~at~~l~~ 152 (152)
T cd06144 138 -----------HSSVEDARAAMRLYR 152 (152)
T ss_pred -----------cCcHHHHHHHHHHhC
Confidence 127889999998874
No 27
>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=96.11 E-value=0.021 Score=47.86 Aligned_cols=82 Identities=20% Similarity=0.176 Sum_probs=55.1
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWE 252 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~ 252 (304)
.+.+++.. ..+.|||+++.|+..|. ... ...+|+..++..+.+ ...+++|+.|+++|++..+.... ..
T Consensus 68 ~~~~fl~~-~~vlVgHn~~fD~~fL~-~~~---~~~iDT~~l~r~~~~-~~~~~~L~~L~~~~~~~~i~~~~--~~---- 135 (150)
T cd06145 68 KLLSLISP-DTILVGHSLENDLKALK-LIH---PRVIDTAILFPHPRG-PPYKPSLKNLAKKYLGRDIQQGE--GG---- 135 (150)
T ss_pred HHHHHhCC-CCEEEEcChHHHHHHhh-ccC---CCEEEcHHhccccCC-CCCChhHHHHHHHHCCcceeCCC--CC----
Confidence 45556642 35689999999999983 221 335798777755443 23478999999999886543210 00
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHH
Q 022027 253 ADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 253 ~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
.-|..||.++..||
T Consensus 136 ---------H~Al~DA~~t~~l~ 149 (150)
T cd06145 136 ---------HDSVEDARAALELV 149 (150)
T ss_pred ---------CCcHHHHHHHHHHh
Confidence 12778999998886
No 28
>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=96.11 E-value=0.023 Score=48.22 Aligned_cols=82 Identities=15% Similarity=0.235 Sum_probs=55.8
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCC---CCCCHHHHHHHHcCcccCCCCccccC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDS---QKWGLASLTEMLVCKELKKPNRIRLG 249 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~---~~~sL~~La~~~Lg~~l~K~~~i~~s 249 (304)
.|.+++.+. -+.|||++..|+..|.. . ...++|+..++..+.. .. .+++|..|+++++|..+.... ..
T Consensus 76 ~~~~~i~~~-~vlVgHn~~fD~~fL~~-~---~~~~iDT~~l~~~~~~-~~~~~~~~~L~~L~~~~~~~~~~~~~--~~- 146 (161)
T cd06137 76 ALWKFIDPD-TILVGHSLQNDLDALRM-I---HTRVVDTAILTREAVK-GPLAKRQWSLRTLCRDFLGLKIQGGG--EG- 146 (161)
T ss_pred HHHHhcCCC-cEEEeccHHHHHHHHhC-c---CCCeeEehhhhhhccC-CCcCCCCccHHHHHHHHCCchhcCCC--CC-
Confidence 455566542 46799999999999832 2 2345799888876443 22 479999999999987654311 11
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 250 NWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 250 ~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
.-|..||.++..||
T Consensus 147 ------------H~A~~DA~at~~l~ 160 (161)
T cd06137 147 ------------HDSLEDALAAREVV 160 (161)
T ss_pred ------------CCcHHHHHHHHHHh
Confidence 12778999998876
No 29
>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=96.10 E-value=0.1 Score=45.55 Aligned_cols=149 Identities=11% Similarity=0.170 Sum_probs=82.8
Q ss_pred CceEEEEeeeecCc-cCCCCCCcEEEEEEEecCCe-EEEEe--------cCC--CCCcHHHHHhHcC--CCceEEEecch
Q 022027 126 QVVVGFDIEWKPTF-RKGVLPRKAAVMQICGDSNH-CYVMQ--------IIH--SGIPPSLQLLLED--STILKVGVGIG 191 (304)
Q Consensus 126 ~~~vgfD~E~~~~~-~~g~~~~~valiQL~~~~~~-~~l~~--------l~~--~~~~~~L~~lL~d--~~i~KVG~~ik 191 (304)
-.+++||+|..... .+.....++..|.++...+. ++.+. ... ..+...+..++.. |. +.+|||+.
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpd-iivgyN~~ 81 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPD-VIYTYNGD 81 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCC-EEEecCCC
Confidence 46789999996321 11111234544444433222 22111 001 1234445555554 65 46899976
Q ss_pred -HHHHHHHHh---cCCccC----------------------C--cchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCC
Q 022027 192 -SDAGKVYRD---YNVSVK----------------------A--SEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKP 243 (304)
Q Consensus 192 -~Dl~~L~~~---~gi~l~----------------------~--~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~ 243 (304)
.|+..|..+ +|+... | .+|+-.++...++ ..+++|+.+++++||......
T Consensus 82 ~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~--l~sy~L~~v~~~~Lg~~k~d~ 159 (195)
T cd05780 82 NFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLN--LTRYTLERVYEELFGIEKEDV 159 (195)
T ss_pred CCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCC--CCcCcHHHHHHHHhCCCCCcC
Confidence 588877643 455321 2 2587555544332 358999999999999753211
Q ss_pred --CccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 022027 244 --NRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVL 278 (304)
Q Consensus 244 --~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L 278 (304)
+.+. .-|....--..-++|+-.||..+++|...|
T Consensus 160 ~~~~i~-~~~~~~~~~~~l~~Y~~~D~~lt~~L~~~~ 195 (195)
T cd05780 160 PGEEIA-EAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CHHHHH-HHHhCCCchHHHHHHhHHHHHHHHHHHhhC
Confidence 1111 124333323456799999999999988753
No 30
>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=96.03 E-value=0.034 Score=43.05 Aligned_cols=74 Identities=15% Similarity=0.076 Sum_probs=50.0
Q ss_pred EEEEeeeecCccCCCCCCcEEEEEEEec-CCeEEEEecCCCCCcHHHHHhHcCCC-ceEEEecchHHHHHHHHhc---CC
Q 022027 129 VGFDIEWKPTFRKGVLPRKAAVMQICGD-SNHCYVMQIIHSGIPPSLQLLLEDST-ILKVGVGIGSDAGKVYRDY---NV 203 (304)
Q Consensus 129 vgfD~E~~~~~~~g~~~~~valiQL~~~-~~~~~l~~l~~~~~~~~L~~lL~d~~-i~KVG~~ik~Dl~~L~~~~---gi 203 (304)
++||+|+.+.. . ...++.++|++.. ++..++++ +.+++.+.. .++|||+...|+..|.+.+ ++
T Consensus 1 ~~~DiEt~~~~-~--~~~~i~~i~~~~~~~~~~~~~~---------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~ 68 (96)
T cd06125 1 IAIDTEATGLD-G--AVHEIIEIALADVNPEDTAVID---------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGL 68 (96)
T ss_pred CEEEEECCCCC-C--CCCcEEEEEEEEccCCCEEEeh---------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCC
Confidence 47899987632 1 2357999999876 35556654 777888876 7899999999988776543 33
Q ss_pred cc----CCcchHHHH
Q 022027 204 SV----KASEDLSYL 214 (304)
Q Consensus 204 ~l----~~~~Dl~~L 214 (304)
.. ...+|+..+
T Consensus 69 ~~p~~~~~~lDT~~l 83 (96)
T cd06125 69 KYPLLAGSWIDTIKL 83 (96)
T ss_pred CCCCcCCcEEEehHH
Confidence 21 234687544
No 31
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.01 E-value=0.17 Score=47.69 Aligned_cols=86 Identities=14% Similarity=0.008 Sum_probs=57.6
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHh---cCCcc--CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSV--KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRI 246 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l--~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i 246 (304)
..|..++.+ -+.||||+..|+..|.+. +|+.. ...+|+..++.. +.++..+++|+.|+++| |+....
T Consensus 86 ~~l~~~l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~-~~~~~~~~kL~~l~~~~-gi~~~~---- 157 (313)
T PRK06063 86 GEVAELLRG--RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARR-LGLGLPNLRLETLAAHW-GVPQQR---- 157 (313)
T ss_pred HHHHHHcCC--CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHH-hccCCCCCCHHHHHHHc-CCCCCC----
Confidence 345666655 367999999999988653 45543 345798777765 44344688999999864 654321
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 247 RLGNWEADVLSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 247 ~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
. +-|..||.++..|+..+.
T Consensus 158 -~-------------H~Al~DA~ata~l~~~ll 176 (313)
T PRK06063 158 -P-------------HDALDDARVLAGILRPSL 176 (313)
T ss_pred -C-------------CCcHHHHHHHHHHHHHHH
Confidence 1 127788888888876663
No 32
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=96.00 E-value=0.057 Score=49.30 Aligned_cols=86 Identities=23% Similarity=0.232 Sum_probs=55.9
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHH--HhCCCCCCCCHHHHHHHHcCcccCCCCccccCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKH--KIGGDSQKWGLASLTEMLVCKELKKPNRIRLGN 250 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~y--lL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~ 250 (304)
.+.+||.. -+.|||++.+|+..|.=.+.-. -+-|++..--+ ++. ...+.||..|++.+||+.+.-++ .
T Consensus 177 ev~klL~g--RIlVGHaLhnDl~~L~l~hp~s--~iRDTs~~~pl~k~~~-~~~tpSLK~Lt~~~Lg~~IQ~Ge--H--- 246 (280)
T KOG2249|consen 177 EVLKLLKG--RILVGHALHNDLQALKLEHPRS--MIRDTSKYPPLMKLLS-KKATPSLKKLTEALLGKDIQVGE--H--- 246 (280)
T ss_pred HHHHHHhC--CEEeccccccHHHHHhhhCchh--hhcccccCchHHHHhh-ccCCccHHHHHHHHhchhhhccc--c---
Confidence 35557765 3569999999999994333211 12255432211 122 23688999999999998774332 1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 251 WEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 251 W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
-..+||.++..||...+.
T Consensus 247 ------------sSvEDA~AtM~LY~~vk~ 264 (280)
T KOG2249|consen 247 ------------SSVEDARATMELYKRVKV 264 (280)
T ss_pred ------------CcHHHHHHHHHHHHHHHH
Confidence 145899999999998753
No 33
>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=95.98 E-value=0.18 Score=43.78 Aligned_cols=101 Identities=14% Similarity=0.148 Sum_probs=61.3
Q ss_pred HHHHHhHcC--CCceEEEecc-hHHHHHHHH---hcCCccC----------------------C--cchHHHHHHHHhCC
Q 022027 172 PSLQLLLED--STILKVGVGI-GSDAGKVYR---DYNVSVK----------------------A--SEDLSYLAKHKIGG 221 (304)
Q Consensus 172 ~~L~~lL~d--~~i~KVG~~i-k~Dl~~L~~---~~gi~l~----------------------~--~~Dl~~LA~ylL~~ 221 (304)
..+..++.+ |. +.+|||+ ..|+..|.. .+|+... + .+|+-.++.....
T Consensus 68 ~~f~~~i~~~dpd-iivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~- 145 (199)
T cd05160 68 KRFFDIIREYDPD-ILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFK- 145 (199)
T ss_pred HHHHHHHHhcCCC-EEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcC-
Confidence 344445544 44 4699999 689988865 3565541 2 2588556654332
Q ss_pred CCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 222 DSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 222 ~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
..+++|+.+++.+++..-.....-....|....--..-++|.-.||..+++|+
T Consensus 146 -l~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~~~~~~l~ 198 (199)
T cd05160 146 -LKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDAELTLQIL 198 (199)
T ss_pred -cccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHHHHHHHhh
Confidence 46899999999999864221111111222111122346799999999999886
No 34
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=95.94 E-value=0.18 Score=45.95 Aligned_cols=85 Identities=19% Similarity=0.168 Sum_probs=57.6
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHh---cCCcc----CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCc
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSV----KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNR 245 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l----~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~ 245 (304)
.+.+++.+. -+.|||++..|...|.+. .|+.. ...+|+..++. .++ ...+++|+.|++.+ |......
T Consensus 80 ~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar-~~~-~~~~~~L~~l~~~~-g~~~~~a-- 153 (250)
T PRK06310 80 QIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAK-EYG-DSPNNSLEALAVHF-NVPYDGN-- 153 (250)
T ss_pred HHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHH-hcc-cCCCCCHHHHHHHC-CCCCCCC--
Confidence 455566543 467999999999888643 45543 23479877775 354 22468999999876 6543211
Q ss_pred cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 246 IRLGNWEADVLSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 246 i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
.-|..||+++..|+..+.
T Consensus 154 ----------------H~Al~Da~at~~vl~~l~ 171 (250)
T PRK06310 154 ----------------HRAMKDVEINIKVFKHLC 171 (250)
T ss_pred ----------------cChHHHHHHHHHHHHHHH
Confidence 227889999999888875
No 35
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.79 E-value=0.29 Score=44.91 Aligned_cols=86 Identities=23% Similarity=0.301 Sum_probs=57.9
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHH---hcCCcc-C-CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYR---DYNVSV-K-ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRI 246 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~---~~gi~l-~-~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i 246 (304)
..+..++.+. +.|||++..|...|.+ .+|... . ..+|+..++...+.. .+++|+.|++. +|.....
T Consensus 139 ~~f~~fl~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~--~~~~L~~L~~~-lgi~~~~---- 209 (257)
T PRK08517 139 EEFRLFLGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES--PRYGLSFLKEL-LGIEIEV---- 209 (257)
T ss_pred HHHHHHHCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccC--CCCCHHHHHHH-cCcCCCC----
Confidence 3566677653 5799999999988854 455432 2 236877777655542 57899999885 5654321
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 247 RLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 247 ~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
. +-|..||.++..|+..+..
T Consensus 210 -~-------------HrAl~DA~ata~ll~~ll~ 229 (257)
T PRK08517 210 -H-------------HRAYADALAAYEIFKICLL 229 (257)
T ss_pred -C-------------CChHHHHHHHHHHHHHHHH
Confidence 1 2277899999998888763
No 36
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=95.60 E-value=0.33 Score=44.06 Aligned_cols=88 Identities=14% Similarity=0.048 Sum_probs=58.0
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHh---cCCcc------CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSV------KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKP 243 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l------~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~ 243 (304)
.+..++.+. ..|+||+..|+..|.+. +|..+ ..++|+..++.+++. + .+++|+.|+++| |+....
T Consensus 79 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p-~-~~~~L~aL~~~~-gi~~~~- 152 (240)
T PRK05711 79 EFLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFP-G-KRNSLDALCKRY-GIDNSH- 152 (240)
T ss_pred HHHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcC-C-CCCCHHHHHHHC-CCCCCC-
Confidence 455555553 46899999999888543 44222 345798777766543 3 467999999986 542211
Q ss_pred CccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC
Q 022027 244 NRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSL 281 (304)
Q Consensus 244 ~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l 281 (304)
+ +..-|-.||.++..+|..|..-
T Consensus 153 ---r------------~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 153 ---R------------TLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred ---C------------CCCCHHHHHHHHHHHHHHHHCc
Confidence 0 0122889999999999888754
No 37
>PRK07740 hypothetical protein; Provisional
Probab=95.46 E-value=0.58 Score=42.51 Aligned_cols=86 Identities=15% Similarity=0.093 Sum_probs=56.9
Q ss_pred HHHhHcCCCceEEEecchHHHHHHHHh----cCCccC-CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcccc
Q 022027 174 LQLLLEDSTILKVGVGIGSDAGKVYRD----YNVSVK-ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRL 248 (304)
Q Consensus 174 L~~lL~d~~i~KVG~~ik~Dl~~L~~~----~gi~l~-~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~ 248 (304)
|..++.+ -+.|||++..|...|.+. ++.... ..+|+..++..+ .+....++|++++.. +|......
T Consensus 135 f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l-~~~~~~~sL~~l~~~-~gi~~~~~----- 205 (244)
T PRK07740 135 FYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLL-AHERDFPTLDDALAY-YGIPIPRR----- 205 (244)
T ss_pred HHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHH-cCCCCCCCHHHHHHH-CCcCCCCC-----
Confidence 3444444 367899999999887542 333443 447997777654 434458899999975 56544211
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC
Q 022027 249 GNWEADVLSKDQLLYAATDAFASWHLYQVLKSL 281 (304)
Q Consensus 249 s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l 281 (304)
.-|..||.++..|+..+...
T Consensus 206 -------------H~Al~Da~ata~l~~~ll~~ 225 (244)
T PRK07740 206 -------------HHALGDALMTAKLWAILLVE 225 (244)
T ss_pred -------------CCcHHHHHHHHHHHHHHHHH
Confidence 12778999999988887543
No 38
>PRK07883 hypothetical protein; Validated
Probab=95.33 E-value=0.47 Score=48.33 Aligned_cols=87 Identities=14% Similarity=0.047 Sum_probs=59.2
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHH---hcCCccC--CcchHHHHHHHHhCC-CCCCCCHHHHHHHHcCcccCCCCcc
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYR---DYNVSVK--ASEDLSYLAKHKIGG-DSQKWGLASLTEMLVCKELKKPNRI 246 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~---~~gi~l~--~~~Dl~~LA~ylL~~-~~~~~sL~~La~~~Lg~~l~K~~~i 246 (304)
.|..|+.+ .+.|||++..|...|.+ .+|+... ..+|+..++..++.. ...+++|++|+++ +|+.....
T Consensus 88 ~f~~fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~-~gi~~~~~--- 161 (557)
T PRK07883 88 AFLEFARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARL-FGATTTPT--- 161 (557)
T ss_pred HHHHHhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHHH-CCcccCCC---
Confidence 45556664 46789999999998864 3566543 347998888765542 2357899999975 57654211
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 247 RLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 247 ~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
+-|..||.++..|+..|..
T Consensus 162 ---------------H~Al~DA~ata~l~~~l~~ 180 (557)
T PRK07883 162 ---------------HRALDDARATVDVLHGLIE 180 (557)
T ss_pred ---------------CCHHHHHHHHHHHHHHHHH
Confidence 2278899988887776654
No 39
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.29 E-value=0.62 Score=42.27 Aligned_cols=85 Identities=15% Similarity=-0.067 Sum_probs=54.8
Q ss_pred HHHhHcCCCceEEEecchHHHHHHHHh----cCCccCC-cchHHHHHHHHhCC----------C--CCCCCHHHHHHHHc
Q 022027 174 LQLLLEDSTILKVGVGIGSDAGKVYRD----YNVSVKA-SEDLSYLAKHKIGG----------D--SQKWGLASLTEMLV 236 (304)
Q Consensus 174 L~~lL~d~~i~KVG~~ik~Dl~~L~~~----~gi~l~~-~~Dl~~LA~ylL~~----------~--~~~~sL~~La~~~L 236 (304)
|..++.+ -+.|||+...|...|.+. ++..+.. .+|+..++..++.. + ...++|+.++++|
T Consensus 123 l~~~~~~--~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~- 199 (239)
T PRK09146 123 LLEALAG--KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRY- 199 (239)
T ss_pred HHHHhCC--CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHc-
Confidence 3444443 467999999999988653 3334433 47998888765321 0 1457899999875
Q ss_pred CcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 237 CKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 237 g~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
|..... . .-|..||.++..|+..+.
T Consensus 200 gl~~~~-----~-------------H~Al~DA~ata~l~~~~~ 224 (239)
T PRK09146 200 GLPAYS-----P-------------HHALTDAIATAELLQAQI 224 (239)
T ss_pred CCCCCC-----C-------------CCcHHHHHHHHHHHHHHH
Confidence 543211 1 228899999999888765
No 40
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.25 E-value=0.34 Score=51.59 Aligned_cols=86 Identities=22% Similarity=0.196 Sum_probs=57.9
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHh---cCCccCCc-chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSVKAS-EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIR 247 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l~~~-~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~ 247 (304)
+.+.+++.+ -+.||||+..|+..|.+. .|+.+.+. +|+..++..++. ...+++|..|++. +|......
T Consensus 78 ~~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p-~~~~~~L~~L~~~-lgl~~~~~---- 149 (820)
T PRK07246 78 RHIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFP-TLEKYSLSHLSRE-LNIDLADA---- 149 (820)
T ss_pred HHHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhC-CCCCCCHHHHHHH-cCCCCCCC----
Confidence 345566665 457999999999998653 35555443 798777765543 4458999999986 56543211
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 248 LGNWEADVLSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 248 ~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
+-|..||.++..|+..|.
T Consensus 150 --------------H~Al~DA~ata~L~~~l~ 167 (820)
T PRK07246 150 --------------HTAIADARATAELFLKLL 167 (820)
T ss_pred --------------CCHHHHHHHHHHHHHHHH
Confidence 127778888877776654
No 41
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=95.08 E-value=0.47 Score=44.79 Aligned_cols=87 Identities=20% Similarity=0.198 Sum_probs=59.2
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHh---cCCc-cC-CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccc
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVS-VK-ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIR 247 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~-l~-~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~ 247 (304)
.|..++.+. ..|||++..|+..|.+. +|+. +. ..+|+..++..+.. ....++|+.|+++ +|... +.
T Consensus 81 ~f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~-~~~~~kL~~L~~~-lgi~~-~~---- 151 (313)
T PRK06807 81 LFLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMK-HAPNHKLETLKRM-LGIRL-SS---- 151 (313)
T ss_pred HHHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhC-CCCCCCHHHHHHH-cCCCC-CC----
Confidence 445566543 35999999999998764 4553 22 34799788776553 3357899999866 46543 11
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCC
Q 022027 248 LGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLP 282 (304)
Q Consensus 248 ~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~ 282 (304)
+-|-.||.++..||..+....
T Consensus 152 --------------H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 152 --------------HNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred --------------cChHHHHHHHHHHHHHHHHhh
Confidence 227789999999988887655
No 42
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=94.97 E-value=0.89 Score=39.80 Aligned_cols=87 Identities=15% Similarity=0.078 Sum_probs=55.6
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHh----cCCccCC-cchHHHHHHHHh----CCCCCCCCHHHHHHHHcCcccCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRD----YNVSVKA-SEDLSYLAKHKI----GGDSQKWGLASLTEMLVCKELKKP 243 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~----~gi~l~~-~~Dl~~LA~ylL----~~~~~~~sL~~La~~~Lg~~l~K~ 243 (304)
.+..++.+ -..|||++..|...|.+. ++..+.. .+|+..++.... .....+++|+.+++++ |.+...
T Consensus 104 ~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~-gi~~~~- 179 (202)
T PRK09145 104 QLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL-DLPVLG- 179 (202)
T ss_pred HHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc-CCCCCC-
Confidence 45556654 357999999999888643 3454443 368765542211 1112368999999775 654321
Q ss_pred CccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 244 NRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 244 ~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
. .-|..||.++..||..|..
T Consensus 180 ----~-------------H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 180 ----R-------------HDALNDAIMAALIFLRLRK 199 (202)
T ss_pred ----C-------------CCcHHHHHHHHHHHHHHHh
Confidence 1 1278999999999998864
No 43
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=94.87 E-value=1.5 Score=39.43 Aligned_cols=87 Identities=14% Similarity=0.037 Sum_probs=57.3
Q ss_pred HHHHhHcCCCceEEEecc-hHHHHHHHH---hcCCcc--CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcc
Q 022027 173 SLQLLLEDSTILKVGVGI-GSDAGKVYR---DYNVSV--KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRI 246 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~i-k~Dl~~L~~---~~gi~l--~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i 246 (304)
.+.+++.+ ....||||. ..|+..|.+ .+|+.. ...+|+..++.. +.+....++|..+++.| |.....
T Consensus 72 ~~~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~-~~~~~~~~~L~~l~~~~-~~~~~~---- 144 (232)
T PRK06309 72 KFIEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQK-YRPDLPKHNLQYLRQVY-GFEENQ---- 144 (232)
T ss_pred HHHHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHH-HcCCCCCCCHHHHHHHc-CCCCCC----
Confidence 34445543 356799995 899988864 345543 244799788765 33333478999999886 543221
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 247 RLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 247 ~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
. .-|..||+++..|+..+..
T Consensus 145 -a-------------H~Al~Da~~t~~vl~~l~~ 164 (232)
T PRK06309 145 -A-------------HRALDDVITLHRVFSALVG 164 (232)
T ss_pred -C-------------CCcHHHHHHHHHHHHHHHH
Confidence 1 1278899999998888653
No 44
>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=94.11 E-value=0.91 Score=48.61 Aligned_cols=65 Identities=20% Similarity=0.146 Sum_probs=44.8
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHh---cCCc-cC-CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCccc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVS-VK-ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKEL 240 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~-l~-~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l 240 (304)
..|.+++.+ -+.||||+..|...|.+. +|+. .. ..+|+..++..++. ...+++|.+|++++ |...
T Consensus 72 ~~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p-~~~~~~L~~l~~~~-gi~~ 141 (850)
T TIGR01407 72 QEIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFP-TEESYQLSELSEAL-GLTH 141 (850)
T ss_pred HHHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcC-CCCCCCHHHHHHHC-CCCC
Confidence 345566654 357999999999888643 4554 23 34799778866543 44689999999884 6544
No 45
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=93.63 E-value=0.28 Score=51.20 Aligned_cols=99 Identities=19% Similarity=0.210 Sum_probs=59.7
Q ss_pred CceEEEecchHHHHHHHHhcCCccCCc--chHHHHHHHHhC-------------------------C-----------CC
Q 022027 182 TILKVGVGIGSDAGKVYRDYNVSVKAS--EDLSYLAKHKIG-------------------------G-----------DS 223 (304)
Q Consensus 182 ~i~KVG~~ik~Dl~~L~~~~gi~l~~~--~Dl~~LA~ylL~-------------------------~-----------~~ 223 (304)
.-+.||||+.+|-..++..|.|.-... +|++.+.--.-| + ..
T Consensus 241 e~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia~~Gm~S~Qrplw~ka~k~k~a~~d~~~~ps~~d~~~pWL~~S 320 (1075)
T KOG3657|consen 241 EQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIAMSGMCSRQRPLWFKARKAKSAMYDSETNPSISDYDNPWLGRS 320 (1075)
T ss_pred CceEEeccccchHHHHHHHHhccccceeeeechhhhhhhhccccccchhHhhhhhhhhhhhhcccCCchhhhhhhhhhhh
Confidence 356799999999999988999865433 587544211100 0 01
Q ss_pred CCCCHHHHHHHHcCcc-cCCCCccccCCCCCCCCCH---HHHHHHHHHHHHHHHHHHHHhC
Q 022027 224 QKWGLASLTEMLVCKE-LKKPNRIRLGNWEADVLSK---DQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 224 ~~~sL~~La~~~Lg~~-l~K~~~i~~s~W~~~pLt~---~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.-.||.++.+.+.|.. +.|.....+-.-...++.+ +-+.|.|.|++++.++|.++-+
T Consensus 321 S~NSL~dVhk~~c~~~~LdKt~Rd~Fvs~~~e~Ire~fq~L~~YCA~Dv~aThqVf~~lfP 381 (1075)
T KOG3657|consen 321 SLNSLVDVHKFHCGIDALDKTPRDSFVSGTKEQIRENFQPLMNYCARDVIATHQVFFRLFP 381 (1075)
T ss_pred hhHHHHHHHHhhCCCCccccchHHhhhcCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhH
Confidence 1235777777787776 7665432211111111111 1348999999999999887743
No 46
>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=93.24 E-value=0.79 Score=37.16 Aligned_cols=83 Identities=19% Similarity=0.082 Sum_probs=54.5
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHhcC-----CccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRDYN-----VSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRI 246 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~g-----i~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i 246 (304)
..+..++.. ...|||+...|...|.+.+. ......+|+..++....+ ....+++..+...+++....+
T Consensus 71 ~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~---- 143 (159)
T cd06127 71 PEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLP-GLRSHRLGLLLAERYGIPLEG---- 143 (159)
T ss_pred HHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcC-CCCcCchHHHHHHHcCCCCCC----
Confidence 456667766 57899999999998865432 222345799878776554 335778888844444542211
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 247 RLGNWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 247 ~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
..-|..||.++..|+
T Consensus 144 --------------~H~Al~Da~~t~~l~ 158 (159)
T cd06127 144 --------------AHRALADALATAELL 158 (159)
T ss_pred --------------CCCcHHHHHHHHHHh
Confidence 123888999998876
No 47
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=93.10 E-value=0.54 Score=42.36 Aligned_cols=80 Identities=19% Similarity=0.053 Sum_probs=51.6
Q ss_pred CceEEEecchHHHHHHHHh---cCCcc---CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCC
Q 022027 182 TILKVGVGIGSDAGKVYRD---YNVSV---KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADV 255 (304)
Q Consensus 182 ~i~KVG~~ik~Dl~~L~~~---~gi~l---~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~p 255 (304)
..+.||||...|...|.+. +|+.. ..++|+..++..+......+++|+.|+++| |+.....
T Consensus 93 ~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~-gi~~~~a------------ 159 (232)
T PRK07942 93 GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHY-GVRLDNA------------ 159 (232)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHc-CCCCCCC------------
Confidence 3466999999999888543 45431 234788666654322112468999999875 6543211
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 256 LSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 256 Lt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.-|..||.++.+|+..|..
T Consensus 160 ------H~Al~Da~ata~l~~~l~~ 178 (232)
T PRK07942 160 ------HEATADALAAARVAWALAR 178 (232)
T ss_pred ------CChHHHHHHHHHHHHHHHH
Confidence 1278899988888887754
No 48
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=92.67 E-value=2.8 Score=45.45 Aligned_cols=84 Identities=23% Similarity=0.207 Sum_probs=54.5
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHh---cCCcc-C-CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccc
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSV-K-ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIR 247 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l-~-~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~ 247 (304)
.|..++.+ .+.||||+..|...|.+. +|+.. . ..+|+..++..++ +...+++|..|++.+ |......
T Consensus 77 ~l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~-p~~~~~~L~~l~~~l-~i~~~~~---- 148 (928)
T PRK08074 77 EIVELLEG--AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILL-PTAESYKLRDLSEEL-GLEHDQP---- 148 (928)
T ss_pred HHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhc-CCCCCCCHHHHHHhC-CCCCCCC----
Confidence 46667764 467999999999988643 45543 2 3479988886544 344688999999874 5543211
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 022027 248 LGNWEADVLSKDQLLYAATDAFASWHLYQVL 278 (304)
Q Consensus 248 ~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L 278 (304)
+-|-.||.++..|+..|
T Consensus 149 --------------H~Al~DA~ata~l~~~l 165 (928)
T PRK08074 149 --------------HRADSDAEVTAELFLQL 165 (928)
T ss_pred --------------CChHHHHHHHHHHHHHH
Confidence 11556666666655555
No 49
>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=92.23 E-value=1.3 Score=38.82 Aligned_cols=102 Identities=13% Similarity=0.133 Sum_probs=58.2
Q ss_pred CcHHHHHhHcC--CCceEEEecchH-HHHHHHH---hcCCcc------------------------CC--cchHHHHHHH
Q 022027 170 IPPSLQLLLED--STILKVGVGIGS-DAGKVYR---DYNVSV------------------------KA--SEDLSYLAKH 217 (304)
Q Consensus 170 ~~~~L~~lL~d--~~i~KVG~~ik~-Dl~~L~~---~~gi~l------------------------~~--~~Dl~~LA~y 217 (304)
+...+..++.. |. +.+|||+.+ |+..|.+ .+|+.. .| .+|+-.+...
T Consensus 54 lL~~f~~~i~~~dPD-vi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~ 132 (193)
T cd05784 54 LLLALIAWFAQYDPD-IIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKT 132 (193)
T ss_pred HHHHHHHHHHhhCCC-EEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHH
Confidence 34444444444 44 458999774 7776654 344432 12 2476444432
Q ss_pred HhCCCCCCCCHHHHHHHHcCcccCC-CC-----ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 022027 218 KIGGDSQKWGLASLTEMLVCKELKK-PN-----RIRLGNWEADVLSKDQLLYAATDAFASWHLYQ 276 (304)
Q Consensus 218 lL~~~~~~~sL~~La~~~Lg~~l~K-~~-----~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~ 276 (304)
. .....+++|+.+++++||..-.. .. ++. .-|...+ ..-++|+..||..+++|++
T Consensus 133 ~-~~kl~sy~L~~Va~~~Lg~~K~~~~~~~~~~eI~-~~~~~~~--~~l~~Y~~~Da~L~l~L~~ 193 (193)
T cd05784 133 A-TYHFESFSLENVAQELLGEGKLIHDVDDRGAEIE-RLFREDK--LALARYNLQDCELVWRIFE 193 (193)
T ss_pred c-cCCCCcCCHHHHHHHHhCCCccccCcccCHHHHH-HHHhhCH--HHHHHHHHHHHHHHHHHhC
Confidence 1 11236899999999999853211 11 111 1233322 3467999999999999863
No 50
>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=92.23 E-value=1.6 Score=35.97 Aligned_cols=81 Identities=21% Similarity=0.122 Sum_probs=55.3
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHH---hcCCccC--CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYR---DYNVSVK--ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRI 246 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~---~~gi~l~--~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i 246 (304)
..|..++.+ ...|||++..|...|.+ .+|+... ..+|+..++..+.. ....++|+.+++.+ |.... .
T Consensus 69 ~~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~-~~~~~~L~~l~~~~-g~~~~-~--- 140 (156)
T cd06130 69 PEIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWP-LLPNHKLNTVAEHL-GIELN-H--- 140 (156)
T ss_pred HHHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhc-cCCCCCHHHHHHHc-CCCcc-C---
Confidence 356667765 46799999999998854 3455432 33799777766544 34578999999874 55332 1
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 247 RLGNWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 247 ~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
.-|..||.++..|+
T Consensus 141 ---------------H~Al~Da~~ta~l~ 154 (156)
T cd06130 141 ---------------HDALEDARACAEIL 154 (156)
T ss_pred ---------------cCchHHHHHHHHHH
Confidence 22778899888876
No 51
>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=92.12 E-value=3.4 Score=45.94 Aligned_cols=87 Identities=17% Similarity=0.179 Sum_probs=60.9
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHh---cCCcc--CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSV--KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRI 246 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l--~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i 246 (304)
+.+..++.+ -+.||||+..|...|.+. +|+.. ...+|+..++..+ .+....++|+.|++++ |.....
T Consensus 262 ~~f~~fl~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l-~p~~k~~kL~~Lak~l-gi~~~~---- 333 (1213)
T TIGR01405 262 EKFKEFFKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARAL-NPEYKSHRLGNICKKL-GVDLDD---- 333 (1213)
T ss_pred HHHHHHhCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHH-hccCCCCCHHHHHHHc-CCCCCC----
Confidence 455666765 467999999999988653 45532 2347997777654 4445689999999885 654321
Q ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 247 RLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 247 ~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.+.|..||.++..|+..|.+
T Consensus 334 --------------~HrAl~DA~aTa~I~~~ll~ 353 (1213)
T TIGR01405 334 --------------HHRADYDAEATAKVFKVMVE 353 (1213)
T ss_pred --------------CcCHHHHHHHHHHHHHHHHH
Confidence 13488899999998888764
No 52
>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=91.92 E-value=1.3 Score=38.43 Aligned_cols=77 Identities=18% Similarity=0.103 Sum_probs=52.2
Q ss_pred CceEEEecchHHHHHHHH---hcCCc---c--CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCC
Q 022027 182 TILKVGVGIGSDAGKVYR---DYNVS---V--KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEA 253 (304)
Q Consensus 182 ~i~KVG~~ik~Dl~~L~~---~~gi~---l--~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~ 253 (304)
..+.|||++..|+..|.+ .+|+. . ...+|+..++..+.+ ..+|+.++++| |+......
T Consensus 102 ~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~----~~~L~~l~~~~-gi~~~~~~--------- 167 (189)
T cd06134 102 RAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG----QTVLAKACQAA-GIEFDNKE--------- 167 (189)
T ss_pred CCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC----CCcHHHHHHHC-CCCCCCCC---------
Confidence 357899999999988864 35552 1 135799888876532 35799999875 65432110
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 254 DVLSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 254 ~pLt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
..-|..||.++..|+..|.
T Consensus 168 -------~H~Al~DA~ata~lf~~l~ 186 (189)
T cd06134 168 -------AHSALYDTQKTAELFCKIV 186 (189)
T ss_pred -------CcChHHHHHHHHHHHHHHH
Confidence 1228899999999998775
No 53
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=91.90 E-value=0.16 Score=49.06 Aligned_cols=89 Identities=21% Similarity=0.201 Sum_probs=61.1
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWE 252 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~ 252 (304)
.|+.|+ ++.-+-|||++..|+..|+-.+ ..++|++++..+..++.....+|..|++.|||+.+. . .....+
T Consensus 286 ~l~~~~-~~~TILVGHSLenDL~aLKl~H----~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq-~-~~~~Hd-- 356 (380)
T KOG2248|consen 286 ELLELI-SKNTILVGHSLENDLKALKLDH----PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQ-E-GVGGHD-- 356 (380)
T ss_pred HHHhhc-CcCcEEEeechhhHHHHHhhhC----CceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHh-c-cCCCCc--
Confidence 466644 4556779999999999995433 355798777766555323577899999999998764 1 111111
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhCC
Q 022027 253 ADVLSKDQLLYAATDAFASWHLYQVLKSL 281 (304)
Q Consensus 253 ~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l 281 (304)
+..||.+++.|.......
T Consensus 357 -----------S~eDA~acm~Lv~~k~~~ 374 (380)
T KOG2248|consen 357 -----------SVEDALACMKLVKLKIKN 374 (380)
T ss_pred -----------cHHHHHHHHHHHHHHHhc
Confidence 678999999887765443
No 54
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=91.48 E-value=1.4 Score=41.43 Aligned_cols=85 Identities=18% Similarity=0.160 Sum_probs=58.2
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHH---hcCCccC--CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccc
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYR---DYNVSVK--ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIR 247 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~---~~gi~l~--~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~ 247 (304)
.|.+++.+ -+.|||++..|+..|.+ .+|+... ..+|+..++..++. ....++|..|++++ |....
T Consensus 73 ~~~~fl~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~-~~~~~~L~~L~~~~-gi~~~------ 142 (309)
T PRK06195 73 KIKHYFNN--NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYS-NIDNARLNTVNNFL-GYEFK------ 142 (309)
T ss_pred HHHHHhCC--CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcC-CCCcCCHHHHHHHc-CCCCc------
Confidence 45556654 46799999999988854 3455433 34798778876543 33578999999885 53210
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 248 LGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 248 ~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
. +-|..||.++.+|+..|.+
T Consensus 143 ~-------------H~Al~DA~ata~l~~~l~~ 162 (309)
T PRK06195 143 H-------------HDALADAMACSNILLNISK 162 (309)
T ss_pred c-------------cCCHHHHHHHHHHHHHHHH
Confidence 1 2377899999888877754
No 55
>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=91.43 E-value=1.7 Score=36.38 Aligned_cols=86 Identities=17% Similarity=0.044 Sum_probs=55.5
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHh---cCCc-----cCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCC
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVS-----VKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKP 243 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~-----l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~ 243 (304)
..|..++.+. ..|||++..|+..|.+. +|.. ....+|+..++..+ .+. ..++|+.+++++ |......
T Consensus 73 ~~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~-~~~-~~~~L~~l~~~~-~i~~~~~ 147 (167)
T cd06131 73 DEFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKK-FPG-KPNSLDALCKRF-GIDNSHR 147 (167)
T ss_pred HHHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHH-cCC-CCCCHHHHHHHC-CCCCCCC
Confidence 3455666653 45899999999888543 3332 12347986666543 333 577999999986 5432110
Q ss_pred CccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 022027 244 NRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVL 278 (304)
Q Consensus 244 ~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L 278 (304)
+..-|..||.++..|+..|
T Consensus 148 ----------------~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 148 ----------------TLHGALLDAELLAEVYLEL 166 (167)
T ss_pred ----------------CCCChHHHHHHHHHHHHHh
Confidence 1123889999999998765
No 56
>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=90.99 E-value=1.6 Score=39.11 Aligned_cols=89 Identities=16% Similarity=0.048 Sum_probs=59.0
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHH---hcCC--c-c---CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYR---DYNV--S-V---KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKP 243 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~---~~gi--~-l---~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~ 243 (304)
.|..++.+ ...|+||+..|+..|.. .+|. . + ..++|+..++..++ ++ .+++|+.|+++| |+.....
T Consensus 75 ~f~~fi~~--~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~-p~-~~~~L~~L~~~~-gi~~~~r 149 (225)
T TIGR01406 75 EFLDFIGG--SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERF-PG-QRNSLDALCKRF-KVDNSHR 149 (225)
T ss_pred HHHHHhCC--CEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHc-CC-CCCCHHHHHHhc-CCCCCCC
Confidence 45556655 34589999999988864 3452 2 1 34579877776654 33 578999999986 5432110
Q ss_pred CccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCC
Q 022027 244 NRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLP 282 (304)
Q Consensus 244 ~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~ 282 (304)
. ..-|..||.++..||..|..-.
T Consensus 150 ---~-------------~H~Al~DA~~~a~v~~~l~~~~ 172 (225)
T TIGR01406 150 ---T-------------LHGALLDAHLLAEVYLALTGGQ 172 (225)
T ss_pred ---C-------------CcCHHHHHHHHHHHHHHHHcCC
Confidence 0 1228899999999999886533
No 57
>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=90.76 E-value=7.6 Score=33.71 Aligned_cols=148 Identities=17% Similarity=0.171 Sum_probs=81.1
Q ss_pred CceEEEEeeeecCcc-CCCCCCcEEEEEEEecCCeEEEEecCC---CCCcHHHHHhHcC--CCceEEEecch-HHHHHHH
Q 022027 126 QVVVGFDIEWKPTFR-KGVLPRKAAVMQICGDSNHCYVMQIIH---SGIPPSLQLLLED--STILKVGVGIG-SDAGKVY 198 (304)
Q Consensus 126 ~~~vgfD~E~~~~~~-~g~~~~~valiQL~~~~~~~~l~~l~~---~~~~~~L~~lL~d--~~i~KVG~~ik-~Dl~~L~ 198 (304)
-..++||+|...... +.....++..|.++...+...++.-.. .++...+..++.. |.+ .+|+|+. .|+..|.
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~lL~~F~~~i~~~dPd~-i~gyN~~~FDlpyl~ 81 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDI-IVGYNSNAFDWPYLV 81 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEEecCCCHHHHHHHHHHHHHHcCCCE-EEecCCCcCcHHHHH
Confidence 367899999863210 111124566666665444444432211 2344455555554 443 5788854 7776665
Q ss_pred H---hcCCccC--------------------C--cchHHHHHHHHhCCCCCCCCHHHHHHHHcCcc--cCCC----Cccc
Q 022027 199 R---DYNVSVK--------------------A--SEDLSYLAKHKIGGDSQKWGLASLTEMLVCKE--LKKP----NRIR 247 (304)
Q Consensus 199 ~---~~gi~l~--------------------~--~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~--l~K~----~~i~ 247 (304)
. .+|+.+. | .+|+-.+..... ...+++|+.+++ +||.. ..|. .++
T Consensus 82 ~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~--~l~~y~L~~Va~-~Lg~~k~~~k~~~~~~~i- 157 (188)
T cd05781 82 ERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP--EVKVKTLENVAE-YLGVMKKSERVLIEWYRI- 157 (188)
T ss_pred HHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC--CCCCCCHHHHHH-HHCCCccccccCCCHHHH-
Confidence 3 4565331 1 357644444322 235899999997 57753 1111 011
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 022027 248 LGNWEADVLSKDQLLYAATDAFASWHLYQVL 278 (304)
Q Consensus 248 ~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L 278 (304)
..-|....-...-.+|...|+..++.|+..+
T Consensus 158 ~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~~ 188 (188)
T cd05781 158 YEYWDDEKKRDILLKYNRDDARSTYGLAEKL 188 (188)
T ss_pred HHHHcCcccHHHHHHHHHHHHHHHHHHHhhC
Confidence 1134332123557799999999999998753
No 58
>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=90.76 E-value=7.4 Score=34.30 Aligned_cols=100 Identities=15% Similarity=0.166 Sum_probs=58.6
Q ss_pred CcHHHHHhHcCCCceEEEecch-HHHHHHHH---hcCCc--------------cCCc--chHHHHHHH------HhCCCC
Q 022027 170 IPPSLQLLLEDSTILKVGVGIG-SDAGKVYR---DYNVS--------------VKAS--EDLSYLAKH------KIGGDS 223 (304)
Q Consensus 170 ~~~~L~~lL~d~~i~KVG~~ik-~Dl~~L~~---~~gi~--------------l~~~--~Dl~~LA~y------lL~~~~ 223 (304)
++..+..++.+. -+.+|+|.. .|+..|.. .+|+. +.+. +|+-..... ..+...
T Consensus 76 lL~~F~~~i~~~-~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~ 154 (204)
T cd05783 76 LIREAFKIISEY-PIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKY 154 (204)
T ss_pred HHHHHHHHHhcC-CEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcccc
Confidence 344555566665 366788866 77777654 45665 1112 466333321 122223
Q ss_pred CCCCHHHHHHHHcCcccCCCCccccCCCCCCCCC-HHHHHHHHHHHHHHHHHHH
Q 022027 224 QKWGLASLTEMLVCKELKKPNRIRLGNWEADVLS-KDQLLYAATDAFASWHLYQ 276 (304)
Q Consensus 224 ~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt-~~Qi~YAA~DA~a~~~L~~ 276 (304)
.+++|+.+++.+||.. |. .+...-|. +. .+-++|+..||..++.|..
T Consensus 155 ~~~~L~~Va~~~lg~~--K~-~~~~~i~~---~~~~~l~~Y~~~D~~lt~~L~~ 202 (204)
T cd05783 155 REYTLDAVAKALLGEG--KV-ELEKNISE---LNLYELAEYNYRDAELTLELTT 202 (204)
T ss_pred ccCcHHHHHHHhcCCC--cc-cCCchhhh---hcHHHHHHhhHHHHHHHHHHhc
Confidence 5889999999999862 11 11101121 23 3356999999999998864
No 59
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=90.08 E-value=3.7 Score=33.99 Aligned_cols=87 Identities=23% Similarity=0.135 Sum_probs=56.7
Q ss_pred HHHHHhHcCCCceEEEecc-hHHHHHHHHh---cCCccC---CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCC
Q 022027 172 PSLQLLLEDSTILKVGVGI-GSDAGKVYRD---YNVSVK---ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPN 244 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~i-k~Dl~~L~~~---~gi~l~---~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~ 244 (304)
..|..++.+. + .|+|+. +.|+..|.+. +|+... ..+|+..++....+ . ..++|+.+++.+.. ....
T Consensus 72 ~~~~~~l~~~-~-~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~-~-~~~~L~~l~~~~~~-~~~~-- 144 (169)
T smart00479 72 EELLEFLKGK-I-LVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNP-G-RKYSLKKLAERLGL-EVIG-- 144 (169)
T ss_pred HHHHHHhcCC-E-EEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCC-C-CCCCHHHHHHHCCC-CCCC--
Confidence 3566677653 3 466666 9999988653 444322 24799777754433 3 48999999988732 2210
Q ss_pred ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 245 RIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 245 ~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
. ...|..||.++..|+..+..
T Consensus 145 ---~------------~H~A~~Da~~t~~l~~~~~~ 165 (169)
T smart00479 145 ---R------------AHRALDDARATAKLFKKLVE 165 (169)
T ss_pred ---C------------CcCcHHHHHHHHHHHHHHHH
Confidence 0 13488999999999988754
No 60
>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=89.40 E-value=2.1 Score=35.09 Aligned_cols=65 Identities=22% Similarity=0.193 Sum_probs=38.8
Q ss_pred HHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHH
Q 022027 192 SDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFAS 271 (304)
Q Consensus 192 ~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~ 271 (304)
.|+..+...-|+.+.---|- +|.+|+|++ .+-+...++++|++-. |.. -|+..|.++
T Consensus 71 K~LAv~a~~~G~~v~PGDDP-lLlAYLlDP--sNt~p~~varRY~~~~-----------W~~---------dA~~RA~~t 127 (138)
T PF09281_consen 71 KDLAVHALREGVVVEPGDDP-LLLAYLLDP--SNTNPEGVARRYLGGE-----------WPE---------DAATRALAT 127 (138)
T ss_dssp HHHHHHHHHTT----B---H-HHHHHHH-T--T--SHHHHHHHH-TS--------------S---------SHHHHHHHH
T ss_pred HHHHHHHHhcCcccCCCCCc-chhhhhcCc--cCCChHHHHHHhcCCC-----------CCc---------cHHHHHHHH
Confidence 45555556778877544455 888899996 5778999999998643 432 278888899
Q ss_pred HHHHHHHh
Q 022027 272 WHLYQVLK 279 (304)
Q Consensus 272 ~~L~~~L~ 279 (304)
.+|++.|.
T Consensus 128 ~~L~~~L~ 135 (138)
T PF09281_consen 128 ARLLRALP 135 (138)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhh
Confidence 88888775
No 61
>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=89.26 E-value=1.9 Score=37.04 Aligned_cols=81 Identities=19% Similarity=0.072 Sum_probs=53.2
Q ss_pred HHHHHhHcC--CCceEEEecc-hHHHHHHHH---hcCCccC--C-cchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCC
Q 022027 172 PSLQLLLED--STILKVGVGI-GSDAGKVYR---DYNVSVK--A-SEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKK 242 (304)
Q Consensus 172 ~~L~~lL~d--~~i~KVG~~i-k~Dl~~L~~---~~gi~l~--~-~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K 242 (304)
+.|..++.. ...+.||||+ ..|+..|.+ .+|+... . .+|+..++..+ . . +|+.|+++++|.....
T Consensus 86 ~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~-~----~-~L~~l~~~~~~~~~~~ 159 (177)
T cd06136 86 NLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFREL-D----Q-SLGSLYKRLFGQEPKN 159 (177)
T ss_pred HHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhh-H----h-hHHHHHHHHhCCCccc
Confidence 346666653 3467899998 799988854 3455432 2 26875565432 2 1 8999999887765432
Q ss_pred CCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 022027 243 PNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQ 276 (304)
Q Consensus 243 ~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~ 276 (304)
. .-|..||.++.+++.
T Consensus 160 ~------------------H~A~~Da~at~~v~~ 175 (177)
T cd06136 160 S------------------HTAEGDVLALLKCAL 175 (177)
T ss_pred c------------------cchHHHHHHHHHHHh
Confidence 1 238899999987764
No 62
>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=88.79 E-value=3.3 Score=36.73 Aligned_cols=93 Identities=15% Similarity=0.046 Sum_probs=58.5
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHhcC---C--ccC-CcchHHHHHHHHhCC-CCCCCCHHHHHHHHcCcccCCCCc
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRDYN---V--SVK-ASEDLSYLAKHKIGG-DSQKWGLASLTEMLVCKELKKPNR 245 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~g---i--~l~-~~~Dl~~LA~ylL~~-~~~~~sL~~La~~~Lg~~l~K~~~ 245 (304)
.|..++.+ -..||||+..|+..|.+.+. . ... .++|+..++.++... +..+++|..+++++ |......
T Consensus 80 ~~~~~~~~--~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~-gl~~~~~-- 154 (217)
T TIGR00573 80 DFADYIRG--AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRY-EITNSHR-- 154 (217)
T ss_pred HHHHHhCC--CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHc-CCCCCCc--
Confidence 45556654 35789999999999976532 1 122 346876666554321 12467999999886 5432100
Q ss_pred cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCc
Q 022027 246 IRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPEP 284 (304)
Q Consensus 246 i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~ 284 (304)
. ..-|..||.++..|+..+......
T Consensus 155 -~-------------~H~Al~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 155 -A-------------LHGALADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred -c-------------cCCHHHHHHHHHHHHHHHHhcchh
Confidence 0 112888999999999998765433
No 63
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=88.66 E-value=5.8 Score=35.05 Aligned_cols=99 Identities=17% Similarity=0.054 Sum_probs=56.3
Q ss_pred HHHHhHcC--CCceEEEecch-HHHHHHHH---hcCCccC----------------C--cchHHHHHHHHhCCCCCCCCH
Q 022027 173 SLQLLLED--STILKVGVGIG-SDAGKVYR---DYNVSVK----------------A--SEDLSYLAKHKIGGDSQKWGL 228 (304)
Q Consensus 173 ~L~~lL~d--~~i~KVG~~ik-~Dl~~L~~---~~gi~l~----------------~--~~Dl~~LA~ylL~~~~~~~sL 228 (304)
.+..++.+ |.+ .+|+|+. .|+..|.. .+|+.+. + .+|+-.+...-......+++|
T Consensus 79 ~f~~~i~~~~Pd~-i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysL 157 (204)
T cd05779 79 RFFEHIREVKPHI-IVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGL 157 (204)
T ss_pred HHHHHHHHhCCCE-EEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccH
Confidence 44444444 444 4788754 67766653 3554322 1 246644443110111247899
Q ss_pred HHHHHHHcCcccCCC--CccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 229 ASLTEMLVCKELKKP--NRIRLGNWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 229 ~~La~~~Lg~~l~K~--~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
+.+++.+||..-... .++. .-|...+ ..-++|.-.||..++.||
T Consensus 158 d~Va~~~Lg~~K~~~~~~~I~-~~~~~~~--~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 158 KAVTKAKLGYDPVELDPEDMV-PLAREDP--QTLASYSVSDAVATYYLY 203 (204)
T ss_pred HHHHHHHhCCCcCcCCHHHHH-HHHhCCc--HHHHhccHHHHHHHHHHh
Confidence 999999999632111 1111 1354432 457899999999999987
No 64
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=88.56 E-value=16 Score=34.19 Aligned_cols=86 Identities=14% Similarity=-0.019 Sum_probs=51.7
Q ss_pred cHHHHHhHcCCCceEEEecchHHHHHHHHhcCCccCC--cchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCcccc
Q 022027 171 PPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKA--SEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRL 248 (304)
Q Consensus 171 ~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~--~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~ 248 (304)
.+.+..++... -+.|+||+..|...|.+ +.....+ ..++.....+. ..+..+++|..|+..| |.. ..
T Consensus 111 ~~~l~~fl~~~-~vlVAHNA~FD~~fL~~-~~~~~~~~~~~ct~~~i~~~-~~~~~~~kL~~La~~~-g~~--~~----- 179 (294)
T PRK09182 111 PAAVDALIAPA-DLIIAHNAGFDRPFLER-FSPVFATKPWACSVSEIDWS-ARGFEGTKLGYLAGQA-GFF--HE----- 179 (294)
T ss_pred HHHHHHHhcCC-CEEEEeCHHHHHHHHHH-HHHhccCCcccccHHHHhhc-cccCCCCCHHHHHHHc-CCC--CC-----
Confidence 34677777764 46799999999999854 3322221 12332222221 1123578999999875 421 10
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 249 GNWEADVLSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 249 s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
..-|..||.++..|+....
T Consensus 180 ------------aHrAl~Da~Ata~ll~~~l 198 (294)
T PRK09182 180 ------------GHRAVDDCQALLELLARPL 198 (294)
T ss_pred ------------CcChHHHHHHHHHHHHHHH
Confidence 1228899999998888543
No 65
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=88.50 E-value=4.9 Score=38.85 Aligned_cols=97 Identities=12% Similarity=0.112 Sum_probs=58.3
Q ss_pred cHHHHHhHcCCCceEEEecchHHHHHHHHhc-------------------------------CCccC-CcchHHHHHHHH
Q 022027 171 PPSLQLLLEDSTILKVGVGIGSDAGKVYRDY-------------------------------NVSVK-ASEDLSYLAKHK 218 (304)
Q Consensus 171 ~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~-------------------------------gi~l~-~~~Dl~~LA~yl 218 (304)
.+.|.+++.+ -+.|+|+...|+..|.+.+ ++... .++|+..++..+
T Consensus 116 l~el~~fL~g--~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl 193 (377)
T PRK05601 116 LKPLDRLIDG--RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQ 193 (377)
T ss_pred HHHHHHHhCC--CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHH
Confidence 3456667765 3579999999999885532 12222 347997888654
Q ss_pred hCCCCCCCCHHHHHHHHcCcccCCCC-ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 022027 219 IGGDSQKWGLASLTEMLVCKELKKPN-RIRLGNWEADVLSKDQLLYAATDAFASWHLYQVL 278 (304)
Q Consensus 219 L~~~~~~~sL~~La~~~Lg~~l~K~~-~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L 278 (304)
.+...++.|..|+++| |+..+... ++.. ..-+.+++ +-.||.++..||..+
T Consensus 194 -~p~l~~~rL~~La~~l-Gi~~p~~~A~~~R-----a~~p~~~l--~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 194 -GVALDDIRIRGVAHTL-GLDAPAAEASVER-----AQVPHRQL--CREETLLVARLYFAL 245 (377)
T ss_pred -cCCCCCCCHHHHHHHh-CCCCCchhhhhhh-----hcCChhhh--hhHHHHHHHHHHHHh
Confidence 4444689999999985 65543210 0110 01111121 224888888888875
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=88.40 E-value=5.4 Score=35.24 Aligned_cols=146 Identities=16% Similarity=0.185 Sum_probs=75.5
Q ss_pred CceEEEEeeeecC---ccCCCCCCcEEEEEEEecC--CeEEEEecCCC---CCcHHHHHhHcC--CCceEEEecc-hHHH
Q 022027 126 QVVVGFDIEWKPT---FRKGVLPRKAAVMQICGDS--NHCYVMQIIHS---GIPPSLQLLLED--STILKVGVGI-GSDA 194 (304)
Q Consensus 126 ~~~vgfD~E~~~~---~~~g~~~~~valiQL~~~~--~~~~l~~l~~~---~~~~~L~~lL~d--~~i~KVG~~i-k~Dl 194 (304)
-..++||+|.... +.++..+..-.++|++... +...++..... .++..+..++.. |. +.+|||+ ..|+
T Consensus 9 lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~E~~lL~~f~~~i~~~dPd-ii~g~N~~~FD~ 87 (207)
T cd05785 9 LRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVLHAEDAAEKELLEELVAIIRERDPD-VIEGHNIFRFDL 87 (207)
T ss_pred ceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeeeccCCCCHHHHHHHHHHHHHHhCCC-EEeccCCcccCH
Confidence 4678999998643 1111112233467776532 21222222111 234444444444 55 4579998 5788
Q ss_pred HHHHH---hcCCcc------------------------------CCc--chHHHHHHHH-h-CCCCCCCCHHHHHHHH--
Q 022027 195 GKVYR---DYNVSV------------------------------KAS--EDLSYLAKHK-I-GGDSQKWGLASLTEML-- 235 (304)
Q Consensus 195 ~~L~~---~~gi~l------------------------------~~~--~Dl~~LA~yl-L-~~~~~~~sL~~La~~~-- 235 (304)
..|.+ .+|+.. .|. +|+-.+...- . .....+++|+.+++.+
T Consensus 88 pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~ 167 (207)
T cd05785 88 PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGL 167 (207)
T ss_pred HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhcc
Confidence 77754 345433 111 4764333210 0 1122478999999986
Q ss_pred cCcc-cC-CCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 236 VCKE-LK-KPNRIRLGNWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 236 Lg~~-l~-K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
++.. .. ..+++ ..-|... ...-++|+..||..++.|+
T Consensus 168 ~~~~k~d~~~~~I-~~l~~~~--~~~l~~Y~~~D~~~t~~l~ 206 (207)
T cd05785 168 ASPDRTYIDGRQI-AEVWRSD--PARLLAYALDDVRETEGLA 206 (207)
T ss_pred cCCCcCCCCHHHH-HHHHhcC--HHHHHHHHHHHHHHHHHhh
Confidence 2221 10 01111 1124332 1457799999999998875
No 67
>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=87.53 E-value=3.7 Score=36.03 Aligned_cols=77 Identities=17% Similarity=0.070 Sum_probs=50.8
Q ss_pred CceEEEecchHHHHHHHHh---cCCc---c--CCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCC
Q 022027 182 TILKVGVGIGSDAGKVYRD---YNVS---V--KASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEA 253 (304)
Q Consensus 182 ~i~KVG~~ik~Dl~~L~~~---~gi~---l--~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~ 253 (304)
..+.|||++..|+..|.+. +|.. . ...+|+..++..+. ...+|+.+++++ |....
T Consensus 105 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~----~~~~L~~l~~~~-gi~~~------------ 167 (200)
T TIGR01298 105 RAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY----GQTVLAKACQAA-GXDFD------------ 167 (200)
T ss_pred CCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc----CcccHHHHHHHc-CCCcc------------
Confidence 3568999999999988543 3432 1 12579988876543 245799999875 54321
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHh
Q 022027 254 DVLSKDQLLYAATDAFASWHLYQVLK 279 (304)
Q Consensus 254 ~pLt~~Qi~YAA~DA~a~~~L~~~L~ 279 (304)
..+..-|..||.++..|+..|.
T Consensus 168 ----~~~~H~Al~Da~ata~lf~~l~ 189 (200)
T TIGR01298 168 ----STQAHSALYDTEKTAELFCEIV 189 (200)
T ss_pred ----ccchhhhHHhHHHHHHHHHHHH
Confidence 0122347789999888887765
No 68
>PRK05168 ribonuclease T; Provisional
Probab=87.38 E-value=5.1 Score=35.40 Aligned_cols=78 Identities=14% Similarity=0.061 Sum_probs=51.6
Q ss_pred CceEEEecchHHHHHHHH---hcCCc---cC--CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCC
Q 022027 182 TILKVGVGIGSDAGKVYR---DYNVS---VK--ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEA 253 (304)
Q Consensus 182 ~i~KVG~~ik~Dl~~L~~---~~gi~---l~--~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~ 253 (304)
..+.|||++..|+..|.+ .+|+. .. .++|+..++..+.+ ..+|..+++++ |..+... ..
T Consensus 114 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~----~~~L~~l~~~~-gl~~~~~---~~----- 180 (211)
T PRK05168 114 RAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG----QTVLAKACQAA-GIEFDNK---EA----- 180 (211)
T ss_pred CceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC----CCCHHHHHHHC-CCCCCCC---CC-----
Confidence 467899999999988854 34542 11 35799888865432 35799999874 5443211 01
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 254 DVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 254 ~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.-|..||.++..|+..|..
T Consensus 181 --------H~Al~DA~ata~l~~~l~~ 199 (211)
T PRK05168 181 --------HSALYDTEKTAELFCEIVN 199 (211)
T ss_pred --------CChHHHHHHHHHHHHHHHH
Confidence 1278899998888887653
No 69
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=87.14 E-value=6.2 Score=34.59 Aligned_cols=91 Identities=12% Similarity=0.097 Sum_probs=59.1
Q ss_pred HHHHHhHcCCCceEEEecch-HHHHHHHHhcCCccCCc--chHHHHH--HHHh-CCCCCCCCHHHHHHHHcCcccCCCCc
Q 022027 172 PSLQLLLEDSTILKVGVGIG-SDAGKVYRDYNVSVKAS--EDLSYLA--KHKI-GGDSQKWGLASLTEMLVCKELKKPNR 245 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik-~Dl~~L~~~~gi~l~~~--~Dl~~LA--~ylL-~~~~~~~sL~~La~~~Lg~~l~K~~~ 245 (304)
+.+..++.+. ..|||++. .|+..| +.+|..+.+. +|+-..+ .... .++..+++|..|+++| |....
T Consensus 76 ~~f~~f~~~~--~lVaHNa~~fD~~fL-~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~-gi~~~---- 147 (195)
T PRK07247 76 AAFKEFVGEL--PLIGYNAQKSDLPIL-AENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL-GIKGR---- 147 (195)
T ss_pred HHHHHHHCCC--eEEEEeCcHhHHHHH-HHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhc-CCCCC----
Confidence 3555667653 47999985 799998 5677765543 4542222 1111 1223579999999864 65321
Q ss_pred cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcc
Q 022027 246 IRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPEPV 285 (304)
Q Consensus 246 i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~~ 285 (304)
. .-|..||.++..||..|......+
T Consensus 148 --~-------------HrAl~DA~~ta~v~~~ll~~~~~~ 172 (195)
T PRK07247 148 --G-------------HNSLEDARMTARVYESFLESDQNK 172 (195)
T ss_pred --C-------------cCCHHHHHHHHHHHHHHHhhccch
Confidence 1 227889999999999998877665
No 70
>PRK11779 sbcB exonuclease I; Provisional
Probab=85.63 E-value=15 Score=36.81 Aligned_cols=88 Identities=14% Similarity=0.104 Sum_probs=51.8
Q ss_pred HHHHhHcCCCceEEEec-chHHHHHHHHhcC---Cc-----c---CCc---chHHHHHHHHhCC----------CCCCCC
Q 022027 173 SLQLLLEDSTILKVGVG-IGSDAGKVYRDYN---VS-----V---KAS---EDLSYLAKHKIGG----------DSQKWG 227 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~-ik~Dl~~L~~~~g---i~-----l---~~~---~Dl~~LA~ylL~~----------~~~~~s 227 (304)
.+..++..+..+.|||+ +..|...+...+. +. . ... +|+..++ |.+.+ +..++.
T Consensus 84 ~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~-~~lrp~~i~~P~~~~g~~s~r 162 (476)
T PRK11779 84 RIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRAC-YALRPEGINWPENEDGLPSFK 162 (476)
T ss_pred HHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHH-HHhccccccCcccccCCCCCc
Confidence 45556654455689997 7899987754331 11 0 111 3443333 22211 124689
Q ss_pred HHHHHHHHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 228 LASLTEMLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 228 L~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
|+.|++++ |+.... . +-|-.||+++..|+..|..
T Consensus 163 Le~L~~~~-gI~~~~-----A-------------HdALsDa~aT~~la~~l~~ 196 (476)
T PRK11779 163 LEHLTKAN-GIEHEN-----A-------------HDAMSDVYATIAMAKLIKQ 196 (476)
T ss_pred HHHHHHHc-CCCCCC-----C-------------CCcHHHHHHHHHHHHHHHH
Confidence 99999885 543211 1 2278899999998888874
No 71
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=85.42 E-value=0.22 Score=52.37 Aligned_cols=85 Identities=24% Similarity=0.306 Sum_probs=61.0
Q ss_pred hHcCCCceEEEecchHHHHHHHHhcCCccC--CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCC
Q 022027 177 LLEDSTILKVGVGIGSDAGKVYRDYNVSVK--ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEAD 254 (304)
Q Consensus 177 lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~--~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~ 254 (304)
+|-+-.+++|||++++|.+.+ ++.+. .++|+..+. +++ ..+..+|.-||.++||..+ |+..-+
T Consensus 1009 ~Li~~GviFVGHGL~nDFrvI----Ni~Vp~~QiiDTv~lf--~~~-s~R~LSLrfLa~~lLg~~I------Q~~~HD-- 1073 (1118)
T KOG1275|consen 1009 LLIQRGVIFVGHGLQNDFRVI----NIHVPEEQIIDTVTLF--RLG-SQRMLSLRFLAWELLGETI------QMEAHD-- 1073 (1118)
T ss_pred HHHHcCcEEEcccccccceEE----EEecChhhheeeeEEE--ecc-cccEEEHHHHHHHHhcchh------hccccc--
Confidence 577888999999999998765 44332 357874333 244 3468899999999998654 332211
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhCCCCcc
Q 022027 255 VLSKDQLLYAATDAFASWHLYQVLKSLPEPV 285 (304)
Q Consensus 255 pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~~ 285 (304)
...||..++.||.+-..|+.+.
T Consensus 1074 ---------SIeDA~taLkLYk~Yl~lkeq~ 1095 (1118)
T KOG1275|consen 1074 ---------SIEDARTALKLYKKYLKLKEQG 1095 (1118)
T ss_pred ---------cHHHHHHHHHHHHHHHHHHHhh
Confidence 4689999999999988887654
No 72
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=82.68 E-value=9.6 Score=34.04 Aligned_cols=86 Identities=12% Similarity=0.006 Sum_probs=55.8
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWE 252 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~ 252 (304)
.+..+.. .-+.||||+..|...| ...+ ...+|+..+|..++. + ..+++..|++.+ +.........
T Consensus 67 v~~~~~~--~~~lVaHNa~FD~~~L-~~~~---~~~idTl~lar~l~p-~-~~~~l~~L~~~~-~l~~~~~~~~------ 131 (219)
T PRK07983 67 VIPHYYG--SEWYVAHNASFDRRVL-PEMP---GEWICTMKLARRLWP-G-IKYSNMALYKSR-KLNVQTPPGL------ 131 (219)
T ss_pred HHHHHcC--CCEEEEeCcHhhHHHH-hCcC---CCcEeHHHHHHHHcc-C-CCCCHHHHHHHc-CCCCCCCCCC------
Confidence 3444433 3577999999999988 3322 345799888876553 3 358999888764 5432110000
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 253 ADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 253 ~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
+..-|..||+++..|+..+.+
T Consensus 132 -------~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 132 -------HHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred -------CCCcHHHHHHHHHHHHHHHHH
Confidence 113388999999999998874
No 73
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=82.47 E-value=13 Score=32.60 Aligned_cols=92 Identities=20% Similarity=0.149 Sum_probs=57.5
Q ss_pred HHHHHhHcCCCceEEEecchHHHHHHHHh---cCCccC---CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCc
Q 022027 172 PSLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSVK---ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNR 245 (304)
Q Consensus 172 ~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l~---~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~ 245 (304)
+.|..++.+.....+. +...|+..|.+. +|+... ..+|+..+.....+ ....++|+.+++++ |.....
T Consensus 84 ~~f~~~~~~~~~~iv~-~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~-~~~~~~L~~~~~~~-gi~~~~--- 157 (207)
T PRK07748 84 EKLAEYDKRCKPTIVT-WGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFG-ERNQTGLWKAIEEY-GKEGTG--- 157 (207)
T ss_pred HHHHHHhCcCCeEEEE-ECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhC-cCCCCCHHHHHHHc-CCCCCC---
Confidence 3566677764444454 468999888653 465432 34577655543333 23568999998875 543210
Q ss_pred cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 022027 246 IRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPE 283 (304)
Q Consensus 246 i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~ 283 (304)
+ ..-|..||.++..|+..|..-+.
T Consensus 158 -~-------------~H~Al~DA~~ta~l~~~l~~~~~ 181 (207)
T PRK07748 158 -K-------------HHCALDDAMTTYNIFKLVEKDKE 181 (207)
T ss_pred -C-------------CcChHHHHHHHHHHHHHHHhCcc
Confidence 0 12388999999999999886543
No 74
>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=79.97 E-value=20 Score=31.64 Aligned_cols=126 Identities=17% Similarity=0.095 Sum_probs=70.2
Q ss_pred CcEEEEEEEe---cCCeEEEEecCC---CCCcHHHHHhHcCCCceEEEecch-HHHHHHHH---hcCCccC---------
Q 022027 146 RKAAVMQICG---DSNHCYVMQIIH---SGIPPSLQLLLEDSTILKVGVGIG-SDAGKVYR---DYNVSVK--------- 206 (304)
Q Consensus 146 ~~valiQL~~---~~~~~~l~~l~~---~~~~~~L~~lL~d~~i~KVG~~ik-~Dl~~L~~---~~gi~l~--------- 206 (304)
.++..|.++. .++..-+..... ..+...+..++.+...+.||||.+ .|+-.|.. .+|+...
T Consensus 51 ~~Iv~Is~~~~~~~~~~~~~~~~~~~~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~ 130 (208)
T cd05782 51 HKVVSISALYRDDDGGFLKVRTLDGADEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKD 130 (208)
T ss_pred CceEEEEEEEEecCCCeEEEeecCCCCHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccch
Confidence 5677777665 223222221111 134455555666533467999985 88887764 3566322
Q ss_pred --------C-cchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCC---ccccCCCCCCCCCHHHHHHHHHHHHHHHHH
Q 022027 207 --------A-SEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPN---RIRLGNWEADVLSKDQLLYAATDAFASWHL 274 (304)
Q Consensus 207 --------~-~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~---~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L 274 (304)
+ .+|+..+.+. .+ ...+.+|+.+++ +||.+ .|.. +.-..-|.... -.+-.+|...||..++.|
T Consensus 131 ~~y~~r~~~~h~DL~~~~~~-~~-~~~~~~L~~va~-~lG~~-~K~d~~G~~v~~~y~~g~-~~~I~~Yc~~Dv~~t~~l 205 (208)
T cd05782 131 WNYRNRYSERHLDLMDLLAF-YG-ARARASLDLLAK-LLGIP-GKMDVDGSQVWELYAEGK-LDEIAEYCETDVLNTYLL 205 (208)
T ss_pred hhccCcCCCCcccHHHHHhc-cC-ccCCCCHHHHHH-HhCCC-CCcCCCHHHHHHHHHcCC-hHHHHHHHHHHHHHHHHH
Confidence 1 4577554432 12 235889999987 46652 2211 00112243322 344669999999999998
Q ss_pred HH
Q 022027 275 YQ 276 (304)
Q Consensus 275 ~~ 276 (304)
|.
T Consensus 206 ~l 207 (208)
T cd05782 206 YL 207 (208)
T ss_pred Hh
Confidence 85
No 75
>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=77.24 E-value=7.6 Score=32.24 Aligned_cols=142 Identities=16% Similarity=0.125 Sum_probs=65.5
Q ss_pred EEEEeeeecCccCCCCCCcEEEEEEEe--cCCeEEEEecCCC--CCcHHHH---HhHcCCCceEEEecc-hHHHHHHHHh
Q 022027 129 VGFDIEWKPTFRKGVLPRKAAVMQICG--DSNHCYVMQIIHS--GIPPSLQ---LLLEDSTILKVGVGI-GSDAGKVYRD 200 (304)
Q Consensus 129 vgfD~E~~~~~~~g~~~~~valiQL~~--~~~~~~l~~l~~~--~~~~~L~---~lL~d~~i~KVG~~i-k~Dl~~L~~~ 200 (304)
+-||+|+.+... + ...+.++.++. .++...+.+.... .-...+. .++.... ..|+|+. ..|...|.+.
T Consensus 1 l~~DIET~Gl~~-~--~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~l~~~~-~iv~yng~~FD~p~L~~~ 76 (164)
T PF13482_consen 1 LFFDIETTGLSP-D--NDTIYLIGVADFDDDEIITFIQWFAEDPDEEEIILEFFELLDEAD-NIVTYNGKNFDIPFLKRR 76 (164)
T ss_dssp --EEEEESS-GG----G---EEEEEEE-ETTTTE-EEEE-GGGHHHHHHHHH--HHHHTT---EEESSTTTTHHHHHHHH
T ss_pred CcEEecCCCCCC-C--CCCEEEEEEEEeCCCceEEeeHhhccCcHHHHHHHHHHHHHhcCC-eEEEEeCcccCHHHHHHH
Confidence 358999986532 1 14577777775 2222223332211 1112222 3455544 3567775 5699888664
Q ss_pred c---CCc-cCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCC----c-c-ccCCCCC---CCCCHHHHHHHHHH
Q 022027 201 Y---NVS-VKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPN----R-I-RLGNWEA---DVLSKDQLLYAATD 267 (304)
Q Consensus 201 ~---gi~-l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~----~-i-~~s~W~~---~pLt~~Qi~YAA~D 267 (304)
+ ++. ....+|+..++.. .. ..+++|..+++. +|..-.+.. . + ....|.. ...-..-+.|.-.|
T Consensus 77 ~~~~~~~~~~~~iDl~~~~~~-~~--~~~~~Lk~ve~~-lg~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~yN~~D 152 (164)
T PF13482_consen 77 AKRYGLPPPFNHIDLLKIIKK-HF--LESYSLKNVEKF-LGIERRDDDISGSESVKLYKEYLETGDPEALEEILEYNEDD 152 (164)
T ss_dssp H-HHHH--GGGEEEHHHHHT--TT--SCCTT--SHHH------------HHHHHHHHHH---TTGGTS--HHHHHHHHHH
T ss_pred HHHcCCCcccchhhHHHHHHh-cc--CCCCCHHHHhhh-cccccccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 4 333 3344798665532 22 257799999887 565443110 0 0 0112211 12345577999999
Q ss_pred HHHHHHHHHHH
Q 022027 268 AFASWHLYQVL 278 (304)
Q Consensus 268 A~a~~~L~~~L 278 (304)
+.++.+|+..|
T Consensus 153 v~~~~~L~~~l 163 (164)
T PF13482_consen 153 VRATRRLYEWL 163 (164)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHh
Confidence 99999999876
No 76
>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=74.58 E-value=29 Score=28.84 Aligned_cols=87 Identities=18% Similarity=0.093 Sum_probs=54.3
Q ss_pred HHHHHhHcCC-CceEEEecchHHHHHHHH---hcCCc-----cCCcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCC
Q 022027 172 PSLQLLLEDS-TILKVGVGIGSDAGKVYR---DYNVS-----VKASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKK 242 (304)
Q Consensus 172 ~~L~~lL~d~-~i~KVG~~ik~Dl~~L~~---~~gi~-----l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K 242 (304)
+.|..++.+. ....+++ .+.|...+.+ .++.. ....+|+..++....+. ...++|.++++.+ |.....
T Consensus 80 ~~~~~~l~~~~~~~~v~~-~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~-~~~~~L~~l~~~~-gi~~~~ 156 (176)
T cd06133 80 KEFLEWLGKNGKYAFVTW-GDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGL-KKRTGLSKALEYL-GLEFEG 156 (176)
T ss_pred HHHHHHHHhCCCeEEEee-cHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCC-CCCCCHHHHHHHC-CCCCCC
Confidence 3566677764 2444554 5888765543 23331 23457998888766543 2589999999765 654431
Q ss_pred CCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 022027 243 PNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVL 278 (304)
Q Consensus 243 ~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L 278 (304)
+. +-|-.||.++..++..|
T Consensus 157 ----~~-------------H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 ----RH-------------HRGLDDARNIARILKRL 175 (176)
T ss_pred ----CC-------------cCcHHHHHHHHHHHHHh
Confidence 11 22778999999888765
No 77
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=74.13 E-value=11 Score=41.69 Aligned_cols=90 Identities=20% Similarity=0.220 Sum_probs=61.8
Q ss_pred CcHHHHHhHcCCCceEEEecchHHHHHHHHh---cCCc-cCCc-chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCC
Q 022027 170 IPPSLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVS-VKAS-EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPN 244 (304)
Q Consensus 170 ~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~-l~~~-~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~ 244 (304)
+++.++.|+.+ -+.|.||+..|+..|... +|+. ..+. +|+-.+|.. |.|...+|+|..|++.+ +..+
T Consensus 491 vL~kf~~~~~d--~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~-L~P~~ksh~Lg~l~kk~-~v~l---- 562 (1444)
T COG2176 491 VLEKFREFIGD--SILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARA-LNPEFKSHRLGTLCKKL-GVEL---- 562 (1444)
T ss_pred HHHHHHHHhcC--cEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHH-hChhhhhcchHHHHHHh-CccH----
Confidence 34567777876 467999999999888654 4543 3444 799777765 66666799999999986 3322
Q ss_pred ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC
Q 022027 245 RIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSL 281 (304)
Q Consensus 245 ~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l 281 (304)
++.+-|--||.++-.++-.+...
T Consensus 563 --------------e~hHRA~yDaeat~~vf~~f~~~ 585 (1444)
T COG2176 563 --------------ERHHRADYDAEATAKVFFVFLKD 585 (1444)
T ss_pred --------------HHhhhhhhhHHHHHHHHHHHHHH
Confidence 34444666777777766665543
No 78
>PRK06722 exonuclease; Provisional
Probab=73.18 E-value=80 Score=29.39 Aligned_cols=88 Identities=15% Similarity=-0.009 Sum_probs=52.4
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHh---cCCccCC-----cchHHHHHHHHhCC-CCCCCCHHHHHHHHcCcccCCC
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSVKA-----SEDLSYLAKHKIGG-DSQKWGLASLTEMLVCKELKKP 243 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l~~-----~~Dl~~LA~ylL~~-~~~~~sL~~La~~~Lg~~l~K~ 243 (304)
.+..++.+. .. |+|+...|+..|.+. +|+.... .+|++.++...... .....+|..+++++ |.....
T Consensus 83 ef~~fig~~-~l-vahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~l-gL~~~g- 158 (281)
T PRK06722 83 KFIQFIGED-SI-FVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQL-GLIWEG- 158 (281)
T ss_pred HHHHHHCCC-cE-EEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHC-CCCCCC-
Confidence 455566653 33 556679999888653 5654322 36776665432211 11356899999885 543211
Q ss_pred CccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 244 NRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 244 ~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
+ ..-|-.||.++..|+..|..
T Consensus 159 ---~-------------~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 159 ---K-------------QHRALADAENTANILLKAYS 179 (281)
T ss_pred ---C-------------CcCcHHHHHHHHHHHHHHhc
Confidence 0 12277889999888888763
No 79
>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=72.07 E-value=38 Score=30.14 Aligned_cols=110 Identities=17% Similarity=0.134 Sum_probs=67.2
Q ss_pred CcHHHHHhHcCCCceEEEecch-HHHHHHHH---hcCCccCC-------------------cchHHHHHHHHhCCCCCCC
Q 022027 170 IPPSLQLLLEDSTILKVGVGIG-SDAGKVYR---DYNVSVKA-------------------SEDLSYLAKHKIGGDSQKW 226 (304)
Q Consensus 170 ~~~~L~~lL~d~~i~KVG~~ik-~Dl~~L~~---~~gi~l~~-------------------~~Dl~~LA~ylL~~~~~~~ 226 (304)
+...+..+++......|+||.+ .|+-.|.. .+|+.+.. -+|++.+.+. -| .+...
T Consensus 40 lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~-~g-~~~~~ 117 (209)
T PF10108_consen 40 LLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSF-YG-AKART 117 (209)
T ss_pred HHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhc-cC-ccccC
Confidence 4455666676666678999977 78877754 36775432 1466433321 12 34688
Q ss_pred CHHHHHHHHcCcccCCCCcccc----CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcc
Q 022027 227 GLASLTEMLVCKELKKPNRIRL----GNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPEPV 285 (304)
Q Consensus 227 sL~~La~~~Lg~~l~K~~~i~~----s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~~ 285 (304)
+|+.||.. +|++- |. .+.. .-|....+ .+-..|.-.||..++.||.++..+....
T Consensus 118 sLd~la~~-lgiPg-K~-~idGs~V~~~y~~g~i-~~I~~YCe~DVl~T~~lylR~~~~~G~l 176 (209)
T PF10108_consen 118 SLDELAAL-LGIPG-KD-DIDGSQVAELYQEGDI-DEIREYCEKDVLNTYLLYLRFELLRGRL 176 (209)
T ss_pred CHHHHHHH-cCCCC-CC-CCCHHHHHHHHHcCCH-HHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence 99988865 57542 32 1111 11221111 2345999999999999999998877643
No 80
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=69.24 E-value=0.15 Score=48.94 Aligned_cols=69 Identities=25% Similarity=0.298 Sum_probs=55.3
Q ss_pred CcEEEEEEEecCCeEEEEecCC--C-CCcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHH
Q 022027 146 RKAAVMQICGDSNHCYVMQIIH--S-GIPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAK 216 (304)
Q Consensus 146 ~~valiQL~~~~~~~~l~~l~~--~-~~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ 216 (304)
++++.+|.++. -.+|++++.. . .+...++.+++++.|.|+-|++.--...+...|||...+++|+ ..+.
T Consensus 74 ~~l~~~q~~~~-~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i~~n~v~~~-q~~d 145 (458)
T KOG2405|consen 74 GKLCWLQVATN-CRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGILLNNVFDT-QVAD 145 (458)
T ss_pred CcchhHHHHHH-HHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhcccceeeecchhhh-hhhh
Confidence 57888888776 4678877643 1 3556889999999999999999998888888999999999988 4443
No 81
>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=68.45 E-value=16 Score=31.35 Aligned_cols=84 Identities=17% Similarity=0.063 Sum_probs=48.9
Q ss_pred HHHHhHcCCCceEEEec-chHHHHHHHHh---cCCcc--------CCcchHHHHHHHH--hCC----------CCCCCCH
Q 022027 173 SLQLLLEDSTILKVGVG-IGSDAGKVYRD---YNVSV--------KASEDLSYLAKHK--IGG----------DSQKWGL 228 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~-ik~Dl~~L~~~---~gi~l--------~~~~Dl~~LA~yl--L~~----------~~~~~sL 228 (304)
.+..++..+....|||+ +..|...|.+. ++... ...+|+-.++... +.+ +..+++|
T Consensus 75 ~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L 154 (183)
T cd06138 75 KIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKL 154 (183)
T ss_pred HHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhH
Confidence 45556654444568986 78999988653 33311 1124665555432 211 1236889
Q ss_pred HHHHHHHcCcccCCCCccccCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q 022027 229 ASLTEMLVCKELKKPNRIRLGNWEADVLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 229 ~~La~~~Lg~~l~K~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
+.|+++| |.... +..-|..||.++..|.
T Consensus 155 ~~l~~~~-gi~~~------------------~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 155 EDLAQAN-GIEHS------------------NAHDALSDVEATIALA 182 (183)
T ss_pred HHHHHHC-CCCcc------------------ccccHHHHHHHHHHHh
Confidence 9999874 54331 1133888998887653
No 82
>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=66.05 E-value=9.2 Score=34.36 Aligned_cols=74 Identities=23% Similarity=0.241 Sum_probs=48.8
Q ss_pred chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCC--CCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcc
Q 022027 209 EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKK--PNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPEPV 285 (304)
Q Consensus 209 ~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K--~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~~ 285 (304)
+|+-.++...+. ..+|+|..+++.+||..-.. .+++ ..-|....--..-++|...||+.+++|...|.-+|-.+
T Consensus 158 ~D~~~~~k~~~~--~~sY~L~~va~~~Lg~~k~di~~~~i-~~~~~~~~~l~~l~~y~~~Da~l~~~L~~kl~il~Ltk 233 (234)
T cd05776 158 CDTYLSAKELIR--CKSYDLTELSQQVLGIERQDIDPEEI-LNMYNDSESLLKLLEHTEKDAYLILQLMFKLNILPLTK 233 (234)
T ss_pred hccHHHHHHHhC--CCCCChHHHHHHHhCcCcccCCHHHH-HHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHCCCcCCC
Confidence 588666655543 36999999999999963211 1111 11243201112356999999999999999998887654
No 83
>KOG2405 consensus Predicted 3'-5' exonuclease [Replication, recombination and repair]
Probab=62.96 E-value=8.9 Score=37.12 Aligned_cols=130 Identities=12% Similarity=0.080 Sum_probs=80.5
Q ss_pred EEEEEEecCCeEEEEecCCCC---CcHHHHHhHcCCCceEEEecchHHHHHHHHhcCCccCCcchHHHHHHHHhCCCC--
Q 022027 149 AVMQICGDSNHCYVMQIIHSG---IPPSLQLLLEDSTILKVGVGIGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDS-- 223 (304)
Q Consensus 149 aliQL~~~~~~~~l~~l~~~~---~~~~L~~lL~d~~i~KVG~~ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~-- 223 (304)
..++++.. ...+++|....+ .....+..|+...+ +- |.+.+...+...|++.+.+++|+ .+|..++.+..
T Consensus 214 ~~m~ia~~-n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDt-Qia~sLve~~e~g 288 (458)
T KOG2405|consen 214 TYMNIADG-NEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDT-QIASSLVEPSEYG 288 (458)
T ss_pred hhhhhccc-chhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHH-HHHHHHhhhHHhc
Confidence 34567765 577888876543 22335666776554 33 89999999988999999999999 56655544321
Q ss_pred CCCCHHHHHHH-HcCc-------ccCCCCc----cc--cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 022027 224 QKWGLASLTEM-LVCK-------ELKKPNR----IR--LGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPE 283 (304)
Q Consensus 224 ~~~sL~~La~~-~Lg~-------~l~K~~~----i~--~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~ 283 (304)
+++....+... .|+. ...+..+ +. ..+|.-+|.++....-++.|+..++.....|...-.
T Consensus 289 rr~p~~~lIsft~Lq~~~~y~~~s~~~~eev~~~l~~dp~~w~irp~te~~~~~~h~dv~~Ll~~~~~l~a~~l 362 (458)
T KOG2405|consen 289 RRHPTSILISFTCLQTYIFYIKASGLIFEEVAKILEADPPRWVIRPSTEIADHLLHRDVISLLGIFDTLVAVCL 362 (458)
T ss_pred ccCCccceeeeEeccccceeehhhhhhHHHHHHHHhcCCCcceecccHHHHHHHHHHHHHHHHHHHhhHhhhCh
Confidence 23333333322 1111 1111111 11 236998999998888899999999886666654433
No 84
>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=62.93 E-value=11 Score=33.65 Aligned_cols=71 Identities=15% Similarity=0.189 Sum_probs=45.2
Q ss_pred chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCC--CccccCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHhCCC
Q 022027 209 EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKP--NRIRLGNWEADVLS-KDQLLYAATDAFASWHLYQVLKSLP 282 (304)
Q Consensus 209 ~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~--~~i~~s~W~~~pLt-~~Qi~YAA~DA~a~~~L~~~L~~l~ 282 (304)
+|+-.++.... ...+++|+.+++++||...... +.+.. -|...+-. ..-++|...||..+++|+.+|.-+.
T Consensus 154 iD~~~~~~~~~--kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~-~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl~~~~ 227 (230)
T cd05777 154 FDLLQVIQRDY--KLRSYSLNSVSAHFLGEQKEDVHYSIITD-LQNGNPETRRRLAVYCLKDAYLPLRLLDKLMCLV 227 (230)
T ss_pred eeHHHHHHHhc--CcccCcHHHHHHHHhCCCCCCCCHHHHHH-HHccCHhHhHHHHHhhHHHHHHHHHHHHHHhhHc
Confidence 46644443222 2368999999999999643211 12211 14322222 3467999999999999999987664
No 85
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=62.24 E-value=42 Score=38.31 Aligned_cols=81 Identities=19% Similarity=0.109 Sum_probs=55.7
Q ss_pred CceEEEecchHHHHHHH---HhcCCc-cC-CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCCCCCCC
Q 022027 182 TILKVGVGIGSDAGKVY---RDYNVS-VK-ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNWEADVL 256 (304)
Q Consensus 182 ~i~KVG~~ik~Dl~~L~---~~~gi~-l~-~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W~~~pL 256 (304)
..+.|+|+...|...|. +.+|+. +. ..+|+..++.. +.+....++|..|++++ |......
T Consensus 499 g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~-l~p~~k~~kL~~LAk~l-GL~~~~~------------- 563 (1437)
T PRK00448 499 DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRF-LYPELKSHRLNTLAKKF-GVELEHH------------- 563 (1437)
T ss_pred CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHH-HcCccccccHHHHHHHc-CCCCCCC-------------
Confidence 46789999999987764 345653 33 34798677655 44344689999999874 6543211
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhCCC
Q 022027 257 SKDQLLYAATDAFASWHLYQVLKSLP 282 (304)
Q Consensus 257 t~~Qi~YAA~DA~a~~~L~~~L~~l~ 282 (304)
+.|-.||.++..|+..|....
T Consensus 564 -----HrAl~DA~aTa~lf~~ll~~l 584 (1437)
T PRK00448 564 -----HRADYDAEATAYLLIKFLKDL 584 (1437)
T ss_pred -----cChHHHHHHHHHHHHHHHHHH
Confidence 338889999999888886544
No 86
>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=61.13 E-value=12 Score=33.70 Aligned_cols=71 Identities=8% Similarity=0.151 Sum_probs=45.3
Q ss_pred CccCCc--chHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccccCCC-CC-C-CCCHHHHHHHHHHHHHHHHHH
Q 022027 203 VSVKAS--EDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIRLGNW-EA-D-VLSKDQLLYAATDAFASWHLY 275 (304)
Q Consensus 203 i~l~~~--~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~~s~W-~~-~-pLt~~Qi~YAA~DA~a~~~L~ 275 (304)
+.+.|. +|+-.++...+. ..+++|+.++.++||...+...--..+.| .. . .-...-++|...||...++|.
T Consensus 155 ~~i~GRi~lD~~~~~r~~~k--l~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l~l~Ll 230 (231)
T cd05778 155 IKIVGRHILNVWRLMRSELA--LTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNLEIL 230 (231)
T ss_pred eEEeeEEEeEhHHHHHHHcC--cccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHHHHHhh
Confidence 445554 587555554333 36899999999999987554321223344 22 1 123446799999999998874
No 87
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=61.06 E-value=91 Score=27.62 Aligned_cols=89 Identities=18% Similarity=0.148 Sum_probs=58.8
Q ss_pred HHHHhHcCCCceEEEecchHHHHHHHHh---cCCccC--CcchHHHHHHHHhCCCCCCCCHHHHHHHHcCcccCCCCccc
Q 022027 173 SLQLLLEDSTILKVGVGIGSDAGKVYRD---YNVSVK--ASEDLSYLAKHKIGGDSQKWGLASLTEMLVCKELKKPNRIR 247 (304)
Q Consensus 173 ~L~~lL~d~~i~KVG~~ik~Dl~~L~~~---~gi~l~--~~~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~l~K~~~i~ 247 (304)
.+..++.+. -..|+|+...|...|... ++..+. ..+|+-.++..... +....+|+.|+. .+|+.......
T Consensus 87 ~~~~~i~~~-~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~-~~~~~~L~~l~~-~~gi~~~~~~~-- 161 (243)
T COG0847 87 EFLDFIGGL-RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFP-GFDRSSLDALAE-RLGIDRNPFHP-- 161 (243)
T ss_pred HHHHHHCCC-CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcC-CCccchHHHHHH-HcCCCcCCcCC--
Confidence 444556554 567999999999988643 444432 33577677766543 336889999999 45654221110
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 248 LGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 248 ~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
.-|..||.++..+|..+..
T Consensus 162 --------------H~Al~Da~~~a~~~~~~~~ 180 (243)
T COG0847 162 --------------HRALFDALALAELFLLLQT 180 (243)
T ss_pred --------------cchHHHHHHHHHHHHHHHh
Confidence 2288899999998888886
No 88
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.93 E-value=38 Score=37.87 Aligned_cols=103 Identities=17% Similarity=0.149 Sum_probs=63.7
Q ss_pred CCCceEEEecch-HHHHHHHHh---cCCc---------------------cCCc--chHHHHHHHHhCCCCCCCCHHHHH
Q 022027 180 DSTILKVGVGIG-SDAGKVYRD---YNVS---------------------VKAS--EDLSYLAKHKIGGDSQKWGLASLT 232 (304)
Q Consensus 180 d~~i~KVG~~ik-~Dl~~L~~~---~gi~---------------------l~~~--~Dl~~LA~ylL~~~~~~~sL~~La 232 (304)
||.+ .+|||+. .|+..|.++ +++. +.|. +|+..++...+. ..+++|..++
T Consensus 599 DPDi-i~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~~~--~~sy~L~~v~ 675 (1172)
T TIGR00592 599 DPDE-IVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKELIR--CKSYDLSELV 675 (1172)
T ss_pred CCCE-EEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHHhC--cCCCCHHHHH
Confidence 7764 5789876 466655442 2222 2333 587666655554 3689999999
Q ss_pred HHHcCcccCC--CCccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcch
Q 022027 233 EMLVCKELKK--PNRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPEPVK 286 (304)
Q Consensus 233 ~~~Lg~~l~K--~~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~~~ 286 (304)
.++||..-.. ...+. .-|....--..-+.|...||..+++|...|.-++-..+
T Consensus 676 ~~~L~~~k~~~~~~~i~-~~~~~~~~~~~~~~y~~~Da~l~~~L~~~l~~l~l~~~ 730 (1172)
T TIGR00592 676 QQILKTERKVIPIDNIN-NMYSESSSLTYLLEHTWKDAMFILQIMCELNVLPLALQ 730 (1172)
T ss_pred HHHhCCCCcccCHHHHH-HHHhCcHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 9999853211 00111 12332111234579999999999999999988886654
No 89
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=43.32 E-value=2.7e+02 Score=25.68 Aligned_cols=109 Identities=17% Similarity=0.126 Sum_probs=60.1
Q ss_pred ceEEEEeeeecCccCCCCCCcEEEEEEEecCCeEEEEecCCCCCcH----HHHHhHcCCCc-eEEEecch-HHHHHHHH-
Q 022027 127 VVVGFDIEWKPTFRKGVLPRKAAVMQICGDSNHCYVMQIIHSGIPP----SLQLLLEDSTI-LKVGVGIG-SDAGKVYR- 199 (304)
Q Consensus 127 ~~vgfD~E~~~~~~~g~~~~~valiQL~~~~~~~~l~~l~~~~~~~----~L~~lL~d~~i-~KVG~~ik-~Dl~~L~~- 199 (304)
..+-||+|+.+....| ..+-++..+...+....+.-.....+. .|..++.++.+ ..|.+|.| .|.-.+.+
T Consensus 99 ~~~FFDiETTGL~~ag---~~I~~~g~a~~~~~~~~Vrq~~lp~p~~E~avle~fl~~~~~~~lvsfNGkaFD~PfikR~ 175 (278)
T COG3359 99 DVAFFDIETTGLDRAG---NTITLVGGARGVDDTMHVRQHFLPAPEEEVAVLENFLHDPDFNMLVSFNGKAFDIPFIKRM 175 (278)
T ss_pred ceEEEeeeccccCCCC---CeEEEEEEEEccCceEEEEeecCCCcchhhHHHHHHhcCCCcceEEEecCcccCcHHHHHH
Confidence 4788999998764322 455566566543333333221111222 46667777632 34666665 67766642
Q ss_pred ---hcCCccCCc-chHHHHHHHHhCCCCCCCCHHHHHHHHcCcc
Q 022027 200 ---DYNVSVKAS-EDLSYLAKHKIGGDSQKWGLASLTEMLVCKE 239 (304)
Q Consensus 200 ---~~gi~l~~~-~Dl~~LA~ylL~~~~~~~sL~~La~~~Lg~~ 239 (304)
.+...+... +|+..-+.-+.+..-.+.+|..+-+ +||+.
T Consensus 176 v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~ 218 (278)
T COG3359 176 VRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIR 218 (278)
T ss_pred HhcccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCcc
Confidence 234444444 7985555544332234678887665 88865
No 90
>PRK05762 DNA polymerase II; Reviewed
Probab=40.82 E-value=2.1e+02 Score=30.64 Aligned_cols=111 Identities=13% Similarity=0.118 Sum_probs=63.8
Q ss_pred CcHHHHHhHcC--CCceEEEecch-HHHHHHHH---hcCCcc-------------------------CC--cchHHHHHH
Q 022027 170 IPPSLQLLLED--STILKVGVGIG-SDAGKVYR---DYNVSV-------------------------KA--SEDLSYLAK 216 (304)
Q Consensus 170 ~~~~L~~lL~d--~~i~KVG~~ik-~Dl~~L~~---~~gi~l-------------------------~~--~~Dl~~LA~ 216 (304)
+...+..++.. |.| .+|||+. .|+..|.+ .+|+.+ .| .+|+-.++.
T Consensus 206 LL~~F~~~i~~~DPDI-IvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k 284 (786)
T PRK05762 206 LLEKFNAWFAEHDPDV-IIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALK 284 (786)
T ss_pred HHHHHHHHHHhcCCCE-EEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHH
Confidence 34444444443 554 5899966 68877764 345432 11 246644443
Q ss_pred HHhCCCCCCCCHHHHHHHHcCcccCC-C-----CccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcc
Q 022027 217 HKIGGDSQKWGLASLTEMLVCKELKK-P-----NRIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKSLPEPV 285 (304)
Q Consensus 217 ylL~~~~~~~sL~~La~~~Lg~~l~K-~-----~~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~l~~~~ 285 (304)
.... ...+++|+.+++++||..-.. . +++ ...|... ...-++|...||..++.|+.++.-++...
T Consensus 285 ~~~~-~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI-~~~~~~~--~~~l~~Y~l~Da~lt~~L~~kl~ll~~~~ 355 (786)
T PRK05762 285 SATW-VFDSFSLEYVSQRLLGEGKAIDDPYDRMDEI-DRRFAED--KPALARYNLKDCELVTRIFEKTKLLPFLL 355 (786)
T ss_pred Hhhc-cCCCCCHHHHHHHHhCCCeeccCccccHHHH-HHHHhhh--HHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 3221 235899999999999853211 0 001 1123211 13457999999999999999765555433
No 91
>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=23.41 E-value=2.6e+02 Score=23.51 Aligned_cols=28 Identities=11% Similarity=0.075 Sum_probs=19.4
Q ss_pred HHHHhHcC----CCceEEEecchHHHHHHHHh
Q 022027 173 SLQLLLED----STILKVGVGIGSDAGKVYRD 200 (304)
Q Consensus 173 ~L~~lL~d----~~i~KVG~~ik~Dl~~L~~~ 200 (304)
.|..++.+ ..+..+||++..|+..|.+.
T Consensus 81 ~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~ 112 (173)
T cd06135 81 ELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKY 112 (173)
T ss_pred HHHHHHHHhcCCCCCceeecchhhCHHHHHHH
Confidence 45555653 34677899999999888553
No 92
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=23.36 E-value=1.7e+02 Score=26.64 Aligned_cols=54 Identities=24% Similarity=0.155 Sum_probs=35.7
Q ss_pred CCCceEEEecchHHHHHHHHhcCCc---------------cCCcchHHHHHHHHhCCCCCCCCHHHHHHHHc
Q 022027 180 DSTILKVGVGIGSDAGKVYRDYNVS---------------VKASEDLSYLAKHKIGGDSQKWGLASLTEMLV 236 (304)
Q Consensus 180 d~~i~KVG~~ik~Dl~~L~~~~gi~---------------l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~L 236 (304)
+.++..|||+.-.|+..|++.+--. ...++|+..++.. .. ....+|+.|++.+-
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~-~~--~~~~~L~~l~~~l~ 215 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEE-CP--GKSTSLQELAEELG 215 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTS-TT--TS-SSHHHHHHHTT
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHh-cc--ccccCHHHHHHHhC
Confidence 3447899999999998887754212 2345788666643 22 25779999998853
No 93
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=22.50 E-value=2.9e+02 Score=27.21 Aligned_cols=101 Identities=13% Similarity=0.177 Sum_probs=61.2
Q ss_pred CcHHHHHhHcCCCceEEEec-chHHHHHHHHhcCCccCCcchHHHHHHHHhCCCCCCCCHHHHHHHHc-----CcccCCC
Q 022027 170 IPPSLQLLLEDSTILKVGVG-IGSDAGKVYRDYNVSVKASEDLSYLAKHKIGGDSQKWGLASLTEMLV-----CKELKKP 243 (304)
Q Consensus 170 ~~~~L~~lL~d~~i~KVG~~-ik~Dl~~L~~~~gi~l~~~~Dl~~LA~ylL~~~~~~~sL~~La~~~L-----g~~l~K~ 243 (304)
+...+...|.-|+...+||+ ++.|=.+-+. +-.+|++|. .-.+ +..+..+|.|=+|+..+- |+.-++.
T Consensus 84 F~~~I~~~ls~P~Tcv~GYNniRFDDEvtRy---~fyRNF~DP-Ya~s--WqngNSRWDLLD~~RacyALRPeGI~Wp~n 157 (475)
T COG2925 84 FAARIHAELTQPNTCVLGYNNIRFDDEVTRY---IFYRNFYDP-YAWS--WQNGNSRWDLLDVVRACYALRPEGINWPEN 157 (475)
T ss_pred HHHHHHHHhCCCCeeeecccccccchHHHHH---HHHHhcCch-hhhh--hcCCCchhHHHHHHHHHHhcCcccCCCCcC
Confidence 44567778888999999997 5666555421 113577776 3333 344457888888887653 2222221
Q ss_pred C---------ccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhC
Q 022027 244 N---------RIRLGNWEADVLSKDQLLYAATDAFASWHLYQVLKS 280 (304)
Q Consensus 244 ~---------~i~~s~W~~~pLt~~Qi~YAA~DA~a~~~L~~~L~~ 280 (304)
. .++..| -+...+..-|-.|+|++..|.+.++.
T Consensus 158 ~dG~pSFkLEhLt~AN----gieH~nAHdAmsDVyATIamAklvk~ 199 (475)
T COG2925 158 DDGLPSFKLEHLTKAN----GIEHSNAHDAMSDVYATIAMAKLVKT 199 (475)
T ss_pred CCCCcchhhHHHhhcc----ccccchhhHHHHHHHHHHHHHHHHHh
Confidence 1 011111 13334567788999999999988875
Done!