Query 013825
Match_columns 436
No_of_seqs 197 out of 1267
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 07:46:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013825.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013825hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09146 DNA polymerase III su 100.0 3.6E-32 7.9E-37 263.6 22.6 177 2-184 41-230 (239)
2 PRK07883 hypothetical protein; 100.0 1E-31 2.2E-36 287.8 24.0 206 2-216 9-218 (557)
3 PRK07942 DNA polymerase III su 100.0 1.8E-31 3.8E-36 257.2 22.4 174 3-182 1-181 (232)
4 PRK06807 DNA polymerase III su 100.0 2.2E-31 4.7E-36 267.4 23.6 172 1-181 1-172 (313)
5 smart00479 EXOIII exonuclease 100.0 4.3E-31 9.3E-36 236.3 23.0 166 9-182 1-168 (169)
6 PRK05711 DNA polymerase III su 100.0 2E-31 4.3E-36 258.7 22.3 166 7-179 3-174 (240)
7 TIGR01406 dnaQ_proteo DNA poly 100.0 2.5E-31 5.3E-36 255.4 22.1 164 9-179 1-170 (225)
8 cd06130 DNA_pol_III_epsilon_li 100.0 3.2E-31 6.9E-36 235.8 20.5 155 10-175 1-155 (156)
9 PRK08517 DNA polymerase III su 100.0 5.1E-31 1.1E-35 258.2 23.3 167 4-181 64-231 (257)
10 TIGR00573 dnaq exonuclease, DN 100.0 3.7E-31 8E-36 252.0 21.7 172 3-181 2-177 (217)
11 PRK06195 DNA polymerase III su 100.0 1.3E-30 2.8E-35 260.9 26.1 166 8-183 1-166 (309)
12 cd06131 DNA_pol_III_epsilon_Ec 100.0 6.8E-31 1.5E-35 237.6 21.4 161 10-177 1-166 (167)
13 PRK06310 DNA polymerase III su 100.0 8.3E-31 1.8E-35 255.3 22.9 168 5-181 4-174 (250)
14 PRK07740 hypothetical protein; 100.0 1.2E-30 2.5E-35 253.5 22.4 174 2-182 53-227 (244)
15 PRK06063 DNA polymerase III su 100.0 1.2E-30 2.7E-35 261.8 22.2 168 6-183 13-181 (313)
16 PRK07748 sporulation inhibitor 100.0 1.1E-30 2.4E-35 246.8 20.1 171 7-181 3-180 (207)
17 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 9.6E-31 2.1E-35 241.9 18.1 158 10-176 1-176 (177)
18 PRK09145 DNA polymerase III su 100.0 5.5E-30 1.2E-34 240.8 22.1 167 6-179 27-199 (202)
19 PRK06309 DNA polymerase III su 100.0 3.8E-30 8.1E-35 247.7 21.4 164 8-182 2-167 (232)
20 PRK05168 ribonuclease T; Provi 100.0 1.1E-29 2.4E-34 241.4 22.1 172 4-182 13-202 (211)
21 TIGR01298 RNaseT ribonuclease 100.0 1.2E-29 2.6E-34 239.3 21.7 170 6-182 6-193 (200)
22 PRK07247 DNA polymerase III su 100.0 1.1E-29 2.3E-34 239.6 21.2 164 8-183 5-171 (195)
23 cd06134 RNaseT DEDDh 3'-5' exo 100.0 2.1E-29 4.5E-34 235.5 20.9 167 7-180 4-188 (189)
24 PRK06722 exonuclease; Provisio 100.0 3E-29 6.6E-34 248.4 21.6 170 6-179 3-179 (281)
25 COG2176 PolC DNA polymerase II 100.0 1.1E-30 2.3E-35 288.8 11.7 200 3-212 416-617 (1444)
26 cd06133 ERI-1_3'hExo_like DEDD 100.0 4.6E-29 1E-33 225.7 20.3 166 10-177 1-175 (176)
27 PRK07246 bifunctional ATP-depe 100.0 1.1E-28 2.3E-33 274.6 23.3 181 3-194 2-185 (820)
28 cd06138 ExoI_N N-terminal DEDD 100.0 1.7E-28 3.8E-33 227.6 17.6 162 11-175 1-183 (183)
29 PRK08074 bifunctional ATP-depe 100.0 4.9E-28 1.1E-32 272.6 23.7 168 7-182 2-170 (928)
30 TIGR01405 polC_Gram_pos DNA po 100.0 9.2E-28 2E-32 274.4 24.3 179 6-194 188-367 (1213)
31 PRK05601 DNA polymerase III su 100.0 1.1E-27 2.3E-32 243.9 21.8 164 5-177 43-245 (377)
32 cd06127 DEDDh DEDDh 3'-5' exon 100.0 1E-27 2.2E-32 209.2 18.0 157 11-175 1-159 (159)
33 TIGR01407 dinG_rel DnaQ family 100.0 1.8E-27 4E-32 265.8 23.3 165 9-182 1-166 (850)
34 PRK07983 exodeoxyribonuclease 99.9 8.8E-27 1.9E-31 223.4 20.0 148 10-182 2-155 (219)
35 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 2.3E-27 5E-32 216.1 11.8 144 11-174 1-160 (161)
36 COG0847 DnaQ DNA polymerase II 99.9 4.7E-26 1E-30 218.2 20.8 164 8-180 13-181 (243)
37 PRK09182 DNA polymerase III su 99.9 5.5E-26 1.2E-30 226.6 20.3 161 7-181 36-201 (294)
38 cd06149 ISG20 DEDDh 3'-5' exon 99.9 2.9E-26 6.4E-31 208.6 13.4 149 11-175 1-157 (157)
39 PTZ00315 2'-phosphotransferase 99.9 2.6E-25 5.7E-30 237.0 22.6 173 8-182 56-256 (582)
40 cd06144 REX4_like DEDDh 3'-5' 99.9 4.8E-26 1E-30 205.4 13.3 148 11-175 1-152 (152)
41 PF00929 RNase_T: Exonuclease; 99.9 5.4E-28 1.2E-32 211.0 0.5 160 11-174 1-164 (164)
42 cd06135 Orn DEDDh 3'-5' exonuc 99.9 1.3E-25 2.8E-30 207.1 15.0 156 10-180 1-171 (173)
43 cd06145 REX1_like DEDDh 3'-5' 99.9 9.9E-26 2.1E-30 203.5 13.9 143 11-175 1-150 (150)
44 PRK11779 sbcB exonuclease I; P 99.9 1.4E-24 3E-29 228.8 21.1 174 5-180 3-197 (476)
45 PRK05359 oligoribonuclease; Pr 99.9 1.4E-24 3E-29 202.3 17.7 162 6-183 1-177 (181)
46 PRK00448 polC DNA polymerase I 99.9 1.1E-24 2.5E-29 251.9 20.6 196 5-210 416-613 (1437)
47 KOG0542 Predicted exonuclease 99.7 9E-17 2E-21 155.7 12.2 170 8-180 56-241 (280)
48 COG5018 KapD Inhibitor of the 99.6 6.4E-16 1.4E-20 142.3 8.3 170 7-179 3-183 (210)
49 COG2925 SbcB Exonuclease I [DN 99.6 2.6E-14 5.7E-19 145.3 13.3 173 5-180 6-200 (475)
50 KOG2249 3'-5' exonuclease [Rep 99.5 1.3E-13 2.7E-18 134.8 14.3 156 8-180 105-265 (280)
51 cd05160 DEDDy_DNA_polB_exo DED 99.4 5.3E-12 1.2E-16 117.7 16.4 132 11-157 2-161 (199)
52 cd06143 PAN2_exo DEDDh 3'-5' e 99.3 1.4E-11 3E-16 115.0 12.9 152 8-175 5-174 (174)
53 COG1949 Orn Oligoribonuclease 99.2 5E-11 1.1E-15 109.7 10.1 165 3-182 1-179 (184)
54 cd06125 DnaQ_like_exo DnaQ-lik 99.1 4.8E-10 1E-14 94.4 11.3 79 11-133 1-83 (96)
55 KOG3242 Oligoribonuclease (3'- 99.1 3.2E-10 6.8E-15 105.4 9.4 162 7-183 25-201 (208)
56 cd05780 DNA_polB_Kod1_like_exo 98.9 4.7E-08 1E-12 91.9 14.8 129 8-161 3-159 (195)
57 COG3359 Predicted exonuclease 98.9 3.9E-08 8.5E-13 95.9 14.3 147 7-183 97-271 (278)
58 PHA02570 dexA exonuclease; Pro 98.8 4.6E-08 1E-12 94.2 13.6 157 11-181 4-199 (220)
59 PF13482 RNase_H_2: RNase_H su 98.8 6.9E-09 1.5E-13 93.5 6.2 115 11-158 1-116 (164)
60 cd05781 DNA_polB_B3_exo DEDDy 98.7 2.9E-07 6.3E-12 86.6 15.0 117 8-157 3-144 (188)
61 KOG2248 3'-5' exonuclease [Rep 98.7 1.2E-07 2.5E-12 98.4 10.8 154 5-179 213-373 (380)
62 cd05779 DNA_polB_epsilon_exo D 98.7 1E-06 2.2E-11 84.3 16.3 147 8-160 2-171 (204)
63 KOG4793 Three prime repair exo 98.6 7.7E-08 1.7E-12 94.9 7.5 173 6-183 11-220 (318)
64 cd05785 DNA_polB_like2_exo Unc 98.6 2.2E-06 4.7E-11 82.0 16.3 126 2-157 3-168 (207)
65 cd06139 DNA_polA_I_Ecoli_like_ 98.6 2.7E-06 5.9E-11 77.8 16.1 145 5-183 2-172 (193)
66 cd05783 DNA_polB_B1_exo DEDDy 98.3 1.6E-05 3.4E-10 76.0 15.3 140 7-157 4-170 (204)
67 cd05777 DNA_polB_delta_exo DED 98.3 3.9E-05 8.5E-10 74.1 17.3 137 7-157 6-182 (230)
68 PRK05755 DNA polymerase I; Pro 98.2 1.5E-05 3.3E-10 90.7 14.8 134 7-182 314-470 (880)
69 cd05784 DNA_polB_II_exo DEDDy 98.2 2.3E-05 5E-10 74.3 12.4 127 9-161 4-157 (193)
70 cd05782 DNA_polB_like1_exo Unc 98.1 0.0001 2.2E-09 70.6 14.5 75 81-157 78-169 (208)
71 PF10108 DNA_pol_B_exo2: Predi 98.0 0.00011 2.4E-09 70.9 14.1 126 26-179 8-171 (209)
72 PF04857 CAF1: CAF1 family rib 98.0 0.0001 2.2E-09 72.7 13.8 161 8-175 22-261 (262)
73 PF01612 DNA_pol_A_exo1: 3'-5' 98.0 0.00034 7.3E-09 62.6 15.6 135 7-181 19-175 (176)
74 cd05778 DNA_polB_zeta_exo inac 97.8 0.00069 1.5E-08 65.8 15.9 171 8-182 4-224 (231)
75 smart00486 POLBc DNA polymeras 97.7 0.00055 1.2E-08 70.7 13.4 157 7-177 2-220 (471)
76 PF03104 DNA_pol_B_exo1: DNA p 97.7 0.00045 9.7E-09 68.4 12.3 131 7-150 156-325 (325)
77 PTZ00166 DNA polymerase delta 97.6 0.0012 2.7E-08 76.8 16.6 158 7-178 263-483 (1054)
78 PRK05762 DNA polymerase II; Re 97.5 0.0023 4.9E-08 72.5 16.1 145 7-177 154-348 (786)
79 PHA02528 43 DNA polymerase; Pr 97.4 0.0038 8.2E-08 71.6 16.9 163 7-176 105-323 (881)
80 cd05776 DNA_polB_alpha_exo ina 97.1 0.0045 9.6E-08 60.2 11.3 145 10-157 5-186 (234)
81 TIGR03491 RecB family nuclease 97.0 0.0089 1.9E-07 63.6 12.8 120 7-157 283-409 (457)
82 cd06146 mut-7_like_exo DEDDy 3 96.9 0.019 4E-07 54.3 12.4 143 5-178 19-192 (193)
83 COG0349 Rnd Ribonuclease D [Tr 96.8 0.027 5.9E-07 58.5 14.0 142 7-192 16-177 (361)
84 KOG0304 mRNA deadenylase subun 96.6 0.03 6.5E-07 54.6 12.2 172 7-180 23-238 (239)
85 PHA02524 43A DNA polymerase su 96.5 0.019 4.1E-07 62.1 10.9 144 7-154 105-283 (498)
86 PRK10829 ribonuclease D; Provi 96.2 0.17 3.6E-06 53.0 15.8 140 6-190 20-179 (373)
87 cd06141 WRN_exo DEDDy 3'-5' ex 96.0 0.11 2.3E-06 47.2 11.6 129 7-178 17-169 (170)
88 cd06129 RNaseD_like DEDDy 3'-5 95.9 0.13 2.8E-06 46.8 11.9 129 7-178 12-160 (161)
89 cd00007 35EXOc 3'-5' exonuclea 95.7 0.081 1.8E-06 45.8 9.2 66 82-155 40-107 (155)
90 KOG1275 PAB-dependent poly(A) 95.6 0.0074 1.6E-07 68.3 2.9 160 6-179 908-1090(1118)
91 TIGR00592 pol2 DNA polymerase 95.6 0.45 9.8E-06 56.6 17.7 141 9-154 505-678 (1172)
92 COG0417 PolB DNA polymerase el 95.5 0.22 4.7E-06 56.9 14.2 131 6-156 152-306 (792)
93 TIGR01388 rnd ribonuclease D. 95.3 0.69 1.5E-05 48.1 15.8 138 6-188 16-173 (367)
94 PHA03036 DNA polymerase; Provi 95.1 0.44 9.6E-06 55.5 14.9 166 8-179 160-390 (1004)
95 KOG4793 Three prime repair exo 93.2 0.12 2.5E-06 52.0 4.6 150 26-183 129-293 (318)
96 PRK05761 DNA polymerase I; Rev 93.2 0.65 1.4E-05 53.1 11.2 96 79-174 208-334 (787)
97 cd06140 DNA_polA_I_Bacillus_li 93.1 4.1 8.8E-05 36.9 14.3 104 8-154 3-108 (178)
98 cd06148 Egl_like_exo DEDDy 3'- 92.7 1.7 3.6E-05 41.0 11.6 139 5-184 7-180 (197)
99 smart00474 35EXOc 3'-5' exonuc 91.5 2.6 5.6E-05 37.1 10.7 88 85-181 64-171 (172)
100 COG0749 PolA DNA polymerase I 90.0 2.9 6.2E-05 46.5 11.4 132 10-182 24-181 (593)
101 KOG1798 DNA polymerase epsilon 88.4 1.9 4.1E-05 52.0 9.0 165 6-181 244-454 (2173)
102 PHA02563 DNA polymerase; Provi 85.2 7.6 0.00017 43.6 11.2 35 85-120 50-91 (630)
103 KOG0969 DNA polymerase delta, 84.9 0.25 5.4E-06 55.8 -0.4 101 8-120 274-380 (1066)
104 cd06142 RNaseD_exo DEDDy 3'-5' 84.5 15 0.00032 32.9 11.1 89 85-182 53-161 (178)
105 TIGR00593 pola DNA polymerase 81.2 9.9 0.00021 44.3 10.5 92 81-181 363-477 (887)
106 KOG3657 Mitochondrial DNA poly 71.3 3.7 7.9E-05 47.1 3.4 38 93-135 240-277 (1075)
107 COG5228 POP2 mRNA deadenylase 69.9 20 0.00043 35.6 7.6 172 7-189 41-261 (299)
108 PF13017 Maelstrom: piRNA path 69.8 6.5 0.00014 38.0 4.4 149 26-178 7-194 (213)
109 KOG0970 DNA polymerase alpha, 55.6 69 0.0015 38.6 9.7 144 8-154 529-707 (1429)
110 cd06147 Rrp6p_like_exo DEDDy 3 54.7 1.6E+02 0.0036 27.1 10.8 87 87-183 68-174 (192)
111 cd09018 DEDDy_polA_RNaseD_like 37.8 1.3E+02 0.0028 25.8 6.8 62 88-157 45-109 (150)
112 cd06128 DNA_polA_exo DEDDy 3'- 25.6 2.6E+02 0.0056 24.4 6.8 59 88-154 45-105 (151)
113 TIGR00592 pol2 DNA polymerase 24.1 39 0.00084 40.7 1.5 93 7-112 197-304 (1172)
114 TIGR02894 DNA_bind_RsfA transc 23.9 25 0.00054 33.0 -0.1 28 395-422 28-56 (161)
No 1
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=3.6e-32 Score=263.55 Aligned_cols=177 Identities=19% Similarity=0.240 Sum_probs=155.4
Q ss_pred CCCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCH
Q 013825 2 GPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (436)
Q Consensus 2 ~~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f 81 (436)
+++..+.+|++||+||||+++ ..++|||||+|.++++.....+.|+++|+|.. +|++.+.++||||.++|+++|+|
T Consensus 41 ~~~~~~~~~vviD~ETTGl~p--~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt~e~l~~ap~~ 116 (239)
T PRK09146 41 DTPLSEVPFVALDFETTGLDA--EQDAIVSIGLVPFTLQRIRCRQARHWVVKPRR--PLEEESVVIHGITHSELQDAPDL 116 (239)
T ss_pred CCCcccCCEEEEEeECCCCCC--CCCcEEEEEEEEEECCeEeecceEEEEECCCC--CCChhhhhhcCCCHHHHhCCCCH
Confidence 457778899999999999997 67999999999999985544678999999998 79999999999999999999999
Q ss_pred HHHHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCC------------CCCCCHHH
Q 013825 82 ADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRR------------AGDMKMAS 149 (436)
Q Consensus 82 ~eVl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~------------~~~~kL~~ 149 (436)
.+++.+|.+++.+.++||||+ .||+.||++++.+++...+ ...+|||+.++++.+.+. .++++|++
T Consensus 117 ~evl~~l~~~~~~~~lVaHna-~FD~~fL~~~l~~~~~~~~-~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~ 194 (239)
T PRK09146 117 ERILDELLEALAGKVVVVHYR-RIERDFLDQALRNRIGEGI-EFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLAD 194 (239)
T ss_pred HHHHHHHHHHhCCCEEEEECH-HHHHHHHHHHHHHhcCCCC-CCceechHHHHHHHcccccccccchhccCCCCCCCHHH
Confidence 999999999999999999999 9999999999988644333 235899999988754321 26789999
Q ss_pred HHHHhCCC-CCCCChHHHHHHHHHHHHHHHHHhhhh
Q 013825 150 LATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFLE 184 (436)
Q Consensus 150 LA~~fGI~-~~~HrALdDAraTa~VLk~L~~~l~le 184 (436)
++++||++ ..+|+|++||++|++||.++.++.+.+
T Consensus 195 l~~~~gl~~~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 195 SRLRYGLPAYSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred HHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 99999999 579999999999999999999887643
No 2
>PRK07883 hypothetical protein; Validated
Probab=100.00 E-value=1e-31 Score=287.80 Aligned_cols=206 Identities=30% Similarity=0.421 Sum_probs=177.2
Q ss_pred CCCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCH
Q 013825 2 GPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (436)
Q Consensus 2 ~~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f 81 (436)
+++..+..||+||+||||+++ ..++|||||||+++++ .+++.|+++|+|.. +++++++++||||++||+++|+|
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~p--~~~~IIEIgaV~v~~g--~iv~~f~~lV~P~~--~i~~~~~~itGIt~e~l~~ap~~ 82 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGSP--AGDAITEIGAVKVRGG--EVLGEFATLVNPGR--PIPPFITVLTGITTAMVAGAPPI 82 (557)
T ss_pred CCCCcCCCEEEEEEecCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEECCCC--CCChhHHhhcCCCHHHHhCCCCH
Confidence 677888999999999999987 5689999999999977 66789999999988 79999999999999999999999
Q ss_pred HHHHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcC-CCCCCCHHHHHHHhCCC-CC
Q 013825 82 ADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGR-RAGDMKMASLATYFGLG-QQ 159 (436)
Q Consensus 82 ~eVl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~-~~~~~kL~~LA~~fGI~-~~ 159 (436)
.+++.+|.+|+++.++||||+ .||+.||+++|.++|++++.+ .++||+.++++.+.+ ...+++|++|+++||++ .+
T Consensus 83 ~evl~~f~~fl~~~~lVaHNa-~FD~~fL~~~~~r~g~~~~~~-~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~~ 160 (557)
T PRK07883 83 EEVLPAFLEFARGAVLVAHNA-PFDIGFLRAAAARCGYPWPGP-PVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTTP 160 (557)
T ss_pred HHHHHHHHHHhcCCEEEEeCc-HHHHHHHHHHHHHcCCCCCCC-CcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccCC
Confidence 999999999999999999999 999999999999999988754 589999998876643 56789999999999999 68
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhh--hcCcchhhhccCCCCCCccccccccCCCCCCCC
Q 013825 160 THRSLDDVRMNLEVLKYCATVLFL--ESSLPDIFTVNSWVSPNATTRSRSNAKSSPEGT 216 (436)
Q Consensus 160 ~HrALdDAraTa~VLk~L~~~l~l--e~slp~l~~~~~~v~~~~~~R~R~~~~~~p~~~ 216 (436)
+|+|++||++|++||.+++.++.. ..++.++......+++ ..+..|...+.+|..|
T Consensus 161 ~H~Al~DA~ata~l~~~l~~~~~~~~~~~~~~l~~~~~~~~~-~~~~~~~~~~~lP~~P 218 (557)
T PRK07883 161 THRALDDARATVDVLHGLIERLGNLGVHTLEELLTYLPRVTP-AQRRKRHLADGLPHAP 218 (557)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHhhhhcCh-hhhcchHHHhhCCCCc
Confidence 999999999999999999999863 2244555554444433 3334566667888876
No 3
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=1.8e-31 Score=257.19 Aligned_cols=174 Identities=20% Similarity=0.206 Sum_probs=151.0
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhC-CCCH
Q 013825 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTF 81 (436)
Q Consensus 3 ~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~-Ap~f 81 (436)
|...+.+||+||+||||+++ ..++|||||+|+++.++ .++++|++||+|.. +|+++++++||||.+|+.+ ++++
T Consensus 1 ~~~~~~~~vv~D~ETTGl~p--~~d~Iieig~v~v~~~g-~~~~~~~~lv~P~~--~i~~~a~~IhGIt~e~l~~~g~~~ 75 (232)
T PRK07942 1 MSWHPGPLAAFDLETTGVDP--ETARIVTAALVVVDADG-EVVESREWLADPGV--EIPEEASAVHGITTEYARAHGRPA 75 (232)
T ss_pred CCcccCcEEEEEeccCCCCC--CCCeeEEEEEEEEeCCC-ccccceEEEECCCC--CCCHHHHHHhCCCHHHHHhhCCCH
Confidence 45678899999999999987 67899999999998532 45678999999998 7999999999999999975 7888
Q ss_pred HHHHHHHHHHH-----cCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 013825 82 ADIADTVFDIL-----HGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGL 156 (436)
Q Consensus 82 ~eVl~~f~efL-----~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI 156 (436)
.+++.+|.+++ .+.++||||+ .||+.||+++++++|.+.+....++|++.+.+.....+.++++|++||++||+
T Consensus 76 ~~vl~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi 154 (232)
T PRK07942 76 AEVLAEIADALREAWARGVPVVVFNA-PYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGV 154 (232)
T ss_pred HHHHHHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCC
Confidence 88998888877 4789999999 99999999999999987664456899999877543334567899999999999
Q ss_pred C-CCCCChHHHHHHHHHHHHHHHHHhh
Q 013825 157 G-QQTHRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 157 ~-~~~HrALdDAraTa~VLk~L~~~l~ 182 (436)
+ .++|+|++||++|++||.++.++..
T Consensus 155 ~~~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 155 RLDNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred CCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 9 5799999999999999999988764
No 4
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=2.2e-31 Score=267.35 Aligned_cols=172 Identities=23% Similarity=0.362 Sum_probs=158.2
Q ss_pred CCCCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCC
Q 013825 1 MGPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPT 80 (436)
Q Consensus 1 ~~~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~ 80 (436)
||......+||+||+||||+++ ..++|||||||.++.+ +++++|+.+|+|.. ++++.++++||||++||+++|+
T Consensus 1 ~~~~~~~~~~Vv~DlETTGl~p--~~~eIIEIgaV~v~~g--~i~~~f~~lVkP~~--~I~~~a~~ihGIT~e~l~~~~~ 74 (313)
T PRK06807 1 MGNISLPLDYVVIDFETTGFNP--YNDKIIQVAAVKYRNH--ELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPT 74 (313)
T ss_pred CCCcCCCCCEEEEEEECCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEECcCC--CCCHhhhccCCCCHHHHhCCCC
Confidence 6777888999999999999987 6789999999999976 67899999999998 7999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCC
Q 013825 81 FADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQT 160 (436)
Q Consensus 81 f~eVl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~~~ 160 (436)
|.+++++|.+|+++.++||||+ .||+.||+++|.++|++++.. .++||+.+++. +.+..++++|.+|+++||++.++
T Consensus 75 ~~evl~~f~~fl~~~~lVaHNa-~FD~~fL~~~~~~~gl~~~~~-~~iDtl~la~~-~~~~~~~~kL~~L~~~lgi~~~~ 151 (313)
T PRK06807 75 IEEVLPLFLAFLHTNVIVAHNA-SFDMRFLKSNVNMLGLPEPKN-KVIDTVFLAKK-YMKHAPNHKLETLKRMLGIRLSS 151 (313)
T ss_pred HHHHHHHHHHHHcCCeEEEEcH-HHHHHHHHHHHHHcCCCCCCC-CEeeHHHHHHH-HhCCCCCCCHHHHHHHcCCCCCC
Confidence 9999999999999999999999 999999999999999987754 49999999875 44566789999999999999889
Q ss_pred CChHHHHHHHHHHHHHHHHHh
Q 013825 161 HRSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 161 HrALdDAraTa~VLk~L~~~l 181 (436)
|||++||++|++||.+|....
T Consensus 152 H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 152 HNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred cChHHHHHHHHHHHHHHHHhh
Confidence 999999999999999988754
No 5
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=100.00 E-value=4.3e-31 Score=236.31 Aligned_cols=166 Identities=27% Similarity=0.415 Sum_probs=150.0
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHH
Q 013825 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (436)
Q Consensus 9 ~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f 88 (436)
.||+||+||||+++ ..++|+|||+|+++++. +.+.|+.+|+|.. +++++++++||||.+++.+++++.+++.+|
T Consensus 1 ~~v~~D~Ettg~~~--~~~~Iieig~v~~~~~~--~~~~f~~~v~p~~--~i~~~~~~~~Git~~~l~~~~~~~~~~~~~ 74 (169)
T smart00479 1 TLVVIDCETTGLDP--GKDEIIEIAAVDVDGGR--IIVVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLEEL 74 (169)
T ss_pred CEEEEEeeCCCCCC--CCCeEEEEEEEEEECCE--eEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 48999999999987 56899999999999983 6689999999966 899999999999999999999999999999
Q ss_pred HHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC-C-CCChHHH
Q 013825 89 FDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ-Q-THRSLDD 166 (436)
Q Consensus 89 ~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~-~-~HrALdD 166 (436)
.+|+++.++|+||+..||+.+|++++.++|+++|.+..++|++.+++..+.. .+++|++++++||++. . .|+|++|
T Consensus 75 ~~~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~--~~~~L~~l~~~~~~~~~~~~H~A~~D 152 (169)
T smart00479 75 LEFLKGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPG--RKYSLKKLAERLGLEVIGRAHRALDD 152 (169)
T ss_pred HHHhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCC--CCCCHHHHHHHCCCCCCCCCcCcHHH
Confidence 9999999999999999999999999999999888766799999988755433 2899999999999983 4 4999999
Q ss_pred HHHHHHHHHHHHHHhh
Q 013825 167 VRMNLEVLKYCATVLF 182 (436)
Q Consensus 167 AraTa~VLk~L~~~l~ 182 (436)
|++|++||+++.++.+
T Consensus 153 a~~t~~l~~~~~~~~~ 168 (169)
T smart00479 153 ARATAKLFKKLVERLL 168 (169)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999987654
No 6
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=2e-31 Score=258.74 Aligned_cols=166 Identities=26% Similarity=0.399 Sum_probs=146.1
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
..+||+||+||||+++. .+++|||||+|.+.++.. +.++|+.||+|.. +|++++.++||||.++|+++|.|+++++
T Consensus 3 ~~r~vvlDtETTGldp~-~~drIIEIGaV~v~~~~~-~~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev~~ 78 (240)
T PRK05711 3 IMRQIVLDTETTGLNQR-EGHRIIEIGAVELINRRL-TGRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEVAD 78 (240)
T ss_pred CCeEEEEEeeCCCcCCC-CCCeEEEEEEEEEECCEE-eccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHHHH
Confidence 46899999999999872 268999999999998743 4468999999988 7999999999999999999999999999
Q ss_pred HHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCC---CCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC---CC
Q 013825 87 TVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPE---PKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ---QT 160 (436)
Q Consensus 87 ~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~---~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~---~~ 160 (436)
+|.+|++++.+||||+ .||++||++++.++|..++. ...++||+.++++.+.. ..++|++||++||++. ..
T Consensus 79 ~f~~fi~~~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~--~~~~L~aL~~~~gi~~~~r~~ 155 (240)
T PRK05711 79 EFLDFIRGAELIIHNA-PFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPG--KRNSLDALCKRYGIDNSHRTL 155 (240)
T ss_pred HHHHHhCCCEEEEEcc-HHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCC--CCCCHHHHHHHCCCCCCCCCC
Confidence 9999999999999999 99999999999999865552 24589999999876543 3579999999999984 46
Q ss_pred CChHHHHHHHHHHHHHHHH
Q 013825 161 HRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 161 HrALdDAraTa~VLk~L~~ 179 (436)
|+|+.||++|++||.++..
T Consensus 156 H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 156 HGALLDAEILAEVYLAMTG 174 (240)
T ss_pred CCHHHHHHHHHHHHHHHHC
Confidence 9999999999999998764
No 7
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.98 E-value=2.5e-31 Score=255.37 Aligned_cols=164 Identities=24% Similarity=0.338 Sum_probs=143.4
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHH
Q 013825 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (436)
Q Consensus 9 ~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f 88 (436)
++|+||+||||+++. .+++|||||||.+.++. ...++|+.||+|.. .|+++++++||||.++++++|+|.+++.+|
T Consensus 1 r~vvlD~ETTGl~p~-~~d~IIEIgav~~~~~~-~~~~~f~~~i~P~~--~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f 76 (225)
T TIGR01406 1 RQIILDTETTGLDPK-GGHRIVEIGAVELVNRM-LTGDNFHVYVNPER--DMPAEAAKVHGITDEFLADKPKFKEIADEF 76 (225)
T ss_pred CEEEEEeeCCCcCCC-CCCeEEEEEEEEEECCc-EecceEEEEECcCC--CCCHHHHhccCCCHHHHhCCCCHHHHHHHH
Confidence 589999999999872 24899999999998763 34578999999998 799999999999999999999999999999
Q ss_pred HHHHcCCEEEEEccccchHHHHHHHHHHcCCCCC---CCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC---CCCC
Q 013825 89 FDILHGRIWAGHNILRFDCARIREAFAEIGRPAP---EPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ---QTHR 162 (436)
Q Consensus 89 ~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p---~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~---~~Hr 162 (436)
.+|+++.++||||+ .||+.||++++.++|...+ ....++||+.++++.+.. ..++|++||++||++. ..|+
T Consensus 77 ~~fi~~~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~--~~~~L~~L~~~~gi~~~~r~~H~ 153 (225)
T TIGR01406 77 LDFIGGSELVIHNA-AFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPG--QRNSLDALCKRFKVDNSHRTLHG 153 (225)
T ss_pred HHHhCCCEEEEEec-HHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCC--CCCCHHHHHHhcCCCCCCCCCcC
Confidence 99999999999999 9999999999999994322 225699999999876533 3689999999999983 4699
Q ss_pred hHHHHHHHHHHHHHHHH
Q 013825 163 SLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 163 ALdDAraTa~VLk~L~~ 179 (436)
|+.||+++++||.++..
T Consensus 154 Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 154 ALLDAHLLAEVYLALTG 170 (225)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 99999999999998765
No 8
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.98 E-value=3.2e-31 Score=235.84 Aligned_cols=155 Identities=25% Similarity=0.429 Sum_probs=141.4
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHH
Q 013825 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVF 89 (436)
Q Consensus 10 fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~ 89 (436)
||+||+||||.. .++|||||+|+++.+ +++++|+.+|+|.. +++++++++||||.+++++++++.+++++|.
T Consensus 1 ~v~~D~Ettg~~----~~~ii~ig~v~~~~~--~~~~~~~~~i~p~~--~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~ 72 (156)
T cd06130 1 FVAIDFETANAD----RASACSIGLVKVRDG--QIVDTFYTLIRPPT--RFDPFNIAIHGITPEDVADAPTFPEVWPEIK 72 (156)
T ss_pred CEEEEEeCCCCC----CCceEEEEEEEEECC--EEEEEEEEEeCcCC--CCChhhccccCcCHHHHhcCCCHHHHHHHHH
Confidence 689999999975 478999999999977 66789999999998 7999999999999999999999999999999
Q ss_pred HHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHHHH
Q 013825 90 DILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRM 169 (436)
Q Consensus 90 efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~~~HrALdDAra 169 (436)
+|+++.++||||+ +||+.||++++.++|++++. ..++|++.++++.+ +..++++|++++++||++..+|+|++||++
T Consensus 73 ~~l~~~~lv~hn~-~fD~~~l~~~~~~~g~~~~~-~~~idt~~~~~~~~-~~~~~~~L~~l~~~~g~~~~~H~Al~Da~~ 149 (156)
T cd06130 73 PFLGGSLVVAHNA-SFDRSVLRAALEAYGLPPPP-YQYLCTVRLARRVW-PLLPNHKLNTVAEHLGIELNHHDALEDARA 149 (156)
T ss_pred HHhCCCEEEEeCh-HHhHHHHHHHHHHcCCCCCC-CCEEEHHHHHHHHh-ccCCCCCHHHHHHHcCCCccCcCchHHHHH
Confidence 9999999999999 99999999999999998764 46999999887654 446789999999999999449999999999
Q ss_pred HHHHHH
Q 013825 170 NLEVLK 175 (436)
Q Consensus 170 Ta~VLk 175 (436)
|+++|-
T Consensus 150 ta~l~~ 155 (156)
T cd06130 150 CAEILL 155 (156)
T ss_pred HHHHHh
Confidence 999984
No 9
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=5.1e-31 Score=258.15 Aligned_cols=167 Identities=20% Similarity=0.361 Sum_probs=151.1
Q ss_pred CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHH
Q 013825 4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (436)
Q Consensus 4 ~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~e 83 (436)
+..+..||+||+||||+.+ ..++|||||||+++++ .++++|+.+|+|. .+++.++++||||++|++++|++.+
T Consensus 64 ~~~~~~~vv~DiETTG~~~--~~~~IIEIGAv~v~~g--~i~~~f~~~v~p~---~ip~~~~~itGIt~e~l~~ap~~~e 136 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKP--KKHQIIEIGAVKVKNG--EIIDRFESFVKAK---EVPEYITELTGITYEDLENAPSLKE 136 (257)
T ss_pred CCCCCCEEEEEEeCCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEECCC---CCChhhhhhcCcCHHHHcCCCCHHH
Confidence 4567899999999999987 5679999999999876 6678999999996 4899999999999999999999999
Q ss_pred HHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCC
Q 013825 84 IADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHR 162 (436)
Q Consensus 84 Vl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~Hr 162 (436)
++.+|.+|++++++||||+ +||+.||++++.++|.++..+ +++||+.++++.+.. .+++|++|+++||++ .++||
T Consensus 137 vl~~f~~fl~~~v~VaHNa-~FD~~fL~~~l~r~g~~~~~~-~~ldtl~la~~~~~~--~~~~L~~L~~~lgi~~~~~Hr 212 (257)
T PRK08517 137 VLEEFRLFLGDSVFVAHNV-NFDYNFISRSLEEIGLGPLLN-RKLCTIDLAKRTIES--PRYGLSFLKELLGIEIEVHHR 212 (257)
T ss_pred HHHHHHHHHCCCeEEEECH-HHHHHHHHHHHHHcCCCCCCC-CcEehHHHHHHHccC--CCCCHHHHHHHcCcCCCCCCC
Confidence 9999999999999999999 999999999999999886543 589999998765532 578999999999999 48999
Q ss_pred hHHHHHHHHHHHHHHHHHh
Q 013825 163 SLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 163 ALdDAraTa~VLk~L~~~l 181 (436)
|++||.+|++||.++..++
T Consensus 213 Al~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 213 AYADALAAYEIFKICLLNL 231 (257)
T ss_pred hHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999876
No 10
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.98 E-value=3.7e-31 Score=251.95 Aligned_cols=172 Identities=20% Similarity=0.253 Sum_probs=149.3
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 3 ~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
+.+....||+||+||||+++ ..+ |||||||++.++. .+.++|+++|+|.. ++++.+.++||||.+|++++|+|.
T Consensus 2 ~~l~~~~fvv~D~ETTGl~~--~~~-IIeIgav~v~~~~-~~~~~f~~li~P~~--~i~~~a~~ihGIt~e~l~~~p~~~ 75 (217)
T TIGR00573 2 RQLVLDTETTGDNETTGLYA--GHD-IIEIGAVEIINRR-ITGNKFHTYIKPDR--PIDPDAIKIHGITDDMLKDKPDFK 75 (217)
T ss_pred ceEEecCEEEEEecCCCCCC--CCC-EEEEEEEEEECCC-EeeeEEEEEECcCC--CCCHHHHhhcCCCHHHHcCCCCHH
Confidence 34667899999999999987 456 9999999987663 45689999999998 799999999999999999999999
Q ss_pred HHHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcC-CCCCCCHHHHHHHhCCCC---
Q 013825 83 DIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGR-RAGDMKMASLATYFGLGQ--- 158 (436)
Q Consensus 83 eVl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~-~~~~~kL~~LA~~fGI~~--- 158 (436)
+++.+|.+|+++.++||||+ .||+.||+++|.+++..++....++|++.+++..+.. ...+++|..++++||++.
T Consensus 76 ev~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~ 154 (217)
T TIGR00573 76 EIAEDFADYIRGAELVIHNA-SFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHR 154 (217)
T ss_pred HHHHHHHHHhCCCEEEEecc-HHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCc
Confidence 99999999999999999999 9999999999999876555445689999987754432 224679999999999983
Q ss_pred CCCChHHHHHHHHHHHHHHHHHh
Q 013825 159 QTHRSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 159 ~~HrALdDAraTa~VLk~L~~~l 181 (436)
.+|+|++||++|++||.++..+.
T Consensus 155 ~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 155 ALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred ccCCHHHHHHHHHHHHHHHHhcc
Confidence 58999999999999999988753
No 11
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=1.3e-30 Score=260.87 Aligned_cols=166 Identities=19% Similarity=0.295 Sum_probs=150.0
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHH
Q 013825 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~ 87 (436)
.+||+||+||||.. .++|||||||+++++ .++++|++||+|.. ..+++.++++||||++||+++|+|.+++++
T Consensus 1 ~~~vviD~ETTg~~----~d~IieIgav~v~~g--~i~~~f~~lv~P~~-~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~ 73 (309)
T PRK06195 1 MNFVAIDFETANEK----RNSPCSIGIVVVKDG--EIVEKVHYLIKPKE-MRFMPINIGIHGIRPHMVEDELEFDKIWEK 73 (309)
T ss_pred CcEEEEEEeCCCCC----CCceEEEEEEEEECC--EEEEEEEEEECCCC-CCCChhheeccCcCHHHHhCCCCHHHHHHH
Confidence 37999999999863 589999999999977 66789999999986 257888999999999999999999999999
Q ss_pred HHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHH
Q 013825 88 VFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDV 167 (436)
Q Consensus 88 f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~~~HrALdDA 167 (436)
|.+|+++.++||||+ .||+.||++++.+++++++.. .++||+.++++ +.+..++++|.+|+++||++..+|||++||
T Consensus 74 ~~~fl~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~-~~idT~~lar~-l~~~~~~~~L~~L~~~~gi~~~~H~Al~DA 150 (309)
T PRK06195 74 IKHYFNNNLVIAHNA-SFDISVLRKTLELYNIPMPSF-EYICTMKLAKN-FYSNIDNARLNTVNNFLGYEFKHHDALADA 150 (309)
T ss_pred HHHHhCCCEEEEECc-HHHHHHHHHHHHHhCCCCCCC-CEEEHHHHHHH-HcCCCCcCCHHHHHHHcCCCCcccCCHHHH
Confidence 999999999999999 999999999999999988765 59999999875 445567899999999999997799999999
Q ss_pred HHHHHHHHHHHHHhhh
Q 013825 168 RMNLEVLKYCATVLFL 183 (436)
Q Consensus 168 raTa~VLk~L~~~l~l 183 (436)
++|++||.++++++..
T Consensus 151 ~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 151 MACSNILLNISKELNS 166 (309)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 9999999999988654
No 12
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.98 E-value=6.8e-31 Score=237.61 Aligned_cols=161 Identities=25% Similarity=0.380 Sum_probs=141.1
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHH
Q 013825 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVF 89 (436)
Q Consensus 10 fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~ 89 (436)
||+||+||||+++ ...++|||||||+++.+.. ..++|+.+|+|.. .++++++++||||.+++++++++.+++.+|.
T Consensus 1 ~v~~D~ETTGl~~-~~~~~iieig~v~v~~~~~-~~~~~~~~v~P~~--~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~ 76 (167)
T cd06131 1 QIVLDTETTGLDP-REGHRIIEIGCVELINRRL-TGNTFHVYINPER--DIPEEAFKVHGITDEFLADKPKFAEIADEFL 76 (167)
T ss_pred CEEEEeeCCCCCC-CCCCeEEEEEEEEEECCcE-eccEEEEEECCCC--CCCHHHHHHhCCCHHHHhcCCCHHHHHHHHH
Confidence 6899999999975 2357999999999988632 4468999999998 6999999999999999999999999999999
Q ss_pred HHHcCCEEEEEccccchHHHHHHHHHHcCCCCC--CCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC---CCCChH
Q 013825 90 DILHGRIWAGHNILRFDCARIREAFAEIGRPAP--EPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ---QTHRSL 164 (436)
Q Consensus 90 efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p--~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~---~~HrAL 164 (436)
+|+++.++||||+ .||+.||++++.++|...+ .+..++||+.++++.+ +. ..++|++++++||++. ++|+|+
T Consensus 77 ~~l~~~~lv~hn~-~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~-~~-~~~~L~~l~~~~~i~~~~~~~H~Al 153 (167)
T cd06131 77 DFIRGAELVIHNA-SFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKF-PG-KPNSLDALCKRFGIDNSHRTLHGAL 153 (167)
T ss_pred HHHCCCeEEEeCh-HHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHc-CC-CCCCHHHHHHHCCCCCCCCCCCChH
Confidence 9999999999999 9999999999999876543 3457999999987654 32 4679999999999983 479999
Q ss_pred HHHHHHHHHHHHH
Q 013825 165 DDVRMNLEVLKYC 177 (436)
Q Consensus 165 dDAraTa~VLk~L 177 (436)
+||++|++||.++
T Consensus 154 ~Da~~~a~l~~~l 166 (167)
T cd06131 154 LDAELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999875
No 13
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=8.3e-31 Score=255.35 Aligned_cols=168 Identities=24% Similarity=0.365 Sum_probs=151.2
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
.++.+||+||+||||+++ ..++|||||+|.+..+ .+++.|+.+|+|.. +|+++++++||||+++|+++|+|.++
T Consensus 4 l~~~~~v~~D~ETTGl~~--~~d~IIEIa~v~v~~~--~~~~~~~~li~P~~--~I~~~a~~ihgIt~e~v~~~p~~~ev 77 (250)
T PRK06310 4 LKDTEFVCLDCETTGLDV--KKDRIIEFAAIRFTFD--EVIDSVEFLINPER--VVSAESQRIHHISDAMLRDKPKIAEV 77 (250)
T ss_pred ccCCcEEEEEEeCCCCCC--CCCeEEEEEEEEEECC--eEEEEEEEEECcCC--CCCHhhhhccCcCHHHHhCCCCHHHH
Confidence 345789999999999987 6789999999999987 56789999999998 79999999999999999999999999
Q ss_pred HHHHHHHHcC-CEEEEEccccchHHHHHHHHHHcCCCCCC-CCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCC
Q 013825 85 ADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPE-PKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTH 161 (436)
Q Consensus 85 l~~f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~-~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~H 161 (436)
+++|.+|+++ .++||||+ .||+.||+++|.++|++++. +..+|||+.+++. +. ..++++|+.|+++||++ ..+|
T Consensus 78 ~~~~~~fl~~~~~lvghn~-~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~-~~-~~~~~~L~~l~~~~g~~~~~aH 154 (250)
T PRK06310 78 FPQIKGFFKEGDYIVGHSV-GFDLQVLSQESERIGETFLSKHYYIIDTLRLAKE-YG-DSPNNSLEALAVHFNVPYDGNH 154 (250)
T ss_pred HHHHHHHhCCCCEEEEECH-HHHHHHHHHHHHHcCCCccccCCcEEehHHHHHh-cc-cCCCCCHHHHHHHCCCCCCCCc
Confidence 9999999986 89999999 99999999999999998764 3569999999874 43 34678999999999999 5799
Q ss_pred ChHHHHHHHHHHHHHHHHHh
Q 013825 162 RSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 162 rALdDAraTa~VLk~L~~~l 181 (436)
||++||.+|++||.++.+++
T Consensus 155 ~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 155 RAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred ChHHHHHHHHHHHHHHHHhc
Confidence 99999999999999998764
No 14
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=1.2e-30 Score=253.45 Aligned_cols=174 Identities=21% Similarity=0.293 Sum_probs=151.9
Q ss_pred CCCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCH
Q 013825 2 GPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (436)
Q Consensus 2 ~~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f 81 (436)
..+..+.+|||||+||||+++. ..++|||||||+++++.. +.++|+.+|+|.. ++++.+.++||||.++++++|+|
T Consensus 53 ~~~~~~~~~vv~D~ETTGl~p~-~~deIIeIgaV~~~~~~i-~~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~ 128 (244)
T PRK07740 53 DIPLTDLPFVVFDLETTGFSPQ-QGDEILSIGAVKTKGGEV-ETDTFYSLVKPKR--PIPEHILELTGITAEDVAFAPPL 128 (244)
T ss_pred CCCccCCCEEEEEEeCCCCCCC-CCCeEEEEEEEEEECCEE-EEEEEEEEeCcCC--CCChhheeccCCCHHHHhCCCCH
Confidence 3456778999999999999872 248999999999998743 4789999999998 79999999999999999999999
Q ss_pred HHHHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCC
Q 013825 82 ADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQT 160 (436)
Q Consensus 82 ~eVl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~ 160 (436)
.+++.+|.+|++++++||||+ .||..||++++.+.... +....++||+.+++. +.+..++++|++++++||++ ..+
T Consensus 129 ~evl~~f~~fi~~~~lVahna-~fD~~fL~~~~~~~~~~-~~~~~~iDt~~l~r~-l~~~~~~~sL~~l~~~~gi~~~~~ 205 (244)
T PRK07740 129 AEVLHRFYAFIGAGVLVAHHA-GHDKAFLRHALWRTYRQ-PFTHRLIDTMFLTKL-LAHERDFPTLDDALAYYGIPIPRR 205 (244)
T ss_pred HHHHHHHHHHhCCCEEEEeCH-HHHHHHHHHHHHHhcCC-CcCCCeechHHHHHH-HcCCCCCCCHHHHHHHCCcCCCCC
Confidence 999999999999999999999 99999999998775432 334569999998764 45555789999999999999 578
Q ss_pred CChHHHHHHHHHHHHHHHHHhh
Q 013825 161 HRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 161 HrALdDAraTa~VLk~L~~~l~ 182 (436)
|+|++||++|++||.+++.++.
T Consensus 206 H~Al~Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 206 HHALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred CCcHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999988764
No 15
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=1.2e-30 Score=261.82 Aligned_cols=168 Identities=23% Similarity=0.336 Sum_probs=149.6
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHH
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl 85 (436)
...+||+||+||||+++ ..++|||||+|+++.++ .+.++|+++|+|.. ++.++++||||++||+++|+|.+++
T Consensus 13 ~~~~fvvlD~ETTGl~p--~~d~IIeIgav~v~~~g-~i~~~~~~lv~P~~----~~~~~~IhGIt~e~l~~ap~f~ev~ 85 (313)
T PRK06063 13 YPRGWAVVDVETSGFRP--GQARIISLAVLGLDADG-NVEQSVVTLLNPGV----DPGPTHVHGLTAEMLEGQPQFADIA 85 (313)
T ss_pred CCCCEEEEEEECCCCCC--CCCEEEEEEEEEEECCc-eeeeEEEEEECcCC----CCCCeecCCCCHHHHhCCCCHHHHH
Confidence 35789999999999987 57899999999998643 56789999999976 2356789999999999999999999
Q ss_pred HHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChH
Q 013825 86 DTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSL 164 (436)
Q Consensus 86 ~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~HrAL 164 (436)
.+|.+|++++++||||+ .||+.||+++|.++|++.+.. .++||+.++++ +.+..++++|++||++||++ .++|||+
T Consensus 86 ~~l~~~l~~~~lVaHNa-~FD~~fL~~~~~r~g~~~~~~-~~ldTl~lar~-~~~~~~~~kL~~l~~~~gi~~~~~H~Al 162 (313)
T PRK06063 86 GEVAELLRGRTLVAHNV-AFDYSFLAAEAERAGAELPVD-QVMCTVELARR-LGLGLPNLRLETLAAHWGVPQQRPHDAL 162 (313)
T ss_pred HHHHHHcCCCEEEEeCH-HHHHHHHHHHHHHcCCCCCCC-CEEehHHHHHH-hccCCCCCCHHHHHHHcCCCCCCCCCcH
Confidence 99999999999999999 999999999999999887754 48999999875 55556799999999999999 5899999
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 013825 165 DDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 165 dDAraTa~VLk~L~~~l~l 183 (436)
+||++|++||.++++++..
T Consensus 163 ~DA~ata~l~~~ll~~~~~ 181 (313)
T PRK06063 163 DDARVLAGILRPSLERARE 181 (313)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999999888654
No 16
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.97 E-value=1.1e-30 Score=246.80 Aligned_cols=171 Identities=18% Similarity=0.211 Sum_probs=146.6
Q ss_pred CCcEEEEEEecCCCCCC----CCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 7 RSEIAFFDVETTVPTRP----GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~----g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
..+||+||+||||.++. +..++|||||||+++++ ++.++|++||+|.....++++++++||||++||.++|+|+
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~--~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ 80 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGC--EVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFE 80 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecC--cChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHH
Confidence 46899999999996531 12479999999999987 5678999999999744699999999999999999999999
Q ss_pred HHHHHHHHHHcC-CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC--C
Q 013825 83 DIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ--Q 159 (436)
Q Consensus 83 eVl~~f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~--~ 159 (436)
+++.+|.+|+++ ..+++||+ .||+.||+++|+++|++.++...++|+..+++..+ +....++|+.++++||++. .
T Consensus 81 evl~~f~~~~~~~~~~iv~~~-~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~-~~~~~~~L~~~~~~~gi~~~~~ 158 (207)
T PRK07748 81 ELVEKLAEYDKRCKPTIVTWG-NMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFF-GERNQTGLWKAIEEYGKEGTGK 158 (207)
T ss_pred HHHHHHHHHhCcCCeEEEEEC-HHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHh-CcCCCCCHHHHHHHcCCCCCCC
Confidence 999999999998 45666777 99999999999999998776556899988766544 3335689999999999993 5
Q ss_pred CCChHHHHHHHHHHHHHHHHHh
Q 013825 160 THRSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 160 ~HrALdDAraTa~VLk~L~~~l 181 (436)
+|||++||++|++||.++.+..
T Consensus 159 ~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 159 HHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred CcChHHHHHHHHHHHHHHHhCc
Confidence 8999999999999999988774
No 17
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.97 E-value=9.6e-31 Score=241.93 Aligned_cols=158 Identities=25% Similarity=0.303 Sum_probs=133.0
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcc-----------eEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCC
Q 013825 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKL-----------EELHNYSTLVRPADPELISSLSVRCNGITPDAVVSS 78 (436)
Q Consensus 10 fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~l-----------evl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~A 78 (436)
|++||+||||++++ ..++|||||||++.+++. .++++|+++|+|.. +|++.++++||||++++.++
T Consensus 1 ~vv~D~ETTGl~~~-~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~--~I~~~a~~IhGIt~e~l~~~ 77 (177)
T cd06136 1 FVFLDLETTGLPKH-NRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR--AISPGASEITGLSNDLLEHK 77 (177)
T ss_pred CeEEeeecCCCCCC-CCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC--cCChhHHHHhCcCHHHHhcC
Confidence 78999999999831 478999999999997642 24578999999998 89999999999999999999
Q ss_pred CCHHH-HHHHHHHHH---cC-CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHH-
Q 013825 79 PTFAD-IADTVFDIL---HG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLAT- 152 (436)
Q Consensus 79 p~f~e-Vl~~f~efL---~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~- 152 (436)
|+|.+ +++.|.+|+ ++ .++||||+.+||+.||++++.++|..++....++||+.++++.. + +|++|++
T Consensus 78 ~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~-~-----~L~~l~~~ 151 (177)
T cd06136 78 APFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD-Q-----SLGSLYKR 151 (177)
T ss_pred CCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-h-----hHHHHHHH
Confidence 98764 445555555 43 58999997579999999999999998775456799999988544 2 8999998
Q ss_pred HhCCC-CCCCChHHHHHHHHHHHHH
Q 013825 153 YFGLG-QQTHRSLDDVRMNLEVLKY 176 (436)
Q Consensus 153 ~fGI~-~~~HrALdDAraTa~VLk~ 176 (436)
+||++ ..+|||++||.+|++||.+
T Consensus 152 ~~~~~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 152 LFGQEPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred HhCCCcccccchHHHHHHHHHHHhh
Confidence 48999 5899999999999999975
No 18
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=5.5e-30 Score=240.82 Aligned_cols=167 Identities=19% Similarity=0.259 Sum_probs=144.4
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHH
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl 85 (436)
.+.+||+||+||||+++ ..++|||||+|+++++.+...+.|+.+|+|.. .++++++++||||.++++++|++.+++
T Consensus 27 ~~~~~vviD~ETTGl~~--~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~--~i~~~~~~ihGIt~~~l~~~~~~~~vl 102 (202)
T PRK09145 27 PPDEWVALDCETTGLDP--RRAEIVSIAAVKIRGNRILTSERLELLVRPPQ--SLSAESIKIHRLRHQDLEDGLSEEEAL 102 (202)
T ss_pred CCCCEEEEEeECCCCCC--CCCceEEEEEEEEECCEEeecCceEEEECCCC--CCCHhHhhhcCcCHHHHhcCCCHHHHH
Confidence 45789999999999987 57899999999999875444478999999997 799999999999999999999999999
Q ss_pred HHHHHHHcCCEEEEEccccchHHHHHHHHHH-cCCCCCCCCceeeHHHHHHHHhcC----CCCCCCHHHHHHHhCCC-CC
Q 013825 86 DTVFDILHGRIWAGHNILRFDCARIREAFAE-IGRPAPEPKGTIDSLALLTQRFGR----RAGDMKMASLATYFGLG-QQ 159 (436)
Q Consensus 86 ~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r-~Gi~~p~~~~~IDTl~Larr~l~~----~~~~~kL~~LA~~fGI~-~~ 159 (436)
++|.+|+.+.++||||+ .||+.||++++.+ ++.+.+ ..++|+..++.....+ ...+++|++++++||++ ..
T Consensus 103 ~~~~~~i~~~~lv~hn~-~fD~~fL~~~~~~~~~~~~~--~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~ 179 (202)
T PRK09145 103 RQLLAFIGNRPLVGYYL-EFDVAMLNRYVRPLLGIPLP--NPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLG 179 (202)
T ss_pred HHHHHHHcCCeEEEeCH-HHHHHHHHHHHHHhcCCCCC--CCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCC
Confidence 99999999999999999 9999999999987 455544 3589998876533222 23468999999999998 57
Q ss_pred CCChHHHHHHHHHHHHHHHH
Q 013825 160 THRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 160 ~HrALdDAraTa~VLk~L~~ 179 (436)
+|+|++||++|++||.++.+
T Consensus 180 ~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 180 RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCcHHHHHHHHHHHHHHHh
Confidence 89999999999999998753
No 19
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.8e-30 Score=247.69 Aligned_cols=164 Identities=27% Similarity=0.358 Sum_probs=145.7
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHH
Q 013825 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~ 87 (436)
.+++|||+||||+++ ..++|||||++. . ...+.|+.+|+|+. +|+++++++||||++||+++|+|.+++++
T Consensus 2 ~~~vv~D~ETTGl~~--~~d~IIeig~v~--~---~~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~~ 72 (232)
T PRK06309 2 PALIFYDTETTGTQI--DKDRIIEIAAYN--G---VTSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQK 72 (232)
T ss_pred CcEEEEEeeCCCCCC--CCCEEEEEEEEc--C---ccccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 469999999999987 678999999963 2 23468999999998 79999999999999999999999999999
Q ss_pred HHHHHcC-CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHH
Q 013825 88 VFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSLD 165 (436)
Q Consensus 88 f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~HrALd 165 (436)
|.+|+.+ .++||||+.+||+.||++++.++|++.+. ..++||+.++++ +.+..++++|+.|+++||++ ..+|||++
T Consensus 73 ~~~fi~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~-~~~iDt~~l~~~-~~~~~~~~~L~~l~~~~~~~~~~aH~Al~ 150 (232)
T PRK06309 73 FIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPPT-LRTIDSLKWAQK-YRPDLPKHNLQYLRQVYGFEENQAHRALD 150 (232)
T ss_pred HHHHHcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCC-CcEEeHHHHHHH-HcCCCCCCCHHHHHHHcCCCCCCCCCcHH
Confidence 9999985 69999995489999999999999998775 459999999875 55666789999999999998 67999999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 013825 166 DVRMNLEVLKYCATVLF 182 (436)
Q Consensus 166 DAraTa~VLk~L~~~l~ 182 (436)
||.+|++||.++++++.
T Consensus 151 Da~~t~~vl~~l~~~~~ 167 (232)
T PRK06309 151 DVITLHRVFSALVGDLS 167 (232)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999988764
No 20
>PRK05168 ribonuclease T; Provisional
Probab=99.97 E-value=1.1e-29 Score=241.44 Aligned_cols=172 Identities=20% Similarity=0.203 Sum_probs=145.7
Q ss_pred CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeC---CcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHH-HhCCC
Q 013825 4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCP---KKLEELHNYSTLVRPADPELISSLSVRCNGITPDA-VVSSP 79 (436)
Q Consensus 4 ~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~---~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~-La~Ap 79 (436)
+.++..|++||+||||+++ ..++|||||||++.. +.+.+.++|+++|+|....+|++.++++||||.++ +++++
T Consensus 13 ~~~~~~~vv~D~ETTGl~~--~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~ 90 (211)
T PRK05168 13 RFRGFLPVVIDVETAGFNA--KTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAV 90 (211)
T ss_pred HhcCCceEEEEeeCCCCCC--CCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCC
Confidence 4567889999999999987 678999999999973 32334689999999953237999999999999886 88999
Q ss_pred CHHHHHHHHHHHHc---------CCEEEEEccccchHHHHHHHHHHcCCCCC-C-CCceeeHHHHHHHHhcCCCCCCCHH
Q 013825 80 TFADIADTVFDILH---------GRIWAGHNILRFDCARIREAFAEIGRPAP-E-PKGTIDSLALLTQRFGRRAGDMKMA 148 (436)
Q Consensus 80 ~f~eVl~~f~efL~---------g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p-~-~~~~IDTl~Larr~l~~~~~~~kL~ 148 (436)
++.+++.+|.+|+. +.++||||+ .||+.||++++.++|+... + +.+++||+.+++..+ +..+|.
T Consensus 91 ~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~----~~~~L~ 165 (211)
T PRK05168 91 SEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLAL----GQTVLA 165 (211)
T ss_pred ChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHc----CCCCHH
Confidence 99999999988875 689999999 9999999999999987532 1 235899999988644 345899
Q ss_pred HHHHHhCCC---CCCCChHHHHHHHHHHHHHHHHHhh
Q 013825 149 SLATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 149 ~LA~~fGI~---~~~HrALdDAraTa~VLk~L~~~l~ 182 (436)
.+|++||++ ..+|+|++||.+|+++|.++++++.
T Consensus 166 ~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 166 KACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred HHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 999999998 2589999999999999999998874
No 21
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.97 E-value=1.2e-29 Score=239.34 Aligned_cols=170 Identities=22% Similarity=0.210 Sum_probs=142.4
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeC---CcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHH-HHhCCCCH
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCP---KKLEELHNYSTLVRPADPELISSLSVRCNGITPD-AVVSSPTF 81 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~---~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e-~La~Ap~f 81 (436)
....+++||+||||+++ ..++|||||||++.. +.....++|+++|+|....+|++++.++||||.+ |+++++++
T Consensus 6 ~~~~~vv~D~ETTGl~~--~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~ 83 (200)
T TIGR01298 6 RGYLPVVVDVETGGFNA--KTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSE 83 (200)
T ss_pred cCCeeEEEEeeCCCCCC--CCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcch
Confidence 35679999999999997 578999999999973 3222246799999985323799999999999975 68999999
Q ss_pred HHHHHHHHHHH---------cCCEEEEEccccchHHHHHHHHHHcCCCC-CC-CCceeeHHHHHHHHhcCCCCCCCHHHH
Q 013825 82 ADIADTVFDIL---------HGRIWAGHNILRFDCARIREAFAEIGRPA-PE-PKGTIDSLALLTQRFGRRAGDMKMASL 150 (436)
Q Consensus 82 ~eVl~~f~efL---------~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~-p~-~~~~IDTl~Larr~l~~~~~~~kL~~L 150 (436)
.+++.+|++++ ++.++||||+ .||+.||+++++++|..+ +. +..++||+.+++..+ +.++|+.+
T Consensus 84 ~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~----~~~~L~~l 158 (200)
T TIGR01298 84 YEALHEIFKVVRKAMKASGCQRAILVGHNA-NFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY----GQTVLAKA 158 (200)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCEEEEECc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc----CcccHHHH
Confidence 99998888887 5789999999 999999999999998753 22 235899999987544 35689999
Q ss_pred HHHhCCC---CCCCChHHHHHHHHHHHHHHHHHhh
Q 013825 151 ATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 151 A~~fGI~---~~~HrALdDAraTa~VLk~L~~~l~ 182 (436)
|++||++ .++|||++||++|++||.++.+++.
T Consensus 159 ~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 159 CQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred HHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 9999998 3689999999999999999998764
No 22
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.1e-29 Score=239.63 Aligned_cols=164 Identities=18% Similarity=0.229 Sum_probs=139.5
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHH
Q 013825 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~ 87 (436)
.+||+||+||||+++ .++|||||||+++++ .++++|++||+|.. ++++.++++||||.+||+++|++.+++.+
T Consensus 5 ~~~vvlD~EtTGl~~---~~eIIeIgaV~v~~g--~~~~~f~~lv~P~~--~i~~~~~~lhGIt~~~v~~ap~~~evl~~ 77 (195)
T PRK07247 5 ETYIAFDLEFNTVNG---VSHIIQVSAVKYDDH--KEVDSFDSYVYTDV--PLQSFINGLTGITADKIADAPKVEEVLAA 77 (195)
T ss_pred CeEEEEEeeCCCCCC---CCeEEEEEEEEEECC--EEEEEEEEEECCCC--CCCccceecCCCCHHHHhCCCCHHHHHHH
Confidence 489999999999974 578999999999987 55689999999998 79999999999999999999999999999
Q ss_pred HHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHH-h--cCCCCCCCHHHHHHHhCCCCCCCChH
Q 013825 88 VFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQR-F--GRRAGDMKMASLATYFGLGQQTHRSL 164 (436)
Q Consensus 88 f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~-l--~~~~~~~kL~~LA~~fGI~~~~HrAL 164 (436)
|.+|+++.++||||+..||+.||++ +|.+.... .++|++..+... . .+...+++|.+||++||++..+|||+
T Consensus 78 f~~f~~~~~lVaHNa~~fD~~fL~~----~g~~~~~~-~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~~~HrAl 152 (195)
T PRK07247 78 FKEFVGELPLIGYNAQKSDLPILAE----NGLDLSDQ-YQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKGRGHNSL 152 (195)
T ss_pred HHHHHCCCeEEEEeCcHhHHHHHHH----cCCCcCCC-ceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCCCCcCCH
Confidence 9999999999999993489999965 46654432 368887654211 1 23457899999999999997789999
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 013825 165 DDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 165 dDAraTa~VLk~L~~~l~l 183 (436)
+||++|+.||.++++....
T Consensus 153 ~DA~~ta~v~~~ll~~~~~ 171 (195)
T PRK07247 153 EDARMTARVYESFLESDQN 171 (195)
T ss_pred HHHHHHHHHHHHHHhhccc
Confidence 9999999999998876543
No 23
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.97 E-value=2.1e-29 Score=235.49 Aligned_cols=167 Identities=22% Similarity=0.238 Sum_probs=137.5
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCC---cceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHH-HhCCCCHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPK---KLEELHNYSTLVRPADPELISSLSVRCNGITPDA-VVSSPTFA 82 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~---~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~-La~Ap~f~ 82 (436)
.-.+|+||+||||+++ ..++|||||||++..+ .+.+.++|+++|+|....+|++.+.++||||.++ +++++...
T Consensus 4 ~~~~vv~D~ETTGl~~--~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~ 81 (189)
T cd06134 4 GFLPVVVDVETGGFNP--QTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEK 81 (189)
T ss_pred cceeEEEEecCCCCCC--CCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchH
Confidence 4568999999999997 6789999999999743 2234689999999953237999999999999986 67777777
Q ss_pred HHHHHHHHHHc---------CCEEEEEccccchHHHHHHHHHHcCCC-CCC-CCceeeHHHHHHHHhcCCCCCCCHHHHH
Q 013825 83 DIADTVFDILH---------GRIWAGHNILRFDCARIREAFAEIGRP-APE-PKGTIDSLALLTQRFGRRAGDMKMASLA 151 (436)
Q Consensus 83 eVl~~f~efL~---------g~vLVaHNa~~FD~~fLr~a~~r~Gi~-~p~-~~~~IDTl~Larr~l~~~~~~~kL~~LA 151 (436)
+++.+|.+++. +.++||||+ .||+.||++++.++|+. .++ +..++||+.|++..+ +.++|+++|
T Consensus 82 ~~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~----~~~~L~~l~ 156 (189)
T cd06134 82 EALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAY----GQTVLAKAC 156 (189)
T ss_pred HHHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHh----CCCcHHHHH
Confidence 77777666653 679999999 99999999999999983 332 235899999988654 346899999
Q ss_pred HHhCCC---CCCCChHHHHHHHHHHHHHHHHH
Q 013825 152 TYFGLG---QQTHRSLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 152 ~~fGI~---~~~HrALdDAraTa~VLk~L~~~ 180 (436)
++||++ .++|+|++||++|+++|.+++++
T Consensus 157 ~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 157 QAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred HHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 999998 26899999999999999998764
No 24
>PRK06722 exonuclease; Provisional
Probab=99.97 E-value=3e-29 Score=248.41 Aligned_cols=170 Identities=16% Similarity=0.233 Sum_probs=146.8
Q ss_pred CCCcEEEEEEecCCCCCC--CCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHH
Q 013825 6 DRSEIAFFDVETTVPTRP--GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~--g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~e 83 (436)
....|+|||+||||. |. ...++|||||||+++++.++++++|+.||+|.. +|+++++++||||++||.++|+|++
T Consensus 3 ~~~~~vViD~ETT~~-p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--~I~~~i~~LTGIT~emV~~AP~f~e 79 (281)
T PRK06722 3 NATHFIVFDIERNFR-PYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--RLTRHTTKLTGITKKDLIGVEKFPQ 79 (281)
T ss_pred CCCEEEEEEeeCCCC-CCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--cCCHhHhhhcCCCHHHHcCCCCHHH
Confidence 458899999999963 31 134899999999999987778899999999998 8999999999999999999999999
Q ss_pred HHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCC--CceeeHHHHHHHHhcCC-CCCCCHHHHHHHhCCCC--
Q 013825 84 IADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEP--KGTIDSLALLTQRFGRR-AGDMKMASLATYFGLGQ-- 158 (436)
Q Consensus 84 Vl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~--~~~IDTl~Larr~l~~~-~~~~kL~~LA~~fGI~~-- 158 (436)
++.+|.+|+++..+|+||+ .||+.||++++.++|++.|.. ..++|+.+++...+.+- ...++|++++++||++.
T Consensus 80 Vl~ef~~fig~~~lvahna-~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~~g 158 (281)
T PRK06722 80 IIEKFIQFIGEDSIFVTWG-KEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEG 158 (281)
T ss_pred HHHHHHHHHCCCcEEEEEe-HHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCCCC
Confidence 9999999999888888888 999999999999999887643 34789988876544321 23578999999999993
Q ss_pred CCCChHHHHHHHHHHHHHHHH
Q 013825 159 QTHRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 159 ~~HrALdDAraTa~VLk~L~~ 179 (436)
.+|||++||++|+++|.++++
T Consensus 159 ~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 159 KQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCcCcHHHHHHHHHHHHHHhc
Confidence 689999999999999999884
No 25
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.97 E-value=1.1e-30 Score=288.81 Aligned_cols=200 Identities=18% Similarity=0.287 Sum_probs=177.2
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 3 ~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
+.+.+.+||+||+||||+++ ..++||||||+++.+| .+++.|+.||+|.. +++..++++||||++||.++++++
T Consensus 416 ~~l~datyVVfDiETTGLs~--~~d~iIE~aAvKikng--~iId~f~~Fi~P~~--pl~~~~telTgITdeml~~a~~i~ 489 (1444)
T COG2176 416 QKLDDATYVVFDIETTGLSP--VYDEIIEIAAVKIKNG--RIIDKFQFFIKPGR--PLSATITELTGITDEMLENAPEIE 489 (1444)
T ss_pred cccccccEEEEEeecCCcCc--ccchhhhheeeeeeCC--cchHHHHHhcCCCC--cCchhhhhccccCHHHHcCCccHH
Confidence 35667899999999999998 7899999999999999 66899999999999 899999999999999999999999
Q ss_pred HHHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCC
Q 013825 83 DIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTH 161 (436)
Q Consensus 83 eVl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~H 161 (436)
+|+.+|.+|+.++++||||+ .||++||+..++++|++... .++|||+.|+| .+.|..++++|..||+.|++. ..+|
T Consensus 490 ~vL~kf~~~~~d~IlVAHNa-sFD~gFl~~~~~k~~~~~~~-~pvIDTL~lar-~L~P~~ksh~Lg~l~kk~~v~le~hH 566 (1444)
T COG2176 490 EVLEKFREFIGDSILVAHNA-SFDMGFLNTNYEKYGLEPLT-NPVIDTLELAR-ALNPEFKSHRLGTLCKKLGVELERHH 566 (1444)
T ss_pred HHHHHHHHHhcCcEEEeccC-ccchhHHHHHHHHhCCcccc-CchhhHHHHHH-HhChhhhhcchHHHHHHhCccHHHhh
Confidence 99999999999999999999 99999999999999988654 45899999977 677888999999999999999 6899
Q ss_pred ChHHHHHHHHHHHHHHHHHhhhhcCcchhhhccC-CCCCCccccccccCCCC
Q 013825 162 RSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNS-WVSPNATTRSRSNAKSS 212 (436)
Q Consensus 162 rALdDAraTa~VLk~L~~~l~le~slp~l~~~~~-~v~~~~~~R~R~~~~~~ 212 (436)
||.+||.+|++||..+++.+... +...+.+.+. ..+.....|.|.++..+
T Consensus 567 RA~yDaeat~~vf~~f~~~~ke~-Gi~~l~eln~~l~~~~~ykr~r~~h~~i 617 (1444)
T COG2176 567 RADYDAEATAKVFFVFLKDLKEK-GITNLSELNDKLSSEDLYKRLRPKHATI 617 (1444)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHh-chhhHHHHhHhhhhhHHHhhccccceEE
Confidence 99999999999999999987744 6666666655 44444567777766544
No 26
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.97 E-value=4.6e-29 Score=225.72 Aligned_cols=166 Identities=23% Similarity=0.281 Sum_probs=144.4
Q ss_pred EEEEEEecCCCCCC---CCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 10 IAFFDVETTVPTRP---GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 10 fV~fDLETTGl~p~---g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
||+||+||||+.+. +..++|||||||+++.++.+++++|+.+|+|.....+++++.++||||.+++++++++.++++
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 69999999999861 124899999999999987667899999999997447999999999999999999999999999
Q ss_pred HHHHHHcCC--EEEEEccccchHHHHHHHHHHcCCC--CCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-C-CC
Q 013825 87 TVFDILHGR--IWAGHNILRFDCARIREAFAEIGRP--APEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-Q-QT 160 (436)
Q Consensus 87 ~f~efL~g~--vLVaHNa~~FD~~fLr~a~~r~Gi~--~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~-~~ 160 (436)
+|.+|+++. .+++||+ .||..+|.+++.+++.. ++....++|+..+++..++. ...++|.+++++||++ . +.
T Consensus 81 ~~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~-~~~~~L~~l~~~~gi~~~~~~ 158 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGL-KKRTGLSKALEYLGLEFEGRH 158 (176)
T ss_pred HHHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCC-CCCCCHHHHHHHCCCCCCCCC
Confidence 999999987 6777777 89999999998888764 34456799999998865543 3689999999999998 3 69
Q ss_pred CChHHHHHHHHHHHHHH
Q 013825 161 HRSLDDVRMNLEVLKYC 177 (436)
Q Consensus 161 HrALdDAraTa~VLk~L 177 (436)
|+|++||++|++||.++
T Consensus 159 H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 159 HRGLDDARNIARILKRL 175 (176)
T ss_pred cCcHHHHHHHHHHHHHh
Confidence 99999999999999986
No 27
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.1e-28 Score=274.63 Aligned_cols=181 Identities=19% Similarity=0.343 Sum_probs=159.0
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 3 ~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
|+....+||+||+||||+++ .++|||||||++.++ .++++|+++|+|.. +|+++++++||||++||+++|+|+
T Consensus 2 ~~~~~~~~vvvD~ETTGl~~---~d~IIeIgaV~v~~g--~i~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ 74 (820)
T PRK07246 2 TQKKLRKYAVVDLEATGAGP---NASIIQVGIVIIEGG--EIIDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFS 74 (820)
T ss_pred ccccCCCEEEEEEecCCcCC---CCeEEEEEEEEEECC--EEEEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHH
Confidence 45667899999999999975 489999999999987 67899999999998 899999999999999999999999
Q ss_pred HHHHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCC
Q 013825 83 DIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTH 161 (436)
Q Consensus 83 eVl~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~H 161 (436)
+++++|.+|+++.++||||+ .||+.||++++.+.|.+++ ..++||+.+++. +.+..++++|++||++||++ .++|
T Consensus 75 ev~~~~~~~l~~~~lVaHN~-~FD~~fL~~~~~~~g~~~~--~~~iDT~~la~~-~~p~~~~~~L~~L~~~lgl~~~~~H 150 (820)
T PRK07246 75 QVARHIYDLIEDCIFVAHNV-KFDANLLAEALFLEGYELR--TPRVDTVELAQV-FFPTLEKYSLSHLSRELNIDLADAH 150 (820)
T ss_pred HHHHHHHHHhCCCEEEEECc-HHHHHHHHHHHHHcCCCCC--CCceeHHHHHHH-HhCCCCCCCHHHHHHHcCCCCCCCC
Confidence 99999999999999999999 9999999999998888765 347999999875 55667789999999999998 5789
Q ss_pred ChHHHHHHHHHHHHHHHHHhhh--hcCcchhhhcc
Q 013825 162 RSLDDVRMNLEVLKYCATVLFL--ESSLPDIFTVN 194 (436)
Q Consensus 162 rALdDAraTa~VLk~L~~~l~l--e~slp~l~~~~ 194 (436)
||++||++|+++|.++.+++.. ...+.++..+.
T Consensus 151 ~Al~DA~ata~L~~~l~~~l~~l~~~~l~~l~~~~ 185 (820)
T PRK07246 151 TAIADARATAELFLKLLQKIESLPKECLERLLEYA 185 (820)
T ss_pred CHHHHHHHHHHHHHHHHHHHhhcCchhHHHHHHHH
Confidence 9999999999999999988742 23445544443
No 28
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.96 E-value=1.7e-28 Score=227.61 Aligned_cols=162 Identities=23% Similarity=0.277 Sum_probs=136.3
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhC-CCCHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTFADIADTVF 89 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~-Ap~f~eVl~~f~ 89 (436)
++||+||||+++ ..++|||||+|+++++.. +++.|+++|+|.....+++.+.++||||.+||++ ++++.+++++|.
T Consensus 1 ~~~D~ETTGl~~--~~d~Iieig~v~v~~~~~-~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~ 77 (183)
T cd06138 1 LFYDYETFGLNP--SFDQILQFAAIRTDENFN-EIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIH 77 (183)
T ss_pred CEEEeecCCCCC--CCCceEEEEEEEECCCCC-CccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHH
Confidence 589999999987 678999999999987643 3488999999985335788999999999999999 899999999999
Q ss_pred HHHc--CCEEEEEccccchHHHHHHHHHHcCCCCCC-----CCceeeHHHHHHHHh--cC----------CCCCCCHHHH
Q 013825 90 DILH--GRIWAGHNILRFDCARIREAFAEIGRPAPE-----PKGTIDSLALLTQRF--GR----------RAGDMKMASL 150 (436)
Q Consensus 90 efL~--g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~-----~~~~IDTl~Larr~l--~~----------~~~~~kL~~L 150 (436)
+|+. +.++||||...||+.||++++.+++.+++. ...++|++.+++..+ .+ ..++++|++|
T Consensus 78 ~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l 157 (183)
T cd06138 78 RLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDL 157 (183)
T ss_pred HHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHH
Confidence 9995 579999983399999999999999876432 234689998887543 11 2357899999
Q ss_pred HHHhCCC-CCCCChHHHHHHHHHHHH
Q 013825 151 ATYFGLG-QQTHRSLDDVRMNLEVLK 175 (436)
Q Consensus 151 A~~fGI~-~~~HrALdDAraTa~VLk 175 (436)
+++||++ .++|||++||++|++|++
T Consensus 158 ~~~~gi~~~~~H~Al~Da~~ta~l~~ 183 (183)
T cd06138 158 AQANGIEHSNAHDALSDVEATIALAK 183 (183)
T ss_pred HHHCCCCccccccHHHHHHHHHHHhC
Confidence 9999999 589999999999999863
No 29
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4.9e-28 Score=272.59 Aligned_cols=168 Identities=24% Similarity=0.378 Sum_probs=153.2
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
.++||+||+||||.++. ..++|||||||++.++ +++++|+++|+|.. +|+++++++||||++||+++|+|.+++.
T Consensus 2 ~~~~vvvD~ETTG~~p~-~~d~IIeigav~v~~~--~i~~~f~~~v~P~~--~i~~~~~~ltGIt~~~l~~ap~f~ev~~ 76 (928)
T PRK08074 2 SKRFVVVDLETTGNSPK-KGDKIIQIAAVVVEDG--EILERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVAP 76 (928)
T ss_pred CCCEEEEEEeCCCCCCC-CCCcEEEEEEEEEECC--EEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHhcCCCHHHHHH
Confidence 46799999999998762 2489999999999887 67899999999998 7999999999999999999999999999
Q ss_pred HHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHH
Q 013825 87 TVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSLD 165 (436)
Q Consensus 87 ~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~HrALd 165 (436)
+|.+|++++++||||+ .||+.||+++|.++|++.+. ..+|||+.+++. +.+...+++|++|+++||++ .++|+|++
T Consensus 77 ~l~~~l~~~~~VaHN~-~FD~~fL~~~~~~~g~~~~~-~~~iDt~~la~~-~~p~~~~~~L~~l~~~l~i~~~~~H~Al~ 153 (928)
T PRK08074 77 EIVELLEGAYFVAHNV-HFDLNFLNEELERAGYTEIH-CPKLDTVELARI-LLPTAESYKLRDLSEELGLEHDQPHRADS 153 (928)
T ss_pred HHHHHhCCCeEEEECh-HHHHHHHHHHHHHcCCCCCC-CCeeeHHHHHHH-hcCCCCCCCHHHHHHhCCCCCCCCCChHH
Confidence 9999999999999999 99999999999999998654 459999999874 55667899999999999998 57999999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 013825 166 DVRMNLEVLKYCATVLF 182 (436)
Q Consensus 166 DAraTa~VLk~L~~~l~ 182 (436)
||++|+++|.+++.++.
T Consensus 154 DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 154 DAEVTAELFLQLLNKLE 170 (928)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999999874
No 30
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.96 E-value=9.2e-28 Score=274.38 Aligned_cols=179 Identities=22% Similarity=0.378 Sum_probs=159.4
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHH
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl 85 (436)
.+.+||+||+||||+++ ..++|||||||+++++ .++++|+++|+|.. +|++.++++||||++||++++++.+++
T Consensus 188 ~~~~~VVfDiETTGL~~--~~d~IIEIGAVkv~~g--~iid~f~~~V~P~~--~I~~~~~~ltGIT~e~L~~ap~~~evl 261 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSP--QYDEIIEFGAVKVKNG--RIIDKFQFFIKPHE--PLSAFVTELTGITQDMLENAPEIEEVL 261 (1213)
T ss_pred cCCcEEEEEeEecCCCC--CCCeEEEEEEEEEECC--eEEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHH
Confidence 56789999999999987 6899999999999987 67799999999998 899999999999999999999999999
Q ss_pred HHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChH
Q 013825 86 DTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSL 164 (436)
Q Consensus 86 ~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~HrAL 164 (436)
++|.+|++++++||||+ .||+.||++++.++|+++. ...++||+.+++. +.+..++++|++||++||++ ..+|||+
T Consensus 262 ~~f~~fl~~~iLVaHNa-~FD~~fL~~~~~r~g~~~~-~~~~IDTl~lar~-l~p~~k~~kL~~Lak~lgi~~~~~HrAl 338 (1213)
T TIGR01405 262 EKFKEFFKDSILVAHNA-SFDIGFLNTNFEKVGLEPL-ENPVIDTLELARA-LNPEYKSHRLGNICKKLGVDLDDHHRAD 338 (1213)
T ss_pred HHHHHHhCCCeEEEECh-HHHHHHHHHHHHHcCCCcc-CCCEeEHHHHHHH-HhccCCCCCHHHHHHHcCCCCCCCcCHH
Confidence 99999999999999998 9999999999999998643 3569999999875 55667899999999999999 5799999
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCcchhhhcc
Q 013825 165 DDVRMNLEVLKYCATVLFLESSLPDIFTVN 194 (436)
Q Consensus 165 dDAraTa~VLk~L~~~l~le~slp~l~~~~ 194 (436)
+||++|++||..+++.+.. .+...+..++
T Consensus 339 ~DA~aTa~I~~~ll~~l~~-~~i~~~~~l~ 367 (1213)
T TIGR01405 339 YDAEATAKVFKVMVEQLKE-KGITNLEELN 367 (1213)
T ss_pred HHHHHHHHHHHHHHHHHHH-cCCccHHHHH
Confidence 9999999999999988753 3444444443
No 31
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.1e-27 Score=243.85 Aligned_cols=164 Identities=16% Similarity=0.263 Sum_probs=139.9
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
..+..||+||+||||+++ ..++|||||||++..++ .+.++|++||+|.. .+.+ ..+||||.+||+++|.|.++
T Consensus 43 ~~~~~fVvlDiETTGLdp--~~drIIeIgAV~i~~~g-~ive~f~tLVnP~~--~~~p--~~LHGIT~e~La~AP~f~eV 115 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHP--STSRLITIDAVTLTADG-EEVEHFHAVLNPGE--DPGP--FHLHGLSAEEFAQGKRFSQI 115 (377)
T ss_pred CCCCCEEEEEEECCCCCC--CCCeEEEEEEEEEEcCC-EEEEEEEEEECcCC--CCCC--ccccCCCHHHHhcCCCHHHH
Confidence 455789999999999998 67999999999998553 56799999999998 3333 37999999999999999999
Q ss_pred HHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCC--------------------------CCCCCCceeeHHHHHHHHh
Q 013825 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGR--------------------------PAPEPKGTIDSLALLTQRF 138 (436)
Q Consensus 85 l~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi--------------------------~~p~~~~~IDTl~Larr~l 138 (436)
+++|.+|+.++++||||+ .||+.||.+++++++. ..+.+..++||+.++++ +
T Consensus 116 l~el~~fL~g~vLVaHNA-~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARr-l 193 (377)
T PRK05601 116 LKPLDRLIDGRTLILHNA-PRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARR-Q 193 (377)
T ss_pred HHHHHHHhCCCEEEEECc-HHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHH-H
Confidence 999999999999999999 9999999999987521 11333468999999885 4
Q ss_pred cCCCCCCCHHHHHHHhCCCC-----------CCCChH--HHHHHHHHHHHHH
Q 013825 139 GRRAGDMKMASLATYFGLGQ-----------QTHRSL--DDVRMNLEVLKYC 177 (436)
Q Consensus 139 ~~~~~~~kL~~LA~~fGI~~-----------~~HrAL--dDAraTa~VLk~L 177 (436)
.+.+++++|.+||++||++. ..|+|| +||+.++++|.++
T Consensus 194 ~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 194 GVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred cCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 46778999999999999974 258888 6999999999886
No 32
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.96 E-value=1e-27 Score=209.16 Aligned_cols=157 Identities=28% Similarity=0.463 Sum_probs=140.3
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~e 90 (436)
|+||+||||+++ ..++|+|||+|.++.+ +++++.|+.+|+|.. .+++.+.++|||+.+++.+++++.+++.+|.+
T Consensus 1 v~~D~Ettg~~~--~~~~iiei~~v~~~~~-~~~~~~~~~~i~p~~--~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~ 75 (159)
T cd06127 1 VVFDTETTGLDP--KKDRIIEIGAVKVDGG-IEIVERFETLVNPGR--PIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75 (159)
T ss_pred CeEEeeCCCcCC--CCCeEEEEEEEEEECC-cChhhhhheeeCcCC--cCCHhheeccCCCHHHHhcCCCHHHHHHHHHH
Confidence 689999999986 6899999999999987 567789999999998 78999999999999999999999999999999
Q ss_pred HHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHH-HHHhCCC-CCCCChHHHHH
Q 013825 91 ILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASL-ATYFGLG-QQTHRSLDDVR 168 (436)
Q Consensus 91 fL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~L-A~~fGI~-~~~HrALdDAr 168 (436)
|+.+.++||||+ .||..+|++.+.++|.++ .+..++|++.+++..+ +....+++..+ ++++|++ ...|+|++||+
T Consensus 76 ~l~~~~~v~~n~-~fD~~~l~~~~~~~~~~~-~~~~~iDt~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~~H~Al~Da~ 152 (159)
T cd06127 76 FLGGRVLVAHNA-SFDLRFLNRELRRLGGPP-LPNPWIDTLRLARRLL-PGLRSHRLGLLLAERYGIPLEGAHRALADAL 152 (159)
T ss_pred HHCCCEEEEeCc-HhhHHHHHHHHHHhCCCC-CCCCeeEHHHHHHHHc-CCCCcCchHHHHHHHcCCCCCCCCCcHHHHH
Confidence 999999999999 999999999999998443 3456999999987554 44467889998 8999998 57999999999
Q ss_pred HHHHHHH
Q 013825 169 MNLEVLK 175 (436)
Q Consensus 169 aTa~VLk 175 (436)
+|++||.
T Consensus 153 ~t~~l~~ 159 (159)
T cd06127 153 ATAELLL 159 (159)
T ss_pred HHHHHhC
Confidence 9999973
No 33
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.95 E-value=1.8e-27 Score=265.81 Aligned_cols=165 Identities=25% Similarity=0.399 Sum_probs=150.7
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHH
Q 013825 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (436)
Q Consensus 9 ~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f 88 (436)
+||+||+||||+++ ..++|||||+|+++++ +++++|+++|+|.. +|+++++++||||++|++++|.|.+++.+|
T Consensus 1 ~~vvvD~ETTG~~~--~~~~IIeig~v~v~~~--~i~~~f~~~v~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l 74 (850)
T TIGR01407 1 RYAVVDLETTGTQL--SFDKIIQIGIVVVEDG--EIVDTFHTDVNPNE--PIPPFIQELTGISDNMLQQAPYFSQVAQEI 74 (850)
T ss_pred CEEEEEEECCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEeCCCC--CCChhhhhhcCcCHHHHhCCCCHHHHHHHH
Confidence 49999999999986 5799999999999877 66789999999998 899999999999999999999999999999
Q ss_pred HHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHH
Q 013825 89 FDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSLDDV 167 (436)
Q Consensus 89 ~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~HrALdDA 167 (436)
.+|+++.++||||+ .||+.||+++|.++|++.. +..++||+.+++. +.+...+++|.+|+++||++ .++|||++||
T Consensus 75 ~~~l~~~~~VahN~-~fD~~fL~~~~~~~g~~~~-~~~~iDt~~l~~~-~~p~~~~~~L~~l~~~~gi~~~~~H~Al~DA 151 (850)
T TIGR01407 75 YDLLEDGIFVAHNV-HFDLNFLAKALKDCGYEPL-PKPRIDTVELAQI-FFPTEESYQLSELSEALGLTHENPHRADSDA 151 (850)
T ss_pred HHHhCCCEEEEeCc-HHHHHHHHHHHHHcCCCCC-CCCeEeHHHHHHH-hcCCCCCCCHHHHHHHCCCCCCCCCChHHHH
Confidence 99999999999999 9999999999999998743 3458999999874 55666789999999999999 5799999999
Q ss_pred HHHHHHHHHHHHHhh
Q 013825 168 RMNLEVLKYCATVLF 182 (436)
Q Consensus 168 raTa~VLk~L~~~l~ 182 (436)
++|+++|.++.+++.
T Consensus 152 ~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 152 QATAELLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999988864
No 34
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.95 E-value=8.8e-27 Score=223.42 Aligned_cols=148 Identities=22% Similarity=0.229 Sum_probs=128.5
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHH
Q 013825 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVF 89 (436)
Q Consensus 10 fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~ 89 (436)
+++||+||||+++ .|||||+|.+.++ .+.+.|+++|+|.. +|++.++++||||++||+++|+|.++++.|
T Consensus 2 ~~vlD~ETTGl~~-----~IieIg~v~v~~~--~i~~~~~~lv~P~~--~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~- 71 (219)
T PRK07983 2 LRVIDTETCGLQG-----GIVEIASVDVIDG--KIVNPMSHLVRPDR--PISPQAMAIHRITEAMVADKPWIEDVIPHY- 71 (219)
T ss_pred eEEEEEECCCCCC-----CCEEEEEEEEECC--EEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHcCCCCHHHHHHHH-
Confidence 7899999999863 4999999999876 56789999999998 799999999999999999999999998874
Q ss_pred HHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC------CCCCCh
Q 013825 90 DILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG------QQTHRS 163 (436)
Q Consensus 90 efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~------~~~HrA 163 (436)
+++.++||||+ .||++||.. ....++||++++++.+ +..+ ++|..|+++||++ ..+|||
T Consensus 72 --~~~~~lVaHNa-~FD~~~L~~----------~~~~~idTl~lar~l~-p~~~-~~l~~L~~~~~l~~~~~~~~~aHrA 136 (219)
T PRK07983 72 --YGSEWYVAHNA-SFDRRVLPE----------MPGEWICTMKLARRLW-PGIK-YSNMALYKSRKLNVQTPPGLHHHRA 136 (219)
T ss_pred --cCCCEEEEeCc-HhhHHHHhC----------cCCCcEeHHHHHHHHc-cCCC-CCHHHHHHHcCCCCCCCCCCCCCcH
Confidence 67889999999 999999952 1235899999998654 5554 8999999999985 359999
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 013825 164 LDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 164 LdDAraTa~VLk~L~~~l~ 182 (436)
++||++|+++|.++++...
T Consensus 137 l~Da~ata~ll~~l~~~~~ 155 (219)
T PRK07983 137 LYDCYITAALLIDIMNTSG 155 (219)
T ss_pred HHHHHHHHHHHHHHHHHcC
Confidence 9999999999999887543
No 35
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=99.95 E-value=2.3e-27 Score=216.13 Aligned_cols=144 Identities=21% Similarity=0.334 Sum_probs=123.5
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCC-------HHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPT-------FAD 83 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~-------f~e 83 (436)
|+||+||||+++ ..++|+|||||.+.++ +++ |+.||+|.. +|+++++++||||.+|++++|+ +++
T Consensus 1 v~lD~EttGl~~--~~d~ii~Ig~V~v~~g--~i~--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~ 72 (161)
T cd06137 1 VALDCEMVGLAD--GDSEVVRISAVDVLTG--EVL--IDSLVRPSV--RVTDWRTRFSGVTPADLEEAAKAGKTIFGWEA 72 (161)
T ss_pred CEEEeeeeeEcC--CCCEEEEEEEEEcCCC--eEE--EeccccCCC--CCCccceeccCCCHHHHhhhhhcCCccccHHH
Confidence 689999999987 5789999999999766 333 889999997 7999999999999999999875 458
Q ss_pred HHHHHHHHHcC-CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCC---CCCCHHHHHHH-hCCCC
Q 013825 84 IADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRA---GDMKMASLATY-FGLGQ 158 (436)
Q Consensus 84 Vl~~f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~---~~~kL~~LA~~-fGI~~ 158 (436)
++++|.+|+++ .++||||+ .||+.||+.. ...++||+.+++..+ +.. .+++|.+||++ ||++.
T Consensus 73 ~~~~~~~~i~~~~vlVgHn~-~fD~~fL~~~----------~~~~iDT~~l~~~~~-~~~~~~~~~~L~~L~~~~~~~~~ 140 (161)
T cd06137 73 ARAALWKFIDPDTILVGHSL-QNDLDALRMI----------HTRVVDTAILTREAV-KGPLAKRQWSLRTLCRDFLGLKI 140 (161)
T ss_pred HHHHHHHhcCCCcEEEeccH-HHHHHHHhCc----------CCCeeEehhhhhhcc-CCCcCCCCccHHHHHHHHCCchh
Confidence 99999999998 89999999 9999999752 124899999988644 433 68999999986 68762
Q ss_pred ----CCCChHHHHHHHHHHH
Q 013825 159 ----QTHRSLDDVRMNLEVL 174 (436)
Q Consensus 159 ----~~HrALdDAraTa~VL 174 (436)
..|+|+.||++|+++|
T Consensus 141 ~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 141 QGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred cCCCCCCCcHHHHHHHHHHh
Confidence 4799999999999987
No 36
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.94 E-value=4.7e-26 Score=218.19 Aligned_cols=164 Identities=26% Similarity=0.408 Sum_probs=148.7
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEe-eeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEEL-HNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl-~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
.++++||+||||.++ ..++|||||+|.+.++ .++ .+|+++|+|.. +|++++.++||||.+++.++|.|.++++
T Consensus 13 ~~~vv~D~ETtg~~~--~~~~iieIgav~~~~~--~i~~~~~~~~v~P~~--~i~~~~~~i~git~e~l~~~p~~~~v~~ 86 (243)
T COG0847 13 TRFVVIDLETTGLNP--KKDRIIEIGAVTLEDG--RIVERSFHTLVNPER--PIPPEIFKIHGITDEMLADAPKFAEVLP 86 (243)
T ss_pred CcEEEEecccCCCCC--CCCceEEEEeEEEECC--eeecceeEEEECCCC--CCChhhhhhcCCCHHHHhcCCCHHHHHH
Confidence 578999999999987 6899999999999998 444 44999999966 7999999999999999999999999999
Q ss_pred HHHHHHcC-CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC---CCCCC
Q 013825 87 TVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG---QQTHR 162 (436)
Q Consensus 87 ~f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~---~~~Hr 162 (436)
+|.+|+.+ +.+||||+ .||+.||+.++.+++..++ ...++|++.+++..+ +....++|+.||.++|++ ...|+
T Consensus 87 ~~~~~i~~~~~~Vahna-~fD~~fl~~~~~~~~~~~~-~~~~~~t~~~~r~~~-~~~~~~~L~~l~~~~gi~~~~~~~H~ 163 (243)
T COG0847 87 EFLDFIGGLRLLVAHNA-AFDVGFLRVESERLGIEIP-GDPVLDTLALARRHF-PGFDRSSLDALAERLGIDRNPFHPHR 163 (243)
T ss_pred HHHHHHCCCCeEEEEch-hhcHHHHHHHHHHcCCCcc-cCceehHHHHHHHHc-CCCccchHHHHHHHcCCCcCCcCCcc
Confidence 99999999 99999999 9999999999999999887 445899999988655 446789999999999999 36799
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 013825 163 SLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 163 ALdDAraTa~VLk~L~~~ 180 (436)
|+.||.++++++..+...
T Consensus 164 Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 164 ALFDALALAELFLLLQTG 181 (243)
T ss_pred hHHHHHHHHHHHHHHHhc
Confidence 999999999999998875
No 37
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=5.5e-26 Score=226.62 Aligned_cols=161 Identities=22% Similarity=0.208 Sum_probs=130.4
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeC---Ccc-eEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCP---KKL-EELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~---~~l-evl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
...+|+||+||||+++ ..++|||||+|+++. |.+ .+.++|+++++|.. +|+++++++||||.+||++++...
T Consensus 36 ~~~~vvlD~ETTGLd~--~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~--~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 36 VRLGVILDTETTGLDP--RKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR--PIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CCeEEEEEeeCCCCCC--CCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC--CCCHHHHHhcCCCHHHHhcCCCcH
Confidence 3579999999999997 679999999999983 322 45688999999998 799999999999999999998765
Q ss_pred HHHHHHHHHHcC-CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCC
Q 013825 83 DIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTH 161 (436)
Q Consensus 83 eVl~~f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~~~H 161 (436)
+. |.+|+.. .++||||+ .||+.||.+.+..+.- ..+.|++..+.. ..+..++++|+.|+.+||....+|
T Consensus 112 ~~---l~~fl~~~~vlVAHNA-~FD~~fL~~~~~~~~~-----~~~~ct~~~i~~-~~~~~~~~kL~~La~~~g~~~~aH 181 (294)
T PRK09182 112 AA---VDALIAPADLIIAHNA-GFDRPFLERFSPVFAT-----KPWACSVSEIDW-SARGFEGTKLGYLAGQAGFFHEGH 181 (294)
T ss_pred HH---HHHHhcCCCEEEEeCH-HHHHHHHHHHHHhccC-----CcccccHHHHhh-ccccCCCCCHHHHHHHcCCCCCCc
Confidence 54 4555554 59999999 9999999987654321 236888865432 223457899999999999556899
Q ss_pred ChHHHHHHHHHHHHHHHHHh
Q 013825 162 RSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 162 rALdDAraTa~VLk~L~~~l 181 (436)
||++||++|++||.+++...
T Consensus 182 rAl~Da~Ata~ll~~~l~~~ 201 (294)
T PRK09182 182 RAVDDCQALLELLARPLPET 201 (294)
T ss_pred ChHHHHHHHHHHHHHHHhhc
Confidence 99999999999999876543
No 38
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.94 E-value=2.9e-26 Score=208.58 Aligned_cols=149 Identities=22% Similarity=0.344 Sum_probs=123.5
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~e 90 (436)
|+||+||||+++.+..++|++|++|.+++. ++ |+++|+|.. +++++++++||||++|++++|++++++++|.+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~---~~--~~~lv~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~ 73 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGD---VL--YDKYIRPEG--PVTDYRTRWSGIRRQHLVNATPFAVAQKEILK 73 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCC---EE--EEEeECCCC--ccCccceECCCCCHHHHhcCCCHHHHHHHHHH
Confidence 689999999997333578889989887443 32 889999998 79999999999999999999999999999999
Q ss_pred HHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHH--HHHH-hcCCCCCCCHHHHHHHh---CCCC--CCCC
Q 013825 91 ILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLAL--LTQR-FGRRAGDMKMASLATYF---GLGQ--QTHR 162 (436)
Q Consensus 91 fL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~L--arr~-l~~~~~~~kL~~LA~~f---GI~~--~~Hr 162 (436)
|+.++++||||+ .||+.||+.. ++. ..++||..+ +++. ..+...+++|+.||++| +++. +.||
T Consensus 74 ~l~~~vlV~Hn~-~~D~~~l~~~-------~~~-~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~ 144 (157)
T cd06149 74 ILKGKVVVGHAI-HNDFKALKYF-------HPK-HMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHS 144 (157)
T ss_pred HcCCCEEEEeCc-HHHHHHhccc-------CCC-cCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcC
Confidence 999999999999 9999999743 222 237888654 4433 24555789999999999 5653 5799
Q ss_pred hHHHHHHHHHHHH
Q 013825 163 SLDDVRMNLEVLK 175 (436)
Q Consensus 163 ALdDAraTa~VLk 175 (436)
|+.||++|+++|+
T Consensus 145 Al~DA~at~~l~~ 157 (157)
T cd06149 145 SVEDARATMELYK 157 (157)
T ss_pred cHHHHHHHHHHhC
Confidence 9999999999985
No 39
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.94 E-value=2.6e-25 Score=237.03 Aligned_cols=173 Identities=18% Similarity=0.210 Sum_probs=142.6
Q ss_pred CcEEEEEEecCCCCCC-CCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 8 SEIAFFDVETTVPTRP-GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~-g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
..|+|||+||||.++. ...++|||||||+++...++++++|++||+|.....++++++++||||++||.++|+|.+++.
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl~ 135 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVYC 135 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 6799999999998752 135899999999998544577899999999987447999999999999999999999999999
Q ss_pred HHHHHHcCC----------EEEEEccccchH-HHHHHHHH---HcCCCCCCCCceeeHHHHHHHHhcC-----------C
Q 013825 87 TVFDILHGR----------IWAGHNILRFDC-ARIREAFA---EIGRPAPEPKGTIDSLALLTQRFGR-----------R 141 (436)
Q Consensus 87 ~f~efL~g~----------vLVaHNa~~FD~-~fLr~a~~---r~Gi~~p~~~~~IDTl~Larr~l~~-----------~ 141 (436)
+|.+|+.+. ++|+||+ .||+ .||.++|. ++++++.+ ..|+|+...+.+.+.+ .
T Consensus 136 ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~~~~~~g~p~~f-~~widLk~~lar~l~p~~~~~~~~~~~~ 213 (582)
T PTZ00315 136 EALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMRVSGQQGTPLSF-QRWCNLKKYMSQLGFGNGSGCGGGATPP 213 (582)
T ss_pred HHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHHHhhhcCCCccc-ceEEEhHHHHHHHhCccccccccccccc
Confidence 999999754 6899999 9999 49999887 45666544 3477764333434333 3
Q ss_pred CCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHHhh
Q 013825 142 AGDMKMASLATYFGLG--QQTHRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 142 ~~~~kL~~LA~~fGI~--~~~HrALdDAraTa~VLk~L~~~l~ 182 (436)
...++|.++++++|++ ..+|||++||++|++||.+|+++..
T Consensus 214 ~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~ 256 (582)
T PTZ00315 214 LGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGL 256 (582)
T ss_pred cCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCC
Confidence 4668999999999998 3689999999999999999988743
No 40
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.93 E-value=4.8e-26 Score=205.45 Aligned_cols=148 Identities=20% Similarity=0.342 Sum_probs=118.2
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~e 90 (436)
|++|+||||+++ .++++||++|.+....+.+ .|++||+|.. +++++++++||||.+||+++|++.+++.+|.+
T Consensus 1 v~lD~EttGl~~---~~~~~~i~~v~~v~~~~~~--~~~~~v~P~~--~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~ 73 (152)
T cd06144 1 VALDCEMVGVGP---DGSESALARVSIVNEDGNV--VYDTYVKPQE--PVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAE 73 (152)
T ss_pred CEEEEEeecccC---CCCEEEEEEEEEEeCCCCE--EEEEEECCCC--CCCcccccCCCCCHHHHcCCCCHHHHHHHHHH
Confidence 689999999986 2367777666544322233 3899999988 79999999999999999999999999999999
Q ss_pred HHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCC-CCCCCHHHHHHH-hCCC--CCCCChHHH
Q 013825 91 ILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRR-AGDMKMASLATY-FGLG--QQTHRSLDD 166 (436)
Q Consensus 91 fL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~-~~~~kL~~LA~~-fGI~--~~~HrALdD 166 (436)
|++++++||||+ .||+.||+. ..+. ..++||..+.. ...+. ..+++|++||++ ||++ ..+|||++|
T Consensus 74 ~l~~~vlVgHn~-~fD~~~L~~-------~~~~-~~~~dt~~l~~-~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~D 143 (152)
T cd06144 74 LLKGRILVGHAL-KNDLKVLKL-------DHPK-KLIRDTSKYKP-LRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVED 143 (152)
T ss_pred HhCCCEEEEcCc-HHHHHHhcC-------cCCC-ccEEEeEEeec-cccccCCCChhHHHHHHHHcCcccCCCCcCcHHH
Confidence 999999999999 999999972 2232 24788876532 22221 468999999997 5997 368999999
Q ss_pred HHHHHHHHH
Q 013825 167 VRMNLEVLK 175 (436)
Q Consensus 167 AraTa~VLk 175 (436)
|++|+++|+
T Consensus 144 A~at~~l~~ 152 (152)
T cd06144 144 ARAAMRLYR 152 (152)
T ss_pred HHHHHHHhC
Confidence 999999984
No 41
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.93 E-value=5.4e-28 Score=210.95 Aligned_cols=160 Identities=33% Similarity=0.551 Sum_probs=135.7
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~e 90 (436)
||||+||||+++ ..++|+|||+|.++.+...+...|+++|+|.....++++++++||||.+++++++++.+++..|.+
T Consensus 1 v~~D~Ettg~~~--~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLDP--RQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSSTT--TTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHH
T ss_pred cEEEeEcCCCCC--CCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhh
Confidence 799999999986 579999999999999965567889999999994469999999999999999999999999999999
Q ss_pred HHc-CCEEEEEccccchHHHHHHHHHHcC-CCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC-C-CCChHHH
Q 013825 91 ILH-GRIWAGHNILRFDCARIREAFAEIG-RPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ-Q-THRSLDD 166 (436)
Q Consensus 91 fL~-g~vLVaHNa~~FD~~fLr~a~~r~G-i~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~-~-~HrALdD 166 (436)
|+. +.++||||+ .||..++...+.+.+ ...+....++|++.+.+..+... ..++|..|+++|+++. . +|+|++|
T Consensus 79 ~~~~~~~~v~~n~-~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~l~~~~~~~~~~~~H~Al~D 156 (164)
T PF00929_consen 79 FLKKNDILVGHNA-SFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNR-KKYSLDDLAEYFGIPFDGTAHDALDD 156 (164)
T ss_dssp HHHHHTEEEETTC-CHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHH-HHHSHHHHHHHTTSSSTSTTTSHHHH
T ss_pred hhhcccccccccc-cchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhcc-ccCCHHHHHHHcCCCCCCCCcChHHH
Confidence 999 789999997 999999999998873 43332234677776655444322 2389999999999994 3 5999999
Q ss_pred HHHHHHHH
Q 013825 167 VRMNLEVL 174 (436)
Q Consensus 167 AraTa~VL 174 (436)
|++|++||
T Consensus 157 a~~t~~l~ 164 (164)
T PF00929_consen 157 ARATAELF 164 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHhCcC
Confidence 99999987
No 42
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.93 E-value=1.3e-25 Score=207.08 Aligned_cols=156 Identities=19% Similarity=0.230 Sum_probs=127.5
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCC--CCCChhhHHhc---CCCHHHHhCCCCHHHH
Q 013825 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADP--ELISSLSVRCN---GITPDAVVSSPTFADI 84 (436)
Q Consensus 10 fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~--~~I~p~a~klt---GIT~e~La~Ap~f~eV 84 (436)
+++||+||||++| ..++|||||||+++++.+++.++|+.+|+|... ..+++++.++| |||+++++++|++.++
T Consensus 1 lv~iD~ETTGl~p--~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~v 78 (173)
T cd06135 1 LVWIDLEMTGLDP--EKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQA 78 (173)
T ss_pred CEEEEEecCCCCC--CCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHH
Confidence 5899999999997 678999999999998877778899999999862 13456777775 9999999999999999
Q ss_pred HHHHHHHHcC------CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeH---HHHHHHHhcCCCCCCCHHHHHHHhC
Q 013825 85 ADTVFDILHG------RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDS---LALLTQRFGRRAGDMKMASLATYFG 155 (436)
Q Consensus 85 l~~f~efL~g------~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDT---l~Larr~l~~~~~~~kL~~LA~~fG 155 (436)
+.+|.+|+.+ .++||||+ .||+.||++++.++|..+. .+.+|+ +.+++ .+.+...+ ++
T Consensus 79 l~~~~~f~~~~~~~~~~~lvgh~~-~FD~~fL~~~~~~~~~~~~--~~~~D~~~l~~l~~-~l~p~~~~---------~~ 145 (173)
T cd06135 79 EAELLEFIKKYVPKGKSPLAGNSV-HQDRRFLDKYMPELEEYLH--YRILDVSSIKELAR-RWYPEIYR---------KA 145 (173)
T ss_pred HHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHHhccCC--cchhhHHHHHHHHH-HhCcHhhh---------cC
Confidence 9999999974 58889998 9999999999999984433 346887 44554 44443321 56
Q ss_pred CC-CCCCChHHHHHHHHHHHHHHHHH
Q 013825 156 LG-QQTHRSLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 156 I~-~~~HrALdDAraTa~VLk~L~~~ 180 (436)
+. ..+|||++||++++.+|+++.+.
T Consensus 146 ~~~~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 146 PKKKGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred CCCCCCcchHHHHHHHHHHHHHHHHH
Confidence 65 57899999999999999997653
No 43
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.93 E-value=9.9e-26 Score=203.55 Aligned_cols=143 Identities=22% Similarity=0.337 Sum_probs=121.5
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCC-CHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSP-TFADIADTVF 89 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap-~f~eVl~~f~ 89 (436)
|++|+||||... +++|++||++.+++. + .|++||+|.. +++++++++||||++||+++| ++++++++|.
T Consensus 1 ~~iD~E~~g~~~---g~ei~~i~~v~~~~~---~--~f~~lv~P~~--~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~ 70 (150)
T cd06145 1 FALDCEMCYTTD---GLELTRVTVVDENGK---V--VLDELVKPDG--EIVDYNTRFSGITEEMLENVTTTLEDVQKKLL 70 (150)
T ss_pred CEEeeeeeeecC---CCEEEEEEEEeCCCC---E--EEEEeECCCC--ccchhccCcCCCCHHHhccCCCCHHHHHHHHH
Confidence 589999999975 499999999988543 2 4999999998 899999999999999999995 9999999999
Q ss_pred HHHc-CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC----CCCCCh
Q 013825 90 DILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG----QQTHRS 163 (436)
Q Consensus 90 efL~-g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~----~~~HrA 163 (436)
+|+. +.++||||+ .||+.||+.. ..+++||+.++++.+. ...+++|+.||++| +.. ..+|||
T Consensus 71 ~fl~~~~vlVgHn~-~fD~~fL~~~----------~~~~iDT~~l~r~~~~-~~~~~~L~~L~~~~~~~~i~~~~~~H~A 138 (150)
T cd06145 71 SLISPDTILVGHSL-ENDLKALKLI----------HPRVIDTAILFPHPRG-PPYKPSLKNLAKKYLGRDIQQGEGGHDS 138 (150)
T ss_pred HHhCCCCEEEEcCh-HHHHHHhhcc----------CCCEEEcHHhccccCC-CCCChhHHHHHHHHCCcceeCCCCCCCc
Confidence 9997 799999999 9999999752 1248999998775443 33478999999987 433 368999
Q ss_pred HHHHHHHHHHHH
Q 013825 164 LDDVRMNLEVLK 175 (436)
Q Consensus 164 LdDAraTa~VLk 175 (436)
++||++|+++|+
T Consensus 139 l~DA~~t~~l~~ 150 (150)
T cd06145 139 VEDARAALELVK 150 (150)
T ss_pred HHHHHHHHHHhC
Confidence 999999999874
No 44
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.93 E-value=1.4e-24 Score=228.76 Aligned_cols=174 Identities=20% Similarity=0.174 Sum_probs=141.5
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhC-CCCHHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTFAD 83 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~-Ap~f~e 83 (436)
.+..+|||||+||||++| ..++|||||||+++.+...+.+.|..+|+|.....+++.+..+||||++|+.+ +.+..+
T Consensus 3 ~~~~~fvv~D~ETTGLdP--~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e 80 (476)
T PRK11779 3 KMQPTFLWHDYETFGANP--ALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAE 80 (476)
T ss_pred CCCCcEEEEEEECCCCCC--CCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHH
Confidence 456789999999999998 68999999999999876555578999999997434678999999999999966 457899
Q ss_pred HHHHHHHHHc--CCEEEEEccccchHHHHHHHHHHcCCC-----CCCCCceeeHHHHHHHHhc--------C----CCCC
Q 013825 84 IADTVFDILH--GRIWAGHNILRFDCARIREAFAEIGRP-----APEPKGTIDSLALLTQRFG--------R----RAGD 144 (436)
Q Consensus 84 Vl~~f~efL~--g~vLVaHNa~~FD~~fLr~a~~r~Gi~-----~p~~~~~IDTl~Larr~l~--------~----~~~~ 144 (436)
++..|.+++. +.++||||..+||..||+.++.+..+. |......+|++.+++..+. + ..++
T Consensus 81 ~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s 160 (476)
T PRK11779 81 FAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPS 160 (476)
T ss_pred HHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCC
Confidence 9999999995 789999984499999999999765432 2222223466666553331 1 2367
Q ss_pred CCHHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHH
Q 013825 145 MKMASLATYFGLG-QQTHRSLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 145 ~kL~~LA~~fGI~-~~~HrALdDAraTa~VLk~L~~~ 180 (436)
++|+.|+++||++ ..+|+|++||++|++|++.+.++
T Consensus 161 ~rLe~L~~~~gI~~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 161 FKLEHLTKANGIEHENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHh
Confidence 9999999999999 68999999999999999999877
No 45
>PRK05359 oligoribonuclease; Provisional
Probab=99.93 E-value=1.4e-24 Score=202.35 Aligned_cols=162 Identities=20% Similarity=0.271 Sum_probs=133.6
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCC--CCCChhhHHhc---CCCHHHHhCCCC
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADP--ELISSLSVRCN---GITPDAVVSSPT 80 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~--~~I~p~a~klt---GIT~e~La~Ap~ 80 (436)
+..+||+||+||||++| ..++|||||||.++++...+.+.|+.+|+|... ..+++++.++| |||.++++++++
T Consensus 1 ~~~~~vvlD~ETTGLdp--~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 1 NEDNLIWIDLEMTGLDP--ERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred CCCcEEEEEeecCCCCC--CCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 35789999999999998 689999999999988744444669999999862 24678899987 899999999999
Q ss_pred HHHHHHHHHHHHc------CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceee--HH-HHHHHHhcCCCCCCCHHHHH
Q 013825 81 FADIADTVFDILH------GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTID--SL-ALLTQRFGRRAGDMKMASLA 151 (436)
Q Consensus 81 f~eVl~~f~efL~------g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~ID--Tl-~Larr~l~~~~~~~kL~~LA 151 (436)
+.+++.+|++|++ +.++||||+ .||..||++++.+++..+. ++++| ++ .+++ .+.++.
T Consensus 79 ~~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~~~~~~~~~l~--~~~~Dv~tl~~l~r-~~~P~~--------- 145 (181)
T PRK05359 79 EAEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLARYMPELEAYFH--YRNLDVSTLKELAR-RWKPEI--------- 145 (181)
T ss_pred HHHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHhcccCC--CcccchhHHHHHHH-HhChhh---------
Confidence 9999999999995 578999998 9999999999998877644 34667 66 5655 455533
Q ss_pred HHhCCC-CCCCChHHHHHHHHHHHHHHHHHhhh
Q 013825 152 TYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 152 ~~fGI~-~~~HrALdDAraTa~VLk~L~~~l~l 183 (436)
+++++ ...|||++||+++++.|+.+.+.++.
T Consensus 146 -~~~~~~~~~HRal~D~~~s~~~~~~~~~~~~~ 177 (181)
T PRK05359 146 -LNGFKKQGTHRALADIRESIAELKYYREHFFK 177 (181)
T ss_pred -hhCCCCcCCcccHHHHHHHHHHHHHHHHHhcc
Confidence 45776 57899999999999999998887653
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.92 E-value=1.1e-24 Score=251.94 Aligned_cols=196 Identities=22% Similarity=0.327 Sum_probs=165.6
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
..+.+||+||+||||+++ ..++|+||||++++.+ .+++.|+.||+|.. ++++.++++||||++++.+++++.++
T Consensus 416 L~~~~~VVfDLETTGL~~--~~deIIEIgAV~V~~G--~iie~F~~~V~P~~--~I~~~~~~LTGIT~e~L~~aps~~Ea 489 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSA--VYDEIIEIGAVKIKNG--EIIDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEV 489 (1437)
T ss_pred hccCcEEEEEhhhcCCCC--chhhhheeeeEEEeCC--eEeeeEEEEECCCC--CCCHHHHHHhCCCHHHHcCCCCHHHH
Confidence 345689999999999987 6899999999999987 56799999999998 79999999999999999999999999
Q ss_pred HHHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCCh
Q 013825 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRS 163 (436)
Q Consensus 85 l~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~HrA 163 (436)
+..|.+|++|.++||||+ .||+.||++++.++|++.+. ..++|++.+++. +.+...+++|.+||++||++ ..+|||
T Consensus 490 L~~f~~figg~vLVAHNa-~FD~~fL~~~l~rlgl~~l~-~~~IDTLelar~-l~p~~k~~kL~~LAk~lGL~~~~~HrA 566 (1437)
T PRK00448 490 LPKFKEFCGDSILVAHNA-SFDVGFINTNYEKLGLEKIK-NPVIDTLELSRF-LYPELKSHRLNTLAKKFGVELEHHHRA 566 (1437)
T ss_pred HHHHHHHhCCCEEEEeCc-cccHHHHHHHHHHcCCcccc-ccceeHHHHHHH-HcCccccccHHHHHHHcCCCCCCCcCh
Confidence 999999999999999999 99999999999999997554 358999998875 44566789999999999999 578999
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCcchhhhccCCCCC-CccccccccCC
Q 013825 164 LDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWVSP-NATTRSRSNAK 210 (436)
Q Consensus 164 LdDAraTa~VLk~L~~~l~le~slp~l~~~~~~v~~-~~~~R~R~~~~ 210 (436)
++||++|++||.++++++. +.++..+...+..+.. ...++.|.+|-
T Consensus 567 l~DA~aTa~lf~~ll~~l~-~~gi~~~~~L~~~~~~~~~~~~~~~~h~ 613 (1437)
T PRK00448 567 DYDAEATAYLLIKFLKDLK-EKGITNLDELNKKLGSEDAYKKARPKHA 613 (1437)
T ss_pred HHHHHHHHHHHHHHHHHHH-HcCCCCHHHHHHHhccccchhccCcccc
Confidence 9999999999999999886 4454444444433322 22344455443
No 47
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.70 E-value=9e-17 Score=155.68 Aligned_cols=170 Identities=18% Similarity=0.263 Sum_probs=139.0
Q ss_pred CcEEEEEEecCCCCCC--CCCCcEEEEEEEEEeCCcceEee-eEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 8 SEIAFFDVETTVPTRP--GQRFAILEFGAILVCPKKLEELH-NYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~--g~~~~IIEIGAV~V~~~~levl~-sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
.-++++|+|+|+-... ....+|||+.+|.++.-.-.+++ +|+.||+|..+..++.+|+.+|||.+++|..||+|.+|
T Consensus 56 dYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~v 135 (280)
T KOG0542|consen 56 DYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQV 135 (280)
T ss_pred ceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHH
Confidence 4578999999996542 13579999999966544333344 99999999987789999999999999999999999999
Q ss_pred HHHHHHHHc--------CC-EEEEEccccchHH-HHHHHHHHcCCCCCCC-CceeeHHHHHHHHhcCCCCCCCHHHHHHH
Q 013825 85 ADTVFDILH--------GR-IWAGHNILRFDCA-RIREAFAEIGRPAPEP-KGTIDSLALLTQRFGRRAGDMKMASLATY 153 (436)
Q Consensus 85 l~~f~efL~--------g~-vLVaHNa~~FD~~-fLr~a~~r~Gi~~p~~-~~~IDTl~Larr~l~~~~~~~kL~~LA~~ 153 (436)
+.+|..|+. |. -+|.. +++|+. ||..+|+..++..|.. ..|||..+.++..+ +.....++..+.++
T Consensus 136 l~~f~~Wlr~~~~~~k~~~~Afvtd--g~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y-~~~~~t~it~mLe~ 212 (280)
T KOG0542|consen 136 LSEFDSWLRKDSLGDKNGKFAFVTD--GDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFY-NRPAPTNITGMLEH 212 (280)
T ss_pred HHHHHHHHHHhhcccccCceEEEeC--chhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHh-cCccccCHHHHHHH
Confidence 999999996 22 33433 389984 8999999999988743 57999999887544 43356689999999
Q ss_pred hCCC--CCCCChHHHHHHHHHHHHHHHHH
Q 013825 154 FGLG--QQTHRSLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 154 fGI~--~~~HrALdDAraTa~VLk~L~~~ 180 (436)
+|++ ...|+++|||++++.|+.+|.+.
T Consensus 213 ~gL~f~Gr~HsGiDDa~Nia~I~~kM~~d 241 (280)
T KOG0542|consen 213 YGLQFEGRAHSGIDDARNIARIAQKMIRD 241 (280)
T ss_pred hCCcccCCcccCchhHHHHHHHHHHHHhC
Confidence 9998 57999999999999999998864
No 48
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.63 E-value=6.4e-16 Score=142.34 Aligned_cols=170 Identities=22% Similarity=0.293 Sum_probs=138.3
Q ss_pred CCcEEEEEEecCCCCCC--CCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 7 RSEIAFFDVETTVPTRP--GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~--g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
...++++|+|.|....- .+..+||||+|-.|+.-.-+++++|+.||||.....++.+|..+|||++..|.+||.|..+
T Consensus 3 ~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v 82 (210)
T COG5018 3 TNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMV 82 (210)
T ss_pred CceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHH
Confidence 35689999999975431 2467999999999876544778999999999987789999999999999999999999999
Q ss_pred HHHHHHHHc------CCEEEEEccccchHHHHHHHHHHcCCCC-CCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 013825 85 ADTVFDILH------GRIWAGHNILRFDCARIREAFAEIGRPA-PEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG 157 (436)
Q Consensus 85 l~~f~efL~------g~vLVaHNa~~FD~~fLr~a~~r~Gi~~-p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~ 157 (436)
+++|..||. ...|+.+ +.+|...|++.+..+++++ ++.-.++|...-+...++- ..-..|...++.+|..
T Consensus 83 ~E~f~r~L~~h~Pr~~~~wa~w--G~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~-pr~tgln~ale~~G~s 159 (210)
T COG5018 83 FEDFIRKLNEHDPRKNSTWATW--GNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGD-PRLTGLNKALEEYGDS 159 (210)
T ss_pred HHHHHHHHHhcCcccCCccccc--cchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcC-CccccHHHHHHHhccc
Confidence 999999996 2346644 4799999999999999883 3335688887666554432 1225799999999998
Q ss_pred --CCCCChHHHHHHHHHHHHHHHH
Q 013825 158 --QQTHRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 158 --~~~HrALdDAraTa~VLk~L~~ 179 (436)
...|||++||+.++++++.+..
T Consensus 160 f~G~~HraldDArn~~rl~klv~~ 183 (210)
T COG5018 160 FTGTHHRALDDARNAYRLFKLVEQ 183 (210)
T ss_pred cCCchhhhHHHHHHHHHHHHHHcc
Confidence 4799999999999999988654
No 49
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.56 E-value=2.6e-14 Score=145.25 Aligned_cols=173 Identities=20% Similarity=0.180 Sum_probs=142.2
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCC-hhhHHhcCCCHHHH-hCCCCHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELIS-SLSVRCNGITPDAV-VSSPTFA 82 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~-p~a~kltGIT~e~L-a~Ap~f~ 82 (436)
....+|+|+|.||.|.+| ..+++.||++|+.+.+-.++.+....|++|.+ +.+| |.+.-+||||+... +.+..-.
T Consensus 6 ~~~~tF~~yDYETfG~~P--a~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsd-DyLP~P~a~LITGITPQ~~~~~G~~E~ 82 (475)
T COG2925 6 TKQPTFLFYDYETFGVHP--ALDRPAQFAGIRTDIEFNIIGEPIVFYCKPAD-DYLPQPGAVLITGITPQEAREKGINEA 82 (475)
T ss_pred CCCCcEEEEehhhcCCCc--ccccchhhheeeccccccccCCCeEEEecCcc-ccCCCCCceeeecCCHHHHHhcCCChH
Confidence 345789999999999998 78999999999999886666677888999998 3555 89999999999887 5677888
Q ss_pred HHHHHHHHHHc--CCEEEEEccccchHHHHHHHHHHcC-----CCCCCCCceeeHHHHHHHHhc--CC----------CC
Q 013825 83 DIADTVFDILH--GRIWAGHNILRFDCARIREAFAEIG-----RPAPEPKGTIDSLALLTQRFG--RR----------AG 143 (436)
Q Consensus 83 eVl~~f~efL~--g~vLVaHNa~~FD~~fLr~a~~r~G-----i~~p~~~~~IDTl~Larr~l~--~~----------~~ 143 (436)
+...+|+.-+. +.+++|||..+||-.+.+..|.|.- ..|.....-+|.+.+.|..+. ++ .+
T Consensus 83 ~F~~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~p 162 (475)
T COG2925 83 AFAARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLP 162 (475)
T ss_pred HHHHHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCc
Confidence 88888888776 7799999999999988888887643 444444556788888776653 21 46
Q ss_pred CCCHHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHH
Q 013825 144 DMKMASLATYFGLG-QQTHRSLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 144 ~~kL~~LA~~fGI~-~~~HrALdDAraTa~VLk~L~~~ 180 (436)
++||+.|.++-|+. .++|+|++|+++|+.+.+.+.++
T Consensus 163 SFkLEhLt~ANgieH~nAHdAmsDVyATIamAklvk~~ 200 (475)
T COG2925 163 SFKLEHLTKANGIEHSNAHDAMSDVYATIAMAKLVKTA 200 (475)
T ss_pred chhhHHHhhccccccchhhHHHHHHHHHHHHHHHHHhh
Confidence 88999999999998 68999999999999988876654
No 50
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.53 E-value=1.3e-13 Score=134.83 Aligned_cols=156 Identities=19% Similarity=0.332 Sum_probs=123.5
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHH
Q 013825 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~ 87 (436)
.++|++|+|+.|.++.|..+.+.-++.|-..++ ++ |..||+|.. +|+.+.++.+||+.+.+.+|.+|+.|..+
T Consensus 105 ~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~--Vv---yDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~aQ~e 177 (280)
T KOG2249|consen 105 TRVVAMDCEMVGVGPDGRESLLARVSIVNYHGH--VV---YDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVAQKE 177 (280)
T ss_pred ceEEEEeeeEeccCCCccceeeeEEEEeeccCc--Ee---eeeecCCCc--ccccceeeecccCHHHhccCccHHHHHHH
Confidence 369999999999998666666666766666555 34 788999999 89999999999999999999999999999
Q ss_pred HHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHH--HHHHhcCCCCCCCHHHHHHHh-CCC--CCCCC
Q 013825 88 VFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLAL--LTQRFGRRAGDMKMASLATYF-GLG--QQTHR 162 (436)
Q Consensus 88 f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~L--arr~l~~~~~~~kL~~LA~~f-GI~--~~~Hr 162 (436)
+.++|.|+|+|||.. ..|+..|.-. .|... +-||-.. +++.+ ......+|..|++.+ |.. ...|+
T Consensus 178 v~klL~gRIlVGHaL-hnDl~~L~l~-------hp~s~-iRDTs~~~pl~k~~-~~~~tpSLK~Lt~~~Lg~~IQ~GeHs 247 (280)
T KOG2249|consen 178 VLKLLKGRILVGHAL-HNDLQALKLE-------HPRSM-IRDTSKYPPLMKLL-SKKATPSLKKLTEALLGKDIQVGEHS 247 (280)
T ss_pred HHHHHhCCEEecccc-ccHHHHHhhh-------Cchhh-hcccccCchHHHHh-hccCCccHHHHHHHHhchhhhccccC
Confidence 999999999999999 8888877654 33322 4455432 12121 233578999999854 665 45699
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 013825 163 SLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 163 ALdDAraTa~VLk~L~~~ 180 (436)
...||++|+++|+.+...
T Consensus 248 SvEDA~AtM~LY~~vk~q 265 (280)
T KOG2249|consen 248 SVEDARATMELYKRVKVQ 265 (280)
T ss_pred cHHHHHHHHHHHHHHHHH
Confidence 999999999999987654
No 51
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=99.43 E-value=5.3e-12 Score=117.69 Aligned_cols=132 Identities=20% Similarity=0.152 Sum_probs=102.2
Q ss_pred EEEEEecCCC----CCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 11 AFFDVETTVP----TRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 11 V~fDLETTGl----~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
++||+||||. ++ ..++|++||++....|... .+.....+.. ..++ ||+..++...++..+++.
T Consensus 2 ~~~DIEt~~~~~~p~~--~~d~Ii~I~~~~~~~g~~~---~~~~~~~~~~-~~~~-------~i~~~~v~~~~~E~~lL~ 68 (199)
T cd05160 2 LSFDIETTPPVGGPEP--DRDPIICITYADSFDGVKV---VFLLKTSTVG-DDIE-------FIDGIEVEYFADEKELLK 68 (199)
T ss_pred ccEEEeecCCCCCcCC--CCCCEEEEEEEEeeCCcee---eEEEeecccC-CcCC-------CCCCceEEEeCCHHHHHH
Confidence 6899999997 55 5799999999988555322 2222222222 0121 888889999999999999
Q ss_pred HHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCC-C--------------------CCceeeHHHHHHHHhcCCC
Q 013825 87 TVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAP-E--------------------PKGTIDSLALLTQRFGRRA 142 (436)
Q Consensus 87 ~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p-~--------------------~~~~IDTl~Larr~l~~~~ 142 (436)
.|.++++. .++||||+..||+++|.+.+.++|++.. . ...++|++.++++.+ + .
T Consensus 69 ~f~~~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~-~-l 146 (199)
T cd05160 69 RFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDF-K-L 146 (199)
T ss_pred HHHHHHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhc-C-c
Confidence 99999986 4999999999999999999999998761 0 124799999987644 3 7
Q ss_pred CCCCHHHHHHHhCCC
Q 013825 143 GDMKMASLATYFGLG 157 (436)
Q Consensus 143 ~~~kL~~LA~~fGI~ 157 (436)
.+|+|+++|+.++..
T Consensus 147 ~sy~L~~v~~~~l~~ 161 (199)
T cd05160 147 KSYTLDAVAEELLGE 161 (199)
T ss_pred ccCCHHHHHHHHhCC
Confidence 899999999988665
No 52
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.33 E-value=1.4e-11 Score=114.99 Aligned_cols=152 Identities=19% Similarity=0.278 Sum_probs=109.5
Q ss_pred CcEEEEEEecCCCCCCCCC-------CcEEEEEEEEEeC-CcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCC
Q 013825 8 SEIAFFDVETTVPTRPGQR-------FAILEFGAILVCP-KKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSP 79 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~-------~~IIEIGAV~V~~-~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap 79 (436)
-+||-+|.|+++..+.|.. .++.-|++|-.++ ..+++ -|..||+|.. +|..+.++.+|||.+++.++.
T Consensus 5 ~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~v--llD~~VkP~~--~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 5 AEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVP--FIDDYISTTE--PVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred eeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCE--EEeeeECCCC--CccCcCccccccCHHHcCccc
Confidence 3566677776666554432 2344444444210 12233 2667999998 899999999999999998764
Q ss_pred ------CHHHHHHHHHHHHc-CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHH
Q 013825 80 ------TFADIADTVFDILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLAT 152 (436)
Q Consensus 80 ------~f~eVl~~f~efL~-g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~ 152 (436)
+++++..++.+++. +.++|||.. ..|+..| ++..|.. .++||..++.. +....++|..|++
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL-~nDL~aL-------~l~hp~~-~viDTa~l~~~---~~~r~~sLk~La~ 148 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGL-AKDFRVI-------NIQVPKE-QVIDTVELFHL---PGQRKLSLRFLAW 148 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccc-hhHHHHh-------cCcCCCc-ceEEcHHhccC---CCCCChhHHHHHH
Confidence 68999999999995 899999999 8887666 4555543 48999765431 2223679999999
Q ss_pred Hh-CCC--CCCCChHHHHHHHHHHHH
Q 013825 153 YF-GLG--QQTHRSLDDVRMNLEVLK 175 (436)
Q Consensus 153 ~f-GI~--~~~HrALdDAraTa~VLk 175 (436)
.| |.. ...|++..||++++++|+
T Consensus 149 ~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 149 YLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 66 555 468999999999999984
No 53
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.23 E-value=5e-11 Score=109.65 Aligned_cols=165 Identities=19% Similarity=0.237 Sum_probs=118.9
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCC--CCCCCChhhHHhc---CCCHHHHhC
Q 013825 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPA--DPELISSLSVRCN---GITPDAVVS 77 (436)
Q Consensus 3 ~~~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~--~~~~I~p~a~klt---GIT~e~La~ 77 (436)
|....+++|.+|+|+||+++ ..++||||+++..+.+-..+.+.+...|.-. ......+++++.| |++....++
T Consensus 1 m~~~~~nLiWIDlEMTGLd~--~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S 78 (184)
T COG1949 1 MSANKNNLIWIDLEMTGLDP--ERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKAS 78 (184)
T ss_pred CCCcCCceEEEeeeeccCCc--CcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHh
Confidence 45678899999999999998 7899999999999887433333344444433 2335678888877 777777788
Q ss_pred CCCHHHHHHHHHHHHc------CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHH--HHHHhcCCCCCCCHHH
Q 013825 78 SPTFADIADTVFDILH------GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLAL--LTQRFGRRAGDMKMAS 149 (436)
Q Consensus 78 Ap~f~eVl~~f~efL~------g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~L--arr~l~~~~~~~kL~~ 149 (436)
..+.+++-.+.++|++ ..+++|-.+ .-|+.||.+++.++.- -+.++.+|+-.+ +.+.+.|+.
T Consensus 79 ~~t~~~aE~~~l~flkkwvp~~~spicGNSI-~qDRrFl~r~MP~Le~--yfHYR~lDVSTlKELa~RW~P~i------- 148 (184)
T COG1949 79 TVTEAEAEAQTLDFLKKWVPKGVSPICGNSI-AQDRRFLFRYMPKLEA--YFHYRYLDVSTLKELARRWNPEI------- 148 (184)
T ss_pred hccHHHHHHHHHHHHHHhCCCCCCCCccchh-hHHHHHHHHHhhhHHH--HhhhHhhhHHHHHHHHHhhCcHh-------
Confidence 9999999999999986 357777776 9999999998866422 123456775433 222344432
Q ss_pred HHHHhCCC-CCCCChHHHHHHHHHHHHHHHHHhh
Q 013825 150 LATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 150 LA~~fGI~-~~~HrALdDAraTa~VLk~L~~~l~ 182 (436)
+.|.. ...|+||+|.+--+.-|++..+.++
T Consensus 149 ---~~~~~K~~~H~Al~DI~ESI~EL~~YR~~f~ 179 (184)
T COG1949 149 ---LAGFKKGGTHRALDDIRESIAELRYYREHFL 179 (184)
T ss_pred ---hhccccccchhHHHHHHHHHHHHHHHHHHhc
Confidence 33443 4689999999999988888776554
No 54
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=99.14 E-value=4.8e-10 Score=94.38 Aligned_cols=79 Identities=29% Similarity=0.357 Sum_probs=62.0
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~e 90 (436)
++||+||||..+ ..++|++|++....++ ..| ++. |.+
T Consensus 1 ~~~DiEt~~~~~--~~~~i~~i~~~~~~~~-----~~~--~~~----------------------------------f~~ 37 (96)
T cd06125 1 IAIDTEATGLDG--AVHEIIEIALADVNPE-----DTA--VID----------------------------------LKD 37 (96)
T ss_pred CEEEEECCCCCC--CCCcEEEEEEEEccCC-----CEE--Eeh----------------------------------HHH
Confidence 479999999987 6789999998865323 122 111 677
Q ss_pred HHcC---CEEEEEccccchHHHHHHHHHHcCCCCCC-CCceeeHHHH
Q 013825 91 ILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE-PKGTIDSLAL 133 (436)
Q Consensus 91 fL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~-~~~~IDTl~L 133 (436)
|+++ .++|+||+ .||+.||++++.+++.+.|. ...++||+.+
T Consensus 38 ~l~~~~~~v~V~hn~-~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 38 ILRDKPLAILVGHNG-SFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHhhCCCCEEEEeCc-HHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 7764 58999999 99999999999999998773 4679999876
No 55
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.11 E-value=3.2e-10 Score=105.35 Aligned_cols=162 Identities=17% Similarity=0.256 Sum_probs=121.9
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCC--CCCCChhhHHhc---CCCHHHHhCCCCH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPAD--PELISSLSVRCN---GITPDAVVSSPTF 81 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~--~~~I~p~a~klt---GIT~e~La~Ap~f 81 (436)
.+++|.+|+|+||++- ..+.|+||+++..+++-..+.+-+...|+-.. .+...+|+.+-| |+|...+++..++
T Consensus 25 ~q~lVWiD~EMTGLdv--ekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl 102 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLDV--EKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITL 102 (208)
T ss_pred cCceEEEeeecccccc--ccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccH
Confidence 4789999999999987 78999999999998885555566777776442 346778888876 7888889999999
Q ss_pred HHHHHHHHHHHc-----CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHH---HHHHhcCCCCCCCHHHHHHH
Q 013825 82 ADIADTVFDILH-----GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLAL---LTQRFGRRAGDMKMASLATY 153 (436)
Q Consensus 82 ~eVl~~f~efL~-----g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~L---arr~l~~~~~~~kL~~LA~~ 153 (436)
+++-+++++|+. |...+|-|..--|+-||+.++...--.. .+++||+-.+ ++ .|.|.. .
T Consensus 103 ~~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~l--hyrivDVStIkeL~~-Rw~P~~----------~ 169 (208)
T KOG3242|consen 103 ADAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHL--HYRIVDVSTIKELAR-RWYPDI----------K 169 (208)
T ss_pred HHHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhc--ceeeeeHHHHHHHHH-HhCchh----------h
Confidence 999999999997 4555666666999999999987653322 3467886543 33 343321 0
Q ss_pred hCCC--CCCCChHHHHHHHHHHHHHHHHHhhh
Q 013825 154 FGLG--QQTHRSLDDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 154 fGI~--~~~HrALdDAraTa~VLk~L~~~l~l 183 (436)
-.-| ...|||++|.+.-++-|+.....+|.
T Consensus 170 ~~aPkK~~~HrAldDI~ESI~ELq~Yr~nifk 201 (208)
T KOG3242|consen 170 ARAPKKKATHRALDDIRESIKELQYYRENIFK 201 (208)
T ss_pred ccCcccccccchHHHHHHHHHHHHHHHHHhcc
Confidence 0112 35899999999999999998877664
No 56
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.88 E-value=4.7e-08 Score=91.93 Aligned_cols=129 Identities=12% Similarity=0.128 Sum_probs=90.9
Q ss_pred CcEEEEEEecC---CCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 8 SEIAFFDVETT---VPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 8 ~~fV~fDLETT---Gl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
-++++||+||+ |+ |....+.|+.||.+....+ .++ . .++.. . ..+....+-.+.
T Consensus 3 l~i~~fDIEt~~~~g~-p~~~~d~Ii~Is~~~~~~~--~~~-~----~~~~~---~------------~~v~~~~~E~~l 59 (195)
T cd05780 3 LKILSFDIEVLNHEGE-PNPEKDPIIMISFADEGGN--KVI-T----WKKFD---L------------PFVEVVKTEKEM 59 (195)
T ss_pred ceEEEEEEEecCCCCC-CCCCCCcEEEEEEecCCCc--eEE-E----ecCCC---C------------CeEEEeCCHHHH
Confidence 36899999998 43 2236799999998653221 111 1 11111 0 023334567889
Q ss_pred HHHHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCCC---------------------CCceeeHHHHHHHHhcC
Q 013825 85 ADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE---------------------PKGTIDSLALLTQRFGR 140 (436)
Q Consensus 85 l~~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~---------------------~~~~IDTl~Larr~l~~ 140 (436)
+..|.++++. .++||||...||+++|.+-+..+|++.+. ....+|++.++++.+
T Consensus 60 L~~F~~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~-- 137 (195)
T cd05780 60 IKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL-- 137 (195)
T ss_pred HHHHHHHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC--
Confidence 9999999984 68999999999999999999999987543 123899999887533
Q ss_pred CCCCCCHHHHHH-HhCCCCCCC
Q 013825 141 RAGDMKMASLAT-YFGLGQQTH 161 (436)
Q Consensus 141 ~~~~~kL~~LA~-~fGI~~~~H 161 (436)
.+.+++|+++|+ ++|.+...+
T Consensus 138 ~l~sy~L~~v~~~~Lg~~k~d~ 159 (195)
T cd05780 138 NLTRYTLERVYEELFGIEKEDV 159 (195)
T ss_pred CCCcCcHHHHHHHHhCCCCCcC
Confidence 467999999988 668875443
No 57
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.87 E-value=3.9e-08 Score=95.93 Aligned_cols=147 Identities=16% Similarity=0.145 Sum_probs=104.2
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCC-HHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPT-FADIA 85 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~-f~eVl 85 (436)
..+++|||+||||+++ .+..|+=.|...+..+.. +|+-... .+|. -..++
T Consensus 97 ~e~~~FFDiETTGL~~--ag~~I~~~g~a~~~~~~~--------~Vrq~~l-------------------p~p~~E~avl 147 (278)
T COG3359 97 AEDVAFFDIETTGLDR--AGNTITLVGGARGVDDTM--------HVRQHFL-------------------PAPEEEVAVL 147 (278)
T ss_pred ccceEEEeeeccccCC--CCCeEEEEEEEEccCceE--------EEEeecC-------------------CCcchhhHHH
Confidence 5679999999999987 567888888877766632 3332221 1111 12245
Q ss_pred HHHHHHHcCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCC------
Q 013825 86 DTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQ------ 159 (436)
Q Consensus 86 ~~f~efL~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~~------ 159 (436)
+.|+....-..||.+|+.+||.+|+++ +.+..++.......+|.+.-+|+.+...+...+|.++-+.+|+...
T Consensus 148 e~fl~~~~~~~lvsfNGkaFD~PfikR-~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~R~edtdG~ 226 (278)
T COG3359 148 ENFLHDPDFNMLVSFNGKAFDIPFIKR-MVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGIRREEDTDGY 226 (278)
T ss_pred HHHhcCCCcceEEEecCcccCcHHHHH-HHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHHHhCccccccCCCc
Confidence 555555555699999999999999996 7777777655556899999999877777889999999999998521
Q ss_pred ---------------------CCChHHHHHHHHHHHHHHHHHhhh
Q 013825 160 ---------------------THRSLDDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 160 ---------------------~HrALdDAraTa~VLk~L~~~l~l 183 (436)
-|.--.|+..+..++.++.+++.-
T Consensus 227 ~~p~lyr~~~~~~dp~ll~~l~~hN~eDvlnL~~i~~h~~~~i~~ 271 (278)
T COG3359 227 DGPELYRLYRRYGDPGLLDGLVLHNREDVLNLPTIIKHVSKKILE 271 (278)
T ss_pred chHHHHHHHHHcCCHHHHHHHHHccHHHHHhHHHHHHHHHHHHHH
Confidence 122245777777777777766553
No 58
>PHA02570 dexA exonuclease; Provisional
Probab=98.85 E-value=4.6e-08 Score=94.21 Aligned_cols=157 Identities=15% Similarity=0.137 Sum_probs=98.9
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcC--CC----HH-----------
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNG--IT----PD----------- 73 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltG--IT----~e----------- 73 (436)
+++|+||.|..+ ...|++||||.+++... ...+|+.+|..+. .+-.......| .. .+
T Consensus 4 lMIDlETmG~~p---~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~--~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~ 77 (220)
T PHA02570 4 FIIDFETFGNTP---DGAVIDLAVIAFEHDPH-NPPTFEELVSRGR--RIKFDLKSQKGKRLFDKSTIEWWKNQSPEARK 77 (220)
T ss_pred EEEEeeccCCCC---CceEEEEEEEEecCCCC-ccccHHHHhhccc--ccccchhhccCCCccCchHHHHHHhCCHHHHH
Confidence 679999999986 68999999999998654 5678887776432 11111111122 11 10
Q ss_pred HHh---CCCCHHHHHHHHHHHHc--C----CEEEEEccccchHHHHHHHHHHc----C--CCCCCC-CceeeHHHHHHHH
Q 013825 74 AVV---SSPTFADIADTVFDILH--G----RIWAGHNILRFDCARIREAFAEI----G--RPAPEP-KGTIDSLALLTQR 137 (436)
Q Consensus 74 ~La---~Ap~f~eVl~~f~efL~--g----~vLVaHNa~~FD~~fLr~a~~r~----G--i~~p~~-~~~IDTl~Larr~ 137 (436)
.+. +..++.+++.+|.+|+. + ...|.-|...||+.+|+.+++++ + .+.|+. ..--|+..+....
T Consensus 78 ~L~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~~ 157 (220)
T PHA02570 78 NLKPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEAT 157 (220)
T ss_pred hccCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhhh
Confidence 111 23678999999999997 2 25566787899999999999998 6 344432 1234555543332
Q ss_pred -hcCCC-----CCCCHHHHHHHhCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 013825 138 -FGRRA-----GDMKMASLATYFGLGQQTHRSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 138 -l~~~~-----~~~kL~~LA~~fGI~~~~HrALdDAraTa~VLk~L~~~l 181 (436)
+.+.. +...|+. .-+|+|++||-.-+..|..-.+..
T Consensus 158 ~l~r~~~~cp~~~g~l~g--------fv~H~sihDcakd~lml~y~~rya 199 (220)
T PHA02570 158 LLTRGMTTCPLPKGTLDG--------FVAHDSIHDCAKDILMLIYAKRYA 199 (220)
T ss_pred hccCCcccCCCcCccccc--------hhhcccHHHHHHHHHHHHHHHHHh
Confidence 34432 1111211 358999999887777776655443
No 59
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.81 E-value=6.9e-09 Score=93.50 Aligned_cols=115 Identities=19% Similarity=0.286 Sum_probs=64.4
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHHH
Q 013825 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (436)
Q Consensus 11 V~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~e 90 (436)
++||+||||+.+ ..+.|.-||++.++.+.... |..+..... .-++.+.++.+
T Consensus 1 l~~DIET~Gl~~--~~~~i~liG~~~~~~~~~~~---~~~~~~~~~-----------------------~ee~~~~~~~~ 52 (164)
T PF13482_consen 1 LFFDIETTGLSP--DNDTIYLIGVADFDDDEIIT---FIQWFAEDP-----------------------DEEEIILEFFE 52 (164)
T ss_dssp --EEEEESS-GG---G---EEEEEEE-ETTTTE----EEEE-GGGH-----------------------HHHHHHHH--H
T ss_pred CcEEecCCCCCC--CCCCEEEEEEEEeCCCceEE---eeHhhccCc-----------------------HHHHHHHHHHH
Confidence 689999999987 56789999999988874422 322222111 11222222224
Q ss_pred HHc-CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC
Q 013825 91 ILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ 158 (436)
Q Consensus 91 fL~-g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~ 158 (436)
++. ...+|+||+..||.++|++.+.+++++. ....+|++..+++.+. .+++|.++++++|+..
T Consensus 53 ~l~~~~~iv~yng~~FD~p~L~~~~~~~~~~~--~~~~iDl~~~~~~~~~---~~~~Lk~ve~~lg~~~ 116 (164)
T PF13482_consen 53 LLDEADNIVTYNGKNFDIPFLKRRAKRYGLPP--PFNHIDLLKIIKKHFL---ESYSLKNVEKFLGIER 116 (164)
T ss_dssp HHHTT--EEESSTTTTHHHHHHHHH-HHHH----GGGEEEHHHHHT-TTS---CCTT--SHHH------
T ss_pred HHhcCCeEEEEeCcccCHHHHHHHHHHcCCCc--ccchhhHHHHHHhccC---CCCCHHHHhhhccccc
Confidence 444 5789999988999999999998888876 3468999998765433 7889999999999875
No 60
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=98.74 E-value=2.9e-07 Score=86.57 Aligned_cols=117 Identities=15% Similarity=0.131 Sum_probs=87.3
Q ss_pred CcEEEEEEecCC---CCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 8 SEIAFFDVETTV---PTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 8 ~~fV~fDLETTG---l~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
-+.++||+||++ + |....+.|+.||+...++. .++ +. ....+..++
T Consensus 3 l~~l~fDIEt~~~~gf-p~~~~d~Ii~Is~~~~~g~-~~~------~~-----------------------~~~~~E~~l 51 (188)
T cd05781 3 LKTLAFDIEVYSKYGT-PNPRRDPIIVISLATSNGD-VEF------IL-----------------------AEGLDDRKI 51 (188)
T ss_pred ceEEEEEEEecCCCCC-CCCCCCCEEEEEEEeCCCC-EEE------EE-----------------------ecCCCHHHH
Confidence 468999999994 3 2225789999998764433 111 10 123567889
Q ss_pred HHHHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCCCC-------------------CceeeHHHHHHHHhcCCC
Q 013825 85 ADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPEP-------------------KGTIDSLALLTQRFGRRA 142 (436)
Q Consensus 85 l~~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~-------------------~~~IDTl~Larr~l~~~~ 142 (436)
+..|.++++. .+++|||...||+++|..-+.++|++.... ...+|++.++++.. .+
T Consensus 52 L~~F~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~--~l 129 (188)
T cd05781 52 IREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP--EV 129 (188)
T ss_pred HHHHHHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC--CC
Confidence 9999999983 589999999999999999999999765411 12799999887543 36
Q ss_pred CCCCHHHHHHHhCCC
Q 013825 143 GDMKMASLATYFGLG 157 (436)
Q Consensus 143 ~~~kL~~LA~~fGI~ 157 (436)
++++|+++|+++|..
T Consensus 130 ~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 130 KVKTLENVAEYLGVM 144 (188)
T ss_pred CCCCHHHHHHHHCCC
Confidence 899999999999875
No 61
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.67 E-value=1.2e-07 Score=98.39 Aligned_cols=154 Identities=19% Similarity=0.295 Sum_probs=117.6
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhC-CCCHHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTFAD 83 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~-Ap~f~e 83 (436)
....+++++|+|+....- +-+++.+++|-.+.. .+ |..+|+|.. +|-.+.++.+|||.+++.+ ..++++
T Consensus 213 ~~~~~i~AlDCEm~~te~---g~el~RVt~VD~~~~--vi---~D~fVkP~~--~VvDy~T~~SGIT~~~~e~~t~tl~d 282 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVTEN---GLELTRVTAVDRDGK--VI---LDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLED 282 (380)
T ss_pred CCCCCeEEEEeeeeeecc---ceeeEEeeeeeccCc--EE---eEEeecCCC--cccccccccccccHHHHhcCccCHHH
Confidence 455789999999999763 478888888887776 33 677999999 7999999999999999975 567999
Q ss_pred HHHHHHHHHc-CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC----
Q 013825 84 IADTVFDILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG---- 157 (436)
Q Consensus 84 Vl~~f~efL~-g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~---- 157 (436)
+..++..|+. +.++|||.. .-|+.-|+-. ...+|||..++....++.....+|..||+-| |..
T Consensus 283 vq~~l~~~~~~~TILVGHSL-enDL~aLKl~----------H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~ 351 (380)
T KOG2248|consen 283 VQKELLELISKNTILVGHSL-ENDLKALKLD----------HPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEG 351 (380)
T ss_pred HHHHHHhhcCcCcEEEeech-hhHHHHHhhh----------CCceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhcc
Confidence 9999999998 679999999 8898887641 1248999744332222101223578888755 332
Q ss_pred CCCCChHHHHHHHHHHHHHHHH
Q 013825 158 QQTHRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 158 ~~~HrALdDAraTa~VLk~L~~ 179 (436)
...|++..||.+++++++....
T Consensus 352 ~~~HdS~eDA~acm~Lv~~k~~ 373 (380)
T KOG2248|consen 352 VGGHDSVEDALACMKLVKLKIK 373 (380)
T ss_pred CCCCccHHHHHHHHHHHHHHHh
Confidence 2569999999999999987544
No 62
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=98.66 E-value=1e-06 Score=84.28 Aligned_cols=147 Identities=14% Similarity=0.120 Sum_probs=91.8
Q ss_pred CcEEEEEEecCCC---CCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCC-CCChhhHHhcCCCHHHHhCCCCHHH
Q 013825 8 SEIAFFDVETTVP---TRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPE-LISSLSVRCNGITPDAVVSSPTFAD 83 (436)
Q Consensus 8 ~~fV~fDLETTGl---~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~-~I~p~a~kltGIT~e~La~Ap~f~e 83 (436)
-+++.||+||.+. -|....+.|++|+.+.-..+ ..+.. ..++.+...+ ...+ +..+.| .-.+....+-.+
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g-~~~~~--~~~~~~~~~~~~~~~-~~~~~~--~~~v~~~~~E~~ 75 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQG-YLIVN--REIVSEDIEDFEYTP-KPEYEG--PFKVFNEPDEKA 75 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCC-EEEec--ccccccccccccccC-CCCCCC--ceEEecCCCHHH
Confidence 3689999999862 13336899999997764333 11110 0010000000 0000 000111 011223567889
Q ss_pred HHHHHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCC--C---C----------CceeeHHHHHHHHhcCCCCCC
Q 013825 84 IADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAP--E---P----------KGTIDSLALLTQRFGRRAGDM 145 (436)
Q Consensus 84 Vl~~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p--~---~----------~~~IDTl~Larr~l~~~~~~~ 145 (436)
.+.+|.+++.. .+++|||...||+++|.+-+..+|+... . . ...+|.+.++++......+++
T Consensus 76 lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sy 155 (204)
T cd05779 76 LLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQ 155 (204)
T ss_pred HHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCc
Confidence 99999999984 4899999999999999999999997644 1 0 116899998876443334689
Q ss_pred CHHHHHHH-hCCCCCC
Q 013825 146 KMASLATY-FGLGQQT 160 (436)
Q Consensus 146 kL~~LA~~-fGI~~~~ 160 (436)
+|+++|++ +|.++..
T Consensus 156 sLd~Va~~~Lg~~K~~ 171 (204)
T cd05779 156 GLKAVTKAKLGYDPVE 171 (204)
T ss_pred cHHHHHHHHhCCCcCc
Confidence 99999994 7886533
No 63
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=98.62 E-value=7.7e-08 Score=94.88 Aligned_cols=173 Identities=18% Similarity=0.207 Sum_probs=128.1
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCc------------------ceEeeeEEEEEcCCCCCCCChhhHHh
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKK------------------LEELHNYSTLVRPADPELISSLSVRC 67 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~------------------levl~sfstLVrP~~~~~I~p~a~kl 67 (436)
.-..|+|+|+|+||+.. +...|.|+....|.... -.++++.+.+..|.. ...+.+.++
T Consensus 11 r~~tf~fldleat~lp~--~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~aeei 86 (318)
T KOG4793|consen 11 RLRTFSFLDLEATGLPG--WIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAEEI 86 (318)
T ss_pred ceeEEEeeeeccccCCc--ccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhhhh
Confidence 34679999999999954 77889998776654110 034567777888888 688899999
Q ss_pred cCCCHHHHhC--CCCHHH-HHHHHHHHHc----CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcC
Q 013825 68 NGITPDAVVS--SPTFAD-IADTVFDILH----GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGR 140 (436)
Q Consensus 68 tGIT~e~La~--Ap~f~e-Vl~~f~efL~----g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~ 140 (436)
||.+++-++- .--|+. +.+-+..|+. --++|+||..+||+.+|.+++++.|+..|.....+|++...+. +.+
T Consensus 87 tgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~a-ld~ 165 (318)
T KOG4793|consen 87 TGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNA-LDR 165 (318)
T ss_pred cccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHH-Hhh
Confidence 9999977632 233443 4445566665 3489999999999999999999999998866567888876553 322
Q ss_pred C---------CCCCCHHHHHHHhCCC---CCCCChHHHHHHHHHHHHHHHHHhhh
Q 013825 141 R---------AGDMKMASLATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 141 ~---------~~~~kL~~LA~~fGI~---~~~HrALdDAraTa~VLk~L~~~l~l 183 (436)
. ..++.|..+..+|--. ...|.|..|+....-++...+.+++.
T Consensus 166 a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR 220 (318)
T KOG4793|consen 166 ANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLR 220 (318)
T ss_pred hcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHh
Confidence 1 3567788887766433 35799999999999999888887765
No 64
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.59 E-value=2.2e-06 Score=81.99 Aligned_cols=126 Identities=23% Similarity=0.295 Sum_probs=91.1
Q ss_pred CCCCCCCcEEEEEEecCCCC------CCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHH
Q 013825 2 GPTQDRSEIAFFDVETTVPT------RPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAV 75 (436)
Q Consensus 2 ~~~~~~~~fV~fDLETTGl~------p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~L 75 (436)
||...+-+++.||+||++.. |....+.|+.||... .++.+. .+.
T Consensus 3 ~~~~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~--~~~~~~------~~~---------------------- 52 (207)
T cd05785 3 GMTFDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRD--NRGWEE------VLH---------------------- 52 (207)
T ss_pred CCCCCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEeccc--CCCcee------eec----------------------
Confidence 67777889999999997642 222467899998742 221100 000
Q ss_pred hCCCCHHHHHHHHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCCC----------------------------C
Q 013825 76 VSSPTFADIADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE----------------------------P 124 (436)
Q Consensus 76 a~Ap~f~eVl~~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~----------------------------~ 124 (436)
....+..+++..|+++++. .++||||...||+++|.+.+.++|++..+ +
T Consensus 53 ~~~~~E~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~ 132 (207)
T cd05785 53 AEDAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIP 132 (207)
T ss_pred cCCCCHHHHHHHHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEec
Confidence 1257788999999999985 69999999999999999999999987631 0
Q ss_pred -CceeeHHHHHHHHh--cCCCCCCCHHHHHHHhCCC
Q 013825 125 -KGTIDSLALLTQRF--GRRAGDMKMASLATYFGLG 157 (436)
Q Consensus 125 -~~~IDTl~Larr~l--~~~~~~~kL~~LA~~fGI~ 157 (436)
...+|++.++++.- ...+.+|+|+++|++||+.
T Consensus 133 Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~ 168 (207)
T cd05785 133 GRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLA 168 (207)
T ss_pred CEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhccc
Confidence 12379998876421 2356899999999999874
No 65
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=98.58 E-value=2.7e-06 Score=77.79 Aligned_cols=145 Identities=14% Similarity=0.190 Sum_probs=98.7
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
+++..++++|+||+|..+ ..+.|+.++...- .+ ..| ++.... ... .+++...++
T Consensus 2 ~~~~~~~a~d~e~~~~~~--~~~~i~~l~~~~~-~~-----~~~--~~~~~~-~~~---------------~~~~~~~~~ 55 (193)
T cd06139 2 LEKAKVFAFDTETTSLDP--MQAELVGISFAVE-PG-----EAY--YIPLGH-DYG---------------GEQLPREEV 55 (193)
T ss_pred CccCCeEEEEeecCCCCc--CCCeEEEEEEEcC-CC-----CEE--EEecCC-Ccc---------------ccCCCHHHH
Confidence 456789999999999875 4577877765421 11 122 222111 011 144568888
Q ss_pred HHHHHHHHcCC--EEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC----
Q 013825 85 ADTVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG---- 157 (436)
Q Consensus 85 l~~f~efL~g~--vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~---- 157 (436)
+..|.+++.+. .+|+||+ .||+.+|++ +|+..+ ..++||+.++. .+.+..+.++|..+++.| +..
T Consensus 56 ~~~l~~~l~~~~~~~v~hn~-k~d~~~l~~----~gi~~~--~~~~Dt~l~a~-ll~p~~~~~~l~~l~~~~l~~~~~~~ 127 (193)
T cd06139 56 LAALKPLLEDPSIKKVGQNL-KFDLHVLAN----HGIELR--GPAFDTMLASY-LLNPGRRRHGLDDLAERYLGHKTISF 127 (193)
T ss_pred HHHHHHHHhCCCCcEEeecc-HHHHHHHHH----CCCCCC--CCcccHHHHHH-HhCCCCCCCCHHHHHHHHhCCCCccH
Confidence 99999999864 7899999 999999864 576644 34799987765 556654356999999876 321
Q ss_pred --------------C-----CCCChHHHHHHHHHHHHHHHHHhhh
Q 013825 158 --------------Q-----QTHRSLDDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 158 --------------~-----~~HrALdDAraTa~VLk~L~~~l~l 183 (436)
. ..|.|..||.++..++..+.+++..
T Consensus 128 ~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 128 EDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 1235888899999999998887653
No 66
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=98.34 E-value=1.6e-05 Score=76.01 Aligned_cols=140 Identities=18% Similarity=0.259 Sum_probs=86.5
Q ss_pred CCcEEEEEEecCCCC----CCC--CCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCC
Q 013825 7 RSEIAFFDVETTVPT----RPG--QRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPT 80 (436)
Q Consensus 7 ~~~fV~fDLETTGl~----p~g--~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~ 80 (436)
+-+++.||+||++.. |.. ..+.|+.|+.. ..++. ..+ .++........+... .-+ ..+....+
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~--~~~~~---~~v-~~~~~~~~~~~~~~~--~~~---~~v~~~~~ 72 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA--GSDGL---KRV-LVLKREGVEGLEGLL--PEG---AEVEFFDS 72 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc--CCCCC---cEE-EEEecCCcccccccC--CCC---CeEEecCC
Confidence 457899999998521 211 23689999875 21211 112 122211100000000 001 11334467
Q ss_pred HHHHHHHHHHHHcC-CEEEEEccccchHHHHHHHHHHcCCC---CCC----------CCceeeHHHHHHHH------hcC
Q 013825 81 FADIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRP---APE----------PKGTIDSLALLTQR------FGR 140 (436)
Q Consensus 81 f~eVl~~f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~---~p~----------~~~~IDTl~Larr~------l~~ 140 (436)
-++++.+|.++++. .++||||...||+++|.+-+.++|++ .+. ....+|.+..++.. ++.
T Consensus 73 E~~lL~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~ 152 (204)
T cd05783 73 EKELIREAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGN 152 (204)
T ss_pred HHHHHHHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhcc
Confidence 88999999999983 58899999999999999999999987 211 23478888765531 222
Q ss_pred CCCCCCHHHHHHHh-CCC
Q 013825 141 RAGDMKMASLATYF-GLG 157 (436)
Q Consensus 141 ~~~~~kL~~LA~~f-GI~ 157 (436)
...+++|+++|+++ |..
T Consensus 153 ~~~~~~L~~Va~~~lg~~ 170 (204)
T cd05783 153 KYREYTLDAVAKALLGEG 170 (204)
T ss_pred ccccCcHHHHHHHhcCCC
Confidence 45799999999977 544
No 67
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=98.30 E-value=3.9e-05 Score=74.07 Aligned_cols=137 Identities=17% Similarity=0.180 Sum_probs=91.9
Q ss_pred CCcEEEEEEecCCC---CCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHH
Q 013825 7 RSEIAFFDVETTVP---TRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (436)
Q Consensus 7 ~~~fV~fDLETTGl---~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~e 83 (436)
.-+.+.||+||+.. .|....++|+.||++.-..+........-..+++.. .++ | ..+....+..+
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~--~~~-------~---~~v~~~~~E~e 73 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCA--PIV-------G---AQVFSFETEEE 73 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCC--CCC-------C---CEEEEECCHHH
Confidence 45689999999852 233467999999998765543222122111233222 221 1 12333568889
Q ss_pred HHHHHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCC--C-------------------------------CCce
Q 013825 84 IADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAP--E-------------------------------PKGT 127 (436)
Q Consensus 84 Vl~~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p--~-------------------------------~~~~ 127 (436)
.+..|.++++. .+++|||...||+++|.+-++++|++.. . ...+
T Consensus 74 LL~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~ 153 (230)
T cd05777 74 LLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQ 153 (230)
T ss_pred HHHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEe
Confidence 99999999984 5999999999999999999988876521 0 0135
Q ss_pred eeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC
Q 013825 128 IDSLALLTQRFGRRAGDMKMASLATYF-GLG 157 (436)
Q Consensus 128 IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~ 157 (436)
+|+..++++.+ .+.+|+|+++|+++ |..
T Consensus 154 iD~~~~~~~~~--kl~sy~L~~Va~~~Lg~~ 182 (230)
T cd05777 154 FDLLQVIQRDY--KLRSYSLNSVSAHFLGEQ 182 (230)
T ss_pred eeHHHHHHHhc--CcccCcHHHHHHHHhCCC
Confidence 68888877643 57899999999955 543
No 68
>PRK05755 DNA polymerase I; Provisional
Probab=98.23 E-value=1.5e-05 Score=90.72 Aligned_cols=134 Identities=16% Similarity=0.216 Sum_probs=96.5
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
...+++||+||+|+++ ..+.|+.|++ ...++ . ..+|.+.. +. .++++
T Consensus 314 ~~~~~a~DtEt~~l~~--~~~~i~~i~l-s~~~g--~-----~~~ip~~~-------------i~----------~~~l~ 360 (880)
T PRK05755 314 AAGLFAFDTETTSLDP--MQAELVGLSF-AVEPG--E-----AAYIPLDQ-------------LD----------REVLA 360 (880)
T ss_pred ccCeEEEEeccCCCCc--ccccEEEEEE-EeCCC--c-----EEEEeccc-------------cc----------HHHHH
Confidence 4578999999999987 5788988875 34333 1 12333211 11 15778
Q ss_pred HHHHHHcCC--EEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCCC-----
Q 013825 87 TVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLGQ----- 158 (436)
Q Consensus 87 ~f~efL~g~--vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~~----- 158 (436)
.|.+++.+. ..|+||+ .||+.+|.+ +|+..+ ..++||+-++ ..+.+.. .++|.+|++.| |...
T Consensus 361 ~l~~~L~d~~v~kV~HNa-kfDl~~L~~----~gi~~~--~~~~DT~iAa-~Ll~~~~-~~~L~~L~~~ylg~~~~~~~~ 431 (880)
T PRK05755 361 ALKPLLEDPAIKKVGQNL-KYDLHVLAR----YGIELR--GIAFDTMLAS-YLLDPGR-RHGLDSLAERYLGHKTISFEE 431 (880)
T ss_pred HHHHHHhCCCCcEEEecc-HhHHHHHHh----CCCCcC--CCcccHHHHH-HHcCCCC-CCCHHHHHHHHhCCCccchHH
Confidence 888888864 4799999 999999984 477654 3489998754 4565544 38999999987 4431
Q ss_pred ---------------CCCChHHHHHHHHHHHHHHHHHhh
Q 013825 159 ---------------QTHRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 159 ---------------~~HrALdDAraTa~VLk~L~~~l~ 182 (436)
..|.|..||.++..++..+.+++.
T Consensus 432 ~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 432 VAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred hcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 237899999999999999998763
No 69
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=98.18 E-value=2.3e-05 Score=74.30 Aligned_cols=127 Identities=14% Similarity=0.180 Sum_probs=84.7
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHH
Q 013825 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (436)
Q Consensus 9 ~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f 88 (436)
++++||+||+|.. .|+.||......+.+. .+.-.. ... |. .+.-.++-.+.+..|
T Consensus 4 ~~~~fDIE~~~~~------~i~~i~~~~~~~~~i~-------~~~~~~--~~~-------~~---~v~~~~~E~~lL~~f 58 (193)
T cd05784 4 KVVSLDIETSMDG------ELYSIGLYGEGQERVL-------MVGDPE--DDA-------PD---NIEWFADEKSLLLAL 58 (193)
T ss_pred cEEEEEeecCCCC------CEEEEEeecCCCCEEE-------EECCCC--CCC-------CC---EEEEECCHHHHHHHH
Confidence 6899999998752 7888887442222111 111111 110 11 123346788899999
Q ss_pred HHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCCCC-----------------------CceeeHHHHHHHHhcCCC
Q 013825 89 FDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPEP-----------------------KGTIDSLALLTQRFGRRA 142 (436)
Q Consensus 89 ~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~-----------------------~~~IDTl~Larr~l~~~~ 142 (436)
.++++. .+++|||...||+.+|.+-+..+|++.... ...+|++.+.++.. ..+
T Consensus 59 ~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~-~kl 137 (193)
T cd05784 59 IAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTAT-YHF 137 (193)
T ss_pred HHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHcc-CCC
Confidence 999984 489999999999999999999998875310 12788888776422 257
Q ss_pred CCCCHHHHHHHh-CCCCCCC
Q 013825 143 GDMKMASLATYF-GLGQQTH 161 (436)
Q Consensus 143 ~~~kL~~LA~~f-GI~~~~H 161 (436)
.+|+|+++|+++ |..+..|
T Consensus 138 ~sy~L~~Va~~~Lg~~K~~~ 157 (193)
T cd05784 138 ESFSLENVAQELLGEGKLIH 157 (193)
T ss_pred CcCCHHHHHHHHhCCCcccc
Confidence 899999999955 4444333
No 70
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.07 E-value=0.0001 Score=70.58 Aligned_cols=75 Identities=19% Similarity=0.271 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCC---------------CceeeHHHHHHHHhcCCCC
Q 013825 81 FADIADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEP---------------KGTIDSLALLTQRFGRRAG 143 (436)
Q Consensus 81 f~eVl~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~---------------~~~IDTl~Larr~l~~~~~ 143 (436)
-.+++..|.++++. .++|+||+..||+++|..-+..+|++.|.. .+.+|++.+++. +. ...
T Consensus 78 E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~-~~-~~~ 155 (208)
T cd05782 78 EKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAF-YG-ARA 155 (208)
T ss_pred HHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhc-cC-ccC
Confidence 36788899888874 589999999999999999999999965522 137899988653 32 246
Q ss_pred CCCHHHHHHHhCCC
Q 013825 144 DMKMASLATYFGLG 157 (436)
Q Consensus 144 ~~kL~~LA~~fGI~ 157 (436)
+++|..+|+++|++
T Consensus 156 ~~~L~~va~~lG~~ 169 (208)
T cd05782 156 RASLDLLAKLLGIP 169 (208)
T ss_pred CCCHHHHHHHhCCC
Confidence 89999999999996
No 71
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=98.04 E-value=0.00011 Score=70.88 Aligned_cols=126 Identities=15% Similarity=0.168 Sum_probs=89.8
Q ss_pred CCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHHHHHc--CCEEEEEccc
Q 013825 26 RFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILH--GRIWAGHNIL 103 (436)
Q Consensus 26 ~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~efL~--g~vLVaHNa~ 103 (436)
-++|+-|+++....++...+.++ -.+ .-..++++.+|.++++ ...+|+||+.
T Consensus 8 f~kIV~Is~~~~~~~~~~~v~s~---~~~-----------------------~~~E~~lL~~F~~~~~~~~p~LVs~NG~ 61 (209)
T PF10108_consen 8 FHKIVCISVVYADDDGQFKVKSL---GGP-----------------------DDDEKELLQDFFDLVEKYNPQLVSFNGR 61 (209)
T ss_pred CCCeEEEEEEEEecCCcEEEEec---cCC-----------------------CCCHHHHHHHHHHHHHhCCCeEEecCCc
Confidence 57899999997775522122221 111 1136778899999997 3579999999
Q ss_pred cchHHHHHHHHHHcCCCCCCC----------------CceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCC--------
Q 013825 104 RFDCARIREAFAEIGRPAPEP----------------KGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQ-------- 159 (436)
Q Consensus 104 ~FD~~fLr~a~~r~Gi~~p~~----------------~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~~~-------- 159 (436)
.||+++|....-.+|++.|.. ...+|++.+.. .++ .....+|+.||+.+|+|..
T Consensus 62 ~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~-~~g-~~~~~sLd~la~~lgiPgK~~idGs~V 139 (209)
T PF10108_consen 62 GFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLS-FYG-AKARTSLDELAALLGIPGKDDIDGSQV 139 (209)
T ss_pred cCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHh-ccC-ccccCCHHHHHHHcCCCCCCCCCHHHH
Confidence 999999999999999887641 23688988754 233 2347799999999999831
Q ss_pred ------------CCChHHHHHHHHHHHHHHHH
Q 013825 160 ------------THRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 160 ------------~HrALdDAraTa~VLk~L~~ 179 (436)
+.=-..||.+|+.||.++..
T Consensus 140 ~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 140 AELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11126799999999988654
No 72
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=98.02 E-value=0.0001 Score=72.69 Aligned_cols=161 Identities=20% Similarity=0.257 Sum_probs=95.4
Q ss_pred CcEEEEEEecCCCCCCC-------------------CCCcEEEEEEEEE-eCCcce----EeeeEEEEEcCCCCCCCChh
Q 013825 8 SEIAFFDVETTVPTRPG-------------------QRFAILEFGAILV-CPKKLE----ELHNYSTLVRPADPELISSL 63 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g-------------------~~~~IIEIGAV~V-~~~~le----vl~sfstLVrP~~~~~I~p~ 63 (436)
-+||.||+|.||+.... ....|+|+|...+ +.++.. .+..|+.++-|.........
T Consensus 22 ~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~~ 101 (262)
T PF04857_consen 22 ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQAS 101 (262)
T ss_dssp SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEHH
T ss_pred CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecch
Confidence 56999999999975532 2458999999999 333211 13344444334332112222
Q ss_pred h---HHhcCCCHHHH-hCCCCHHHHHH-----HHHHHH-------c-CCEEEEEccccchHHHHHHHHHHcCCCCCC---
Q 013825 64 S---VRCNGITPDAV-VSSPTFADIAD-----TVFDIL-------H-GRIWAGHNILRFDCARIREAFAEIGRPAPE--- 123 (436)
Q Consensus 64 a---~kltGIT~e~L-a~Ap~f~eVl~-----~f~efL-------~-g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~--- 123 (436)
+ .+-+|+.-+.+ .++.++....+ +...+- . ..+|||||. -+|+.+|-+.|-. +.|.
T Consensus 102 sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~-~~Dl~~l~~~f~~---~LP~t~~ 177 (262)
T PF04857_consen 102 SLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNG-LYDLMYLYKKFIG---PLPETLE 177 (262)
T ss_dssp HHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESST-HHHHHHHHHHHTT---S--SSHH
T ss_pred hHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeCh-HhHHHHHHHHhcC---CCCCCHH
Confidence 2 23568876665 45655544332 221111 1 379999999 9999998887643 3332
Q ss_pred ---------CCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC--------------------------CCCCChHHHHH
Q 013825 124 ---------PKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG--------------------------QQTHRSLDDVR 168 (436)
Q Consensus 124 ---------~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~--------------------------~~~HrALdDAr 168 (436)
...++||.-|+.. .. ....+|+.|++.++.. ...|.|-.||.
T Consensus 178 eF~~~~~~~FP~i~DtK~la~~-~~--~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~ 254 (262)
T PF04857_consen 178 EFKELLRELFPRIYDTKYLAEE-CP--GKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAY 254 (262)
T ss_dssp HHHHHHHHHSSSEEEHHHHHTS-TT--TS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHHH
T ss_pred HHHHHHHHHCcccccHHHHHHh-cc--ccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHHH
Confidence 1238888766542 11 2466899999999853 23899999999
Q ss_pred HHHHHHH
Q 013825 169 MNLEVLK 175 (436)
Q Consensus 169 aTa~VLk 175 (436)
+|+.+|.
T Consensus 255 mTg~~F~ 261 (262)
T PF04857_consen 255 MTGCVFI 261 (262)
T ss_dssp HHHHHHH
T ss_pred HHHHHHc
Confidence 9999985
No 73
>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=97.99 E-value=0.00034 Score=62.64 Aligned_cols=135 Identities=19% Similarity=0.252 Sum_probs=87.3
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
..+++.||+||+|..+... -..+..+-+..+ ....++.+... .... +++
T Consensus 19 ~~~~~a~D~E~~~~~~~~~---~~~~~~iq~~~~------~~~~i~~~~~~-~~~~---------------------~~~ 67 (176)
T PF01612_consen 19 NAKVLAFDTETTGLDPYSY---NPKIALIQLATG------EGCYIIDPIDL-GDNW---------------------ILD 67 (176)
T ss_dssp TTSEEEEEEEEETSTSTTS---SEEEEEEEEEES------CEEEEECGTTS-TTTT---------------------HHH
T ss_pred CCCeEEEEEEECCCCcccc---CCeEEEEEEecC------CCceeeeeccc-cccc---------------------hHH
Confidence 4569999999999876222 233444444444 11234444431 0000 667
Q ss_pred HHHHHHc--CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-C-CC----C
Q 013825 87 TVFDILH--GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-G-LG----Q 158 (436)
Q Consensus 87 ~f~efL~--g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-G-I~----~ 158 (436)
.+.+++. +...||||+ .||..+|.+. +|+... .++|+ .++...+..... ++|..|+..| | .. .
T Consensus 68 ~l~~ll~~~~i~kv~~n~-~~D~~~L~~~---~~i~~~---~~~D~-~l~~~~l~~~~~-~~L~~L~~~~l~~~~~~~~~ 138 (176)
T PF01612_consen 68 ALKELLEDPNIIKVGHNA-KFDLKWLYRS---FGIDLK---NVFDT-MLAAYLLDPTRS-YSLKDLAEEYLGNIDLDKKE 138 (176)
T ss_dssp HHHHHHTTTTSEEEESSH-HHHHHHHHHH---HTS--S---SEEEH-HHHHHHTTTSTT-SSHHHHHHHHHSEEE-GHCC
T ss_pred HHHHHHhCCCccEEEEEE-echHHHHHHH---hccccC---Cccch-hhhhhccccccc-ccHHHHHHHHhhhccCcHHH
Confidence 7888888 458999999 9999999886 577543 48999 566655555433 9999998866 6 32 1
Q ss_pred --CCC---C---------hHHHHHHHHHHHHHHHHHh
Q 013825 159 --QTH---R---------SLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 159 --~~H---r---------ALdDAraTa~VLk~L~~~l 181 (436)
... + |..||..+.++++.+..++
T Consensus 139 ~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 139 QMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp TTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred hhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 112 2 5669999999999988764
No 74
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=97.84 E-value=0.00069 Score=65.80 Aligned_cols=171 Identities=12% Similarity=0.049 Sum_probs=107.7
Q ss_pred CcEEEEEEecCC---CCCCCCCCcEEEEEEEEEeCCcceEe---eeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCH
Q 013825 8 SEIAFFDVETTV---PTRPGQRFAILEFGAILVCPKKLEEL---HNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (436)
Q Consensus 8 ~~fV~fDLETTG---l~p~g~~~~IIEIGAV~V~~~~levl---~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f 81 (436)
-+++.||+||.+ ..|....+.|+.|+.+.-+.+..... .....++.+... ..... .....+....+.-.++.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~-~~~~~~~~~~v~~~~~E 81 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKS-NASNG-RIRSGLSGIPVEVVESE 81 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccc-hhhhh-ccccCCCCCeEEEeCCH
Confidence 467899999875 23444789999999885554421111 111233443331 11000 00112333345556788
Q ss_pred HHHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCCC---------------------C-----------CCc
Q 013825 82 ADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAP---------------------E-----------PKG 126 (436)
Q Consensus 82 ~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p---------------------~-----------~~~ 126 (436)
.+.+.+|.+++. -.+++|||+..||+++|.+-++.+++... + ...
T Consensus 82 ~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi 161 (231)
T cd05778 82 LELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRH 161 (231)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEE
Confidence 888888888887 46999999999999999888877665321 0 012
Q ss_pred eeeHHHHHHHHhcCCCCCCCHHHHHH-HhCCCC--CCCChHHHHH------HHHHHHHHHHHHhh
Q 013825 127 TIDSLALLTQRFGRRAGDMKMASLAT-YFGLGQ--QTHRSLDDVR------MNLEVLKYCATVLF 182 (436)
Q Consensus 127 ~IDTl~Larr~l~~~~~~~kL~~LA~-~fGI~~--~~HrALdDAr------aTa~VLk~L~~~l~ 182 (436)
.+|++.++++.+ .+.+|+|+++|. ++|-.. -.|..+.+.. ....++.+|+++..
T Consensus 162 ~lD~~~~~r~~~--kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~ 224 (231)
T cd05778 162 ILNVWRLMRSEL--ALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVR 224 (231)
T ss_pred EeEhHHHHHHHc--CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHH
Confidence 568888877644 668999999999 456543 3566666653 55677777777654
No 75
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=97.70 E-value=0.00055 Score=70.67 Aligned_cols=157 Identities=17% Similarity=0.211 Sum_probs=102.9
Q ss_pred CCcEEEEEEecCCCC---CCCC--CCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCH
Q 013825 7 RSEIAFFDVETTVPT---RPGQ--RFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (436)
Q Consensus 7 ~~~fV~fDLETTGl~---p~g~--~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f 81 (436)
...+++||+||+... |... .+.|+.|+.+.-..+.............+.. .+ .|+. +......
T Consensus 2 ~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~--~~-------~~~~---~~~~~~E 69 (471)
T smart00486 2 PLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK--EI-------DGVE---VYEFNNE 69 (471)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC--CC-------CCCe---EEecCCH
Confidence 356899999998753 2212 5899999888877764322222222334433 22 2222 2222367
Q ss_pred HHHHHHHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCCC--------------------------------CCc
Q 013825 82 ADIADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE--------------------------------PKG 126 (436)
Q Consensus 82 ~eVl~~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~--------------------------------~~~ 126 (436)
.+.+..|.+++.. .+++|||...||+.+|...+..+++.... ...
T Consensus 70 ~~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~ 149 (471)
T smart00486 70 KELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRL 149 (471)
T ss_pred HHHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEE
Confidence 7888888888873 58999999889999999998877764320 124
Q ss_pred eeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCC---------------------ChHHHHHHHHHHHHHH
Q 013825 127 TIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTH---------------------RSLDDVRMNLEVLKYC 177 (436)
Q Consensus 127 ~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~-~~~H---------------------rALdDAraTa~VLk~L 177 (436)
.+|+..++++.+ .+.+++|+.+++++... .... --+.||..+.+++.++
T Consensus 150 ~~Dl~~~~~~~~--kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 150 VIDLYNLYKNKL--KLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEhHHHHHHHh--CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 789998887655 36899999999976432 2111 1155777788877775
No 76
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=97.69 E-value=0.00045 Score=68.39 Aligned_cols=131 Identities=17% Similarity=0.192 Sum_probs=86.4
Q ss_pred CCcEEEEEEecCCCCC---CCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHH
Q 013825 7 RSEIAFFDVETTVPTR---PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p---~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~e 83 (436)
.-.++.||+||..... ....++|+.|+++....+...........+.+.. .... ...+.-..+..+
T Consensus 156 ~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~--~~~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 156 PLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCD--SIED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSC--CTTC---------TTEEEEESSHHH
T ss_pred ccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCC--CCCC---------CcEEEEECCHHH
Confidence 4578999999988651 2368999999998876541111122222233333 1111 223444578889
Q ss_pred HHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCC--------CC-------------------------CCCce
Q 013825 84 IADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRP--------AP-------------------------EPKGT 127 (436)
Q Consensus 84 Vl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~--------~p-------------------------~~~~~ 127 (436)
.+..|.+++. -.+++|||...||+.+|.+-++.+|+. +. ....+
T Consensus 225 lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gr~~ 304 (325)
T PF03104_consen 225 LLEAFLDIIQEYDPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSRKFSRIDIPGRLV 304 (325)
T ss_dssp HHHHHHHHHHHHS-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCTTEEEEEETTSEE
T ss_pred HHHHHHHHHHhcCCcEEEEecccCCCHHHHHHHHHHhCccccccccccccceeEEeecccccccCCCcceeEEEECCChH
Confidence 9999999887 469999999999999999999988533 10 01247
Q ss_pred eeHHHHHHHHhcCCCCCCCHHHH
Q 013825 128 IDSLALLTQRFGRRAGDMKMASL 150 (436)
Q Consensus 128 IDTl~Larr~l~~~~~~~kL~~L 150 (436)
+|++.++++.+ ++.+|+|+++
T Consensus 305 ~D~~~~~~~~~--~l~sY~L~~V 325 (325)
T PF03104_consen 305 LDLYRLARKDY--KLDSYSLDNV 325 (325)
T ss_dssp EEHHHHHHHHS----SS-SHHHH
T ss_pred hHHHHHHHhhC--CCCCCCCCCC
Confidence 89999988766 6788999864
No 77
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.64 E-value=0.0012 Score=76.78 Aligned_cols=158 Identities=15% Similarity=0.174 Sum_probs=101.5
Q ss_pred CCcEEEEEEecCCCC----CCCCCCcEEEEEEEEEeCCcce-EeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCH
Q 013825 7 RSEIAFFDVETTVPT----RPGQRFAILEFGAILVCPKKLE-ELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (436)
Q Consensus 7 ~~~fV~fDLETTGl~----p~g~~~~IIEIGAV~V~~~~le-vl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f 81 (436)
.-+++.||+||.+.. |....+.||+||.+....|... ....+-...++.. ++ .| ..+....+.
T Consensus 263 plrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~c~--~i-------~g---~~V~~f~sE 330 (1054)
T PTZ00166 263 PLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECA--SI-------AG---ANVLSFETE 330 (1054)
T ss_pred CcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCccc--cC-------CC---ceEEEeCCH
Confidence 346899999998632 3335799999999876654211 1111111122111 11 22 223345678
Q ss_pred HHHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCC-C---------------------C-----------CC
Q 013825 82 ADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPA-P---------------------E-----------PK 125 (436)
Q Consensus 82 ~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~-p---------------------~-----------~~ 125 (436)
.+.+..|.+++. -.+++|||+..||+++|.+-++.+|+.. . + ..
T Consensus 331 ~eLL~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR 410 (1054)
T PTZ00166 331 KELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGR 410 (1054)
T ss_pred HHHHHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeE
Confidence 888999988887 4699999999999999999888876541 0 0 01
Q ss_pred ceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCCCC--CCC-------------------hHHHHHHHHHHHHHHH
Q 013825 126 GTIDSLALLTQRFGRRAGDMKMASLATYF-GLGQQ--THR-------------------SLDDVRMNLEVLKYCA 178 (436)
Q Consensus 126 ~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~~~--~Hr-------------------ALdDAraTa~VLk~L~ 178 (436)
..+|++.++++. ..+.+|+|++++.+| |.... .|. .+.||..+.+++.++.
T Consensus 411 ~~iDl~~~~~~~--~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 411 IQFDVMDLIRRD--YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred EEEEHHHHHHHh--cCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 367888887754 357899999999965 54321 111 2567777777776653
No 78
>PRK05762 DNA polymerase II; Reviewed
Probab=97.51 E-value=0.0023 Score=72.54 Aligned_cols=145 Identities=12% Similarity=0.148 Sum_probs=98.7
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
.-+++.||+||++. .+|+.||..-...+ .-..+.+.. ... .+.+...++-.+.+.
T Consensus 154 ~lrvlsfDIE~~~~------~~i~sI~~~~~~~~-------~vi~ig~~~--~~~----------~~~v~~~~sE~~LL~ 208 (786)
T PRK05762 154 PLKVVSLDIETSNK------GELYSIGLEGCGQR-------PVIMLGPPN--GEA----------LDFLEYVADEKALLE 208 (786)
T ss_pred CCeEEEEEEEEcCC------CceEEeeecCCCCC-------eEEEEECCC--CCC----------cceEEEcCCHHHHHH
Confidence 45799999999874 25878876411111 112233222 110 011445678889999
Q ss_pred HHHHHHcC---CEEEEEccccchHHHHHHHHHHcCCCCCC------------C------------CceeeHHHHHHHHhc
Q 013825 87 TVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE------------P------------KGTIDSLALLTQRFG 139 (436)
Q Consensus 87 ~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~------------~------------~~~IDTl~Larr~l~ 139 (436)
.|.+++.. .+++|||...||+++|.+-+..+|++... + ...+|++.++++.+
T Consensus 209 ~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~- 287 (786)
T PRK05762 209 KFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSAT- 287 (786)
T ss_pred HHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhh-
Confidence 99999984 59999999999999999999999876320 0 12789999887543
Q ss_pred CCCCCCCHHHHHHHhCCC-CCCCC----------------------hHHHHHHHHHHHHHH
Q 013825 140 RRAGDMKMASLATYFGLG-QQTHR----------------------SLDDVRMNLEVLKYC 177 (436)
Q Consensus 140 ~~~~~~kL~~LA~~fGI~-~~~Hr----------------------ALdDAraTa~VLk~L 177 (436)
..+.+++|+++|+.+... ...|+ .+.||..|.+++.++
T Consensus 288 ~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 288 WVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred ccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 357899999999987554 22222 367888888888743
No 79
>PHA02528 43 DNA polymerase; Provisional
Probab=97.45 E-value=0.0038 Score=71.57 Aligned_cols=163 Identities=13% Similarity=0.096 Sum_probs=98.1
Q ss_pred CCcEEEEEEecCC----CCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCC-CCCC-ChhhHHhcCCCHHHHhCCCC
Q 013825 7 RSEIAFFDVETTV----PTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPAD-PELI-SSLSVRCNGITPDAVVSSPT 80 (436)
Q Consensus 7 ~~~fV~fDLETTG----l~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~-~~~I-~p~a~kltGIT~e~La~Ap~ 80 (436)
.-+++.||+||+. ++|....+.|+.||.. +.+. ..+..+.-+.. ++.. .+.. ...-...-.+....+
T Consensus 105 ~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~--~~~~----~~~~v~~~~~~~~~~~~~~~~-~~~~~~~v~~~~~~s 177 (881)
T PHA02528 105 KIRIANLDIEVTAEDGFPDPEEAKYEIDAITHY--DSID----DRFYVFDLGSVEEWDAKGDEV-PQEILDKVVYMPFDT 177 (881)
T ss_pred CccEEEEEEEECCCCCCCCcccCCCcEEEEEEe--cCCC----CEEEEEEecCcccccccCCcc-cccccCCeeEEEcCC
Confidence 4578999999976 2221125689999872 2221 22222321111 0000 0000 000011111223567
Q ss_pred HHHHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHH-cCCCC-------CC--------------------CCceee
Q 013825 81 FADIADTVFDILH---GRIWAGHNILRFDCARIREAFAE-IGRPA-------PE--------------------PKGTID 129 (436)
Q Consensus 81 f~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r-~Gi~~-------p~--------------------~~~~ID 129 (436)
-.+.+..|.+|+. -.+++|||...||+++|.+-+++ +|+.. .. ....+|
T Consensus 178 E~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD 257 (881)
T PHA02528 178 EREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILD 257 (881)
T ss_pred HHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEe
Confidence 8899999999996 36999999999999999888875 45331 10 012567
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHH-HhCCCCCCC------------------ChHHHHHHHHHHHHH
Q 013825 130 SLALLTQRFGRRAGDMKMASLAT-YFGLGQQTH------------------RSLDDVRMNLEVLKY 176 (436)
Q Consensus 130 Tl~Larr~l~~~~~~~kL~~LA~-~fGI~~~~H------------------rALdDAraTa~VLk~ 176 (436)
.+.+++......+.+|+|+++|+ +||.....| =.+.||+.+.+++.+
T Consensus 258 ~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 258 YLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 78877753334678999999999 478763222 236788888888877
No 80
>cd05776 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are
Probab=97.13 E-value=0.0045 Score=60.20 Aligned_cols=145 Identities=14% Similarity=0.172 Sum_probs=93.2
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcc-------eEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKL-------EELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 10 fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~l-------evl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
++.|-+-|.--.. ....+|+.|+++....=.. .-...+.++++|......++...+.-......+.-..+..
T Consensus 5 v~sls~~T~~n~k-~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~E~ 83 (234)
T cd05776 5 VMSLSIKTVLNSK-TNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENER 83 (234)
T ss_pred EEEEEeEEEecCc-CCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCCHH
Confidence 4555666643222 2368999998887652110 1123456677887631222222222222223355567889
Q ss_pred HHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCC-CC-------------------------CCceeeHHHH
Q 013825 83 DIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPA-PE-------------------------PKGTIDSLAL 133 (436)
Q Consensus 83 eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~-p~-------------------------~~~~IDTl~L 133 (436)
+.+..|.++++ -.+++|||...||+.+|.+-+..+|++. .. ..-.+|+...
T Consensus 84 ~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~ 163 (234)
T cd05776 84 ALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLS 163 (234)
T ss_pred HHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHH
Confidence 99999999987 4699999999999999999988877652 10 0125778887
Q ss_pred HHHHhcCCCCCCCHHHHHH-HhCCC
Q 013825 134 LTQRFGRRAGDMKMASLAT-YFGLG 157 (436)
Q Consensus 134 arr~l~~~~~~~kL~~LA~-~fGI~ 157 (436)
++..+ + ..+|+|+++|+ ++|..
T Consensus 164 ~k~~~-~-~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 164 AKELI-R-CKSYDLTELSQQVLGIE 186 (234)
T ss_pred HHHHh-C-CCCCChHHHHHHHhCcC
Confidence 76543 3 68999999999 66765
No 81
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=96.98 E-value=0.0089 Score=63.64 Aligned_cols=120 Identities=14% Similarity=0.154 Sum_probs=84.0
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
....++||+||+. ...-...||++..+++.. .+.|..++.... ....+++.
T Consensus 283 ~~~~~ffDiEt~P-----~~~~~yL~G~~~~~~~~~--~~~~~~fla~~~----------------------~~E~~~~~ 333 (457)
T TIGR03491 283 APGELIFDIESDP-----DENLDYLHGFLVVDKGQE--NEKYRPFLAEDP----------------------NTEELAWQ 333 (457)
T ss_pred CCccEEEEecCCC-----CCCCceEEEEEEecCCCC--CcceeeeecCCc----------------------hHHHHHHH
Confidence 3567899999983 245677899977665421 123544443222 12345677
Q ss_pred HHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCCCC----CCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 013825 87 TVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAPE----PKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG 157 (436)
Q Consensus 87 ~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~----~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~ 157 (436)
+|.+|+. +..++.|| .|....|++.+.++|.+... ..+++|+....++.+.-..++|+|.+++.++|..
T Consensus 334 ~f~~~l~~~~~~~i~hY~--~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~~ 409 (457)
T TIGR03491 334 QFLQLLQSYPDAPIYHYG--ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGFE 409 (457)
T ss_pred HHHHHHHHCCCCeEEeeC--HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCcc
Confidence 7777776 44677777 59999999999999876311 1258999998887664455899999999999987
No 82
>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=96.85 E-value=0.019 Score=54.25 Aligned_cols=143 Identities=14% Similarity=0.102 Sum_probs=87.8
Q ss_pred CCCCcEEEEEEecCCCCCC--CCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 5 QDRSEIAFFDVETTVPTRP--GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~--g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
.....++.||+|+++.... ...-.++||+. .+. ..+|++.. +.. ..-+
T Consensus 19 l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat----~~~-------~~lid~~~---~~~----------------~~~~ 68 (193)
T cd06146 19 LEAGRVVGIDSEWKPSFLGDSDPRVAILQLAT----EDE-------VFLLDLLA---LEN----------------LESE 68 (193)
T ss_pred hccCCEEEEECccCCCccCCCCCCceEEEEec----CCC-------EEEEEchh---ccc----------------cchH
Confidence 4567899999999865431 13457888873 221 22444433 110 0111
Q ss_pred HHHHHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCC---------CCCCCHHHHH
Q 013825 83 DIADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRR---------AGDMKMASLA 151 (436)
Q Consensus 83 eVl~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~---------~~~~kL~~LA 151 (436)
...+.+.+++.+ -+-|||++ ++|..+|.+.+...+........++|+..+++...... ...++|..|+
T Consensus 69 ~~~~~L~~ll~d~~i~KVg~~~-~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~ 147 (193)
T cd06146 69 DWDRLLKRLFEDPDVLKLGFGF-KQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLV 147 (193)
T ss_pred HHHHHHHHHhCCCCeeEEEech-HHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHH
Confidence 222345666664 34599999 99999998766432110112346899998877433221 2467999999
Q ss_pred HHh-CCC--C---------------CCCChHHHHHHHHHHHHHHH
Q 013825 152 TYF-GLG--Q---------------QTHRSLDDVRMNLEVLKYCA 178 (436)
Q Consensus 152 ~~f-GI~--~---------------~~HrALdDAraTa~VLk~L~ 178 (436)
+.+ |.+ + +-+=|..||..+.+|+.+|.
T Consensus 148 ~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 148 QEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 976 432 1 23568899999999998865
No 83
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.79 E-value=0.027 Score=58.49 Aligned_cols=142 Identities=18% Similarity=0.154 Sum_probs=93.3
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
...++.+|+||.|..+ ..+ +.|.|-+..+. . ..+|+|..+ + .+. +
T Consensus 16 ~~~~iAiDTEf~r~~t--~~p---~LcLIQi~~~e-----~-~~lIdpl~~--~---------------~d~-------~ 60 (361)
T COG0349 16 GSKAIAIDTEFMRLRT--YYP---RLCLIQISDGE-----G-ASLIDPLAG--I---------------LDL-------P 60 (361)
T ss_pred CCCceEEecccccccc--cCC---ceEEEEEecCC-----C-ceEeccccc--c---------------ccc-------c
Confidence 4679999999999876 444 34566666652 1 457887762 1 111 1
Q ss_pred HHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--CC--
Q 013825 87 TVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--QQ-- 159 (436)
Q Consensus 87 ~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~--~~-- 159 (436)
-|...+.+ .+=|=|++ +||+.+|...| |+-+ .+++||.- +.+..+... +++|.+|++.+ |+. +.
T Consensus 61 ~l~~Ll~d~~v~KIfHaa-~~DL~~l~~~~---g~~p---~plfdTqi-Aa~l~g~~~-~~gl~~Lv~~ll~v~ldK~~q 131 (361)
T COG0349 61 PLVALLADPNVVKIFHAA-RFDLEVLLNLF---GLLP---TPLFDTQI-AAKLAGFGT-SHGLADLVEELLGVELDKSEQ 131 (361)
T ss_pred hHHHHhcCCceeeeeccc-cccHHHHHHhc---CCCC---CchhHHHH-HHHHhCCcc-cccHHHHHHHHhCCccccccc
Confidence 23333332 23377999 99999998877 4432 23799975 444554433 89999999865 665 21
Q ss_pred ----CCC---------hHHHHHHHHHHHHHHHHHhhhhcCcchhhh
Q 013825 160 ----THR---------SLDDVRMNLEVLKYCATVLFLESSLPDIFT 192 (436)
Q Consensus 160 ----~Hr---------ALdDAraTa~VLk~L~~~l~le~slp~l~~ 192 (436)
.+| |..||....+++.++.+++..+.-.+.+..
T Consensus 132 ~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~~ 177 (361)
T COG0349 132 RSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAED 177 (361)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHH
Confidence 122 689999999999999998876665555443
No 84
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=96.64 E-value=0.03 Score=54.55 Aligned_cols=172 Identities=16% Similarity=0.125 Sum_probs=107.5
Q ss_pred CCcEEEEEEecCCC--CCCC-----------------CCCcEEEEEEEEEeCCcceE---eeeEEEEE---cCC-C-CCC
Q 013825 7 RSEIAFFDVETTVP--TRPG-----------------QRFAILEFGAILVCPKKLEE---LHNYSTLV---RPA-D-PEL 59 (436)
Q Consensus 7 ~~~fV~fDLETTGl--~p~g-----------------~~~~IIEIGAV~V~~~~lev---l~sfstLV---rP~-~-~~~ 59 (436)
+-+||++|+|--|. .|.+ ..-.+||+|.-..+.++... .+.++.-. ++. + ...
T Consensus 23 ~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~a~ 102 (239)
T KOG0304|consen 23 DYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMYAQ 102 (239)
T ss_pred hCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCCCCCceeEEecccCCchhhccch
Confidence 45799999998883 1111 23479999999998643222 11333222 222 2 012
Q ss_pred CChhhHHhcCCCHHHHh-CCCCHHHHHHHHHH---HHc-CCEEEEEccccchHHHHHHHHHHcCCCCCC----------C
Q 013825 60 ISSLSVRCNGITPDAVV-SSPTFADIADTVFD---ILH-GRIWAGHNILRFDCARIREAFAEIGRPAPE----------P 124 (436)
Q Consensus 60 I~p~a~kltGIT~e~La-~Ap~f~eVl~~f~e---fL~-g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~----------~ 124 (436)
-+-+..+-+||.-+-.+ .+....+..+.+.. .+. .-.||.+.. .+|.++|-+.+-...+|-.. .
T Consensus 103 ~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs-~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~f 181 (239)
T KOG0304|consen 103 DSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHS-GYDFGYLLKILTGKPLPETEEEFFEIVRQLF 181 (239)
T ss_pred hhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeec-cchHHHHHHHHcCCCCcchHHHHHHHHHHHc
Confidence 22345567899887774 34444443333322 222 458999887 89999998877654333211 1
Q ss_pred CceeeHHHHHHHHhcCCCCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHH
Q 013825 125 KGTIDSLALLTQRFGRRAGDMKMASLATYFGLG--QQTHRSLDDVRMNLEVLKYCATV 180 (436)
Q Consensus 125 ~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI~--~~~HrALdDAraTa~VLk~L~~~ 180 (436)
..++|+..+++..-+. .-...|..+|..+++. ..+|.|-.|++.|+.+|.++.+.
T Consensus 182 p~vYDiK~l~~~c~~~-~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 182 PFVYDVKYLMKFCEGL-SLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred chhhhHHHHHHhhhhh-hhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHhc
Confidence 2467776665432121 1256899999999999 57999999999999999997653
No 85
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=96.50 E-value=0.019 Score=62.07 Aligned_cols=144 Identities=13% Similarity=0.098 Sum_probs=84.4
Q ss_pred CCcEEEEEEecCCCCCCC---CCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhc-C-CCHHHHhCCCCH
Q 013825 7 RSEIAFFDVETTVPTRPG---QRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCN-G-ITPDAVVSSPTF 81 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g---~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~klt-G-IT~e~La~Ap~f 81 (436)
.-+++.+|+|+|+..-|. ...+|.-|+-.....+ -+.|..+.-.+..+.+.+....++ + +..-.+-..++-
T Consensus 105 ~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~sE 180 (498)
T PHA02524 105 DVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNG----KKTYYIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFEDE 180 (498)
T ss_pred hceEEEEEEEecCCCCCChhhcCCceEEEEeeecccC----CccEEEEeccccccCCCcccccccccccCCeEEEEeCCH
Confidence 356899999998753221 2344555544433311 123433321111112221111110 1 111122446788
Q ss_pred HHHHHHHHHHHcC---CEEEEEccccchHHHHHHHHHH-cCCC-------CCC-------------------CCceeeHH
Q 013825 82 ADIADTVFDILHG---RIWAGHNILRFDCARIREAFAE-IGRP-------APE-------------------PKGTIDSL 131 (436)
Q Consensus 82 ~eVl~~f~efL~g---~vLVaHNa~~FD~~fLr~a~~r-~Gi~-------~p~-------------------~~~~IDTl 131 (436)
.+.+.+|.+|+.. .+++|||+..||+++|.+-++. +|+. +-. ....+|.+
T Consensus 181 ~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl~ 260 (498)
T PHA02524 181 VDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDYM 260 (498)
T ss_pred HHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeEHH
Confidence 9999999999984 6999999999999998888764 6653 100 01257888
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHh
Q 013825 132 ALLTQRFGRRAGDMKMASLATYF 154 (436)
Q Consensus 132 ~Larr~l~~~~~~~kL~~LA~~f 154 (436)
.++++.-...+.+|+|++++..+
T Consensus 261 ~l~kk~s~~~l~sYsL~~Vs~~~ 283 (498)
T PHA02524 261 DVFKKFSFTPMPDYKLGNVGYRE 283 (498)
T ss_pred HHHHHhhhccCCCCCHHHHHHHh
Confidence 88874313467899999998744
No 86
>PRK10829 ribonuclease D; Provisional
Probab=96.22 E-value=0.17 Score=53.03 Aligned_cols=140 Identities=17% Similarity=0.112 Sum_probs=90.0
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHH
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl 85 (436)
....+++||+|+.+...-...-.+|||+ .+. -..+|+|-. +.. +
T Consensus 20 ~~~~~lalDtEf~~~~ty~~~l~LiQl~-----~~~------~~~LiD~l~---~~d----------------------~ 63 (373)
T PRK10829 20 RAFPAIALDTEFVRTRTYYPQLGLIQLY-----DGE------QLSLIDPLG---ITD----------------------W 63 (373)
T ss_pred hcCCeEEEecccccCccCCCceeEEEEe-----cCC------ceEEEecCC---ccc----------------------h
Confidence 4567899999999876411124455554 221 124777665 110 2
Q ss_pred HHHHHHHcCC--EEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--C--
Q 013825 86 DTVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--Q-- 158 (436)
Q Consensus 86 ~~f~efL~g~--vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~--~-- 158 (436)
..|.+++.+. +-|.|++ ++|+.+|.+. +|+.+ ..++||.-. ...++.. ..++|..|++.+ |+. +
T Consensus 64 ~~L~~ll~~~~ivKV~H~~-~~Dl~~l~~~---~g~~p---~~~fDTqia-a~~lg~~-~~~gl~~Lv~~~lgv~ldK~~ 134 (373)
T PRK10829 64 SPFKALLRDPQVTKFLHAG-SEDLEVFLNA---FGELP---QPLIDTQIL-AAFCGRP-LSCGFASMVEEYTGVTLDKSE 134 (373)
T ss_pred HHHHHHHcCCCeEEEEeCh-HhHHHHHHHH---cCCCc---CCeeeHHHH-HHHcCCC-ccccHHHHHHHHhCCccCccc
Confidence 3455566643 3479999 9999998654 36643 348999754 4455532 257899988754 764 1
Q ss_pred -------------CCCChHHHHHHHHHHHHHHHHHhhhhcCcchh
Q 013825 159 -------------QTHRSLDDVRMNLEVLKYCATVLFLESSLPDI 190 (436)
Q Consensus 159 -------------~~HrALdDAraTa~VLk~L~~~l~le~slp~l 190 (436)
+-+=|..||..+..++.++.+.+....-+.++
T Consensus 135 ~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~~~w~ 179 (373)
T PRK10829 135 SRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGWLPAA 179 (373)
T ss_pred ccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHH
Confidence 12447899999999999999887654544443
No 87
>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=95.97 E-value=0.11 Score=47.17 Aligned_cols=129 Identities=21% Similarity=0.277 Sum_probs=82.6
Q ss_pred CCcEEEEEEecCCCCC--CCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 7 RSEIAFFDVETTVPTR--PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p--~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
...++.||+|+++... ....-.++||+. ++ ...++++... ...
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~~----~~-------~~~l~~~~~~------------------------~~~ 61 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLAT----ES-------RCLLFQLAHM------------------------DKL 61 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEec----CC-------cEEEEEhhhh------------------------hcc
Confidence 6789999999998653 113466777762 22 1235554441 111
Q ss_pred HHHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC-C--
Q 013825 85 ADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG-Q-- 158 (436)
Q Consensus 85 l~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~-~-- 158 (436)
.+.|.+++.+ ...|+|++ .+|+..|.+. +|+... .++|+..++. .+.+.....+|..+++.| |.. .
T Consensus 62 ~~~l~~ll~~~~i~kv~~~~-k~D~~~L~~~---~g~~~~---~~~Dl~~aa~-ll~~~~~~~~l~~l~~~~l~~~~~k~ 133 (170)
T cd06141 62 PPSLKQLLEDPSILKVGVGI-KGDARKLARD---FGIEVR---GVVDLSHLAK-RVGPRRKLVSLARLVEEVLGLPLSKP 133 (170)
T ss_pred cHHHHHHhcCCCeeEEEeee-HHHHHHHHhH---cCCCCC---CeeeHHHHHH-HhCCCcCCccHHHHHHHHcCcccCCC
Confidence 2345566653 45699999 9999988643 466532 3699987655 455433346999999987 542 1
Q ss_pred ----------------CCCChHHHHHHHHHHHHHHH
Q 013825 159 ----------------QTHRSLDDVRMNLEVLKYCA 178 (436)
Q Consensus 159 ----------------~~HrALdDAraTa~VLk~L~ 178 (436)
+-|=|..||..+.+++..+.
T Consensus 134 k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 134 KKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 13457889999998888764
No 88
>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=95.94 E-value=0.13 Score=46.81 Aligned_cols=129 Identities=19% Similarity=0.153 Sum_probs=82.0
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHH
Q 013825 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~ 86 (436)
...++.||+|+.........-.++||+. ..+. ..++++..... ..+
T Consensus 12 ~~~~ig~D~E~~~~~~~~~~~~liQl~~---~~~~-------~~l~d~~~~~~------------------------~~~ 57 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYYGEVALIQLCV---SEEK-------CYLFDPLSLSV------------------------DWQ 57 (161)
T ss_pred CCCEEEEECCccCCCCCCCceEEEEEEE---CCCC-------EEEEecccCcc------------------------CHH
Confidence 6789999999998754222456677754 1121 23555444100 123
Q ss_pred HHHHHHcCC--EEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--C---
Q 013825 87 TVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--Q--- 158 (436)
Q Consensus 87 ~f~efL~g~--vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~--~--- 158 (436)
.+.+++.+. +.|+|++ ..|+..|.+. +|+... .++|+...+. .+++. ...+|+.+++.| |.. +
T Consensus 58 ~L~~lL~d~~i~Kvg~~~-k~D~~~L~~~---~gi~~~---~~~D~~~aa~-ll~~~-~~~~L~~l~~~~lg~~l~K~~~ 128 (161)
T cd06129 58 GLKMLLENPSIVKALHGI-EGDLWKLLRD---FGEKLQ---RLFDTTIAAN-LKGLP-ERWSLASLVEHFLGKTLDKSIS 128 (161)
T ss_pred HHHHHhCCCCEEEEEecc-HHHHHHHHHH---cCCCcc---cHhHHHHHHH-HhCCC-CCchHHHHHHHHhCCCCCccce
Confidence 455566643 5699999 9999888643 466532 3689987544 55543 356899999976 653 0
Q ss_pred ------------CCCChHHHHHHHHHHHHHHH
Q 013825 159 ------------QTHRSLDDVRMNLEVLKYCA 178 (436)
Q Consensus 159 ------------~~HrALdDAraTa~VLk~L~ 178 (436)
+-|=|..||..+.+++.++.
T Consensus 129 ~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 129 CADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 24668889999999988753
No 89
>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=95.68 E-value=0.081 Score=45.76 Aligned_cols=66 Identities=17% Similarity=0.297 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHcCC--EEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhC
Q 013825 82 ADIADTVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFG 155 (436)
Q Consensus 82 ~eVl~~f~efL~g~--vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fG 155 (436)
..+.+.+.+++.+. ..|+||+ .||+.+|.+. +...+ ..++||+-++ ..+.+...+++|+.+++.|.
T Consensus 40 ~~~~~~l~~~l~~~~~~~v~~~~-k~d~~~L~~~----~~~~~--~~~~D~~~~a-yll~~~~~~~~l~~l~~~~l 107 (155)
T cd00007 40 EEDLEALKELLEDEDITKVGHDA-KFDLVVLARD----GIELP--GNIFDTMLAA-YLLNPGEGSHSLDDLAKEYL 107 (155)
T ss_pred HHHHHHHHHHHcCCCCcEEeccH-HHHHHHHHHC----CCCCC--CCcccHHHHH-HHhCCCCCcCCHHHHHHHHc
Confidence 45666788888753 5899999 9999998643 44333 3479997654 46666542469999999873
No 90
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=95.63 E-value=0.0074 Score=68.27 Aligned_cols=160 Identities=20% Similarity=0.274 Sum_probs=100.9
Q ss_pred CCCcEEEEEEecCCCCC-------CCCCCcEE----EEEEEEEeCCc--ceEeeeEEEEEcCCCCCCCChhhHHhcCCCH
Q 013825 6 DRSEIAFFDVETTVPTR-------PGQRFAIL----EFGAILVCPKK--LEELHNYSTLVRPADPELISSLSVRCNGITP 72 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p-------~g~~~~II----EIGAV~V~~~~--levl~sfstLVrP~~~~~I~p~a~kltGIT~ 72 (436)
...++|.+|-|..-++. .|...-|= .+|-|.+-.|. ++-+-=-.-||--.+ .+..+.++..||-.
T Consensus 908 k~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d--~VvDYLTqySGI~P 985 (1118)
T KOG1275|consen 908 KSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDD--KVVDYLTQYSGIKP 985 (1118)
T ss_pred CCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchh--HHHHHHHHhcCCCc
Confidence 34678999998877654 11111111 23333322221 111111112444444 67788999999999
Q ss_pred HHHhCC------CCHHHHHHHHHHHHc-CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCC
Q 013825 73 DAVVSS------PTFADIADTVFDILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDM 145 (436)
Q Consensus 73 e~La~A------p~f~eVl~~f~efL~-g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~ 145 (436)
.+|... .++.-+..++.=.++ |.++|||.. .-|...| ++-.|..+ ++||+.+.+ + +.....
T Consensus 986 GDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL-~nDFrvI-------Ni~Vp~~Q-iiDTv~lf~--~-~s~R~L 1053 (1118)
T KOG1275|consen 986 GDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGL-QNDFRVI-------NIHVPEEQ-IIDTVTLFR--L-GSQRML 1053 (1118)
T ss_pred cccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccc-cccceEE-------EEecChhh-heeeeEEEe--c-ccccEE
Confidence 998432 355666677666666 899999998 6665444 55545443 899987643 2 222345
Q ss_pred CHHHHHHHh-CCC--CCCCChHHHHHHHHHHHHHHHH
Q 013825 146 KMASLATYF-GLG--QQTHRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 146 kL~~LA~~f-GI~--~~~HrALdDAraTa~VLk~L~~ 179 (436)
+|.-||.++ |-. ..+|++..||+.++++|++.++
T Consensus 1054 SLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1054 SLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred EHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHH
Confidence 899999877 433 5799999999999999998765
No 91
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.62 E-value=0.45 Score=56.60 Aligned_cols=141 Identities=13% Similarity=0.073 Sum_probs=94.7
Q ss_pred cEEEEEEe--cCCCCCCCCCCcEEEEEEEEEeCCcc------e-EeeeEEEEEcCCCCCCCChh-hHHhcCCCHHHHhCC
Q 013825 9 EIAFFDVE--TTVPTRPGQRFAILEFGAILVCPKKL------E-ELHNYSTLVRPADPELISSL-SVRCNGITPDAVVSS 78 (436)
Q Consensus 9 ~fV~fDLE--TTGl~p~g~~~~IIEIGAV~V~~~~l------e-vl~sfstLVrP~~~~~I~p~-a~kltGIT~e~La~A 78 (436)
+++++|+- +..++. ...+++.|+++....... . ....+...++|.. ..+|.. .....|+....|..-
T Consensus 505 Pl~vLdFsi~SlyPsi--~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~-~~~p~~~~~~~~~~~~~~L~~~ 581 (1172)
T TIGR00592 505 PLVVLDFSMKSLNPSI--IRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKD-CSFPLDLKGEFPGKKPSLVEDL 581 (1172)
T ss_pred CeEEEEeeeEEecCcc--ccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCC-CCCCchhhhhhhccCCcEEEEe
Confidence 46666555 544433 467899998888765211 0 1123444556632 123322 223456666667777
Q ss_pred CCHHHHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCCC--------------------CCCceeeHHHHHH
Q 013825 79 PTFADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAP--------------------EPKGTIDSLALLT 135 (436)
Q Consensus 79 p~f~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p--------------------~~~~~IDTl~Lar 135 (436)
.+-.+.+..|+++++ -.+++|||...||+.+|..-+.+++++.- ...-++|+...++
T Consensus 582 ~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k 661 (1172)
T TIGR00592 582 ATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAK 661 (1172)
T ss_pred cCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHH
Confidence 888999999999986 46999999999999999998888877631 1123678888876
Q ss_pred HHhcCCCCCCCHHHHHHHh
Q 013825 136 QRFGRRAGDMKMASLATYF 154 (436)
Q Consensus 136 r~l~~~~~~~kL~~LA~~f 154 (436)
..+ ...+|+|+++++.+
T Consensus 662 ~~~--~~~sy~L~~v~~~~ 678 (1172)
T TIGR00592 662 ELI--RCKSYDLSELVQQI 678 (1172)
T ss_pred HHh--CcCCCCHHHHHHHH
Confidence 655 36899999999966
No 92
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=95.54 E-value=0.22 Score=56.87 Aligned_cols=131 Identities=15% Similarity=0.134 Sum_probs=87.1
Q ss_pred CCCcEEEEEEecCCCCC---CCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHH
Q 013825 6 DRSEIAFFDVETTVPTR---PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p---~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~ 82 (436)
..-++++||+||.+... ++..+.++.|+...-..+... ..+.. . ...|.. +....+-.
T Consensus 152 p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~--------~~~~~--~------~~~~~~---v~~~~~e~ 212 (792)
T COG0417 152 PPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI--------EVFIY--T------SGEGFS---VEVVISEA 212 (792)
T ss_pred CCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc--------ccccc--c------CCCCce---eEEecCHH
Confidence 34678999999988432 224677888866655444221 11111 0 111111 45556678
Q ss_pred HHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCCC---------------C---CCceeeHHHHHHHHhcCC
Q 013825 83 DIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAP---------------E---PKGTIDSLALLTQRFGRR 141 (436)
Q Consensus 83 eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p---------------~---~~~~IDTl~Larr~l~~~ 141 (436)
+++..|.+++. ..+++|||...||+.+|.+-+.++|++.. . ....+|....++. -...
T Consensus 213 e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~-~~~~ 291 (792)
T COG0417 213 ELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRR-RPLN 291 (792)
T ss_pred HHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhh-hhcc
Confidence 88889988886 56999999988999999999999998765 1 1246888887663 1124
Q ss_pred CCCCCHHHHHHHhCC
Q 013825 142 AGDMKMASLATYFGL 156 (436)
Q Consensus 142 ~~~~kL~~LA~~fGI 156 (436)
+..++|+..++.+..
T Consensus 292 ~~~ysl~~v~~~~l~ 306 (792)
T COG0417 292 LKSYSLEAVSEALLG 306 (792)
T ss_pred cccccHHHHHHHhcc
Confidence 678999999776644
No 93
>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=95.26 E-value=0.69 Score=48.14 Aligned_cols=138 Identities=16% Similarity=0.108 Sum_probs=85.7
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHH
Q 013825 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl 85 (436)
....++.||+|+.....-...-.++||+. ++ ...+|+|-.. . .+
T Consensus 16 ~~~~~ia~DtE~~~~~~y~~~l~LiQia~----~~-------~~~liD~~~~--~-----------------------~~ 59 (367)
T TIGR01388 16 RTFPFVALDTEFVRERTFWPQLGLIQVAD----GE-------QLALIDPLVI--I-----------------------DW 59 (367)
T ss_pred hcCCEEEEeccccCCCCCCCcceEEEEee----CC-------eEEEEeCCCc--c-----------------------cH
Confidence 34679999999988754111235566642 22 1236766541 0 02
Q ss_pred HHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--CC-
Q 013825 86 DTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--QQ- 159 (436)
Q Consensus 86 ~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~--~~- 159 (436)
..|.+++.+ .+.|+|++ .+|+.+|...+ ...+ ..++||+- +...+++.. .+++..|++.| |+. +.
T Consensus 60 ~~L~~lL~d~~i~KV~h~~-k~Dl~~L~~~~----~~~~--~~~fDtql-Aa~lL~~~~-~~~l~~Lv~~~Lg~~l~K~~ 130 (367)
T TIGR01388 60 SPLKELLRDESVVKVLHAA-SEDLEVFLNLF----GELP--QPLFDTQI-AAAFCGFGM-SMGYAKLVQEVLGVELDKSE 130 (367)
T ss_pred HHHHHHHCCCCceEEEeec-HHHHHHHHHHh----CCCC--CCcccHHH-HHHHhCCCC-CccHHHHHHHHcCCCCCccc
Confidence 334455553 45799999 99999986542 2233 23799975 444666543 36899998765 653 11
Q ss_pred -----CCC---------hHHHHHHHHHHHHHHHHHhhhhcCcc
Q 013825 160 -----THR---------SLDDVRMNLEVLKYCATVLFLESSLP 188 (436)
Q Consensus 160 -----~Hr---------ALdDAraTa~VLk~L~~~l~le~slp 188 (436)
..+ |..||..+..++..+.+++....-+.
T Consensus 131 ~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~g~~~ 173 (367)
T TIGR01388 131 SRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEESGRLA 173 (367)
T ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHH
Confidence 133 78889999999999888876544433
No 94
>PHA03036 DNA polymerase; Provisional
Probab=95.09 E-value=0.44 Score=55.51 Aligned_cols=166 Identities=10% Similarity=-0.000 Sum_probs=96.1
Q ss_pred CcEEEEEEecCCCC--CCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCC-HHHH--------h
Q 013825 8 SEIAFFDVETTVPT--RPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGIT-PDAV--------V 76 (436)
Q Consensus 8 ~~fV~fDLETTGl~--p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT-~e~L--------a 76 (436)
..|++||+|+-... |....+.|++|+.+.++..+. +.--++++..-.....+.-...-|++ .+.+ .
T Consensus 160 ~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~~~~---~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (1004)
T PHA03036 160 RSYLFLDIECHFDKKFPSVFINPVSHISCCYIDLSGK---EKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSKEL 236 (1004)
T ss_pred ceeEEEEEEeccCCCCCCcccCcceEEEEEEEecCCC---eeEEEEeccccccccccccceeeeeeccccccccCCceee
Confidence 57999999997522 223568999999877776543 22235666643211111111222221 1111 1
Q ss_pred CCCCHHHHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCC--------------------------------
Q 013825 77 SSPTFADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPA-------------------------------- 121 (436)
Q Consensus 77 ~Ap~f~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~-------------------------------- 121 (436)
--.+..+ +-.|.+++. -.+++|+|+..||++.|..-++.+...-
T Consensus 237 ~~~sE~~-ml~~~~~i~~~d~D~i~~yNg~nFD~~Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~gg~~~ 315 (1004)
T PHA03036 237 ILCSEIV-LLRIAKKLLELEFDYVVTFNGHNFDLRYISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKGVGGVAN 315 (1004)
T ss_pred ecCCHHH-HHHHHHHHHhcCCCEEEeccCCCcchHHHHHHHHHhccCceeeccCCCcccccceeeccccccccccCcccc
Confidence 1234444 336666665 4699999999999999888877752200
Q ss_pred -------CCCCceeeHHHHHHHHhcCCCCCCCHHHHHHH-hCC--C-----CC----CCChHHHHHHHHHHHHHHHH
Q 013825 122 -------PEPKGTIDSLALLTQRFGRRAGDMKMASLATY-FGL--G-----QQ----THRSLDDVRMNLEVLKYCAT 179 (436)
Q Consensus 122 -------p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~-fGI--~-----~~----~HrALdDAraTa~VLk~L~~ 179 (436)
-....++|.+...++.+ ++.+|+|+++++. |+. - .. .-.-..|+...+.+|...+.
T Consensus 316 ~t~~i~~~~G~i~fDLy~~i~k~~--~L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl~ 390 (1004)
T PHA03036 316 TTYHINNNNGTIFFDLYTFIQKTE--KLDSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVLS 390 (1004)
T ss_pred ceEEecccCCeEEEEhHHHHhhhc--CcccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhhc
Confidence 01134678888776544 5689999999997 333 0 00 01112466666666666543
No 95
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=93.20 E-value=0.12 Score=52.04 Aligned_cols=150 Identities=16% Similarity=0.068 Sum_probs=91.0
Q ss_pred CCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCC--CCHHHHHHHHHHHHcC-------CE
Q 013825 26 RFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSS--PTFADIADTVFDILHG-------RI 96 (436)
Q Consensus 26 ~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~A--p~f~eVl~~f~efL~g-------~v 96 (436)
+..+++|.+--+...+. ..+..++++.. ++.. .-+.-+..|+..+ +.......-|..+.+. ..
T Consensus 129 ~~~dfpil~qela~lg~---~lpq~lvcvds---lpa~--~ald~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~ 200 (318)
T KOG4793|consen 129 NEYDFPILAQELAGLGY---SLPQDLVCVDS---LPAL--NALDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVA 200 (318)
T ss_pred CccccHHHHHHHHhcCc---cchhhhcCcch---hHHH--HHHhhhcCcccCCCCCcccccchHHHhhhcccCCCcceee
Confidence 34455554444444332 34555666665 3211 1111144444333 2333333334444442 23
Q ss_pred EEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhc---C-CCCCCCHHHHHHHhCCC--CCCCChHHHHHHH
Q 013825 97 WAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFG---R-RAGDMKMASLATYFGLG--QQTHRSLDDVRMN 170 (436)
Q Consensus 97 LVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~---~-~~~~~kL~~LA~~fGI~--~~~HrALdDAraT 170 (436)
.+.||+..|+..|..+++-|.+.+-+.+...|+.|-+++.... + -...++++.|+.++... ..+|||+.|+.++
T Consensus 201 e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~~ 280 (318)
T KOG4793|consen 201 EGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPTPKLVSSLEALATYYSLTPELDAHRALSDVLLL 280 (318)
T ss_pred ecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCCCccchhHHHHHHHhhcCcccchhhhccccchh
Confidence 4568888899999999988877665555556777766544332 2 12467899999999886 4799999999999
Q ss_pred HHHHHHHHHHhhh
Q 013825 171 LEVLKYCATVLFL 183 (436)
Q Consensus 171 a~VLk~L~~~l~l 183 (436)
-++++++-..+++
T Consensus 281 ~k~~q~~~idlla 293 (318)
T KOG4793|consen 281 SKVFQKLTIDLLA 293 (318)
T ss_pred hhHHHHhhhhhhh
Confidence 9999997665543
No 96
>PRK05761 DNA polymerase I; Reviewed
Probab=93.19 E-value=0.65 Score=53.08 Aligned_cols=96 Identities=15% Similarity=0.257 Sum_probs=67.4
Q ss_pred CCHHHHHHHHHHHHcC-CEEEEEccccchHHHHHHHHHHcCCCCCCC-------CceeeHHHHHHHH----h--cCC--C
Q 013825 79 PTFADIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEP-------KGTIDSLALLTQR----F--GRR--A 142 (436)
Q Consensus 79 p~f~eVl~~f~efL~g-~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~-------~~~IDTl~Larr~----l--~~~--~ 142 (436)
.+-.+++.+|.+++.. .+.|.+|...||+++|.+-+..+|++.... ...+|....++.. + ..+ .
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~ 287 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRH 287 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeec
Confidence 6788899999999983 467779999999999999999999875411 1126665543311 1 111 2
Q ss_pred CCCCHHHHHH-HhCCCCC-C-------------CChHHHHHHHHHHH
Q 013825 143 GDMKMASLAT-YFGLGQQ-T-------------HRSLDDVRMNLEVL 174 (436)
Q Consensus 143 ~~~kL~~LA~-~fGI~~~-~-------------HrALdDAraTa~VL 174 (436)
.+++|+..++ ++|.++. . .=.+.||..+.+++
T Consensus 288 ~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 288 REARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 3789999999 6677631 1 12488999999985
No 97
>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=93.08 E-value=4.1 Score=36.91 Aligned_cols=104 Identities=11% Similarity=0.068 Sum_probs=64.9
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHH
Q 013825 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~ 87 (436)
.+.+.+|+|++|.++ ....++-| .+..+. . ..+|.+.. . + .+...
T Consensus 3 ~~~~~~~~~~~~~~~--~~~~l~~i---~l~~~~----~--~~~i~~~~--~----------~------------~~~~~ 47 (178)
T cd06140 3 ADEVALYVELLGENY--HTADIIGL---ALANGG----G--AYYIPLEL--A----------L------------LDLAA 47 (178)
T ss_pred CCceEEEEEEcCCCc--ceeeEEEE---EEEeCC----c--EEEEeccc--h----------H------------HHHHH
Confidence 457889999999875 34455433 332221 1 12444322 1 0 13455
Q ss_pred HHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh
Q 013825 88 VFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF 154 (436)
Q Consensus 88 f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f 154 (436)
|.+++.+ ...++||+ .+|+.+|. ++|+..+. ...||+- +.-.+.+...++++..++..|
T Consensus 48 l~~~l~~~~~~ki~~d~-K~~~~~l~----~~gi~~~~--~~fDt~l-aaYLL~p~~~~~~l~~l~~~y 108 (178)
T cd06140 48 LKEWLEDEKIPKVGHDA-KRAYVALK----RHGIELAG--VAFDTML-AAYLLDPTRSSYDLADLAKRY 108 (178)
T ss_pred HHHHHhCCCCceeccch-hHHHHHHH----HCCCcCCC--cchhHHH-HHHHcCCCCCCCCHHHHHHHH
Confidence 6667764 46899999 99988875 46776553 3689975 454677755556999998876
No 98
>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=92.72 E-value=1.7 Score=41.04 Aligned_cols=139 Identities=14% Similarity=0.117 Sum_probs=83.3
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 5 ~~~~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
..+..++.||+|+++.+..+ .-.++||+.- .+ -..++++... .. .. .
T Consensus 7 l~~~~~i~~D~E~~~~~~~~-~~~LiQia~~---~~-------~v~l~D~~~~---~~----------------~~---~ 53 (197)
T cd06148 7 LKKQKVIGLDCEGVNLGRKG-KLCLVQIATR---TG-------QIYLFDILKL---GS----------------IV---F 53 (197)
T ss_pred hhhCCEEEEEcccccCCCCC-CEEEEEEeeC---CC-------cEEEEEhhhc---cc----------------hh---H
Confidence 45678999999999876522 3445555421 12 1224554431 00 00 1
Q ss_pred HHHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCC-------CCCCHHHHHHHh-
Q 013825 85 ADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRA-------GDMKMASLATYF- 154 (436)
Q Consensus 85 l~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~-------~~~kL~~LA~~f- 154 (436)
.+.+.+++.+ ...|+|++ ++|..+|.. .+|+... .++||... ...+.+.. ...+|..+++.|
T Consensus 54 ~~~L~~iLe~~~i~Kv~h~~-k~D~~~L~~---~~gi~~~---~~fDt~iA-~~lL~~~~~~~~~~~~~~~L~~l~~~~l 125 (197)
T cd06148 54 INGLKDILESKKILKVIHDC-RRDSDALYH---QYGIKLN---NVFDTQVA-DALLQEQETGGFNPDRVISLVQLLDKYL 125 (197)
T ss_pred HHHHHHHhcCCCccEEEEec-hhHHHHHHH---hcCcccc---ceeeHHHH-HHHHHHHhcCCccccccccHHHHHHHhh
Confidence 2345555653 35699999 999988743 4466532 36899754 33443311 134788888765
Q ss_pred CCCC-------------------------CCCChHHHHHHHHHHHHHHHHHhhhh
Q 013825 155 GLGQ-------------------------QTHRSLDDVRMNLEVLKYCATVLFLE 184 (436)
Q Consensus 155 GI~~-------------------------~~HrALdDAraTa~VLk~L~~~l~le 184 (436)
|++. +-+=|..||..+..++..+...+...
T Consensus 126 ~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 126 YISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred CCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 4321 12447899999999999998887654
No 99
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=91.45 E-value=2.6 Score=37.06 Aligned_cols=88 Identities=17% Similarity=0.245 Sum_probs=55.5
Q ss_pred HHHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC-CC-
Q 013825 85 ADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG-QQ- 159 (436)
Q Consensus 85 l~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~-~~- 159 (436)
...+.+++.. ...|+||+ .+|+.+|+ ++|+... .++|++-.+. .+.+....++|..++..| +.. ..
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~-k~~~~~L~----~~gi~~~---~~~D~~laay-ll~p~~~~~~l~~l~~~~l~~~~~~~ 134 (172)
T smart00474 64 LEILKDLLEDETITKVGHNA-KFDLHVLA----RFGIELE---NIFDTMLAAY-LLLGGPSKHGLATLLKEYLGVELDKE 134 (172)
T ss_pred HHHHHHHhcCCCceEEEech-HHHHHHHH----HCCCccc---chhHHHHHHH-HHcCCCCcCCHHHHHHHHhCCCCCcc
Confidence 3446666663 46899999 99999986 3677654 2489976543 455544436999998876 443 11
Q ss_pred -----------CC----ChHHHHHHHHHHHHHHHHHh
Q 013825 160 -----------TH----RSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 160 -----------~H----rALdDAraTa~VLk~L~~~l 181 (436)
.. -|..||.++.+++..+.+++
T Consensus 135 ~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 135 EQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred cCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 01 14556666666666655543
No 100
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=90.01 E-value=2.9 Score=46.48 Aligned_cols=132 Identities=17% Similarity=0.222 Sum_probs=84.7
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHHHHHHH
Q 013825 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVF 89 (436)
Q Consensus 10 fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eVl~~f~ 89 (436)
.+.+|+||+|+++ ....++-++...-. .. .||.-.. + +..-++...+.
T Consensus 24 ~~a~~~et~~l~~--~~~~lvg~s~~~~~-------~~--~yi~~~~------------~---------~~~~~~~~~l~ 71 (593)
T COG0749 24 NIAFDTETDGLDP--HGADLVGLSVASEE-------EA--AYIPLLH------------G---------PEQLNVLAALK 71 (593)
T ss_pred cceeeccccccCc--ccCCeeEEEeeccc-------cc--eeEeecc------------c---------hhhhhhHHHHH
Confidence 3899999999987 45666555443222 11 1222111 1 11112778889
Q ss_pred HHHcCC--EEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHhCC-CCC-------
Q 013825 90 DILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGL-GQQ------- 159 (436)
Q Consensus 90 efL~g~--vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~fGI-~~~------- 159 (436)
.|+... ..|+||. .||..+|.. +|+. + ....||+ |+.-.+.+..+.+.|+.|+..|.- ...
T Consensus 72 ~~l~~~~~~kv~~~~-K~d~~~l~~----~Gi~-~--~~~~Dtm-lasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~ 142 (593)
T COG0749 72 PLLEDEGIKKVGQNL-KYDYKVLAN----LGIE-P--GVAFDTM-LASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAG 142 (593)
T ss_pred HHhhCcccchhcccc-chhHHHHHH----cCCc-c--cchHHHH-HHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhc
Confidence 999854 5899999 999888754 5744 2 2468997 445455666678999999998832 110
Q ss_pred ----------------CCChHHHHHHHHHHHHHHHHHhh
Q 013825 160 ----------------THRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 160 ----------------~HrALdDAraTa~VLk~L~~~l~ 182 (436)
.-.+..||..+.++...+...+.
T Consensus 143 kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~ 181 (593)
T COG0749 143 KGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELL 181 (593)
T ss_pred cccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 22356788888888888886543
No 101
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=88.44 E-value=1.9 Score=52.00 Aligned_cols=165 Identities=13% Similarity=0.111 Sum_probs=96.7
Q ss_pred CCCcEEEEEEecCCCC---CCCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCC------HHHHh
Q 013825 6 DRSEIAFFDVETTVPT---RPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGIT------PDAVV 76 (436)
Q Consensus 6 ~~~~fV~fDLETTGl~---p~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT------~e~La 76 (436)
.+..+++||+|||-+. |+...++|--|+. .+++.+.-+. |-+ -+++.+..+.=-. .-.+-
T Consensus 244 adp~VlAFDIETtKlPLKFPDae~DqIMMISY-MiDGqGfLIt-------NRE---iVs~DIedfEYTPKpE~eG~F~v~ 312 (2173)
T KOG1798|consen 244 ADPRVLAFDIETTKLPLKFPDAESDQIMMISY-MIDGQGFLIT-------NRE---IVSEDIEDFEYTPKPEYEGPFCVF 312 (2173)
T ss_pred CCceEEEEeeecccCCCCCCCcccceEEEEEE-EecCceEEEe-------chh---hhccchhhcccCCccccccceEEe
Confidence 3567999999999851 2235677877743 4555432111 111 1111111111000 00134
Q ss_pred CCCCHHHHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCCCCCC------------Cc---eeeHHHHHHHHh
Q 013825 77 SSPTFADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAPEP------------KG---TIDSLALLTQRF 138 (436)
Q Consensus 77 ~Ap~f~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~------------~~---~IDTl~Larr~l 138 (436)
+.+.-...+.+|++.++ -.++|.+|+.=||++|+.+-...+|+....- .+ ..|..+..++--
T Consensus 313 Ne~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDS 392 (2173)
T KOG1798|consen 313 NEPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDS 392 (2173)
T ss_pred cCCcHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcc
Confidence 56677888899988887 4699999998899999999999998765421 11 233333322211
Q ss_pred cCCCCCCCHHHHHHH-hCCC---------------CCC---CChHHHHHHHHHHHHHHHHHh
Q 013825 139 GRRAGDMKMASLATY-FGLG---------------QQT---HRSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 139 ~~~~~~~kL~~LA~~-fGI~---------------~~~---HrALdDAraTa~VLk~L~~~l 181 (436)
.--.|+..|.+..+. +|-. ++. -=+..||.+|.-+|.+..+-+
T Consensus 393 YLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhPF 454 (2173)
T KOG1798|consen 393 YLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHPF 454 (2173)
T ss_pred cCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhhH
Confidence 112467777777663 3321 122 344899999999998877654
No 102
>PHA02563 DNA polymerase; Provisional
Probab=85.16 E-value=7.6 Score=43.58 Aligned_cols=35 Identities=23% Similarity=0.208 Sum_probs=28.0
Q ss_pred HHHHHHHHc-------CCEEEEEccccchHHHHHHHHHHcCCC
Q 013825 85 ADTVFDILH-------GRIWAGHNILRFDCARIREAFAEIGRP 120 (436)
Q Consensus 85 l~~f~efL~-------g~vLVaHNa~~FD~~fLr~a~~r~Gi~ 120 (436)
+++|++|+. ..++..||. .||..||...+.+++..
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN~-~FD~~Fil~~L~~~~~~ 91 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHNL-KFDGSFILKWLLRNGFN 91 (630)
T ss_pred HHHHHHHHhhccccccceEEEEecC-CccHHHHHHHHHhhccc
Confidence 347777776 568889995 99999999999887743
No 103
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=84.87 E-value=0.25 Score=55.75 Aligned_cols=101 Identities=17% Similarity=0.231 Sum_probs=64.4
Q ss_pred CcEEEEEEecCCCCC---CCCCCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCCHHHH
Q 013825 8 SEIAFFDVETTVPTR---PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (436)
Q Consensus 8 ~~fV~fDLETTGl~p---~g~~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~f~eV 84 (436)
-.++-||+|+.|-.+ ...-+.||+|+-+....|..+. | ++-.. .+. ...+|.-.+|-....-.++
T Consensus 274 lrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~p---f---~rnvf--~l~----~capI~G~~V~~~~~e~el 341 (1066)
T KOG0969|consen 274 LRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEP---F---VRNVF--TLK----TCAPIVGSNVHSYETEKEL 341 (1066)
T ss_pred ccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCch---H---HHhhh--ccc----CcCCCCCceeEEeccHHHH
Confidence 457889999999432 1256788999877665553221 2 22111 111 1244555556555566666
Q ss_pred HHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCC
Q 013825 85 ADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRP 120 (436)
Q Consensus 85 l~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~ 120 (436)
++.+..|+. -.+++|||+..||+..|-.-.+.+|++
T Consensus 342 L~~W~~firevDPDvI~GYNi~nFDiPYll~RA~~L~Ie 380 (1066)
T KOG0969|consen 342 LESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIE 380 (1066)
T ss_pred HHHHHHHHHhcCCCeEecccccccccceecChHhhcCcc
Confidence 666666664 689999999999999877766777765
No 104
>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=84.50 E-value=15 Score=32.94 Aligned_cols=89 Identities=19% Similarity=0.243 Sum_probs=58.1
Q ss_pred HHHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC-CCC
Q 013825 85 ADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG-QQT 160 (436)
Q Consensus 85 l~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~-~~~ 160 (436)
.+.|.+++.+ ...|+||+ .+|+..|...+ |+. . ..+.|++ ++...+.+... .+|+.+++.| +.. ...
T Consensus 53 ~~~l~~ll~~~~i~kv~~d~-K~~~~~L~~~~---gi~-~--~~~~D~~-laayLl~p~~~-~~l~~l~~~~l~~~~~~~ 123 (178)
T cd06142 53 LSPLKELLADPNIVKVFHAA-REDLELLKRDF---GIL-P--QNLFDTQ-IAARLLGLGDS-VGLAALVEELLGVELDKG 123 (178)
T ss_pred HHHHHHHHcCCCceEEEecc-HHHHHHHHHHc---CCC-C--CCcccHH-HHHHHhCCCcc-ccHHHHHHHHhCCCCCcc
Confidence 3445566663 46899999 99988876432 776 3 2368997 45556776543 5999998865 554 110
Q ss_pred ----------------CChHHHHHHHHHHHHHHHHHhh
Q 013825 161 ----------------HRSLDDVRMNLEVLKYCATVLF 182 (436)
Q Consensus 161 ----------------HrALdDAraTa~VLk~L~~~l~ 182 (436)
+-+..||.++.+++..+.+++.
T Consensus 124 ~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~ 161 (178)
T cd06142 124 EQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161 (178)
T ss_pred cccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 0256667778888777776654
No 105
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=81.19 E-value=9.9 Score=44.32 Aligned_cols=92 Identities=12% Similarity=0.013 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC
Q 013825 81 FADIADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG 157 (436)
Q Consensus 81 f~eVl~~f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~ 157 (436)
...+...|..++.+ ...|+||+ .||+.+|. ++|+.... .+.||+-. ...+.+... .+|+.++..| +..
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~-K~d~~~l~----~~gi~~~~--~~~Dt~la-~yll~~~~~-~~l~~la~~yl~~~ 433 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDA-KFLMHLLK----REGIELGG--VIFDTMLA-AYLLDPAQV-STLDTLARRYLVEE 433 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeH-HHHHHHHH----hCCCCCCC--cchhHHHH-HHHcCCCCC-CCHHHHHHHHcCcc
Confidence 44566778888875 35799999 99999986 46876543 36899854 446666443 4999998876 311
Q ss_pred ---------C----C-------CCChHHHHHHHHHHHHHHHHHh
Q 013825 158 ---------Q----Q-------THRSLDDVRMNLEVLKYCATVL 181 (436)
Q Consensus 158 ---------~----~-------~HrALdDAraTa~VLk~L~~~l 181 (436)
. . ..-|..||.+|..++..+..++
T Consensus 434 ~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l 477 (887)
T TIGR00593 434 LILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKEL 477 (887)
T ss_pred cccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 0 0136678889999998887775
No 106
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=71.27 E-value=3.7 Score=47.15 Aligned_cols=38 Identities=32% Similarity=0.540 Sum_probs=28.9
Q ss_pred cCCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHH
Q 013825 93 HGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLT 135 (436)
Q Consensus 93 ~g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Lar 135 (436)
.+.++||||. .||+..+++++. +.-- ..+++|||.|-.
T Consensus 240 ke~liVGHNV-sfDRaRirEeY~---i~~S-k~rFlDTMSlHi 277 (1075)
T KOG3657|consen 240 KEQLIVGHNV-SFDRARIREEYN---INGS-KIRFLDTMSLHI 277 (1075)
T ss_pred CCceEEeccc-cchHHHHHHHHh---cccc-ceeeeechhhhh
Confidence 3679999999 999999998875 3322 235899998744
No 107
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=69.88 E-value=20 Score=35.63 Aligned_cols=172 Identities=15% Similarity=0.130 Sum_probs=99.5
Q ss_pred CCcEEEEEEecCCCCC--CC-----------------CCCcEEEEEEEEEeCCcceEe--e--eEEEEEcCCCCCCCChh
Q 013825 7 RSEIAFFDVETTVPTR--PG-----------------QRFAILEFGAILVCPKKLEEL--H--NYSTLVRPADPELISSL 63 (436)
Q Consensus 7 ~~~fV~fDLETTGl~p--~g-----------------~~~~IIEIGAV~V~~~~levl--~--sfstLVrP~~~~~I~p~ 63 (436)
+-++|-+|+|..|.-. .| .--.||++|...-+..+.... . .|+.-.++... -..++
T Consensus 41 rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~d-mya~E 119 (299)
T COG5228 41 RYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKD-MYATE 119 (299)
T ss_pred hCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhh-hcchH
Confidence 4568899999988421 11 123799999988876543322 2 35555666651 22222
Q ss_pred hH---HhcCCCHHHHhC-CCCHHHHHHHHHHHHc--------CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHH
Q 013825 64 SV---RCNGITPDAVVS-SPTFADIADTVFDILH--------GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSL 131 (436)
Q Consensus 64 a~---kltGIT~e~La~-Ap~f~eVl~~f~efL~--------g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl 131 (436)
.. +-.||.-+.-+. +... .+|-+.+- .-+||.+.. .+|.++|-..+-.. +.|.. .-|-.
T Consensus 120 SieLL~ksgIdFkkHe~~GI~v----~eF~elLm~SGLvm~e~VtWitfHs-aYDfgyLikilt~~--plP~~--~EdFy 190 (299)
T COG5228 120 SIELLRKSGIDFKKHENLGIDV----FEFSELLMDSGLVMDESVTWITFHS-AYDFGYLIKILTND--PLPNN--KEDFY 190 (299)
T ss_pred HHHHHHHcCCChhhHhhcCCCH----HHHHHHHhccCceeccceEEEEeec-chhHHHHHHHHhcC--CCCcc--HHHHH
Confidence 22 234665443322 2222 23334332 358888777 89999998877543 33322 22333
Q ss_pred HHHHHHhcCCC------------CCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHHhhhhcCcch
Q 013825 132 ALLTQRFGRRA------------GDMKMASLATYFGLG--QQTHRSLDDVRMNLEVLKYCATVLFLESSLPD 189 (436)
Q Consensus 132 ~Larr~l~~~~------------~~~kL~~LA~~fGI~--~~~HrALdDAraTa~VLk~L~~~l~le~slp~ 189 (436)
.+... +.++. -+-.|.++++-+++. .+.|.|-.||+.|++.|.....++|-...-..
T Consensus 191 ~~l~~-yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F~~sig~~ 261 (299)
T COG5228 191 WWLHQ-YFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTSIGQS 261 (299)
T ss_pred HHHHH-HCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhheecccccHH
Confidence 33322 22211 123467777777776 47899999999999999887777765443333
No 108
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=69.80 E-value=6.5 Score=37.99 Aligned_cols=149 Identities=9% Similarity=0.046 Sum_probs=82.4
Q ss_pred CCcEEEEEEEEEeCCcceEeeeEEEEEcCCCCCCCC-h-----hhHHhcCCCHHHHhCCC-CHHHHHHHHHHHHcC----
Q 013825 26 RFAILEFGAILVCPKKLEELHNYSTLVRPADPELIS-S-----LSVRCNGITPDAVVSSP-TFADIADTVFDILHG---- 94 (436)
Q Consensus 26 ~~~IIEIGAV~V~~~~levl~sfstLVrP~~~~~I~-p-----~a~kltGIT~e~La~Ap-~f~eVl~~f~efL~g---- 94 (436)
..-..|||++.+.-..+ +.+.|+++|+|+.. +.- . .+...|+|..+--+.+. .+..++.++.+|++.
T Consensus 7 ~y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~-p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~~ 84 (213)
T PF13017_consen 7 EYVPAEIAICKFSLKEG-IIDSFHTFINPGQI-PLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNKGG 84 (213)
T ss_pred cEEeEEEEEEEEecCCc-cchhhhcccCCCCC-CcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcCCC
Confidence 45688999999987765 66899999999972 211 1 22234566655444444 699999999999972
Q ss_pred -C--EEEEEcc-ccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHH----hcC---CCCCCCHHHHHHHhC--------
Q 013825 95 -R--IWAGHNI-LRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQR----FGR---RAGDMKMASLATYFG-------- 155 (436)
Q Consensus 95 -~--vLVaHNa-~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~----l~~---~~~~~kL~~LA~~fG-------- 155 (436)
. +++.-.- .......|+..+...+.... ..+.+...|+-.. +.. +....+..-....+.
T Consensus 85 ~~~~~i~~~~~~~~~V~~cl~~La~~a~~~~~--~~v~~~~~lf~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~ 162 (213)
T PF13017_consen 85 EKMPPIFTKRDQIPRVQSCLKWLAKKAGEDND--FKVYDFEYLFFDLKNEKVDYRWDRQDFPSKTIADALFPKDFFEYSS 162 (213)
T ss_pred CCcceEEEeHhHHHHHHHHHHHHHHhcCCCcc--eEeecHHHHHHHHHHHHhhcccccccCchHHHHHHHccchhhhccC
Confidence 1 2332211 12223345555555555433 2245544443321 111 111222222222222
Q ss_pred -C--------CCCCCChHHHHHHHHHHHHHHH
Q 013825 156 -L--------GQQTHRSLDDVRMNLEVLKYCA 178 (436)
Q Consensus 156 -I--------~~~~HrALdDAraTa~VLk~L~ 178 (436)
+ +...+.|+..+..++-.+-..+
T Consensus 163 ~~~C~~He~~d~~~~Ca~s~v~r~ay~i~d~~ 194 (213)
T PF13017_consen 163 NIRCDFHEEIDRSKYCALSTVKRWAYTISDYM 194 (213)
T ss_pred CCceeecccCCCcccchhHHHHHHHHHHHHHH
Confidence 1 1236888888888887775554
No 109
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=55.60 E-value=69 Score=38.55 Aligned_cols=144 Identities=13% Similarity=0.166 Sum_probs=86.3
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCcc-------eEeeeEEEEEcCCCCCCCChhhHHhcCCCHHHHhCCCC
Q 013825 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKL-------EELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPT 80 (436)
Q Consensus 8 ~~fV~fDLETTGl~p~g~~~~IIEIGAV~V~~~~l-------evl~sfstLVrP~~~~~I~p~a~kltGIT~e~La~Ap~ 80 (436)
-....+-++|+--.. ....+|+-|++.....-.+ .....|..+++|.. ..+|-...++-.-..--+.-.-+
T Consensus 529 l~llsL~i~T~~N~k-~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~-~~fP~g~~ela~~k~~~v~~~~s 606 (1429)
T KOG0970|consen 529 LTLLSLNIRTSMNPK-QNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPG-TSFPLGLKELAKQKLSKVVLHNS 606 (1429)
T ss_pred eeEEEeeeeehhccc-cchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCC-CcCCchHHHHHHhccCceEEecC
Confidence 456777888876433 2457888887776543211 12345778899986 23332111211110001344556
Q ss_pred HHHHHHHHHHHHc---CCEEEEEccccchHHHHHHHHHHcCCC-----------CCCC--------------CceeeHHH
Q 013825 81 FADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRP-----------APEP--------------KGTIDSLA 132 (436)
Q Consensus 81 f~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~a~~r~Gi~-----------~p~~--------------~~~IDTl~ 132 (436)
-...+..|+..++ -.++||||+..|++..|-..+..+.++ |+.. -+.+|-+.
T Consensus 607 ErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~CD~~ 686 (1429)
T KOG0970|consen 607 ERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMCDLN 686 (1429)
T ss_pred HHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccceEEeehH
Confidence 6778888888886 469999997799999886665554443 2210 12455556
Q ss_pred HHHHHhcCCCCCCCHHHHHHHh
Q 013825 133 LLTQRFGRRAGDMKMASLATYF 154 (436)
Q Consensus 133 Larr~l~~~~~~~kL~~LA~~f 154 (436)
++.+-+-+ ..+|.|.+|++..
T Consensus 687 ~~a~~lik-~~S~~LseL~q~~ 707 (1429)
T KOG0970|consen 687 LAARELIK-AQSYSLSELSQQI 707 (1429)
T ss_pred HHHHhhhc-cccccHHHHHHHH
Confidence 66655544 4688999998865
No 110
>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=54.71 E-value=1.6e+02 Score=27.09 Aligned_cols=87 Identities=10% Similarity=0.108 Sum_probs=53.9
Q ss_pred HHHHHHc--CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--C---
Q 013825 87 TVFDILH--GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--Q--- 158 (436)
Q Consensus 87 ~f~efL~--g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~--~--- 158 (436)
.|.+++. +...|+||. ..|+..|++ ++|+.... .+|++-. ...+.+. . ..++.+++.| +.. .
T Consensus 68 ~L~~~L~~~~i~kv~~d~-K~~~~~L~~---~~gi~~~~---~fD~~la-aYLL~p~-~-~~l~~l~~~yl~~~~~k~~~ 137 (192)
T cd06147 68 ILNEVFTDPNILKVFHGA-DSDIIWLQR---DFGLYVVN---LFDTGQA-ARVLNLP-R-HSLAYLLQKYCNVDADKKYQ 137 (192)
T ss_pred HHHHHhcCCCceEEEech-HHHHHHHHH---HhCCCcCc---hHHHHHH-HHHhCCC-c-ccHHHHHHHHhCCCcchhhh
Confidence 3555665 357899999 888888753 55776442 3899754 4467776 4 4999998876 433 0
Q ss_pred ----CCCC--------hHHHHHHHHHHHHHHHHHhhh
Q 013825 159 ----QTHR--------SLDDVRMNLEVLKYCATVLFL 183 (436)
Q Consensus 159 ----~~Hr--------ALdDAraTa~VLk~L~~~l~l 183 (436)
..+. +..||.++.++...+..++..
T Consensus 138 ~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e 174 (192)
T cd06147 138 LADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLE 174 (192)
T ss_pred ccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 1111 334455666666666665543
No 111
>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=37.79 E-value=1.3e+02 Score=25.82 Aligned_cols=62 Identities=18% Similarity=0.206 Sum_probs=40.9
Q ss_pred HHHHHc--CCEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC
Q 013825 88 VFDILH--GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG 157 (436)
Q Consensus 88 f~efL~--g~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f-GI~ 157 (436)
+.+++. +...|+||+ .+|+.+|+ +.|+.... ...|++-. ...+.+..++.+++.|++.| +..
T Consensus 45 l~~~l~~~~~~kv~~d~-K~~~~~L~----~~~~~~~~--~~~D~~la-ayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKALKVGQNL-KYDRGILL----NYFIELRG--IAFDTMLE-AYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCCceeeecH-HHHHHHHH----HcCCccCC--cchhHHHH-HHHhCCCCCCCCHHHHHHHHhCCC
Confidence 455565 356789999 99988875 34655442 36899765 44666643235899998876 543
No 112
>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=25.64 E-value=2.6e+02 Score=24.41 Aligned_cols=59 Identities=24% Similarity=0.329 Sum_probs=39.1
Q ss_pred HHHHHcC--CEEEEEccccchHHHHHHHHHHcCCCCCCCCceeeHHHHHHHHhcCCCCCCCHHHHHHHh
Q 013825 88 VFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF 154 (436)
Q Consensus 88 f~efL~g--~vLVaHNa~~FD~~fLr~a~~r~Gi~~p~~~~~IDTl~Larr~l~~~~~~~kL~~LA~~f 154 (436)
|.+|+.. ...++||. .+++.+| .++|+.... ...|++ |+.-.+.+......++.++..|
T Consensus 45 l~~~l~~~~~~ki~~d~-K~~~~~l----~~~gi~l~~--~~fD~~-LAaYLL~p~~~~~~l~~la~~y 105 (151)
T cd06128 45 LKPLLEDEKALKVGQNL-KYDRVIL----ANYGIELRG--IAFDTM-LEAYLLDPVAGRHDMDSLAERW 105 (151)
T ss_pred HHHHHcCCCCCEEeeeh-HHHHHHH----HHCCCCCCC--cchhHH-HHHHHcCCCCCCCCHHHHHHHH
Confidence 5566663 45688888 6666665 467877543 358997 4555677754413999998887
No 113
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.11 E-value=39 Score=40.71 Aligned_cols=93 Identities=17% Similarity=0.129 Sum_probs=53.0
Q ss_pred CCcEEEEEEecCCCC-------CCCCCCcEEEEEEEEEe-----CCcceEeeeEEEEEcCCCCCCCChhhHHhcCCCHHH
Q 013825 7 RSEIAFFDVETTVPT-------RPGQRFAILEFGAILVC-----PKKLEELHNYSTLVRPADPELISSLSVRCNGITPDA 74 (436)
Q Consensus 7 ~~~fV~fDLETTGl~-------p~g~~~~IIEIGAV~V~-----~~~levl~sfstLVrP~~~~~I~p~a~kltGIT~e~ 74 (436)
..+++.||+|+-+.. +....+.|++|+...+. ++. +....--+-+.+. ..|+-..
T Consensus 197 ~~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~~~~~~~~~-~~~~~~~~~~~~~------------~~~~~~~ 263 (1172)
T TIGR00592 197 ELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWDYES-EPEARVVTWKKPD------------KPTTGSY 263 (1172)
T ss_pred cccccccccccccccccccCcccccccccccccccccccccccccCC-CccchhhhccCcc------------ccCCCcc
Confidence 456788999976421 22356889999864222 110 0000000001111 1122223
Q ss_pred HhCCCCHHHHHHHHHHHHc---CCEEEEEccccchHHHHHH
Q 013825 75 VVSSPTFADIADTVFDILH---GRIWAGHNILRFDCARIRE 112 (436)
Q Consensus 75 La~Ap~f~eVl~~f~efL~---g~vLVaHNa~~FD~~fLr~ 112 (436)
+...++..+.+..|.+++. ..+++|+|+..||+..+..
T Consensus 264 v~~~~~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~~ 304 (1172)
T TIGR00592 264 VESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLAD 304 (1172)
T ss_pred ceeccchHHHHhhHHHHHhhcCcchhcccccccCccceecC
Confidence 3444667777777777775 3589999999999987766
No 114
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=23.90 E-value=25 Score=33.03 Aligned_cols=28 Identities=29% Similarity=0.366 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhhhccCC-CCCCccccee
Q 013825 395 TVLDACEVIVRKLVEDSG-SSSEWRHVVT 422 (436)
Q Consensus 395 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 422 (436)
.=|.+|+.++++|+.-|+ ++-.|+.+|-
T Consensus 28 TQL~AFeEvg~~L~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 28 TQLSAFEEVGRALNRTAAACGFRWNAYVR 56 (161)
T ss_pred HHHHHHHHHHHHHcccHHHhcchHHHHHH
Confidence 347899999999999998 8999999993
Done!