Query 025709
Match_columns 249
No_of_seqs 151 out of 1317
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 08:42:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025709.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025709hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3242 Oligoribonuclease (3'- 100.0 1.2E-44 2.7E-49 296.7 13.6 182 66-247 23-204 (208)
2 COG1949 Orn Oligoribonuclease 100.0 2.4E-44 5.1E-49 292.5 13.9 181 66-247 3-183 (184)
3 PRK05359 oligoribonuclease; Pr 100.0 8.8E-41 1.9E-45 282.3 19.0 179 68-247 2-180 (181)
4 cd06135 Orn DEDDh 3'-5' exonuc 100.0 7E-38 1.5E-42 262.6 17.0 172 71-242 1-172 (173)
5 PRK09146 DNA polymerase III su 100.0 1.1E-30 2.4E-35 229.6 21.7 170 60-245 38-230 (239)
6 PRK09145 DNA polymerase III su 100.0 5.3E-30 1.1E-34 219.5 19.6 161 67-240 27-199 (202)
7 PRK05711 DNA polymerase III su 100.0 5.4E-30 1.2E-34 225.2 19.5 156 68-240 3-174 (240)
8 TIGR01406 dnaQ_proteo DNA poly 100.0 1.9E-29 4.1E-34 219.9 19.5 153 70-240 1-170 (225)
9 PRK07740 hypothetical protein; 100.0 6.7E-29 1.5E-33 218.9 20.7 162 65-243 55-227 (244)
10 PRK06310 DNA polymerase III su 100.0 1.2E-28 2.5E-33 218.1 20.3 158 68-242 6-174 (250)
11 cd06131 DNA_pol_III_epsilon_Ec 100.0 1.4E-28 3.1E-33 203.6 18.4 151 71-238 1-166 (167)
12 PRK07942 DNA polymerase III su 100.0 2.9E-28 6.2E-33 213.4 19.6 166 65-242 2-180 (232)
13 PRK08517 DNA polymerase III su 100.0 4.2E-28 9.1E-33 215.3 20.8 159 65-242 64-231 (257)
14 TIGR00573 dnaq exonuclease, DN 100.0 3.7E-28 8.1E-33 210.5 19.2 159 68-242 6-177 (217)
15 PRK06063 DNA polymerase III su 100.0 3.1E-28 6.7E-33 221.7 19.4 159 65-242 11-179 (313)
16 TIGR01298 RNaseT ribonuclease 100.0 8.6E-28 1.9E-32 206.0 18.7 168 65-242 4-192 (200)
17 COG2176 PolC DNA polymerase II 100.0 3.3E-29 7.3E-34 250.6 11.0 177 43-243 400-587 (1444)
18 PRK05168 ribonuclease T; Provi 100.0 1.3E-27 2.8E-32 206.4 19.3 167 67-242 15-201 (211)
19 PRK06309 DNA polymerase III su 100.0 1.5E-27 3.3E-32 208.7 19.2 154 69-242 2-166 (232)
20 cd06134 RNaseT DEDDh 3'-5' exo 100.0 1.2E-27 2.6E-32 203.2 17.7 165 69-241 5-188 (189)
21 PRK06807 DNA polymerase III su 100.0 2.6E-27 5.5E-32 215.6 20.4 156 68-242 7-172 (313)
22 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 4.2E-28 9.1E-33 204.0 14.1 155 71-237 1-176 (177)
23 smart00479 EXOIII exonuclease 100.0 8.5E-27 1.8E-31 191.6 19.4 156 70-243 1-168 (169)
24 cd06138 ExoI_N N-terminal DEDD 99.9 5.9E-27 1.3E-31 197.9 16.4 155 72-236 1-183 (183)
25 cd06130 DNA_pol_III_epsilon_li 99.9 1.4E-26 3E-31 188.9 17.4 145 71-236 1-155 (156)
26 PRK06195 DNA polymerase III su 99.9 3.9E-26 8.4E-31 207.7 18.9 153 69-242 1-164 (309)
27 PRK07246 bifunctional ATP-depe 99.9 3.2E-26 6.9E-31 231.2 20.0 157 68-243 6-171 (820)
28 PRK05601 DNA polymerase III su 99.9 1E-25 2.2E-30 206.8 21.4 155 65-238 42-245 (377)
29 PRK07883 hypothetical protein; 99.9 4.9E-26 1.1E-30 221.4 20.5 161 65-243 11-183 (557)
30 PRK07748 sporulation inhibitor 99.9 4.5E-26 9.6E-31 196.1 16.9 159 68-241 3-179 (207)
31 cd06127 DEDDh DEDDh 3'-5' exon 99.9 9.5E-26 2.1E-30 181.6 16.5 147 72-235 1-158 (159)
32 TIGR01405 polC_Gram_pos DNA po 99.9 2.2E-25 4.8E-30 230.7 21.1 159 67-243 188-356 (1213)
33 PRK08074 bifunctional ATP-depe 99.9 2.1E-25 4.4E-30 228.2 20.6 159 68-244 2-171 (928)
34 cd06133 ERI-1_3'hExo_like DEDD 99.9 3.4E-25 7.4E-30 183.9 17.7 156 71-238 1-175 (176)
35 TIGR01407 dinG_rel DnaQ family 99.9 3.1E-25 6.6E-30 225.3 20.0 155 70-242 1-165 (850)
36 PRK07247 DNA polymerase III su 99.9 1.7E-25 3.6E-30 191.2 14.9 153 68-242 4-169 (195)
37 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 3.1E-26 6.7E-31 189.9 10.0 136 72-235 1-160 (161)
38 cd06149 ISG20 DEDDh 3'-5' exon 99.9 8.8E-26 1.9E-30 186.6 11.3 140 72-236 1-157 (157)
39 PRK06722 exonuclease; Provisio 99.9 1.1E-24 2.3E-29 195.2 17.6 158 68-239 4-178 (281)
40 PRK07983 exodeoxyribonuclease 99.9 1.7E-24 3.6E-29 188.1 17.1 138 71-241 2-153 (219)
41 cd06145 REX1_like DEDDh 3'-5' 99.9 8.3E-25 1.8E-29 179.4 12.0 136 72-236 1-150 (150)
42 PRK09182 DNA polymerase III su 99.9 7.8E-24 1.7E-28 191.2 17.5 153 65-240 33-199 (294)
43 PRK11779 sbcB exonuclease I; P 99.9 1.9E-23 4E-28 199.2 19.2 165 68-241 5-197 (476)
44 cd06144 REX4_like DEDDh 3'-5' 99.9 2.8E-24 6.1E-29 176.4 10.5 142 72-236 1-152 (152)
45 PTZ00315 2'-phosphotransferase 99.9 1.8E-22 3.8E-27 194.5 20.7 191 43-240 29-253 (582)
46 COG0847 DnaQ DNA polymerase II 99.9 1.6E-22 3.5E-27 177.1 18.0 156 69-241 13-181 (243)
47 PF00929 RNase_T: Exonuclease; 99.9 1.6E-24 3.5E-29 174.7 1.7 154 72-235 1-164 (164)
48 PRK00448 polC DNA polymerase I 99.9 1.5E-21 3.3E-26 204.6 16.9 158 68-243 418-585 (1437)
49 COG2925 SbcB Exonuclease I [DN 99.7 7.5E-16 1.6E-20 140.6 11.6 165 68-240 8-199 (475)
50 KOG2249 3'-5' exonuclease [Rep 99.5 7.5E-13 1.6E-17 116.1 12.4 142 70-239 106-263 (280)
51 KOG0542 Predicted exonuclease 99.4 2.3E-12 4.9E-17 112.4 13.4 168 66-239 53-239 (280)
52 COG5018 KapD Inhibitor of the 99.4 1.3E-12 2.9E-17 107.7 7.6 164 69-239 4-182 (210)
53 cd06143 PAN2_exo DEDDh 3'-5' e 99.3 5E-12 1.1E-16 105.9 9.8 121 90-236 32-174 (174)
54 cd05160 DEDDy_DNA_polB_exo DED 99.3 1.9E-11 4.2E-16 103.9 10.8 97 72-188 2-104 (199)
55 PHA02570 dexA exonuclease; Pro 99.2 1.9E-10 4E-15 99.2 12.2 162 72-241 4-198 (220)
56 cd06125 DnaQ_like_exo DnaQ-lik 99.2 6E-10 1.3E-14 84.7 11.5 91 72-234 1-94 (96)
57 KOG2248 3'-5' exonuclease [Rep 99.0 8.2E-09 1.8E-13 96.2 12.9 148 66-242 213-375 (380)
58 cd06139 DNA_polA_I_Ecoli_like_ 98.6 9.6E-07 2.1E-11 73.8 12.0 137 67-243 3-171 (193)
59 cd05780 DNA_polB_Kod1_like_exo 98.5 1.5E-06 3.2E-11 74.1 10.8 91 68-188 2-97 (195)
60 PF13482 RNase_H_2: RNase_H su 98.4 4.1E-07 8.9E-12 74.6 4.8 91 72-198 1-92 (164)
61 cd05781 DNA_polB_B3_exo DEDDy 98.4 3.3E-06 7.1E-11 71.8 10.4 82 68-187 2-88 (188)
62 PRK05755 DNA polymerase I; Pro 98.3 1.1E-05 2.3E-10 83.3 13.0 130 68-244 314-471 (880)
63 COG3359 Predicted exonuclease 98.0 2.2E-05 4.8E-10 68.9 8.5 98 68-208 97-199 (278)
64 cd05779 DNA_polB_epsilon_exo D 98.0 5E-05 1.1E-09 65.5 10.1 106 69-187 2-113 (204)
65 cd05777 DNA_polB_delta_exo DED 97.9 4.8E-05 1E-09 66.5 8.8 100 66-186 4-110 (230)
66 cd05785 DNA_polB_like2_exo Unc 97.9 6.6E-05 1.4E-09 64.8 9.2 84 66-187 6-98 (207)
67 KOG4793 Three prime repair exo 97.7 0.0001 2.2E-09 65.5 6.8 171 66-242 10-218 (318)
68 PF04857 CAF1: CAF1 family rib 97.6 0.00069 1.5E-08 60.4 11.3 165 69-236 22-261 (262)
69 cd05783 DNA_polB_B1_exo DEDDy 97.6 0.00032 6.9E-09 60.5 8.6 101 67-188 3-112 (204)
70 PF03104 DNA_pol_B_exo1: DNA p 97.4 0.00069 1.5E-08 61.1 8.2 101 67-186 155-261 (325)
71 cd05784 DNA_polB_II_exo DEDDy 97.3 0.0015 3.2E-08 55.8 8.6 89 68-187 2-91 (193)
72 PTZ00166 DNA polymerase delta 97.2 0.0014 3.1E-08 68.9 8.9 100 66-185 261-368 (1054)
73 cd05778 DNA_polB_zeta_exo inac 97.1 0.0026 5.7E-08 55.7 8.7 107 68-184 3-118 (231)
74 cd05782 DNA_polB_like1_exo Unc 96.8 0.0076 1.6E-07 52.0 8.7 77 76-188 41-118 (208)
75 PF01612 DNA_pol_A_exo1: 3'-5' 96.8 0.045 9.7E-07 44.5 12.8 42 148-197 65-106 (176)
76 KOG1275 PAB-dependent poly(A) 96.6 0.0036 7.8E-08 63.7 6.1 161 60-240 901-1090(1118)
77 PRK05762 DNA polymerase II; Re 96.6 0.037 7.9E-07 56.8 13.4 90 67-187 153-243 (786)
78 smart00486 POLBc DNA polymeras 96.6 0.012 2.6E-07 55.4 9.0 99 68-186 2-108 (471)
79 PHA02528 43 DNA polymerase; Pr 96.0 0.041 8.9E-07 57.0 9.9 103 67-184 104-215 (881)
80 cd06146 mut-7_like_exo DEDDy 3 95.8 0.14 3.1E-06 43.4 10.9 84 152-239 74-192 (193)
81 COG0349 Rnd Ribonuclease D [Tr 95.0 0.1 2.3E-06 48.6 8.0 125 69-244 17-168 (361)
82 cd00007 35EXOc 3'-5' exonuclea 95.0 0.65 1.4E-05 36.4 11.7 55 146-211 40-94 (155)
83 cd06141 WRN_exo DEDDy 3'-5' ex 94.8 0.28 6.2E-06 40.1 9.3 121 68-239 17-169 (170)
84 cd06129 RNaseD_like DEDDy 3'-5 93.1 1 2.2E-05 36.8 9.5 80 152-239 59-160 (161)
85 PRK10829 ribonuclease D; Provi 92.7 2 4.3E-05 40.5 11.9 123 68-243 21-171 (373)
86 KOG0304 mRNA deadenylase subun 92.3 2.2 4.9E-05 37.2 10.7 166 68-241 23-238 (239)
87 COG0417 PolB DNA polymerase el 91.3 0.99 2.2E-05 46.5 8.8 97 65-188 150-252 (792)
88 PF10108 DNA_pol_B_exo2: Predi 91.0 0.33 7.2E-06 42.1 4.4 36 144-183 36-72 (209)
89 KOG3657 Mitochondrial DNA poly 90.5 0.17 3.6E-06 51.6 2.3 35 165-201 242-276 (1075)
90 TIGR01388 rnd ribonuclease D. 90.4 13 0.00028 34.8 14.8 39 152-198 62-100 (367)
91 KOG4793 Three prime repair exo 89.5 0.49 1.1E-05 42.5 4.2 97 149-245 182-294 (318)
92 cd05776 DNA_polB_alpha_exo ina 88.6 0.65 1.4E-05 40.6 4.3 42 142-186 79-121 (234)
93 TIGR03491 RecB family nuclease 87.2 6.2 0.00013 38.0 10.5 95 68-198 283-383 (457)
94 KOG1798 DNA polymerase epsilon 84.5 4.1 8.9E-05 44.5 8.1 100 66-187 243-357 (2173)
95 TIGR00592 pol2 DNA polymerase 83.7 5.7 0.00012 42.8 9.1 109 68-187 505-624 (1172)
96 cd06148 Egl_like_exo DEDDy 3'- 82.9 27 0.00059 29.4 12.0 28 217-244 152-179 (197)
97 COG0749 PolA DNA polymerase I 82.2 9.8 0.00021 38.0 9.4 130 72-245 25-183 (593)
98 PRK05761 DNA polymerase I; Rev 82.1 4 8.7E-05 42.1 7.0 41 143-188 208-249 (787)
99 PHA02524 43A DNA polymerase su 81.7 1.9 4.1E-05 42.1 4.2 39 143-184 178-217 (498)
100 COG5228 POP2 mRNA deadenylase 81.7 9.1 0.0002 33.7 8.0 166 68-245 41-256 (299)
101 PHA03036 DNA polymerase; Provi 80.2 8.7 0.00019 40.7 8.7 112 65-186 156-279 (1004)
102 cd06140 DNA_polA_I_Bacillus_li 77.0 32 0.00069 27.9 9.7 83 69-197 3-85 (178)
103 KOG0969 DNA polymerase delta, 69.3 0.75 1.6E-05 46.9 -2.1 94 67-181 272-372 (1066)
104 TIGR00592 pol2 DNA polymerase 56.8 5.8 0.00012 42.8 1.5 95 66-181 195-304 (1172)
105 PF13017 Maelstrom: piRNA path 50.9 1.5E+02 0.0033 25.4 9.2 75 84-160 6-82 (213)
106 KOG0970 DNA polymerase alpha, 50.4 56 0.0012 35.2 7.3 109 65-184 525-644 (1429)
107 smart00474 35EXOc 3'-5' exonuc 47.8 49 0.0011 26.0 5.4 41 149-198 64-104 (172)
108 TIGR00593 pola DNA polymerase 39.4 66 0.0014 33.9 6.0 91 145-243 363-478 (887)
109 PF11288 DUF3089: Protein of u 37.7 44 0.00096 28.9 3.8 42 142-183 74-117 (207)
110 cd09018 DEDDy_polA_RNaseD_like 34.0 1.2E+02 0.0025 23.4 5.5 38 152-197 45-82 (150)
111 PHA02563 DNA polymerase; Provi 31.6 48 0.001 33.5 3.4 38 149-186 50-88 (630)
112 cd06142 RNaseD_exo DEDDy 3'-5' 27.8 1.8E+02 0.0039 23.2 5.7 38 152-197 56-93 (178)
113 PHA01746 hypothetical protein 27.8 65 0.0014 25.2 2.8 56 87-158 34-89 (131)
114 PF03337 Pox_F12L: Poxvirus F1 26.2 55 0.0012 33.1 2.7 45 142-186 251-298 (651)
115 PF12083 DUF3560: Domain of un 21.2 1.8E+02 0.0038 23.2 4.2 27 161-187 40-67 (126)
116 COG4674 Uncharacterized ABC-ty 20.9 1.7E+02 0.0036 25.8 4.3 26 76-101 132-169 (249)
No 1
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=100.00 E-value=1.2e-44 Score=296.71 Aligned_cols=182 Identities=60% Similarity=0.959 Sum_probs=176.0
Q ss_pred ccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCH
Q 025709 66 EYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 145 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~ 145 (249)
....++||+|||||||+..+|+|||||||++||.++...+.|+++|+++.++++.|++||+.||+.+|||..++++..++
T Consensus 23 ~l~q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl 102 (208)
T KOG3242|consen 23 KLKQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITL 102 (208)
T ss_pred cccCceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCcccCCCCCCCCCcHH
Q 025709 146 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRAL 225 (249)
Q Consensus 146 ~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~~~l~~~~~HrAl 225 (249)
.||..++++|++.++++|.++|+|++++.|+.||.++||.+-..++++.+|++++.+||+||+|....+.|.....|||+
T Consensus 103 ~~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL~~Rw~P~~~~~aPkK~~~HrAl 182 (208)
T KOG3242|consen 103 ADAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKELARRWYPDIKARAPKKKATHRAL 182 (208)
T ss_pred HHHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHHHHHhCchhhccCcccccccchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999988889999999999
Q ss_pred HHHHHHHHHHHHHHHHhcCcCC
Q 025709 226 DDIRESIMELKYYKENIFKTNL 247 (249)
Q Consensus 226 ~Da~aT~~ll~~~~~~~~~~~~ 247 (249)
+|++.+++.|+|||+++|+++.
T Consensus 183 dDI~ESI~ELq~Yr~nifkk~~ 204 (208)
T KOG3242|consen 183 DDIRESIKELQYYRENIFKKST 204 (208)
T ss_pred HHHHHHHHHHHHHHHHhccCcc
Confidence 9999999999999999999853
No 2
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=100.00 E-value=2.4e-44 Score=292.49 Aligned_cols=181 Identities=48% Similarity=0.709 Sum_probs=174.4
Q ss_pred ccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCH
Q 025709 66 EYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 145 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~ 145 (249)
....++||||||||||+|.+|+|||||+|++|++++.+.+++...|+++.+.+..|++||+.+|+.+||+....++..++
T Consensus 3 ~~~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~ 82 (184)
T COG1949 3 ANKNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTE 82 (184)
T ss_pred CcCCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccH
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCcccCCCCCCCCCcHH
Q 025709 146 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRAL 225 (249)
Q Consensus 146 ~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~~~l~~~~~HrAl 225 (249)
.+|..+.++||+++++.+.++++|+++.-|++||-++||++..+|+++.+||+++.+||+||.|....+ +.+...|+||
T Consensus 83 ~~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVSTlKELa~RW~P~i~~~-~~K~~~H~Al 161 (184)
T COG1949 83 AEAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVSTLKELARRWNPEILAG-FKKGGTHRAL 161 (184)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHHHHHHHHhhCcHhhhc-cccccchhHH
Confidence 999999999999999998889999999999999999999999999999999999999999999998766 8899999999
Q ss_pred HHHHHHHHHHHHHHHHhcCcCC
Q 025709 226 DDIRESIMELKYYKENIFKTNL 247 (249)
Q Consensus 226 ~Da~aT~~ll~~~~~~~~~~~~ 247 (249)
+|++.++..|+|||++||++++
T Consensus 162 ~DI~ESI~EL~~YR~~f~~~~~ 183 (184)
T COG1949 162 DDIRESIAELRYYREHFLKPAP 183 (184)
T ss_pred HHHHHHHHHHHHHHHHhccCCC
Confidence 9999999999999999999976
No 3
>PRK05359 oligoribonuclease; Provisional
Probab=100.00 E-value=8.8e-41 Score=282.29 Aligned_cols=179 Identities=48% Similarity=0.711 Sum_probs=162.0
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
..+|||||+|||||+|.+|+|||||||+++++...+.+.++.+|+|+..++..++.|+..+|.+||||+++++++|++.+
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~e 81 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAE 81 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHHH
Confidence 46899999999999999999999999999888766777899999998877666789999888999999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCcccCCCCCCCCCcHHHH
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDD 227 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~~~l~~~~~HrAl~D 227 (249)
++.+|++|++++++.+.+++||||+.||+.||++++++++.+++++++|++++++++++|+|.. .++++....|||++|
T Consensus 82 ~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P~~-~~~~~~~~~HRal~D 160 (181)
T PRK05359 82 AEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKPEI-LNGFKKQGTHRALAD 160 (181)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhChhh-hhCCCCcCCcccHHH
Confidence 9999999998766544567899999999999999999999999999999999989999999985 346777889999999
Q ss_pred HHHHHHHHHHHHHHhcCcCC
Q 025709 228 IRESIMELKYYKENIFKTNL 247 (249)
Q Consensus 228 a~aT~~ll~~~~~~~~~~~~ 247 (249)
|++|+++|++|++.+|+..+
T Consensus 161 ~~~s~~~~~~~~~~~~~~~~ 180 (181)
T PRK05359 161 IRESIAELKYYREHFFKLAP 180 (181)
T ss_pred HHHHHHHHHHHHHHhccCCC
Confidence 99999999999999998754
No 4
>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=100.00 E-value=7e-38 Score=262.56 Aligned_cols=172 Identities=61% Similarity=0.941 Sum_probs=153.2
Q ss_pred EEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHH
Q 025709 71 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEK 150 (249)
Q Consensus 71 ~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~ 150 (249)
+||||+||||++|.+++|||||||.+++....+.+.|+.+|+|...++..+++|+..+|.+|||+++++.++|++.+++.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~ 80 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEA 80 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHH
Confidence 58999999999999999999999988887655667899999998876555567888888899999999999999999999
Q ss_pred HHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCcccCCCCCCCCCcHHHHHHH
Q 025709 151 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDIRE 230 (249)
Q Consensus 151 ~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~~~l~~~~~HrAl~Da~a 230 (249)
+|.+|++++...+..++||||+.||+.||++++++++.+++++.+|++++.+++++++|...+.++....+|||++||++
T Consensus 81 ~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p~~~~~~~~~~~~HrAl~Da~~ 160 (173)
T cd06135 81 ELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYPEIYRKAPKKKGTHRALDDIRE 160 (173)
T ss_pred HHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCcHhhhcCCCCCCCcchHHHHHH
Confidence 99999987543334678999999999999999999888888999999998899999999876667778889999999999
Q ss_pred HHHHHHHHHHHh
Q 025709 231 SIMELKYYKENI 242 (249)
Q Consensus 231 T~~ll~~~~~~~ 242 (249)
|+.+|++|++.+
T Consensus 161 ~~~~~~~~~~~~ 172 (173)
T cd06135 161 SIAELKYYRENI 172 (173)
T ss_pred HHHHHHHHHHHh
Confidence 999999999876
No 5
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=1.1e-30 Score=229.58 Aligned_cols=170 Identities=17% Similarity=0.162 Sum_probs=141.0
Q ss_pred CCCcccccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHH
Q 025709 60 QTPLEFEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVL 139 (249)
Q Consensus 60 ~~~~~~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l 139 (249)
...+.+....+||+||+||||++|.+|+|||||+|.+++......+.++++|+|..++ ++.+. .+||||++++
T Consensus 38 ~~~~~~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i----~~~~~---~IhGIt~e~l 110 (239)
T PRK09146 38 VSPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPL----EEESV---VIHGITHSEL 110 (239)
T ss_pred CCCCCCcccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCC----Chhhh---hhcCCCHHHH
Confidence 4555577789999999999999999999999999976655444456789999998765 34444 4569999999
Q ss_pred hcCCCHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhc-cCCCCCceeehhHHHHHHHHHCCCc-------
Q 025709 140 HSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDL-ASLFSHVLVDVSSIKALCMRWYPRD------- 211 (249)
Q Consensus 140 ~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~-~~~~~~~~iD~~sl~~la~r~~p~~------- 211 (249)
.++|++.+++.+|.+|+++ .++||||+.||+.||++.+.++ +..++++++|| ++++++++|..
T Consensus 111 ~~ap~~~evl~~l~~~~~~------~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDT---l~Lar~l~~~~~~~~~~~ 181 (239)
T PRK09146 111 QDAPDLERILDELLEALAG------KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDT---MEIEARIQRKQAGGLWNR 181 (239)
T ss_pred hCCCCHHHHHHHHHHHhCC------CEEEEECHHHHHHHHHHHHHHhcCCCCCCceech---HHHHHHHcccccccccch
Confidence 9999999999999999986 4689999999999999999765 44677889999 56777765532
Q ss_pred ------c---------cCCCCCCCCCcHHHHHHHHHHHHHHHHHHhcCc
Q 025709 212 ------Y---------RKVPSKEQKHRALDDIRESIMELKYYKENIFKT 245 (249)
Q Consensus 212 ------~---------~~~l~~~~~HrAl~Da~aT~~ll~~~~~~~~~~ 245 (249)
. .++++..++|||++||.+|++++..+.+.+|..
T Consensus 182 ~~~~~~~~~~L~~l~~~~gl~~~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 182 LKGKKPESIRLADSRLRYGLPAYSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred hccCCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 1 135778899999999999999999999999876
No 6
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=5.3e-30 Score=219.53 Aligned_cols=161 Identities=22% Similarity=0.267 Sum_probs=131.7
Q ss_pred cCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 67 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 67 ~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
.+.+||+||+||||++|..++|||||+|.+++......+.|+.+|+|...+ +++++ .+||||+++++++|++.
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i----~~~~~---~ihGIt~~~l~~~~~~~ 99 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSL----SAESI---KIHRLRHQDLEDGLSEE 99 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCC----CHhHh---hhcCcCHHHHhcCCCHH
Confidence 357999999999999999999999999988776655557899999998654 56666 45699999999999999
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHh-ccCCCCCceeehhHHHH-HHHHHCCC-cc---------cC
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPD-LASLFSHVLVDVSSIKA-LCMRWYPR-DY---------RK 214 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~-~~~~~~~~~iD~~sl~~-la~r~~p~-~~---------~~ 214 (249)
+++.+|.+|+++ .++||||+.||+.||++++.+ ++..++++++|+++++. ...+.+|. .. .+
T Consensus 100 ~vl~~~~~~i~~------~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~ 173 (202)
T PRK09145 100 EALRQLLAFIGN------RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHL 173 (202)
T ss_pred HHHHHHHHHHcC------CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHc
Confidence 999999999986 468999999999999999865 46678889999987652 22223343 11 24
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHHHHH
Q 025709 215 VPSKEQKHRALDDIRESIMELKYYKE 240 (249)
Q Consensus 215 ~l~~~~~HrAl~Da~aT~~ll~~~~~ 240 (249)
+++..++|+|++||++|++|+..++.
T Consensus 174 gi~~~~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 174 DLPVLGRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHh
Confidence 67778899999999999999988753
No 7
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=5.4e-30 Score=225.21 Aligned_cols=156 Identities=19% Similarity=0.160 Sum_probs=127.9
Q ss_pred CCcEEEEEEecCCCCCC-CCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 68 KMPLVWIDLEMTGLKIE-VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~-~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
.++||+||+||||++|. .|+|||||||...+... .++.|+.+|+|..++ ++.+. .+||||++++.++|++.
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~-~~~~f~~~i~P~~~i----~~~a~---~VHGIT~e~l~~~p~f~ 74 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINRRL-TGRNFHVYIKPDRLV----DPEAL---AVHGITDEFLADKPTFA 74 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEE-eccEEEEEECcCCcC----CHHHh---hhcCCCHHHHcCCCCHH
Confidence 47899999999999997 89999999995443332 356799999997765 55565 45699999999999999
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCC-----CceeehhHHHHHHHHHCCCccc--------
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-----HVLVDVSSIKALCMRWYPRDYR-------- 213 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-----~~~iD~~sl~~la~r~~p~~~~-------- 213 (249)
+++.+|++|+++ .+|||||+.||+.||++++.+++..++ +.++|+ +.++++++|....
T Consensus 75 ev~~~f~~fi~~------~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDT---l~lar~~~p~~~~~L~aL~~~ 145 (240)
T PRK05711 75 EVADEFLDFIRG------AELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDT---LAMARRMFPGKRNSLDALCKR 145 (240)
T ss_pred HHHHHHHHHhCC------CEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeH---HHHHHHHcCCCCCCHHHHHHH
Confidence 999999999987 468999999999999999988874443 568999 6788888886432
Q ss_pred CCCCCC--CCCcHHHHHHHHHHHHHHHHH
Q 025709 214 KVPSKE--QKHRALDDIRESIMELKYYKE 240 (249)
Q Consensus 214 ~~l~~~--~~HrAl~Da~aT~~ll~~~~~ 240 (249)
++++.. ..|+|+.||++|++||..+..
T Consensus 146 ~gi~~~~r~~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 146 YGIDNSHRTLHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHC
Confidence 455543 469999999999999988753
No 8
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.97 E-value=1.9e-29 Score=219.94 Aligned_cols=153 Identities=18% Similarity=0.227 Sum_probs=125.3
Q ss_pred cEEEEEEecCCCCCCC-CceEEEEEE-EEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 70 PLVWIDLEMTGLKIEV-DRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 70 ~~V~lDlETTGL~p~~-d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
++|+||+||||++|.. ++||||||| +.++.. .++.|+.+|+|..++ ++.++ .+||||+++++++|++.+
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~--~~~~f~~~i~P~~~i----~~~a~---~vhGIt~e~l~~~p~f~e 71 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRML--TGDNFHVYVNPERDM----PAEAA---KVHGITDEFLADKPKFKE 71 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcE--ecceEEEEECcCCCC----CHHHH---hccCCCHHHHhCCCCHHH
Confidence 4899999999999986 899999999 444333 356799999998765 45565 556999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC--C-CC--CceeehhHHHHHHHHHCCCcc--------cC
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS--L-FS--HVLVDVSSIKALCMRWYPRDY--------RK 214 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~--~-~~--~~~iD~~sl~~la~r~~p~~~--------~~ 214 (249)
++.+|++|+++ .++||||+.||+.||+.++.+++. . +. ++++|+ +.++++++|... .+
T Consensus 72 v~~~f~~fi~~------~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDT---l~lar~~~p~~~~~L~~L~~~~ 142 (225)
T TIGR01406 72 IADEFLDFIGG------SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDT---LAMARERFPGQRNSLDALCKRF 142 (225)
T ss_pred HHHHHHHHhCC------CEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEH---HHHHHHHcCCCCCCHHHHHHhc
Confidence 99999999987 468999999999999999988873 2 32 679999 578888888643 23
Q ss_pred CCCC--CCCCcHHHHHHHHHHHHHHHHH
Q 025709 215 VPSK--EQKHRALDDIRESIMELKYYKE 240 (249)
Q Consensus 215 ~l~~--~~~HrAl~Da~aT~~ll~~~~~ 240 (249)
+++. ...|+|+.||++++++|..+..
T Consensus 143 gi~~~~r~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 143 KVDNSHRTLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred CCCCCCCCCcCHHHHHHHHHHHHHHHHc
Confidence 5544 3579999999999999988754
No 9
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=6.7e-29 Score=218.91 Aligned_cols=162 Identities=20% Similarity=0.171 Sum_probs=134.0
Q ss_pred cccCCcEEEEEEecCCCCCCC-CceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC
Q 025709 65 FEYKMPLVWIDLEMTGLKIEV-DRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 143 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~-d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p 143 (249)
.....+||+||+||||++|.. ++|||||||.+++... ..+.|+.+|+|..++ ++.+. .+||||+++++++|
T Consensus 55 ~~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i-~~~~f~~lv~P~~~i----~~~~~---~ltGIt~e~l~~ap 126 (244)
T PRK07740 55 PLTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEV-ETDTFYSLVKPKRPI----PEHIL---ELTGITAEDVAFAP 126 (244)
T ss_pred CccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEE-EEEEEEEEeCcCCCC----Chhhe---eccCCCHHHHhCCC
Confidence 456789999999999999986 8999999997766554 346789999998765 45555 67799999999999
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHH-hccCCCCCceeehhHHHHHHHHHCCCcc---------c
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMP-DLASLFSHVLVDVSSIKALCMRWYPRDY---------R 213 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~-~~~~~~~~~~iD~~sl~~la~r~~p~~~---------~ 213 (249)
++.+++.+|.+|+++ .++||||+.||+.||++.+. .++.+++++++|+. .+++.+.|... .
T Consensus 127 ~~~evl~~f~~fi~~------~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~---~l~r~l~~~~~~~sL~~l~~~ 197 (244)
T PRK07740 127 PLAEVLHRFYAFIGA------GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTM---FLTKLLAHERDFPTLDDALAY 197 (244)
T ss_pred CHHHHHHHHHHHhCC------CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechH---HHHHHHcCCCCCCCHHHHHHH
Confidence 999999999999986 46899999999999999874 45667788999994 45666666532 2
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 214 KVPSKEQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 214 ~~l~~~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
++++..++|+|++||++|++++..+.+.+.
T Consensus 198 ~gi~~~~~H~Al~Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 198 YGIPIPRRHHALGDALMTAKLWAILLVEAQ 227 (244)
T ss_pred CCcCCCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 467778899999999999999999876654
No 10
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.2e-28 Score=218.11 Aligned_cols=158 Identities=21% Similarity=0.275 Sum_probs=129.0
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
+++||+||+||||++|.+|+|||||+|.+++... .+.++.+|+|..++ ++.+. .+||||+++++++|++.+
T Consensus 6 ~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~--~~~~~~li~P~~~I----~~~a~---~ihgIt~e~v~~~p~~~e 76 (250)
T PRK06310 6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEV--IDSVEFLINPERVV----SAESQ---RIHHISDAMLRDKPKIAE 76 (250)
T ss_pred CCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeE--EEEEEEEECcCCCC----CHhhh---hccCcCHHHHhCCCCHHH
Confidence 4789999999999999999999999997665432 35688999998766 34444 456999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCC---CCceeehhHHHHHHHHHCCCcc--------cCCC
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF---SHVLVDVSSIKALCMRWYPRDY--------RKVP 216 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~---~~~~iD~~sl~~la~r~~p~~~--------~~~l 216 (249)
++.+|.+|+++. .++||||+.||+.||++++.+.+..+ +++++|| ..+++++.+... .+++
T Consensus 77 v~~~~~~fl~~~-----~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDt---l~lar~~~~~~~~~L~~l~~~~g~ 148 (250)
T PRK06310 77 VFPQIKGFFKEG-----DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDT---LRLAKEYGDSPNNSLEALAVHFNV 148 (250)
T ss_pred HHHHHHHHhCCC-----CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEeh---HHHHHhcccCCCCCHHHHHHHCCC
Confidence 999999999752 47999999999999999999887644 3679999 466776632211 2466
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 217 SKEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 217 ~~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
+..++|||++||.+|++|++++.+.+
T Consensus 149 ~~~~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 149 PYDGNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CCCCCcChHHHHHHHHHHHHHHHHhc
Confidence 77889999999999999999987653
No 11
>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=99.96 E-value=1.4e-28 Score=203.59 Aligned_cols=151 Identities=21% Similarity=0.206 Sum_probs=121.0
Q ss_pred EEEEEEecCCCCC-CCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHH
Q 025709 71 LVWIDLEMTGLKI-EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 149 (249)
Q Consensus 71 ~V~lDlETTGL~p-~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~ 149 (249)
||+||+||||++| ..++|||||+|.+++... ..+.|+.+|+|..++ ++.++ .+||||++++++++++.+++
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~-~~~~~~~~v~P~~~i----~~~~~---~ihGIt~e~l~~~~~~~~v~ 72 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRL-TGNTFHVYINPERDI----PEEAF---KVHGITDEFLADKPKFAEIA 72 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcE-eccEEEEEECCCCCC----CHHHH---HHhCCCHHHHhcCCCHHHHH
Confidence 6899999999999 679999999996554332 345788999998754 56666 45599999999999999999
Q ss_pred HHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC----CCCCceeehhHHHHHHHHHCCCcc--------cCCCC
Q 025709 150 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS----LFSHVLVDVSSIKALCMRWYPRDY--------RKVPS 217 (249)
Q Consensus 150 ~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~----~~~~~~iD~~sl~~la~r~~p~~~--------~~~l~ 217 (249)
.+|.+|+++ .++||||+.||+.||++++.+.+. ..++.++|+ +.++++++|... .++++
T Consensus 73 ~~l~~~l~~------~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt---~~~~~~~~~~~~~~L~~l~~~~~i~ 143 (167)
T cd06131 73 DEFLDFIRG------AELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDT---LALARKKFPGKPNSLDALCKRFGID 143 (167)
T ss_pred HHHHHHHCC------CeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEh---HHHHHHHcCCCCCCHHHHHHHCCCC
Confidence 999999986 468999999999999999988643 234678999 456777776422 13555
Q ss_pred C--CCCCcHHHHHHHHHHHHHHH
Q 025709 218 K--EQKHRALDDIRESIMELKYY 238 (249)
Q Consensus 218 ~--~~~HrAl~Da~aT~~ll~~~ 238 (249)
. .++|+|++||++|++++.++
T Consensus 144 ~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 144 NSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCCChHHHHHHHHHHHHHh
Confidence 4 35799999999999999764
No 12
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=2.9e-28 Score=213.38 Aligned_cols=166 Identities=16% Similarity=0.091 Sum_probs=129.7
Q ss_pred cccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhc-CC
Q 025709 65 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS-GL 143 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~-~p 143 (249)
++...+||+||+||||++|..++|||||+|.++.+... .+.++++|+|..++ ++.++ .+||||++++.+ ++
T Consensus 2 ~~~~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~-~~~~~~lv~P~~~i----~~~a~---~IhGIt~e~l~~~g~ 73 (232)
T PRK07942 2 SWHPGPLAAFDLETTGVDPETARIVTAALVVVDADGEV-VESREWLADPGVEI----PEEAS---AVHGITTEYARAHGR 73 (232)
T ss_pred CcccCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCcc-ccceEEEECCCCCC----CHHHH---HHhCCCHHHHHhhCC
Confidence 57788999999999999999999999999977632221 24678999998765 45555 456999999975 78
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCC--CCCceeehhHHHHHHHHHCCCc---c------
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL--FSHVLVDVSSIKALCMRWYPRD---Y------ 212 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~--~~~~~iD~~sl~~la~r~~p~~---~------ 212 (249)
++.+++.+|..++.+....+ .+|||||+.||+.||++++.+++.. .+.+++|+. .+++.+.+.. .
T Consensus 74 ~~~~vl~e~~~~l~~~~~~~-~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~---~l~~~~~~~~~~~~~L~~l~ 149 (232)
T PRK07942 74 PAAEVLAEIADALREAWARG-VPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPY---VIDKAVDRYRKGKRTLTALC 149 (232)
T ss_pred CHHHHHHHHHHHHHHHhhcC-CEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHH---HHHhhhhcccCCCCCHHHHH
Confidence 89999999999997543222 4689999999999999999988753 356789995 4555443321 1
Q ss_pred -cCCCCCCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 213 -RKVPSKEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 213 -~~~l~~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
.++++..++|||++||++|++|+..+.+.+
T Consensus 150 ~~~gi~~~~aH~Al~Da~ata~l~~~l~~~~ 180 (232)
T PRK07942 150 EHYGVRLDNAHEATADALAAARVAWALARRF 180 (232)
T ss_pred HHcCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 256778899999999999999999887655
No 13
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=4.2e-28 Score=215.26 Aligned_cols=159 Identities=17% Similarity=0.206 Sum_probs=131.0
Q ss_pred cccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCC
Q 025709 65 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 144 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~ 144 (249)
.+.+..||+||+||||++|..++|||||||.+++... .+.|+.+|+|+ .+ ++.++ .+||||++++.++|+
T Consensus 64 ~~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i--~~~f~~~v~p~-~i----p~~~~---~itGIt~e~l~~ap~ 133 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEI--IDRFESFVKAK-EV----PEYIT---ELTGITYEDLENAPS 133 (257)
T ss_pred CCCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEE--EEEEEEEECCC-CC----Chhhh---hhcCcCHHHHcCCCC
Confidence 4678899999999999999999999999996543322 24688999985 33 45555 567999999999999
Q ss_pred HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC-CCCCceeehhHHHHHHHHHCCCcc--------cCC
Q 025709 145 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDY--------RKV 215 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iD~~sl~~la~r~~p~~~--------~~~ 215 (249)
+.+|+.+|.+|+++ .++||||+.||+.||++++.+++. .+.++.+|+ +.++++++|... .++
T Consensus 134 ~~evl~~f~~fl~~------~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldt---l~la~~~~~~~~~~L~~L~~~lg 204 (257)
T PRK08517 134 LKEVLEEFRLFLGD------SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCT---IDLAKRTIESPRYGLSFLKELLG 204 (257)
T ss_pred HHHHHHHHHHHHCC------CeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEeh---HHHHHHHccCCCCCHHHHHHHcC
Confidence 99999999999986 468999999999999999988875 466789999 567777766422 135
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 216 PSKEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 216 l~~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
++...+|||++||.+|+++++.+...+
T Consensus 205 i~~~~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 205 IEIEVHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred cCCCCCCChHHHHHHHHHHHHHHHHHh
Confidence 677799999999999999999987654
No 14
>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=99.96 E-value=3.7e-28 Score=210.49 Aligned_cols=159 Identities=16% Similarity=0.125 Sum_probs=126.6
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEE-EcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACII-TDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv-~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
...||+||+||||++|..+ |||||+|. .++.. ..+.|+.+|+|..++ ++.+. .+||||++++.++|++.
T Consensus 6 ~~~fvv~D~ETTGl~~~~~-IIeIgav~v~~~~~--~~~~f~~li~P~~~i----~~~a~---~ihGIt~e~l~~~p~~~ 75 (217)
T TIGR00573 6 LDTETTGDNETTGLYAGHD-IIEIGAVEIINRRI--TGNKFHTYIKPDRPI----DPDAI---KIHGITDDMLKDKPDFK 75 (217)
T ss_pred ecCEEEEEecCCCCCCCCC-EEEEEEEEEECCCE--eeeEEEEEECcCCCC----CHHHH---hhcCCCHHHHcCCCCHH
Confidence 4789999999999999888 99999996 55543 245789999998655 44555 55699999999999999
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC--CCCCceeehhHHHHHHHHHCCCcc--------cCCC
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS--LFSHVLVDVSSIKALCMRWYPRDY--------RKVP 216 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~--~~~~~~iD~~sl~~la~r~~p~~~--------~~~l 216 (249)
+++.+|.+|+++ .++||||+.||+.||++++.+++. +.+++++|+..+.+..+...|... .+++
T Consensus 76 ev~~~~~~~~~~------~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl 149 (217)
T TIGR00573 76 EIAEDFADYIRG------AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEI 149 (217)
T ss_pred HHHHHHHHHhCC------CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCC
Confidence 999999999986 468999999999999999988754 345678999655544444444211 1355
Q ss_pred CCC--CCCcHHHHHHHHHHHHHHHHHHh
Q 025709 217 SKE--QKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 217 ~~~--~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
+.. .+|+|++||++|+++++.+.+..
T Consensus 150 ~~~~~~~H~Al~DA~~ta~l~~~l~~~~ 177 (217)
T TIGR00573 150 TNSHRALHGALADAFILAKLYLVMTGKQ 177 (217)
T ss_pred CCCCcccCCHHHHHHHHHHHHHHHHhcc
Confidence 554 78999999999999999987664
No 15
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.96 E-value=3.1e-28 Score=221.75 Aligned_cols=159 Identities=18% Similarity=0.157 Sum_probs=130.8
Q ss_pred cccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCC
Q 025709 65 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 144 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~ 144 (249)
..++.+||+||+||||++|.+++|||||+|.++++.. +.+.|+.+|+|.... .++ .+||||++++.++|+
T Consensus 11 ~~~~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~-i~~~~~~lv~P~~~~------~~~---~IhGIt~e~l~~ap~ 80 (313)
T PRK06063 11 SHYPRGWAVVDVETSGFRPGQARIISLAVLGLDADGN-VEQSVVTLLNPGVDP------GPT---HVHGLTAEMLEGQPQ 80 (313)
T ss_pred cCCCCCEEEEEEECCCCCCCCCEEEEEEEEEEECCce-eeeEEEEEECcCCCC------CCe---ecCCCCHHHHhCCCC
Confidence 3557899999999999999999999999997754333 235788999996432 222 466999999999999
Q ss_pred HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCC-CceeehhHHHHHHHHHCCCccc---------C
Q 025709 145 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRWYPRDYR---------K 214 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-~~~iD~~sl~~la~r~~p~~~~---------~ 214 (249)
+.+++.+|.+|+++ .++||||+.||+.||++++.+++..++ +.++|+ +.+++++.|.... +
T Consensus 81 f~ev~~~l~~~l~~------~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldT---l~lar~~~~~~~~~kL~~l~~~~ 151 (313)
T PRK06063 81 FADIAGEVAELLRG------RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCT---VELARRLGLGLPNLRLETLAAHW 151 (313)
T ss_pred HHHHHHHHHHHcCC------CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEeh---HHHHHHhccCCCCCCHHHHHHHc
Confidence 99999999999986 478999999999999999998886554 468999 5778887765433 3
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 215 VPSKEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 215 ~l~~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
+++..++|||++||++|++++..+.+..
T Consensus 152 gi~~~~~H~Al~DA~ata~l~~~ll~~~ 179 (313)
T PRK06063 152 GVPQQRPHDALDDARVLAGILRPSLERA 179 (313)
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 5677899999999999999998887665
No 16
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.96 E-value=8.6e-28 Score=205.97 Aligned_cols=168 Identities=20% Similarity=0.185 Sum_probs=127.5
Q ss_pred cccCCcEEEEEEecCCCCCCCCceEEEEEEEE--cCc-EeeeeccceEEecCC--CcccccchhhhhhhhhccCCcHH-H
Q 025709 65 FEYKMPLVWIDLEMTGLKIEVDRILEIACIIT--DGK-LTKSVEGPDLVIHQT--KECLDSMGEWCQNHHEASGLTKK-V 138 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~--dg~-~~~~~~~~~~~I~p~--~~~~~~~~~~~~~~h~~tGIt~~-~ 138 (249)
.+....+|+||+||||++|.+|+|||||+|.+ ++. .....+.|+.+++|. .++ +..+. .+||||++ +
T Consensus 4 ~~~~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i----~~~a~---~ihGIt~~~~ 76 (200)
T TIGR01298 4 RFRGYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANI----QPEAL---EFTGIDLDHP 76 (200)
T ss_pred hhcCCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCC----CHHHH---HccCCChhhh
Confidence 45667899999999999999999999999954 222 222346789999984 333 34444 56699975 6
Q ss_pred HhcCCCHHHHHHHHHHHHhcccCC---CCcEEEEecHHHHHHHHHHHHHhccCC---C-CCceeehhHHHHHHHHHCCCc
Q 025709 139 LHSGLTEREAEKQVVEFVKKNVGT---YTPLLAGNSVYVDFMFLKKYMPDLASL---F-SHVLVDVSSIKALCMRWYPRD 211 (249)
Q Consensus 139 l~~~p~~~ea~~~~~~fl~~~~~~---~~~~lVghn~~FD~~fL~~~~~~~~~~---~-~~~~iD~~sl~~la~r~~p~~ 211 (249)
+.+++++.+++.+++.|+.+.... +..++||||+.||+.||++++.+++.. + ++.++|| +.+++..+|..
T Consensus 77 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDT---l~lar~~~~~~ 153 (200)
T TIGR01298 77 LRGAVSEYEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDT---ATLAGLAYGQT 153 (200)
T ss_pred hhcCcchHHHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEH---HHHHHHHcCcc
Confidence 999999999999999998643211 235799999999999999999887642 2 3568999 56777777653
Q ss_pred c------cCCCCC--CCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 212 Y------RKVPSK--EQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 212 ~------~~~l~~--~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
. .++++. .++|||++||.+|++|+..+.+.+
T Consensus 154 ~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 154 VLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred cHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHH
Confidence 2 245553 589999999999999999887665
No 17
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.96 E-value=3.3e-29 Score=250.62 Aligned_cols=177 Identities=19% Similarity=0.266 Sum_probs=154.5
Q ss_pred cccCCCCcchhccccCCCCCcccccCCcEEEEEEecCCCCCCCCceEEEEEE-EEcCcEeeeeccceEEecCCCcccccc
Q 025709 43 SKANSSSNLTLENQQNSQTPLEFEYKMPLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSM 121 (249)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~lDlETTGL~p~~d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~ 121 (249)
-+.++|.+++.||..++.-. +..||+||+|||||+|..+.||||||+ +..|+.+ +.|+.+|+|..++
T Consensus 400 anlvdD~vpiv~N~~d~~l~-----datyVVfDiETTGLs~~~d~iIE~aAvKikng~iI---d~f~~Fi~P~~pl---- 467 (1444)
T COG2176 400 ANLVDDGVPIVYNPDDQKLD-----DATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRII---DKFQFFIKPGRPL---- 467 (1444)
T ss_pred eeeccCCCceecCccccccc-----cccEEEEEeecCCcCcccchhhhheeeeeeCCcch---HHHHHhcCCCCcC----
Confidence 45589999999998775555 488999999999999999999999999 6677765 5789999999887
Q ss_pred hhhhhhhhhccCCcHHHHhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC-CCCCceeehhHH
Q 025709 122 GEWCQNHHEASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSI 200 (249)
Q Consensus 122 ~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iD~~sl 200 (249)
+...+ ++||||++||.+++++.+|+.+|.+|+++ +++|+||++||.+||+..+.+++. ++.+++|||
T Consensus 468 ~~~~t---elTgITdeml~~a~~i~~vL~kf~~~~~d------~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDT--- 535 (1444)
T COG2176 468 SATIT---ELTGITDEMLENAPEIEEVLEKFREFIGD------SILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDT--- 535 (1444)
T ss_pred chhhh---hccccCHHHHcCCccHHHHHHHHHHHhcC------cEEEeccCccchhHHHHHHHHhCCccccCchhhH---
Confidence 34444 89999999999999999999999999998 689999999999999999988875 678999999
Q ss_pred HHHHHHHCCCcccCC---------CCCCCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 201 KALCMRWYPRDYRKV---------PSKEQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 201 ~~la~r~~p~~~~~~---------l~~~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
++|||.++|...+++ +....+|||.+|+.+|+.++.++.+...
T Consensus 536 L~lar~L~P~~ksh~Lg~l~kk~~v~le~hHRA~yDaeat~~vf~~f~~~~k 587 (1444)
T COG2176 536 LELARALNPEFKSHRLGTLCKKLGVELERHHRADYDAEATAKVFFVFLKDLK 587 (1444)
T ss_pred HHHHHHhChhhhhcchHHHHHHhCccHHHhhhhhhhHHHHHHHHHHHHHHHH
Confidence 789999999876653 4668999999999999999999877653
No 18
>PRK05168 ribonuclease T; Provisional
Probab=99.96 E-value=1.3e-27 Score=206.44 Aligned_cols=167 Identities=19% Similarity=0.204 Sum_probs=128.3
Q ss_pred cCCcEEEEEEecCCCCCCCCceEEEEEEEEc----CcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHH-Hhc
Q 025709 67 YKMPLVWIDLEMTGLKIEVDRILEIACIITD----GKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV-LHS 141 (249)
Q Consensus 67 ~~~~~V~lDlETTGL~p~~d~IIEIgaVv~d----g~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~-l~~ 141 (249)
....+|+||+||||++|.+|+|||||+|.+. |.+ ...+.|+++|+|+... .+++.++ .+||||+++ +++
T Consensus 15 ~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i-~~~~~f~~lv~P~~~~--~i~~~~~---~ihGIt~e~~~~~ 88 (211)
T PRK05168 15 RGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWL-YPDETLHFHVEPFEGA--NLEPEAL---AFNGIDPDNPLRG 88 (211)
T ss_pred cCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcE-eccceEEEEECCCCCC--CCCHHHH---hhcCCCchhhhhc
Confidence 3578899999999999999999999999542 332 2346799999995321 1255565 566999875 899
Q ss_pred CCCHHHHHHHHHHHHhcccCC---CCcEEEEecHHHHHHHHHHHHHhccC---CC-CCceeehhHHHHHHHHHCCCcc--
Q 025709 142 GLTEREAEKQVVEFVKKNVGT---YTPLLAGNSVYVDFMFLKKYMPDLAS---LF-SHVLVDVSSIKALCMRWYPRDY-- 212 (249)
Q Consensus 142 ~p~~~ea~~~~~~fl~~~~~~---~~~~lVghn~~FD~~fL~~~~~~~~~---~~-~~~~iD~~sl~~la~r~~p~~~-- 212 (249)
++++.+++.++++|+++.... +..++||||+.||+.||++++.+++. ++ +++++|| ..++++++|...
T Consensus 89 ~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt---~~lar~~~~~~~L~ 165 (211)
T PRK05168 89 AVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDT---ATLSGLALGQTVLA 165 (211)
T ss_pred CCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeH---HHHHHHHcCCCCHH
Confidence 999999999999999854321 12579999999999999999988763 22 3579999 567777776522
Q ss_pred ----cCCCCC--CCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 213 ----RKVPSK--EQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 213 ----~~~l~~--~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
.++++. ..+|||++||.+|++++..+.+.+
T Consensus 166 ~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 166 KACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred HHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 245553 579999999999999999988765
No 19
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.5e-27 Score=208.71 Aligned_cols=154 Identities=22% Similarity=0.256 Sum_probs=126.4
Q ss_pred CcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHH
Q 025709 69 MPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 148 (249)
Q Consensus 69 ~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea 148 (249)
.++|+||+||||+++.+|+|||||+| ++.. .+.|+.+++|..++ ++.+. .+||||+++++++|++.++
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v--~~~~---~~~f~~lv~P~~~I----~~~a~---~IhGIt~e~v~~~p~f~ev 69 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAY--NGVT---SESFQTLVNPEIPI----PAEAS---KIHGITTDEVADAPKFPEA 69 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEE--cCcc---ccEEEEEeCCCCCC----ChhHH---hhcCCCHHHHhCCCCHHHH
Confidence 46999999999999999999999996 3222 35688999998766 34444 5569999999999999999
Q ss_pred HHHHHHHHhcccCCCCcEEEEec-HHHHHHHHHHHHHhccCC-CCCceeehhHHHHHHHHHCCCccc---------CCCC
Q 025709 149 EKQVVEFVKKNVGTYTPLLAGNS-VYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYR---------KVPS 217 (249)
Q Consensus 149 ~~~~~~fl~~~~~~~~~~lVghn-~~FD~~fL~~~~~~~~~~-~~~~~iD~~sl~~la~r~~p~~~~---------~~l~ 217 (249)
+.+|.+|+++. .++|||| +.||+.||++++.+.+.. ..++++|+ ..++++++|.... ++++
T Consensus 70 ~~~~~~fi~~~-----~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt---~~l~~~~~~~~~~~~L~~l~~~~~~~ 141 (232)
T PRK06309 70 YQKFIEFCGTD-----NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDS---LKWAQKYRPDLPKHNLQYLRQVYGFE 141 (232)
T ss_pred HHHHHHHHcCC-----CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeH---HHHHHHHcCCCCCCCHHHHHHHcCCC
Confidence 99999999752 5789999 599999999999888764 34689999 5677887775432 4567
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 218 KEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 218 ~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
..++|||++||.+|+++|+.+.+.+
T Consensus 142 ~~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 142 ENQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 7889999999999999999987653
No 20
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.96 E-value=1.2e-27 Score=203.24 Aligned_cols=165 Identities=19% Similarity=0.210 Sum_probs=124.0
Q ss_pred CcEEEEEEecCCCCCCCCceEEEEEEEEc-C-c-EeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHH-HhcCCC
Q 025709 69 MPLVWIDLEMTGLKIEVDRILEIACIITD-G-K-LTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV-LHSGLT 144 (249)
Q Consensus 69 ~~~V~lDlETTGL~p~~d~IIEIgaVv~d-g-~-~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~-l~~~p~ 144 (249)
--+|+||+||||++|.+|+|||||||.+. + + .....+.|+++++|+... .+++.+. .+||||+++ +++++.
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~--~i~~~~~---~ihGIt~~~~~~~~~~ 79 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGA--NLDPAAL---EFNGIDPFHPFRFAVD 79 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCC--CCCHHHH---hhcCCCchhhhccccc
Confidence 35789999999999999999999999542 2 1 222346799999995321 1244444 566999876 788898
Q ss_pred HHHHHHHHHHHHhcccCC---CCcEEEEecHHHHHHHHHHHHHhccC---CC-CCceeehhHHHHHHHHHCCCcc-----
Q 025709 145 EREAEKQVVEFVKKNVGT---YTPLLAGNSVYVDFMFLKKYMPDLAS---LF-SHVLVDVSSIKALCMRWYPRDY----- 212 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~---~~~~lVghn~~FD~~fL~~~~~~~~~---~~-~~~~iD~~sl~~la~r~~p~~~----- 212 (249)
..+++.+|+.|+.+.... +..+|||||+.||+.||++++.+++. ++ +++++|+ +.+++.++|...
T Consensus 80 ~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt---~~la~~~~~~~~L~~l~ 156 (189)
T cd06134 80 EKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDT---ATLAGLAYGQTVLAKAC 156 (189)
T ss_pred hHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEH---HHHHHHHhCCCcHHHHH
Confidence 899999999888754321 12579999999999999999988875 33 3568999 567777777531
Q ss_pred -cCCCC--CCCCCcHHHHHHHHHHHHHHHHHH
Q 025709 213 -RKVPS--KEQKHRALDDIRESIMELKYYKEN 241 (249)
Q Consensus 213 -~~~l~--~~~~HrAl~Da~aT~~ll~~~~~~ 241 (249)
.++++ ..++|+|++||++|++|+..+.+.
T Consensus 157 ~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 157 QAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred HHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 24565 357999999999999999988753
No 21
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=2.6e-27 Score=215.60 Aligned_cols=156 Identities=17% Similarity=0.173 Sum_probs=129.2
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
+++||+||+||||++|..++|||||||.+++.. +.+.|+.+|+|..++ ++.++ .+||||+++++++|++.+
T Consensus 7 ~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~--i~~~f~~lVkP~~~I----~~~a~---~ihGIT~e~l~~~~~~~e 77 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHE--LVDQFVSYVNPERPI----PDRIT---SLTGITNYRVSDAPTIEE 77 (313)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEECCE--EEEEEEEEECcCCCC----CHhhh---ccCCCCHHHHhCCCCHHH
Confidence 689999999999999999999999999655433 235788999998755 45555 567999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCC-CCCceeehhHHHHHHHHHCCCccc---------CCCC
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYR---------KVPS 217 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~-~~~~~iD~~sl~~la~r~~p~~~~---------~~l~ 217 (249)
++.+|++|+++ .++||||+.||+.||.+.+.+++.. ..++++|+ ..++++++|.... ++++
T Consensus 78 vl~~f~~fl~~------~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDt---l~la~~~~~~~~~~kL~~L~~~lgi~ 148 (313)
T PRK06807 78 VLPLFLAFLHT------NVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDT---VFLAKKYMKHAPNHKLETLKRMLGIR 148 (313)
T ss_pred HHHHHHHHHcC------CeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeH---HHHHHHHhCCCCCCCHHHHHHHcCCC
Confidence 99999999987 3589999999999999999988864 45679999 4667777775433 3456
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 218 KEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 218 ~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
. ++|||++||++|++|+..+....
T Consensus 149 ~-~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 149 L-SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred C-CCcChHHHHHHHHHHHHHHHHhh
Confidence 6 89999999999999998776544
No 22
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.96 E-value=4.2e-28 Score=204.01 Aligned_cols=155 Identities=16% Similarity=0.155 Sum_probs=117.8
Q ss_pred EEEEEEecCCCC-CCCCceEEEEEEEEcCcEee-----------eeccceEEecCCCcccccchhhhhhhhhccCCcHHH
Q 025709 71 LVWIDLEMTGLK-IEVDRILEIACIITDGKLTK-----------SVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV 138 (249)
Q Consensus 71 ~V~lDlETTGL~-p~~d~IIEIgaVv~dg~~~~-----------~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~ 138 (249)
||+||+|||||+ +.+|+|||||+|.+++.... +.++|+++|+|..++ ++.+. .+||||+++
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I----~~~a~---~IhGIt~e~ 73 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAI----SPGAS---EITGLSNDL 73 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcC----ChhHH---HHhCcCHHH
Confidence 689999999999 68899999999965543211 124689999998766 34444 456999999
Q ss_pred HhcCCCHHH-HHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccCCCC--CceeehhHHHHHHHHHCCCcc--
Q 025709 139 LHSGLTERE-AEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASLFS--HVLVDVSSIKALCMRWYPRDY-- 212 (249)
Q Consensus 139 l~~~p~~~e-a~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~~~--~~~iD~~sl~~la~r~~p~~~-- 212 (249)
+.++|++.+ +.+.+.+|++... +..+|||||+ .||+.||++++.+++..++ +.++|+ +.+++++.|++.
T Consensus 74 l~~~~~~~~~~~~~l~~f~~~~~--~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDt---l~l~r~~~~~L~~l 148 (177)
T cd06136 74 LEHKAPFDSDTANLIKLFLRRQP--KPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDS---LPAFRELDQSLGSL 148 (177)
T ss_pred HhcCCCccHHHHHHHHHHHHhcC--CCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEe---HHHHhhhHhhHHHH
Confidence 999888664 6666777776421 1257999998 8999999999998876554 456898 456676666432
Q ss_pred ---cCCCCCCCCCcHHHHHHHHHHHHHH
Q 025709 213 ---RKVPSKEQKHRALDDIRESIMELKY 237 (249)
Q Consensus 213 ---~~~l~~~~~HrAl~Da~aT~~ll~~ 237 (249)
.++++..++|||++||.+|++++.+
T Consensus 149 ~~~~~~~~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 149 YKRLFGQEPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHhCCCcccccchHHHHHHHHHHHhh
Confidence 2577888999999999999999864
No 23
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.95 E-value=8.5e-27 Score=191.64 Aligned_cols=156 Identities=29% Similarity=0.359 Sum_probs=125.3
Q ss_pred cEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHH
Q 025709 70 PLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 149 (249)
Q Consensus 70 ~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~ 149 (249)
.||+||+||||+++..++|||||+|.+++.. ..+.|+.+|+|...+ +++++ .+||||++++.+++++.+++
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~--~~~~f~~~v~p~~~i----~~~~~---~~~Git~~~l~~~~~~~~~~ 71 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGR--IIVVFDTYVKPDRPI----TDYAT---EIHGITPEMLDDAPTFEEVL 71 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCE--eEEEEEEEECCCCCC----CHHHH---HHhCCCHHHHhCCCCHHHHH
Confidence 4899999999999999999999999777654 345789999996544 66777 55699999999999999999
Q ss_pred HHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccCC--CCCceeehhHHHHHHHHHCCCcc--------cCCCCC
Q 025709 150 KQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASL--FSHVLVDVSSIKALCMRWYPRDY--------RKVPSK 218 (249)
Q Consensus 150 ~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~--~~~~~iD~~sl~~la~r~~p~~~--------~~~l~~ 218 (249)
.+|.+|+++. ++|+||. .||+.||++++.+.+.. +.++++|+. .+++.+.|... .++++.
T Consensus 72 ~~~~~~l~~~------~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~---~~~~~~~~~~~~~L~~l~~~~~~~~ 142 (169)
T smart00479 72 EELLEFLKGK------ILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTL---KLARALNPGRKYSLKKLAERLGLEV 142 (169)
T ss_pred HHHHHHhcCC------EEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHH---HHHHHHCCCCCCCHHHHHHHCCCCC
Confidence 9999999873 4566666 99999999999887653 345689994 56666665321 235555
Q ss_pred CCC-CcHHHHHHHHHHHHHHHHHHhc
Q 025709 219 EQK-HRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 219 ~~~-HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
.++ |+|++||++|+++++.+.+..+
T Consensus 143 ~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 143 IGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 555 9999999999999999987765
No 24
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.95 E-value=5.9e-27 Score=197.86 Aligned_cols=155 Identities=21% Similarity=0.238 Sum_probs=117.7
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhc-CCCHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS-GLTEREAEK 150 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~-~p~~~ea~~ 150 (249)
+|||+||||+++.+|+|||||+|.+++....+ +.|+.+|+|+.... +++.+. .+||||++++++ +|++.+++.
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~-~~~~~~v~p~~~~~--~~~~a~---~ihGIt~e~l~~~~~~~~~~l~ 74 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEI-EPFNIFCRLPPDVL--PSPEAL---IVTGITPQQLLKEGLSEYEFIA 74 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCc-cceeEEEeCCCCCC--CCHHHH---HHhCCCHHHHHhcCCCHHHHHH
Confidence 58999999999999999999999887764434 67899999875321 123333 456999999999 899999999
Q ss_pred HHHHHHhcccCCCCcEEEEec-HHHHHHHHHHHHHhccC-CC------CCceeehhHHHHHHHHHCCC----------cc
Q 025709 151 QVVEFVKKNVGTYTPLLAGNS-VYVDFMFLKKYMPDLAS-LF------SHVLVDVSSIKALCMRWYPR----------DY 212 (249)
Q Consensus 151 ~~~~fl~~~~~~~~~~lVghn-~~FD~~fL~~~~~~~~~-~~------~~~~iD~~sl~~la~r~~p~----------~~ 212 (249)
+|.+|+++. ..++|||| +.||+.||++++.+.+. ++ ++..+|+..+.++.+.+.|. ..
T Consensus 75 ~~~~~~~~~----~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~ 150 (183)
T cd06138 75 KIHRLFNTP----GTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKP 150 (183)
T ss_pred HHHHHHccC----CCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCc
Confidence 999999741 24678986 89999999999987763 22 34568886555555444341 11
Q ss_pred ---------cCCCCCCCCCcHHHHHHHHHHHHH
Q 025709 213 ---------RKVPSKEQKHRALDDIRESIMELK 236 (249)
Q Consensus 213 ---------~~~l~~~~~HrAl~Da~aT~~ll~ 236 (249)
.++++..++|||++||++|++|++
T Consensus 151 ~~~L~~l~~~~gi~~~~~H~Al~Da~~ta~l~~ 183 (183)
T cd06138 151 SFKLEDLAQANGIEHSNAHDALSDVEATIALAK 183 (183)
T ss_pred chhHHHHHHHCCCCccccccHHHHHHHHHHHhC
Confidence 135677899999999999999874
No 25
>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=99.95 E-value=1.4e-26 Score=188.87 Aligned_cols=145 Identities=17% Similarity=0.110 Sum_probs=117.5
Q ss_pred EEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHH
Q 025709 71 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEK 150 (249)
Q Consensus 71 ~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~ 150 (249)
||+||+||||.+ .++|||||+|..++... .++++.+|+|+.++ ++.++ .+||||++++++++++.+++.
T Consensus 1 ~v~~D~Ettg~~--~~~ii~ig~v~~~~~~~--~~~~~~~i~p~~~~----~~~~~---~i~GIt~e~l~~~~~~~~v~~ 69 (156)
T cd06130 1 FVAIDFETANAD--RASACSIGLVKVRDGQI--VDTFYTLIRPPTRF----DPFNI---AIHGITPEDVADAPTFPEVWP 69 (156)
T ss_pred CEEEEEeCCCCC--CCceEEEEEEEEECCEE--EEEEEEEeCcCCCC----Chhhc---cccCcCHHHHhcCCCHHHHHH
Confidence 689999999976 57999999996654432 25688999998754 44455 567999999999999999999
Q ss_pred HHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCC-CCCceeehhHHHHHHHHHCCCccc---------CCCCCCC
Q 025709 151 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYR---------KVPSKEQ 220 (249)
Q Consensus 151 ~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~-~~~~~iD~~sl~~la~r~~p~~~~---------~~l~~~~ 220 (249)
+|.+|+++ .++||||+.||+.||++++.+.+.. .+.+++|+. .+++.++|.... ++++..
T Consensus 70 ~l~~~l~~------~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~---~~~~~~~~~~~~~~L~~l~~~~g~~~~- 139 (156)
T cd06130 70 EIKPFLGG------SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTV---RLARRVWPLLPNHKLNTVAEHLGIELN- 139 (156)
T ss_pred HHHHHhCC------CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHH---HHHHHHhccCCCCCHHHHHHHcCCCcc-
Confidence 99999987 4789999999999999999888753 457899994 566666665322 356666
Q ss_pred CCcHHHHHHHHHHHHH
Q 025709 221 KHRALDDIRESIMELK 236 (249)
Q Consensus 221 ~HrAl~Da~aT~~ll~ 236 (249)
+|||++||++|++++-
T Consensus 140 ~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 140 HHDALEDARACAEILL 155 (156)
T ss_pred CcCchHHHHHHHHHHh
Confidence 9999999999999984
No 26
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=3.9e-26 Score=207.69 Aligned_cols=153 Identities=15% Similarity=0.168 Sum_probs=123.4
Q ss_pred CcEEEEEEecCCCCCCCCceEEEEEEEE-cCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 69 MPLVWIDLEMTGLKIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 69 ~~~V~lDlETTGL~p~~d~IIEIgaVv~-dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
+.||+||+||||. ..|+|||||+|.+ +++.. +.|+++|+|.... +++.++ .+||||+++++++|++.+
T Consensus 1 ~~~vviD~ETTg~--~~d~IieIgav~v~~g~i~---~~f~~lv~P~~~~---~~~~~~---~IhGIT~e~v~~ap~f~e 69 (309)
T PRK06195 1 MNFVAIDFETANE--KRNSPCSIGIVVVKDGEIV---EKVHYLIKPKEMR---FMPINI---GIHGIRPHMVEDELEFDK 69 (309)
T ss_pred CcEEEEEEeCCCC--CCCceEEEEEEEEECCEEE---EEEEEEECCCCCC---CChhhe---eccCcCHHHHhCCCCHHH
Confidence 4799999999975 5689999999955 44332 4688999997531 134444 567999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCC-CceeehhHHHHHHHHHCCCcccC---------CCC
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRWYPRDYRK---------VPS 217 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-~~~iD~~sl~~la~r~~p~~~~~---------~l~ 217 (249)
++.+|.+|+++ .++||||+.||+.||++++.+++..++ ++++|| +.++++++|....+ +++
T Consensus 70 v~~~~~~fl~~------~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT---~~lar~l~~~~~~~~L~~L~~~~gi~ 140 (309)
T PRK06195 70 IWEKIKHYFNN------NLVIAHNASFDISVLRKTLELYNIPMPSFEYICT---MKLAKNFYSNIDNARLNTVNNFLGYE 140 (309)
T ss_pred HHHHHHHHhCC------CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEH---HHHHHHHcCCCCcCCHHHHHHHcCCC
Confidence 99999999986 479999999999999999988876544 579999 57788888865433 444
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 218 KEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 218 ~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
..+|||++||++|++++..+.+..
T Consensus 141 -~~~H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 141 -FKHHDALADAMACSNILLNISKEL 164 (309)
T ss_pred -CcccCCHHHHHHHHHHHHHHHHHh
Confidence 369999999999999998886653
No 27
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=3.2e-26 Score=231.21 Aligned_cols=157 Identities=15% Similarity=0.185 Sum_probs=132.2
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
...||+||+||||+++ .|+|||||||.+++... .+.|+++|+|..++ ++.++ .+||||+++++++|++.+
T Consensus 6 ~~~~vvvD~ETTGl~~-~d~IIeIgaV~v~~g~i--~~~f~~lv~P~~~i----~~~~~---~ltGIt~e~l~~ap~~~e 75 (820)
T PRK07246 6 LRKYAVVDLEATGAGP-NASIIQVGIVIIEGGEI--IDSYTTDVNPHEPL----DEHIK---HLTGITDQQLAQAPDFSQ 75 (820)
T ss_pred CCCEEEEEEecCCcCC-CCeEEEEEEEEEECCEE--EEEEEEEeCcCCCC----CHhHh---hcCCCCHHHHhcCCCHHH
Confidence 5789999999999997 59999999995543322 25789999998766 44454 577999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCcccC---------CCCC
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRK---------VPSK 218 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~~---------~l~~ 218 (249)
++.+|.+|+++ .++||||+.||+.||++.+.+.+..+.++++|| +.++++++|....+ +++.
T Consensus 76 v~~~~~~~l~~------~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT---~~la~~~~p~~~~~~L~~L~~~lgl~~ 146 (820)
T PRK07246 76 VARHIYDLIED------CIFVAHNVKFDANLLAEALFLEGYELRTPRVDT---VELAQVFFPTLEKYSLSHLSRELNIDL 146 (820)
T ss_pred HHHHHHHHhCC------CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeH---HHHHHHHhCCCCCCCHHHHHHHcCCCC
Confidence 99999999987 579999999999999999877777777889999 57889988875443 5677
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 219 EQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 219 ~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
.++|||++||++|++|+..+.+.+-
T Consensus 147 ~~~H~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 147 ADAHTAIADARATAELFLKLLQKIE 171 (820)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 7899999999999999999887663
No 28
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=1e-25 Score=206.79 Aligned_cols=155 Identities=14% Similarity=0.077 Sum_probs=125.5
Q ss_pred cccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCC
Q 025709 65 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 144 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~ 144 (249)
.+...+||+||+|||||+|..|+|||||||.+..... +.+.|+.+|+|..... .+ .+||||+++++++|+
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~-ive~f~tLVnP~~~~~----p~-----~LHGIT~e~La~AP~ 111 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGE-EVEHFHAVLNPGEDPG----PF-----HLHGLSAEEFAQGKR 111 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCE-EEEEEEEEECcCCCCC----Cc-----cccCCCHHHHhcCCC
Confidence 4566899999999999999999999999995442222 2367999999986431 11 356999999999999
Q ss_pred HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhc----------------------------cCCCCCceee
Q 025709 145 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDL----------------------------ASLFSHVLVD 196 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~----------------------------~~~~~~~~iD 196 (249)
+.+++.+|.+||++ .+|||||+.||+.||++++.++ +.++++.++|
T Consensus 112 f~eVl~el~~fL~g------~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iD 185 (377)
T PRK05601 112 FSQILKPLDRLIDG------RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVD 185 (377)
T ss_pred HHHHHHHHHHHhCC------CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEE
Confidence 99999999999997 4799999999999999988653 1245677999
Q ss_pred hhHHHHHHHHHCCCcccC---------CCCC----------CCCCcHH--HHHHHHHHHHHHH
Q 025709 197 VSSIKALCMRWYPRDYRK---------VPSK----------EQKHRAL--DDIRESIMELKYY 238 (249)
Q Consensus 197 ~~sl~~la~r~~p~~~~~---------~l~~----------~~~HrAl--~Da~aT~~ll~~~ 238 (249)
| +.++++++|....+ +++. ...|+|+ +|++.+++++...
T Consensus 186 T---L~LARrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 186 T---LATARRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred h---HHHHHHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 9 68999999876543 4444 6678888 6999999999875
No 29
>PRK07883 hypothetical protein; Validated
Probab=99.94 E-value=4.9e-26 Score=221.36 Aligned_cols=161 Identities=20% Similarity=0.211 Sum_probs=133.0
Q ss_pred cccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCC
Q 025709 65 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 144 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~ 144 (249)
......||+||+||||++|..++|||||+|.+++... .+.|+.+|+|...+ ++.+. .+||||++++.++|+
T Consensus 11 ~~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~i--v~~f~~lV~P~~~i----~~~~~---~itGIt~e~l~~ap~ 81 (557)
T PRK07883 11 PLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEV--LGEFATLVNPGRPI----PPFIT---VLTGITTAMVAGAPP 81 (557)
T ss_pred CCcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEE--EEEEEEEECCCCCC----ChhHH---hhcCCCHHHHhCCCC
Confidence 3446899999999999999999999999996654432 24688999997665 44454 567999999999999
Q ss_pred HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCC-CceeehhHHHHHHHHHCC--Cccc--------
Q 025709 145 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRWYP--RDYR-------- 213 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-~~~iD~~sl~~la~r~~p--~~~~-------- 213 (249)
+.+++.+|.+|+++ .++||||+.||+.||++++.+++..++ +.++|| +.++++++| ....
T Consensus 82 ~~evl~~f~~fl~~------~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDT---l~lar~l~~~~~~~~~~L~~L~~ 152 (557)
T PRK07883 82 IEEVLPAFLEFARG------AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCT---VRLARRVLPRDEAPNVRLSTLAR 152 (557)
T ss_pred HHHHHHHHHHHhcC------CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEec---HHHHHHhcccCCCCCCCHHHHHH
Confidence 99999999999986 478999999999999999999887654 679999 567788776 2222
Q ss_pred -CCCCCCCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 214 -KVPSKEQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 214 -~~l~~~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
++++..++|+|++||.+|++++..+.+.+.
T Consensus 153 ~~gi~~~~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 153 LFGATTTPTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred HCCcccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356778899999999999999998877664
No 30
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.94 E-value=4.5e-26 Score=196.10 Aligned_cols=159 Identities=18% Similarity=0.231 Sum_probs=120.4
Q ss_pred CCcEEEEEEecCCCCCC------CCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhc
Q 025709 68 KMPLVWIDLEMTGLKIE------VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS 141 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~------~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~ 141 (249)
..+||+||+||||+++. .++|||||||.+++.. +.+.|+.+|+|.... .+++.++ .+||||++++.+
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~--i~~~f~~lV~P~~~~--~i~~~~~---~ltGIt~~~l~~ 75 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCE--VEDTFSSYVKPKTFP--SLTERCK---SFLGITQEDVDK 75 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCc--ChhhhcceECCCccC--ccChhhh---hhcCcCHHHHcc
Confidence 46899999999998753 4799999999655432 236799999997521 2356666 567999999999
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCC--CCceeehhHHHHHHHHHCCCcc-------
Q 025709 142 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF--SHVLVDVSSIKALCMRWYPRDY------- 212 (249)
Q Consensus 142 ~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~--~~~~iD~~sl~~la~r~~p~~~------- 212 (249)
+|++.+++.+|.+|+++. ..++| ||+.||+.||++.+.+++..+ ...++|+. .+.+++++...
T Consensus 76 ap~~~evl~~f~~~~~~~----~~~iv-~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~---~~~~~~~~~~~~~~L~~~ 147 (207)
T PRK07748 76 GISFEELVEKLAEYDKRC----KPTIV-TWGNMDMKVLKHNCEKAGVPFPFKGQCRDLS---LEYKKFFGERNQTGLWKA 147 (207)
T ss_pred CCCHHHHHHHHHHHhCcC----CeEEE-EECHHHHHHHHHHHHHcCCCCcccccceeHH---HHHHHHhCcCCCCCHHHH
Confidence 999999999999999862 13444 557999999999998877543 34688884 33445544321
Q ss_pred --cCCCCC-CCCCcHHHHHHHHHHHHHHHHHH
Q 025709 213 --RKVPSK-EQKHRALDDIRESIMELKYYKEN 241 (249)
Q Consensus 213 --~~~l~~-~~~HrAl~Da~aT~~ll~~~~~~ 241 (249)
.++++. ..+|||++||++|+++++.+...
T Consensus 148 ~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 148 IEEYGKEGTGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred HHHcCCCCCCCCcChHHHHHHHHHHHHHHHhC
Confidence 245664 46899999999999999998766
No 31
>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=99.94 E-value=9.5e-26 Score=181.58 Aligned_cols=147 Identities=26% Similarity=0.327 Sum_probs=119.9
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 151 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~ 151 (249)
|++|+||||++|..++|||||+|+++... ...+.++.+|+|+..+ .+.+. .++||+++++.+++++.+++.+
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~-~~~~~~~~~i~p~~~~----~~~~~---~~~gi~~~~~~~~~~~~~~~~~ 72 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGI-EIVERFETLVNPGRPI----PPEAT---AIHGITDEMLADAPPFEEVLPE 72 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCc-ChhhhhheeeCcCCcC----CHhhe---eccCCCHHHHhcCCCHHHHHHH
Confidence 58999999999999999999999877662 2346789999998754 34444 4579999999999999999999
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC-CCCCceeehhHHHHHHHHHCCCcc----------cCCCCCCC
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDY----------RKVPSKEQ 220 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iD~~sl~~la~r~~p~~~----------~~~l~~~~ 220 (249)
|.+|+++ .++||||+.||+.||++.+.+++. .++..++|+. .+.+.+++... .++....+
T Consensus 73 ~~~~l~~------~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~---~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 143 (159)
T cd06127 73 FLEFLGG------RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTL---RLARRLLPGLRSHRLGLLLAERYGIPLEG 143 (159)
T ss_pred HHHHHCC------CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHH---HHHHHHcCCCCcCchHHHHHHHcCCCCCC
Confidence 9999986 468999999999999999988763 5667899995 44555554322 12456788
Q ss_pred CCcHHHHHHHHHHHH
Q 025709 221 KHRALDDIRESIMEL 235 (249)
Q Consensus 221 ~HrAl~Da~aT~~ll 235 (249)
+|+|++||++|+++|
T Consensus 144 ~H~Al~Da~~t~~l~ 158 (159)
T cd06127 144 AHRALADALATAELL 158 (159)
T ss_pred CCCcHHHHHHHHHHh
Confidence 999999999999987
No 32
>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=99.94 E-value=2.2e-25 Score=230.73 Aligned_cols=159 Identities=19% Similarity=0.266 Sum_probs=133.9
Q ss_pred cCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 67 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 67 ~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
...+||+||+|||||++..++|||||||.+++... .+.|+.+|+|..++ ++.++ .+||||++++.+++++.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~i--id~f~~~V~P~~~I----~~~~~---~ltGIT~e~L~~ap~~~ 258 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRI--IDKFQFFIKPHEPL----SAFVT---ELTGITQDMLENAPEIE 258 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeE--EEEEEEEECCCCCC----CHHHH---HHhCCCHHHHhCCCCHH
Confidence 35799999999999999999999999995544322 25689999998765 45555 67799999999999999
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC-CCCCceeehhHHHHHHHHHCCCccc---------CCC
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDYR---------KVP 216 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iD~~sl~~la~r~~p~~~~---------~~l 216 (249)
+++.+|++|+++ .+|||||+.||+.||++.+.+++. +++++++|| +.+++.++|.... +++
T Consensus 259 evl~~f~~fl~~------~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDT---l~lar~l~p~~k~~kL~~Lak~lgi 329 (1213)
T TIGR01405 259 EVLEKFKEFFKD------SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDT---LELARALNPEYKSHRLGNICKKLGV 329 (1213)
T ss_pred HHHHHHHHHhCC------CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEH---HHHHHHHhccCCCCCHHHHHHHcCC
Confidence 999999999986 579999999999999999998875 477889999 5678888876543 356
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 217 SKEQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 217 ~~~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
+..++|||++||.+|++++..+.+.+.
T Consensus 330 ~~~~~HrAl~DA~aTa~I~~~ll~~l~ 356 (1213)
T TIGR01405 330 DLDDHHRADYDAEATAKVFKVMVEQLK 356 (1213)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 677899999999999999999887664
No 33
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=2.1e-25 Score=228.19 Aligned_cols=159 Identities=17% Similarity=0.233 Sum_probs=133.5
Q ss_pred CCcEEEEEEecCCCCCCC-CceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 68 KMPLVWIDLEMTGLKIEV-DRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~-d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
.++||+||+||||++|.. ++|||||||.+++... .+.|+.+|+|..++ ++.+. .+||||+++++++|++.
T Consensus 2 ~~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i--~~~f~~~v~P~~~i----~~~~~---~ltGIt~~~l~~ap~f~ 72 (928)
T PRK08074 2 SKRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEI--LERFSSFVNPERPI----PPFIT---ELTGISEEMVKQAPLFE 72 (928)
T ss_pred CCCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEE--EEEEEEEECcCCCC----CHHHh---hcCCCCHHHHhcCCCHH
Confidence 367999999999999875 8999999995543322 25789999998765 45555 67799999999999999
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC-CCCCceeehhHHHHHHHHHCCCcccC---------CC
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDYRK---------VP 216 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iD~~sl~~la~r~~p~~~~~---------~l 216 (249)
+++.+|.+|+++ .++||||+.||+.||++++.+.|. +++++++|| +++++.++|....+ ++
T Consensus 73 ev~~~l~~~l~~------~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt---~~la~~~~p~~~~~~L~~l~~~l~i 143 (928)
T PRK08074 73 DVAPEIVELLEG------AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDT---VELARILLPTAESYKLRDLSEELGL 143 (928)
T ss_pred HHHHHHHHHhCC------CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeH---HHHHHHhcCCCCCCCHHHHHHhCCC
Confidence 999999999986 578999999999999999988875 456789999 67888888875543 56
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHHhcC
Q 025709 217 SKEQKHRALDDIRESIMELKYYKENIFK 244 (249)
Q Consensus 217 ~~~~~HrAl~Da~aT~~ll~~~~~~~~~ 244 (249)
+..++|||++||++|++++..+.+.+..
T Consensus 144 ~~~~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 144 EHDQPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred CCCCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 7889999999999999999999877643
No 34
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.94 E-value=3.4e-25 Score=183.87 Aligned_cols=156 Identities=21% Similarity=0.214 Sum_probs=120.1
Q ss_pred EEEEEEecCCCCCCC-----CceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCH
Q 025709 71 LVWIDLEMTGLKIEV-----DRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 145 (249)
Q Consensus 71 ~V~lDlETTGL~p~~-----d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~ 145 (249)
||+||+||||+++.+ ++|||||||+++++.....+.|+.+|+|+... .++++++ .+||||.+++.++|++
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~--~i~~~~~---~i~gIt~e~l~~~~~~ 75 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINP--KLSDFCT---ELTGITQEDVDNAPSF 75 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCC--chhHHHH---HhcCcCHHHHhcCCCH
Confidence 689999999999875 99999999988776543456899999998721 2356666 5579999999999999
Q ss_pred HHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC----CCCCceeehhHHHHHHHHHCCCcc---------
Q 025709 146 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS----LFSHVLVDVSSIKALCMRWYPRDY--------- 212 (249)
Q Consensus 146 ~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~----~~~~~~iD~~sl~~la~r~~p~~~--------- 212 (249)
.+|+.+|.+|+++.. + .+++||..||..+|.+++.+.+. ++.++++|++.+. ++.+|...
T Consensus 76 ~~vl~~~~~~l~~~~---~-~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~---~~~~~~~~~~~L~~l~~ 148 (176)
T cd06133 76 PEVLKEFLEWLGKNG---K-YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEF---AKFYGLKKRTGLSKALE 148 (176)
T ss_pred HHHHHHHHHHHHhCC---C-eEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHH---HHHhCCCCCCCHHHHHH
Confidence 999999999999731 1 24455569999999888765542 4567899996544 44444321
Q ss_pred cCCCCCC-CCCcHHHHHHHHHHHHHHH
Q 025709 213 RKVPSKE-QKHRALDDIRESIMELKYY 238 (249)
Q Consensus 213 ~~~l~~~-~~HrAl~Da~aT~~ll~~~ 238 (249)
.++++.. ..|+|++||++|+++++++
T Consensus 149 ~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 149 YLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred HCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 2456655 8999999999999999875
No 35
>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=99.93 E-value=3.1e-25 Score=225.34 Aligned_cols=155 Identities=19% Similarity=0.311 Sum_probs=130.8
Q ss_pred cEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHH
Q 025709 70 PLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 149 (249)
Q Consensus 70 ~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~ 149 (249)
.||+||+||||++|..++|||||+|.+++... .+.|+++|+|..++ ++.++ .+||||++++.++|++.+++
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i--~~~f~~~v~P~~~i----~~~~~---~ltGIt~e~l~~ap~~~ev~ 71 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEI--VDTFHTDVNPNEPI----PPFIQ---ELTGISDNMLQQAPYFSQVA 71 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEE--EEEEEEEeCCCCCC----Chhhh---hhcCcCHHHHhCCCCHHHHH
Confidence 48999999999999999999999996543322 25789999998765 44554 57799999999999999999
Q ss_pred HHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCC-CCCceeehhHHHHHHHHHCCCccc---------CCCCCC
Q 025709 150 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYR---------KVPSKE 219 (249)
Q Consensus 150 ~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~-~~~~~iD~~sl~~la~r~~p~~~~---------~~l~~~ 219 (249)
.+|.+|+++ .++||||+.||+.||++++.+.|.. ++++.+|+ +.+++.++|.... ++++..
T Consensus 72 ~~l~~~l~~------~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt---~~l~~~~~p~~~~~~L~~l~~~~gi~~~ 142 (850)
T TIGR01407 72 QEIYDLLED------GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDT---VELAQIFFPTEESYQLSELSEALGLTHE 142 (850)
T ss_pred HHHHHHhCC------CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeH---HHHHHHhcCCCCCCCHHHHHHHCCCCCC
Confidence 999999986 4689999999999999999888764 67889999 5778888886543 356778
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHh
Q 025709 220 QKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 220 ~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
++|||++||.+|++++.++.+.+
T Consensus 143 ~~H~Al~DA~ata~l~~~l~~~~ 165 (850)
T TIGR01407 143 NPHRADSDAQATAELLLLLFEKM 165 (850)
T ss_pred CCCChHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999987765
No 36
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=1.7e-25 Score=191.18 Aligned_cols=153 Identities=18% Similarity=0.161 Sum_probs=113.5
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
...||+||+||||+++ .++|||||||.+++... .+.|+.+|+|..++ +..++ .+||||+++++++|++.+
T Consensus 4 ~~~~vvlD~EtTGl~~-~~eIIeIgaV~v~~g~~--~~~f~~lv~P~~~i----~~~~~---~lhGIt~~~v~~ap~~~e 73 (195)
T PRK07247 4 LETYIAFDLEFNTVNG-VSHIIQVSAVKYDDHKE--VDSFDSYVYTDVPL----QSFIN---GLTGITADKIADAPKVEE 73 (195)
T ss_pred CCeEEEEEeeCCCCCC-CCeEEEEEEEEEECCEE--EEEEEEEECCCCCC----Cccce---ecCCCCHHHHhCCCCHHH
Confidence 4689999999999985 68999999995544332 24688999998765 33444 577999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHH-HHHHHHHHHHHhccCCCC-CceeehhHHHHHHHHH--CCCccc---------C
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVY-VDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRW--YPRDYR---------K 214 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~-FD~~fL~~~~~~~~~~~~-~~~iD~~sl~~la~r~--~p~~~~---------~ 214 (249)
++.+|.+|+++ .++||||+. ||+.||++. +..+. ...+|+... .+.++. +|.... +
T Consensus 74 vl~~f~~f~~~------~~lVaHNa~~fD~~fL~~~----g~~~~~~~~idt~~~-~~~~~~~~~~~~~~~~L~~La~~~ 142 (195)
T PRK07247 74 VLAAFKEFVGE------LPLIGYNAQKSDLPILAEN----GLDLSDQYQVDLYDE-AFERRSSDLNGIANLKLQTVADFL 142 (195)
T ss_pred HHHHHHHHHCC------CeEEEEeCcHhHHHHHHHc----CCCcCCCceeehHHH-HHHhhccccCCCCCCCHHHHHHhc
Confidence 99999999987 468999996 899999864 22222 235676322 123333 343332 3
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 215 VPSKEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 215 ~l~~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
+++. .+|||++||++|+.+++++....
T Consensus 143 gi~~-~~HrAl~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 143 GIKG-RGHNSLEDARMTARVYESFLESD 169 (195)
T ss_pred CCCC-CCcCCHHHHHHHHHHHHHHHhhc
Confidence 4554 68999999999999999886653
No 37
>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=99.93 E-value=3.1e-26 Score=189.85 Aligned_cols=136 Identities=20% Similarity=0.249 Sum_probs=106.8
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEE-cCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCC------
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT------ 144 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~-dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~------ 144 (249)
|+|||||||++|..++|||||+|.. +|+.. |+.+|+|..++ +++.+ .+||||+++++++|+
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~-----~~~~v~P~~~i----~~~~~---~i~GIt~~~l~~a~~~~~~~~ 68 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVL-----IDSLVRPSVRV----TDWRT---RFSGVTPADLEEAAKAGKTIF 68 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEE-----EeccccCCCCC----Cccce---eccCCCHHHHhhhhhcCCccc
Confidence 6899999999999999999999955 66553 56789998766 33444 567999999998875
Q ss_pred -HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCc---cc-------
Q 025709 145 -EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRD---YR------- 213 (249)
Q Consensus 145 -~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~---~~------- 213 (249)
+.+++.+|++|+++. .+|||||+.||+.||+.. +++++|| ..+++++.|.. ..
T Consensus 69 ~~~~~~~~~~~~i~~~-----~vlVgHn~~fD~~fL~~~--------~~~~iDT---~~l~~~~~~~~~~~~~~~L~~L~ 132 (161)
T cd06137 69 GWEAARAALWKFIDPD-----TILVGHSLQNDLDALRMI--------HTRVVDT---AILTREAVKGPLAKRQWSLRTLC 132 (161)
T ss_pred cHHHHHHHHHHhcCCC-----cEEEeccHHHHHHHHhCc--------CCCeeEe---hhhhhhccCCCcCCCCccHHHHH
Confidence 358999999999852 479999999999999852 5678999 46677776653 11
Q ss_pred ---CCCCC---CCCCcHHHHHHHHHHHH
Q 025709 214 ---KVPSK---EQKHRALDDIRESIMEL 235 (249)
Q Consensus 214 ---~~l~~---~~~HrAl~Da~aT~~ll 235 (249)
++++. ..+|+|++||++|++|+
T Consensus 133 ~~~~~~~~~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 133 RDFLGLKIQGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred HHHCCchhcCCCCCCCcHHHHHHHHHHh
Confidence 23333 46899999999999986
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=99.93 E-value=8.8e-26 Score=186.57 Aligned_cols=140 Identities=24% Similarity=0.308 Sum_probs=108.7
Q ss_pred EEEEEecCCCCCC--CCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHH
Q 025709 72 VWIDLEMTGLKIE--VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 149 (249)
Q Consensus 72 V~lDlETTGL~p~--~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~ 149 (249)
|+|||||||++|. .++|++||+|..+|... ++.+|+|..++ +.+.+ .+||||+++++++|++.+++
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~-----~~~lv~P~~~i----~~~~~---~i~GIt~~~l~~a~~~~~v~ 68 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVL-----YDKYIRPEGPV----TDYRT---RWSGIRRQHLVNATPFAVAQ 68 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEE-----EEEeECCCCcc----Cccce---ECCCCCHHHHhcCCCHHHHH
Confidence 6899999999997 47888888886666653 67899998776 34444 56799999999999999999
Q ss_pred HHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHH--CCCcccC------------C
Q 025709 150 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRW--YPRDYRK------------V 215 (249)
Q Consensus 150 ~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~--~p~~~~~------------~ 215 (249)
.+|.+|+++ .+|||||+.||+.||+.. ..++.++|+.++. +.++. +|....+ +
T Consensus 69 ~~l~~~l~~------~vlV~Hn~~~D~~~l~~~------~~~~~~~Dt~~l~-~~~~~~~~p~~~~~~L~~L~~~~~~~~ 135 (157)
T cd06149 69 KEILKILKG------KVVVGHAIHNDFKALKYF------HPKHMTRDTSTIP-LLNRKAGFPENCRVSLKVLAKRLLHRD 135 (157)
T ss_pred HHHHHHcCC------CEEEEeCcHHHHHHhccc------CCCcCEEECcccc-cchhhcCCcccCChhHHHHHHHHcChh
Confidence 999999986 479999999999999955 2334578886653 34433 5643322 2
Q ss_pred CCC-CCCCcHHHHHHHHHHHHH
Q 025709 216 PSK-EQKHRALDDIRESIMELK 236 (249)
Q Consensus 216 l~~-~~~HrAl~Da~aT~~ll~ 236 (249)
++. .++|||++||++|++++|
T Consensus 136 i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 136 IQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred hcCCCCCcCcHHHHHHHHHHhC
Confidence 333 568999999999999985
No 39
>PRK06722 exonuclease; Provisional
Probab=99.93 E-value=1.1e-24 Score=195.22 Aligned_cols=158 Identities=13% Similarity=0.088 Sum_probs=116.6
Q ss_pred CCcEEEEEEecCCCCC---CCCceEEEEEEEEc-CcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC
Q 025709 68 KMPLVWIDLEMTGLKI---EVDRILEIACIITD-GKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 143 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p---~~d~IIEIgaVv~d-g~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p 143 (249)
...||+||+||||... ..++|||||||.++ +... +.+.|+.+|+|..++ +.+|+ .+||||++|+.++|
T Consensus 4 ~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~-Ivd~F~sLV~P~~~I----~~~i~---~LTGIT~emV~~AP 75 (281)
T PRK06722 4 ATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMK-VIGEFSELVKPGARL----TRHTT---KLTGITKKDLIGVE 75 (281)
T ss_pred CCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCcee-EEeeEEEEECCCCcC----CHhHh---hhcCCCHHHHcCCC
Confidence 4789999999996432 23899999999655 4333 335799999998655 56776 67799999999999
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCC----CceeehhHHHH-HHHHHCCC---cc---
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS----HVLVDVSSIKA-LCMRWYPR---DY--- 212 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~----~~~iD~~sl~~-la~r~~p~---~~--- 212 (249)
++.+++.+|.+|+++. ++|+||+.||+.||++.+.+++..++ .+++|+..+.. +.+++.+. +.
T Consensus 76 ~f~eVl~ef~~fig~~------~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~ 149 (281)
T PRK06722 76 KFPQIIEKFIQFIGED------SIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAV 149 (281)
T ss_pred CHHHHHHHHHHHHCCC------cEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHH
Confidence 9999999999999862 35666779999999999988775433 23577743321 12233222 11
Q ss_pred -cCCCCC-CCCCcHHHHHHHHHHHHHHHH
Q 025709 213 -RKVPSK-EQKHRALDDIRESIMELKYYK 239 (249)
Q Consensus 213 -~~~l~~-~~~HrAl~Da~aT~~ll~~~~ 239 (249)
.++++. +.+|||++||++|++++..+.
T Consensus 150 ~~lgL~~~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 150 EQLGLIWEGKQHRALADAENTANILLKAY 178 (281)
T ss_pred HHCCCCCCCCCcCcHHHHHHHHHHHHHHh
Confidence 245664 568999999999999997765
No 40
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.93 E-value=1.7e-24 Score=188.09 Aligned_cols=138 Identities=18% Similarity=0.175 Sum_probs=110.0
Q ss_pred EEEEEEecCCCCCCCCceEEEEEE-EEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHH
Q 025709 71 LVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 149 (249)
Q Consensus 71 ~V~lDlETTGL~p~~d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~ 149 (249)
+++||+||||+++ +|||||+| +.+++.. +.|+.+|+|..++ +..++ .+||||+++++++|++.+++
T Consensus 2 ~~vlD~ETTGl~~---~IieIg~v~v~~~~i~---~~~~~lv~P~~~i----~~~~~---~ihgIt~e~v~~ap~~~ev~ 68 (219)
T PRK07983 2 LRVIDTETCGLQG---GIVEIASVDVIDGKIV---NPMSHLVRPDRPI----SPQAM---AIHRITEAMVADKPWIEDVI 68 (219)
T ss_pred eEEEEEECCCCCC---CCEEEEEEEEECCEEE---EEEEEEECcCCCC----CHHHh---hcCCCCHHHHcCCCCHHHHH
Confidence 7899999999985 49999999 5666543 4688999998765 44555 56699999999999999998
Q ss_pred HHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCccc--------CCCC----
Q 025709 150 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYR--------KVPS---- 217 (249)
Q Consensus 150 ~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~--------~~l~---- 217 (249)
.+ |++. .+|||||+.||+.||.. +..+++|| ++++|+++|.... +++.
T Consensus 69 ~~---~~~~------~~lVaHNa~FD~~~L~~--------~~~~~idT---l~lar~l~p~~~~~l~~L~~~~~l~~~~~ 128 (219)
T PRK07983 69 PH---YYGS------EWYVAHNASFDRRVLPE--------MPGEWICT---MKLARRLWPGIKYSNMALYKSRKLNVQTP 128 (219)
T ss_pred HH---HcCC------CEEEEeCcHhhHHHHhC--------cCCCcEeH---HHHHHHHccCCCCCHHHHHHHcCCCCCCC
Confidence 86 4443 57999999999999963 34678999 6889999987442 1222
Q ss_pred -CCCCCcHHHHHHHHHHHHHHHHHH
Q 025709 218 -KEQKHRALDDIRESIMELKYYKEN 241 (249)
Q Consensus 218 -~~~~HrAl~Da~aT~~ll~~~~~~ 241 (249)
..++|||++||.+|++||.++.+.
T Consensus 129 ~~~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 129 PGLHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 257999999999999999998753
No 41
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.92 E-value=8.3e-25 Score=179.41 Aligned_cols=136 Identities=20% Similarity=0.268 Sum_probs=105.8
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC-CHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL-TEREAEK 150 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p-~~~ea~~ 150 (249)
|++||||||++.. ++|++||+|..+|+. .|+.+|+|..++ +++.+ .+||||+++++++| ++.+++.
T Consensus 1 ~~iD~E~~g~~~g-~ei~~i~~v~~~~~~-----~f~~lv~P~~~i----~~~~t---~itGIt~~~l~~a~~~~~~v~~ 67 (150)
T cd06145 1 FALDCEMCYTTDG-LELTRVTVVDENGKV-----VLDELVKPDGEI----VDYNT---RFSGITEEMLENVTTTLEDVQK 67 (150)
T ss_pred CEEeeeeeeecCC-CEEEEEEEEeCCCCE-----EEEEeECCCCcc----chhcc---CcCCCCHHHhccCCCCHHHHHH
Confidence 5899999999976 999999999655543 278999998766 44444 67799999999985 9999999
Q ss_pred HHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCcccC----------C--CCC
Q 025709 151 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRK----------V--PSK 218 (249)
Q Consensus 151 ~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~~----------~--l~~ 218 (249)
+|.+|+++. .+|||||+.||+.||+. ++++++||. .+++++.|....+ + +..
T Consensus 68 ~~~~fl~~~-----~vlVgHn~~fD~~fL~~--------~~~~~iDT~---~l~r~~~~~~~~~~L~~L~~~~~~~~i~~ 131 (150)
T cd06145 68 KLLSLISPD-----TILVGHSLENDLKALKL--------IHPRVIDTA---ILFPHPRGPPYKPSLKNLAKKYLGRDIQQ 131 (150)
T ss_pred HHHHHhCCC-----CEEEEcChHHHHHHhhc--------cCCCEEEcH---HhccccCCCCCChhHHHHHHHHCCcceeC
Confidence 999999731 57999999999999985 345689994 4556554432211 1 122
Q ss_pred -CCCCcHHHHHHHHHHHHH
Q 025709 219 -EQKHRALDDIRESIMELK 236 (249)
Q Consensus 219 -~~~HrAl~Da~aT~~ll~ 236 (249)
..+|||++||++|++|++
T Consensus 132 ~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 132 GEGGHDSVEDARAALELVK 150 (150)
T ss_pred CCCCCCcHHHHHHHHHHhC
Confidence 578999999999999874
No 42
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=7.8e-24 Score=191.20 Aligned_cols=153 Identities=19% Similarity=0.204 Sum_probs=110.1
Q ss_pred cccCCcEEEEEEecCCCCCCCCceEEEEEEEEc----CcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHh
Q 025709 65 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITD----GKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 140 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~d----g~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~ 140 (249)
......+|+||+|||||+|.+|+|||||+|.++ |.+..+.+.|+.+++|..++ ++.++ .+||||++++.
T Consensus 33 ~~~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I----~~~~t---~IhGIt~e~v~ 105 (294)
T PRK09182 33 GEFVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPI----PPEIT---RLTGITDEMVA 105 (294)
T ss_pred CCCCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCC----CHHHH---HhcCCCHHHHh
Confidence 455678999999999999999999999999654 55444456789999998765 44444 56799999999
Q ss_pred cCCCHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHH-CCCcc-------
Q 025709 141 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRW-YPRDY------- 212 (249)
Q Consensus 141 ~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~-~p~~~------- 212 (249)
+++...+ +|.+|++.. .+|||||+.||+.||+++++.+.. .++.|+.... .| .+...
T Consensus 106 ~~~~~~~---~l~~fl~~~-----~vlVAHNA~FD~~fL~~~~~~~~~---~~~~ct~~~i----~~~~~~~~~~kL~~L 170 (294)
T PRK09182 106 GQTIDPA---AVDALIAPA-----DLIIAHNAGFDRPFLERFSPVFAT---KPWACSVSEI----DWSARGFEGTKLGYL 170 (294)
T ss_pred cCCCcHH---HHHHHhcCC-----CEEEEeCHHHHHHHHHHHHHhccC---CcccccHHHH----hhccccCCCCCHHHH
Confidence 9886544 456666641 478999999999999998765432 2234442111 11 11111
Q ss_pred --cCCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 025709 213 --RKVPSKEQKHRALDDIRESIMELKYYKE 240 (249)
Q Consensus 213 --~~~l~~~~~HrAl~Da~aT~~ll~~~~~ 240 (249)
.++ ...++|||++||.+|++||.....
T Consensus 171 a~~~g-~~~~aHrAl~Da~Ata~ll~~~l~ 199 (294)
T PRK09182 171 AGQAG-FFHEGHRAVDDCQALLELLARPLP 199 (294)
T ss_pred HHHcC-CCCCCcChHHHHHHHHHHHHHHHh
Confidence 134 356899999999999999996653
No 43
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.91 E-value=1.9e-23 Score=199.19 Aligned_cols=165 Identities=20% Similarity=0.196 Sum_probs=122.7
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhc-CCCHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS-GLTER 146 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~-~p~~~ 146 (249)
...|||+|+||||++|..|+|||||+|.+++....+.+.++.+++|....+.. ++.+ .+||||++++.+ +.++.
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~-p~a~----~IhGIT~e~l~~~g~~e~ 79 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPS-PEAV----LITGITPQEALEKGLPEA 79 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCC-HHHH----HHhCCCHHHHHhcCCCHH
Confidence 46799999999999999999999999988776555566789999998643211 3333 456999999854 56799
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEec-HHHHHHHHHHHHHhcc-C------CCCCceeehhHHHHHHHHHCCCc-------
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNS-VYVDFMFLKKYMPDLA-S------LFSHVLVDVSSIKALCMRWYPRD------- 211 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn-~~FD~~fL~~~~~~~~-~------~~~~~~iD~~sl~~la~r~~p~~------- 211 (249)
+++.+|.+|+.. ++ .++|||| ++||..||++.+.+-. . ..++..+|+..+.++++.+.|..
T Consensus 80 e~~~~i~~~l~~---~~-~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~ 155 (476)
T PRK11779 80 EFAARIHAEFSQ---PG-TCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENE 155 (476)
T ss_pred HHHHHHHHHHhc---CC-CEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccc
Confidence 999999999962 12 4689996 7999999999874321 1 11233456655566666654421
Q ss_pred ---c---------cCCCCCCCCCcHHHHHHHHHHHHHHHHHH
Q 025709 212 ---Y---------RKVPSKEQKHRALDDIRESIMELKYYKEN 241 (249)
Q Consensus 212 ---~---------~~~l~~~~~HrAl~Da~aT~~ll~~~~~~ 241 (249)
. .++++..++|||++||++|+++++.+++.
T Consensus 156 ~g~~s~rLe~L~~~~gI~~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 156 DGLPSFKLEHLTKANGIEHENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred cCCCCCcHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHh
Confidence 1 13678899999999999999999998876
No 44
>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=99.91 E-value=2.8e-24 Score=176.43 Aligned_cols=142 Identities=20% Similarity=0.218 Sum_probs=100.0
Q ss_pred EEEEEecCCCCCCCCceEEEEEE-EEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEK 150 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~ 150 (249)
|+|||||||++|. ++++||+.| +.+.+... .|+.+|+|..++ +.++. .+||||+++++++|++.+++.
T Consensus 1 v~lD~EttGl~~~-~~~~~i~~v~~v~~~~~~---~~~~~v~P~~~i----~~~~~---~ihGIt~~~v~~a~~~~~~~~ 69 (152)
T cd06144 1 VALDCEMVGVGPD-GSESALARVSIVNEDGNV---VYDTYVKPQEPV----TDYRT---AVSGIRPEHLKDAPDFEEVQK 69 (152)
T ss_pred CEEEEEeecccCC-CCEEEEEEEEEEeCCCCE---EEEEEECCCCCC----Ccccc---cCCCCCHHHHcCCCCHHHHHH
Confidence 6899999999986 467777766 44433322 268899998655 44555 567999999999999999999
Q ss_pred HHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHH-CCC--cc---c--CCCCC-CCC
Q 025709 151 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRW-YPR--DY---R--KVPSK-EQK 221 (249)
Q Consensus 151 ~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~-~p~--~~---~--~~l~~-~~~ 221 (249)
+|.+|+++ .++||||+.||+.||+... ..+.++|+..+..+...+ .+. +. . .+++. .++
T Consensus 70 ~l~~~l~~------~vlVgHn~~fD~~~L~~~~------~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~ 137 (152)
T cd06144 70 KVAELLKG------RILVGHALKNDLKVLKLDH------PKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGE 137 (152)
T ss_pred HHHHHhCC------CEEEEcCcHHHHHHhcCcC------CCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCC
Confidence 99999986 4789999999999998432 224566765432111111 010 00 0 13332 368
Q ss_pred CcHHHHHHHHHHHHH
Q 025709 222 HRALDDIRESIMELK 236 (249)
Q Consensus 222 HrAl~Da~aT~~ll~ 236 (249)
|||++||++|+++++
T Consensus 138 H~Al~DA~at~~l~~ 152 (152)
T cd06144 138 HSSVEDARAAMRLYR 152 (152)
T ss_pred cCcHHHHHHHHHHhC
Confidence 999999999999875
No 45
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.90 E-value=1.8e-22 Score=194.55 Aligned_cols=191 Identities=14% Similarity=0.133 Sum_probs=132.5
Q ss_pred cccCCCCcchhccccCCCCCcccccC-CcEEEEEEecCCCCCC---CCceEEEEEEEEcCcEeeeeccceEEecCCCccc
Q 025709 43 SKANSSSNLTLENQQNSQTPLEFEYK-MPLVWIDLEMTGLKIE---VDRILEIACIITDGKLTKSVEGPDLVIHQTKECL 118 (249)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~V~lDlETTGL~p~---~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~ 118 (249)
++..-.|....+..+...+.....+. +.||+||+||||+++. .++|||||||+++.....+.+.|+.+|+|....
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~q~~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p- 107 (582)
T PTZ00315 29 QRPQRNTVAAAQSAASSQFPEIAPQPFDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNP- 107 (582)
T ss_pred ccccccCcChhhhhhcccCcccccCCCCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCC-
Confidence 33433444443333333333333333 8999999999999874 489999999977532112235799999997531
Q ss_pred ccchhhhhhhhhccCCcHHHHhcCCCHHHHHHHHHHHHhccc-C---CCCcEEEEecHHHHH-HHHHHHHHh---ccCCC
Q 025709 119 DSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQVVEFVKKNV-G---TYTPLLAGNSVYVDF-MFLKKYMPD---LASLF 190 (249)
Q Consensus 119 ~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~~~~fl~~~~-~---~~~~~lVghn~~FD~-~fL~~~~~~---~~~~~ 190 (249)
.++++|+ .+||||++++.++|+|.+++.+|.+|+++.. + +....+|+||+.||+ .||.+++.. .+.++
T Consensus 108 -~Ls~fct---~LTGITqe~V~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~ 183 (582)
T PTZ00315 108 -VLSRFCT---ELTGITQSMVSRADPFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPL 183 (582)
T ss_pred -CCChhHh---hhcCcCHHHHhcCCCHHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCc
Confidence 2477887 6789999999999999999999999998752 1 112357899999998 599998863 34444
Q ss_pred CC-ceeehhHHHHHHHHHCCCc-----------cc---------CCCC-CCCCCcHHHHHHHHHHHHHHHHH
Q 025709 191 SH-VLVDVSSIKALCMRWYPRD-----------YR---------KVPS-KEQKHRALDDIRESIMELKYYKE 240 (249)
Q Consensus 191 ~~-~~iD~~sl~~la~r~~p~~-----------~~---------~~l~-~~~~HrAl~Da~aT~~ll~~~~~ 240 (249)
.+ .++|+.. .+++.++|.. .. .+++ .+..|||++||++|+.++..+..
T Consensus 184 ~f~~widLk~--~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~ 253 (582)
T PTZ00315 184 SFQRWCNLKK--YMSQLGFGNGSGCGGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLR 253 (582)
T ss_pred ccceEEEhHH--HHHHHhCccccccccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHH
Confidence 33 4666542 4566666631 11 2344 45689999999999999998754
No 46
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.90 E-value=1.6e-22 Score=177.11 Aligned_cols=156 Identities=24% Similarity=0.274 Sum_probs=128.1
Q ss_pred CcEEEEEEecCCCCCCCCceEEEEEE-EEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 69 MPLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 69 ~~~V~lDlETTGL~p~~d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
..+|+||+||||+++.+++|||||+| +.++++. ...|+.+++|..+++ +... .++|||.+++.++|.+.+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~--~~~~~~~v~P~~~i~----~~~~---~i~git~e~l~~~p~~~~ 83 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIV--ERSFHTLVNPERPIP----PEIF---KIHGITDEMLADAPKFAE 83 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeee--cceeEEEECCCCCCC----hhhh---hhcCCCHHHHhcCCCHHH
Confidence 68999999999999999999999999 5665554 234889999965542 2222 566999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCC-CCceeehhHHHHHHHHHCCCccc---------CCCC
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF-SHVLVDVSSIKALCMRWYPRDYR---------KVPS 217 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~-~~~~iD~~sl~~la~r~~p~~~~---------~~l~ 217 (249)
++.++.+|+++. .++||||+.||+.||+..+.+++... ...++|+ +.++++.+|+... +++.
T Consensus 84 v~~~~~~~i~~~-----~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t---~~~~r~~~~~~~~~~L~~l~~~~gi~ 155 (243)
T COG0847 84 VLPEFLDFIGGL-----RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDT---LALARRHFPGFDRSSLDALAERLGID 155 (243)
T ss_pred HHHHHHHHHCCC-----CeEEEEchhhcHHHHHHHHHHcCCCcccCceehH---HHHHHHHcCCCccchHHHHHHHcCCC
Confidence 999999999972 46999999999999999998887543 5678899 6788998888332 2455
Q ss_pred --CCCCCcHHHHHHHHHHHHHHHHHH
Q 025709 218 --KEQKHRALDDIRESIMELKYYKEN 241 (249)
Q Consensus 218 --~~~~HrAl~Da~aT~~ll~~~~~~ 241 (249)
....|+|+.||+++++++.+....
T Consensus 156 ~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 156 RNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred cCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 567899999999999998887764
No 47
>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=99.89 E-value=1.6e-24 Score=174.67 Aligned_cols=154 Identities=24% Similarity=0.295 Sum_probs=112.8
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 151 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~ 151 (249)
|+||+||||+++..++|||||+|..++......+.++.+|+|.... .++++++. +||||.+++.+++++.+++.+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~--~i~~~~~~---~~gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPP--KISPWATK---VHGITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHC--SSEHHHHH---HHHHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccc--cCCHHHee---ecCCcccccccCCcHHHHHHh
Confidence 7899999999998999999999966655432235688999998751 34778874 459999999999999999999
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhcc-CCCC--CceeehhHHHHHHHHHC--CCcc----cCCCCCCC-C
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLA-SLFS--HVLVDVSSIKALCMRWY--PRDY----RKVPSKEQ-K 221 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~-~~~~--~~~iD~~sl~~la~r~~--p~~~----~~~l~~~~-~ 221 (249)
|.+|+++. .++||||+.||..++...+.+++ ..++ ..++|+..+......-+ +.+. .++++... +
T Consensus 76 ~~~~~~~~-----~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~ 150 (164)
T PF00929_consen 76 FEEFLKKN-----DILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGTA 150 (164)
T ss_dssp HHHHHHHH-----TEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTSTT
T ss_pred hhhhhhcc-----cccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCCC
Confidence 99999953 47999999999999998886653 3332 33555543222211111 1111 23444444 7
Q ss_pred CcHHHHHHHHHHHH
Q 025709 222 HRALDDIRESIMEL 235 (249)
Q Consensus 222 HrAl~Da~aT~~ll 235 (249)
|+|++||++|+++|
T Consensus 151 H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 151 HDALDDARATAELF 164 (164)
T ss_dssp TSHHHHHHHHHHHH
T ss_pred cChHHHHHHHhCcC
Confidence 99999999999986
No 48
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.87 E-value=1.5e-21 Score=204.65 Aligned_cols=158 Identities=20% Similarity=0.259 Sum_probs=132.3
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
..+||++|+||||+++..++|||||+|..+.... .+.|+.+|+|..++ ++.++ .+||||++++.+++++.+
T Consensus 418 ~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~i--ie~F~~~V~P~~~I----~~~~~---~LTGIT~e~L~~aps~~E 488 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEI--IDKFEFFIKPGHPL----SAFTT---ELTGITDDMVKDAPSIEE 488 (1437)
T ss_pred cCcEEEEEhhhcCCCCchhhhheeeeEEEeCCeE--eeeEEEEECCCCCC----CHHHH---HHhCCCHHHHcCCCCHHH
Confidence 4679999999999999999999999995543322 26789999998765 45555 667999999999999999
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC-CCCCceeehhHHHHHHHHHCCCccc---------CCCC
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDYR---------KVPS 217 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iD~~sl~~la~r~~p~~~~---------~~l~ 217 (249)
++.+|.+|+++ .++||||+.||+.||++.+.+++. .+..+.+|+ +++++.++|.... +++.
T Consensus 489 aL~~f~~figg------~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDT---Lelar~l~p~~k~~kL~~LAk~lGL~ 559 (1437)
T PRK00448 489 VLPKFKEFCGD------SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDT---LELSRFLYPELKSHRLNTLAKKFGVE 559 (1437)
T ss_pred HHHHHHHHhCC------CEEEEeCccccHHHHHHHHHHcCCccccccceeH---HHHHHHHcCccccccHHHHHHHcCCC
Confidence 99999999987 478999999999999999999876 467789999 5677888775432 3667
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 218 KEQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 218 ~~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
...+|||++||.+|++++..+.+.+.
T Consensus 560 ~~~~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 560 LEHHHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred CCCCcChHHHHHHHHHHHHHHHHHHH
Confidence 78889999999999999999876653
No 49
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.65 E-value=7.5e-16 Score=140.61 Aligned_cols=165 Identities=18% Similarity=0.177 Sum_probs=129.6
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHH-HhcCCCHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV-LHSGLTER 146 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~-l~~~p~~~ 146 (249)
.-.|.|.|.||.|.+|..|++.|+|+|.+|.+.+++++...++++|....+.. +..| -+||||++. .+.|.++.
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~-P~a~----LITGITPQ~~~~~G~~E~ 82 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQ-PGAV----LITGITPQEAREKGINEA 82 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCC-CCce----eeecCCHHHHHhcCCChH
Confidence 46799999999999999999999999999999999999999999998865432 4444 468999955 57899999
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHh-c----cCCC--CCceeehhHHHHHHHHHCCCccc------
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPD-L----ASLF--SHVLVDVSSIKALCMRWYPRDYR------ 213 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~-~----~~~~--~~~~iD~~sl~~la~r~~p~~~~------ 213 (249)
+.+..+..-+.. +++|++..+|++||-.+.+..|-+ + ...| ++..+|..-+++.|..+.|....
T Consensus 83 ~F~~~I~~~ls~---P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~d 159 (475)
T COG2925 83 AFAARIHAELTQ---PNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDD 159 (475)
T ss_pred HHHHHHHHHhCC---CCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCC
Confidence 999999887764 455654445779998888876632 2 1112 34567776668899999886431
Q ss_pred -------------CCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 025709 214 -------------KVPSKEQKHRALDDIRESIMELKYYKE 240 (249)
Q Consensus 214 -------------~~l~~~~~HrAl~Da~aT~~ll~~~~~ 240 (249)
.++.+.++|+||+|++||+.+.|..|+
T Consensus 160 G~pSFkLEhLt~ANgieH~nAHdAmsDVyATIamAklvk~ 199 (475)
T COG2925 160 GLPSFKLEHLTKANGIEHSNAHDAMSDVYATIAMAKLVKT 199 (475)
T ss_pred CCcchhhHHHhhccccccchhhHHHHHHHHHHHHHHHHHh
Confidence 256899999999999999999988765
No 50
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.46 E-value=7.5e-13 Score=116.10 Aligned_cols=142 Identities=23% Similarity=0.293 Sum_probs=101.6
Q ss_pred cEEEEEEecCCCCCCCCceEEEEEE-EEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHH
Q 025709 70 PLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 148 (249)
Q Consensus 70 ~~V~lDlETTGL~p~~d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea 148 (249)
.+|++||||.|..|+. +.=.+|=| +++-....+ |+.+|+|..++- +|-+ .++||+++.+.++++|..|
T Consensus 106 r~vAmDCEMVG~Gp~G-~~s~lARvSIVN~~G~Vv---yDkyVkP~~~Vt----DyRT---~vSGIrpehm~~A~pf~~a 174 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDG-RESLLARVSIVNYHGHVV---YDKYVKPTEPVT----DYRT---RVSGIRPEHMRDAMPFKVA 174 (280)
T ss_pred eEEEEeeeEeccCCCc-cceeeeEEEEeeccCcEe---eeeecCCCcccc----ccee---eecccCHHHhccCccHHHH
Confidence 6999999999999862 22333433 334333322 678999998873 3433 6789999999999999999
Q ss_pred HHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehh---------------HHHHHHHHHCCCccc
Q 025709 149 EKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS---------------SIKALCMRWYPRDYR 213 (249)
Q Consensus 149 ~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~---------------sl~~la~r~~p~~~~ 213 (249)
-.+++++|.++ +||||-+..|+.-|.-..++-- +.||+ +|..|++.++...
T Consensus 175 Q~ev~klL~gR------IlVGHaLhnDl~~L~l~hp~s~------iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~-- 240 (280)
T KOG2249|consen 175 QKEVLKLLKGR------ILVGHALHNDLQALKLEHPRSM------IRDTSKYPPLMKLLSKKATPSLKKLTEALLGKD-- 240 (280)
T ss_pred HHHHHHHHhCC------EEeccccccHHHHHhhhCchhh------hcccccCchHHHHhhccCCccHHHHHHHHhchh--
Confidence 99999999984 6999999999999987654321 23332 3444555544332
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHH
Q 025709 214 KVPSKEQKHRALDDIRESIMELKYYK 239 (249)
Q Consensus 214 ~~l~~~~~HrAl~Da~aT~~ll~~~~ 239 (249)
+. ...|+..+||++|++||+..+
T Consensus 241 --IQ-~GeHsSvEDA~AtM~LY~~vk 263 (280)
T KOG2249|consen 241 --IQ-VGEHSSVEDARATMELYKRVK 263 (280)
T ss_pred --hh-ccccCcHHHHHHHHHHHHHHH
Confidence 22 233999999999999997764
No 51
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.43 E-value=2.3e-12 Score=112.35 Aligned_cols=168 Identities=13% Similarity=0.145 Sum_probs=123.6
Q ss_pred ccCCcEEEEEEecCCCCCC----CCceEEEEEEEEcCc-EeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHh
Q 025709 66 EYKMPLVWIDLEMTGLKIE----VDRILEIACIITDGK-LTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 140 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL~p~----~d~IIEIgaVv~dg~-~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~ 140 (249)
...+.++++|.|+|.-+-. ..+|||+.||..+.. ...+.+.|+.+|+|.... .++++|+ .+|||..+.+.
T Consensus 53 q~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np--~LS~fC~---~lTgI~Q~tVD 127 (280)
T KOG0542|consen 53 QPFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENP--RLSDFCT---SLTGIQQETVD 127 (280)
T ss_pred CccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCc--hHHHHHH---HhhCchHhhhc
Confidence 4567899999999976543 379999999955433 333444899999997643 5689998 88999999999
Q ss_pred cCCCHHHHHHHHHHHHhcc--cCC-CCcEEEEecHHHH-HHHHHHHHHhccCCC---CCceeehhHHHHHHHHH-CCCcc
Q 025709 141 SGLTEREAEKQVVEFVKKN--VGT-YTPLLAGNSVYVD-FMFLKKYMPDLASLF---SHVLVDVSSIKALCMRW-YPRDY 212 (249)
Q Consensus 141 ~~p~~~ea~~~~~~fl~~~--~~~-~~~~lVghn~~FD-~~fL~~~~~~~~~~~---~~~~iD~~sl~~la~r~-~p~~~ 212 (249)
.+|++.+|+.+|..|+... .+. |..-+|... .-| ..||..++..-+... -+.+||+...+..-.+. .|...
T Consensus 128 ~a~~f~~vl~~f~~Wlr~~~~~~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~i 206 (280)
T KOG0542|consen 128 EAPTFPQVLSEFDSWLRKDSLGDKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNI 206 (280)
T ss_pred cCCCHHHHHHHHHHHHHHhhcccccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCH
Confidence 9999999999999999875 223 566677765 444 567888875544332 24799998776544433 34322
Q ss_pred -----cCCCC-CCCCCcHHHHHHHHHHHHHHHH
Q 025709 213 -----RKVPS-KEQKHRALDDIRESIMELKYYK 239 (249)
Q Consensus 213 -----~~~l~-~~~~HrAl~Da~aT~~ll~~~~ 239 (249)
.+++. .+.+|++++||+..+.+++.+.
T Consensus 207 t~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~kM~ 239 (280)
T KOG0542|consen 207 TGMLEHYGLQFEGRAHSGIDDARNIARIAQKMI 239 (280)
T ss_pred HHHHHHhCCcccCCcccCchhHHHHHHHHHHHH
Confidence 34554 5678999999999999987764
No 52
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.37 E-value=1.3e-12 Score=107.75 Aligned_cols=164 Identities=18% Similarity=0.103 Sum_probs=118.9
Q ss_pred CcEEEEEEecCCCC----CCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCC
Q 025709 69 MPLVWIDLEMTGLK----IEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 144 (249)
Q Consensus 69 ~~~V~lDlETTGL~----p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~ 144 (249)
..+++||+|.|-.+ +...+||||+|.+++.-...+.+.|+.+|+|.... .+...|+ .+|||+...+.++|.
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P--~Lt~~Ck---slt~I~Q~~VD~api 78 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFP--KLTKRCK---SLTKITQKQVDEAPI 78 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCc--hHHHHHH---Hhhhhhhhhccccch
Confidence 46899999998554 34679999999865433222336789999997753 4578898 788999999999999
Q ss_pred HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC---CCCCceeehhHHHHHHHHHCCCc-------ccC
Q 025709 145 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS---LFSHVLVDVSSIKALCMRWYPRD-------YRK 214 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~---~~~~~~iD~~sl~~la~r~~p~~-------~~~ 214 (249)
+..++++|..||.++-+..-+.+ +....+|...|.+.+...+. ++.-+.+|++.-+.-.++. |+. ..+
T Consensus 79 fs~v~E~f~r~L~~h~Pr~~~~w-a~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~-pr~tgln~ale~~ 156 (210)
T COG5018 79 FSMVFEDFIRKLNEHDPRKNSTW-ATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGD-PRLTGLNKALEEY 156 (210)
T ss_pred HHHHHHHHHHHHHhcCcccCCcc-ccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcC-CccccHHHHHHHh
Confidence 99999999999999865422223 34568999999888755543 3445789987655433322 321 113
Q ss_pred CC-CCCCCCcHHHHHHHHHHHHHHHH
Q 025709 215 VP-SKEQKHRALDDIRESIMELKYYK 239 (249)
Q Consensus 215 ~l-~~~~~HrAl~Da~aT~~ll~~~~ 239 (249)
+. -.+..|||++||+.+.++++..-
T Consensus 157 G~sf~G~~HraldDArn~~rl~klv~ 182 (210)
T COG5018 157 GDSFTGTHHRALDDARNAYRLFKLVE 182 (210)
T ss_pred ccccCCchhhhHHHHHHHHHHHHHHc
Confidence 33 35788999999999999998763
No 53
>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=99.35 E-value=5e-12 Score=105.88 Aligned_cols=121 Identities=17% Similarity=0.262 Sum_probs=83.4
Q ss_pred EEEEE-EEcC----cEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC------CHHHHHHHHHHHHhc
Q 025709 90 EIACI-ITDG----KLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL------TEREAEKQVVEFVKK 158 (249)
Q Consensus 90 EIgaV-v~dg----~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p------~~~ea~~~~~~fl~~ 158 (249)
|+|=| ++|. .... -++.+|+|..++.+ +.+ ..+|||++++.++. ++.++..++.+++..
T Consensus 32 ~LaRVsiVd~~~~~~g~v---llD~~VkP~~~V~D----YrT---~~SGIt~~~L~~a~~~~~~~t~~~v~~~l~~li~~ 101 (174)
T cd06143 32 SLARVSVVRGEGELEGVP---FIDDYISTTEPVVD----YLT---RFSGIKPGDLDPKTSSKNLTTLKSAYLKLRLLVDL 101 (174)
T ss_pred eeEEEEEEcCCCCcCCCE---EEeeeECCCCCccC----cCc---cccccCHHHcCccccccccCCHHHHHHHHHHHcCC
Confidence 66655 5562 2222 25689999887743 444 67899999998764 588899999998864
Q ss_pred ccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHH-----------HHHHHHHCCCcccCCCCCCCCCcHHHH
Q 025709 159 NVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSI-----------KALCMRWYPRDYRKVPSKEQKHRALDD 227 (249)
Q Consensus 159 ~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl-----------~~la~r~~p~~~~~~l~~~~~HrAl~D 227 (249)
. .+||||....|+..|+-..| +..++||+.+ ..|++.++.... ....|+.++|
T Consensus 102 ~-----tILVGHsL~nDL~aL~l~hp------~~~viDTa~l~~~~~~r~~sLk~La~~~L~~~I-----Q~~~HdSvED 165 (174)
T cd06143 102 G-----CIFVGHGLAKDFRVINIQVP------KEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKI-----QSETHDSIED 165 (174)
T ss_pred C-----CEEEeccchhHHHHhcCcCC------CcceEEcHHhccCCCCCChhHHHHHHHHcCCcc-----cCCCcCcHHH
Confidence 2 58999999999999985422 2346666533 334444433222 2358999999
Q ss_pred HHHHHHHHH
Q 025709 228 IRESIMELK 236 (249)
Q Consensus 228 a~aT~~ll~ 236 (249)
|++|++||+
T Consensus 166 ArAam~Ly~ 174 (174)
T cd06143 166 ARTALKLYR 174 (174)
T ss_pred HHHHHHHhC
Confidence 999999984
No 54
>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=99.30 E-value=1.9e-11 Score=103.87 Aligned_cols=97 Identities=19% Similarity=0.175 Sum_probs=72.8
Q ss_pred EEEEEecCCC----CCCCCceEEEEEEEE-cCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 72 VWIDLEMTGL----KIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 72 V~lDlETTGL----~p~~d~IIEIgaVv~-dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
++||+||||+ ++..|+|++||++.. +|.... +.....+... ...|++..++...+++.
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~----~~~~~~~~~~-------------~~~~i~~~~v~~~~~E~ 64 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVV----FLLKTSTVGD-------------DIEFIDGIEVEYFADEK 64 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceee----EEEeecccCC-------------cCCCCCCceEEEeCCHH
Confidence 6899999999 888999999999964 665432 1111111111 01166777788889999
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccC
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 188 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 188 (249)
+++..|+++++.+- +.++||||+ .||++||...+..++.
T Consensus 65 ~lL~~f~~~i~~~d---pdiivg~N~~~FD~~~L~~R~~~~~~ 104 (199)
T cd05160 65 ELLKRFFDIIREYD---PDILTGYNIDDFDLPYLLKRAEALGI 104 (199)
T ss_pred HHHHHHHHHHHhcC---CCEEEEeccCCCcHHHHHHHHHHhCC
Confidence 99999999999752 357999999 9999999998876664
No 55
>PHA02570 dexA exonuclease; Provisional
Probab=99.21 E-value=1.9e-10 Score=99.16 Aligned_cols=162 Identities=18% Similarity=0.206 Sum_probs=107.4
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecC-----------CC-ccc--ccchhhhhhhhhccCCcHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQ-----------TK-ECL--DSMGEWCQNHHEASGLTKK 137 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p-----------~~-~~~--~~~~~~~~~~h~~tGIt~~ 137 (249)
++||+||.|..|. ..||+||||.++.... .+..|+.+|.. .. ... .++.+|.++.-+. .+
T Consensus 4 lMIDlETmG~~p~-AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EA----R~ 77 (220)
T PHA02570 4 FIIDFETFGNTPD-GAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEA----RK 77 (220)
T ss_pred EEEEeeccCCCCC-ceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHH----HH
Confidence 5799999999975 7999999999887544 34555554531 11 111 2345554432110 11
Q ss_pred HHh---cCCCHHHHHHHHHHHHhcccC-CCCcEEEEecHHHHHHHHHHHHHhc----c--CCCCC---ceeehhHHHHHH
Q 025709 138 VLH---SGLTEREAEKQVVEFVKKNVG-TYTPLLAGNSVYVDFMFLKKYMPDL----A--SLFSH---VLVDVSSIKALC 204 (249)
Q Consensus 138 ~l~---~~p~~~ea~~~~~~fl~~~~~-~~~~~lVghn~~FD~~fL~~~~~~~----~--~~~~~---~~iD~~sl~~la 204 (249)
.+. +..++.+++.+|.+||..+.. .....+.|+...||..+|...+.++ + ...|+ .-.|++++.+.
T Consensus 78 ~L~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~- 156 (220)
T PHA02570 78 NLKPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEA- 156 (220)
T ss_pred hccCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhh-
Confidence 222 346899999999999997642 2335678999999999999998776 5 34443 36789887652
Q ss_pred HHHCCC------cccCCCCCCCCCcHHHHHHHHHHHHHHHHHH
Q 025709 205 MRWYPR------DYRKVPSKEQKHRALDDIRESIMELKYYKEN 241 (249)
Q Consensus 205 ~r~~p~------~~~~~l~~~~~HrAl~Da~aT~~ll~~~~~~ 241 (249)
+++-+ +++..++.-.+|+|+.||..-+..|.|.+..
T Consensus 157 -~~l~r~~~~cp~~~g~l~gfv~H~sihDcakd~lml~y~~ry 198 (220)
T PHA02570 157 -TLLTRGMTTCPLPKGTLDGFVAHDSIHDCAKDILMLIYAKRY 198 (220)
T ss_pred -hhccCCcccCCCcCccccchhhcccHHHHHHHHHHHHHHHHH
Confidence 22111 2234566678999999999988888776543
No 56
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=99.16 E-value=6e-10 Score=84.70 Aligned_cols=91 Identities=26% Similarity=0.366 Sum_probs=67.3
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 151 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~ 151 (249)
+++|+||||+++..++|++|++...++... .++ +
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~-------~~~---------------------~------------------ 34 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDT-------AVI---------------------D------------------ 34 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCE-------EEe---------------------h------------------
Confidence 479999999999999999999874320110 000 1
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCC---CCCceeehhHHHHHHHHHCCCcccCCCCCCCCCcHHHHH
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL---FSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDI 228 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~---~~~~~iD~~sl~~la~r~~p~~~~~~l~~~~~HrAl~Da 228 (249)
|.+|+++.. +.++||||+.||+.||++++.+++.. ++.+++|+..+ |++||
T Consensus 35 f~~~l~~~~---~~v~V~hn~~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l-----------------------~~~~~ 88 (96)
T cd06125 35 LKDILRDKP---LAILVGHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIKL-----------------------AADDV 88 (96)
T ss_pred HHHHHhhCC---CCEEEEeCcHHhHHHHHHHHHHcCCCCCCcCCcEEEehHH-----------------------hhhhH
Confidence 778887631 14789999999999999999887643 35679999432 88998
Q ss_pred HHHHHH
Q 025709 229 RESIME 234 (249)
Q Consensus 229 ~aT~~l 234 (249)
+.++++
T Consensus 89 ~~~~~~ 94 (96)
T cd06125 89 ENTLQI 94 (96)
T ss_pred HHHHHh
Confidence 888765
No 57
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.97 E-value=8.2e-09 Score=96.24 Aligned_cols=148 Identities=22% Similarity=0.305 Sum_probs=108.6
Q ss_pred ccCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhc-CCC
Q 025709 66 EYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS-GLT 144 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~-~p~ 144 (249)
....+.+++||||....-. -++..|++|=.+++.. ++.+|.|..++.++. + ..+|||++++++ ..+
T Consensus 213 ~~~~~i~AlDCEm~~te~g-~el~RVt~VD~~~~vi-----~D~fVkP~~~VvDy~----T---~~SGIT~~~~e~~t~t 279 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVTENG-LELTRVTAVDRDGKVI-----LDTFVKPNKPVVDYN----T---RYSGITEEDLENSTIT 279 (380)
T ss_pred CCCCCeEEEEeeeeeeccc-eeeEEeeeeeccCcEE-----eEEeecCCCcccccc----c---ccccccHHHHhcCccC
Confidence 3347889999999987755 6777777775665552 568899999886543 2 567999999974 568
Q ss_pred HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehh--------------HHHHHHHHHCCC
Q 025709 145 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS--------------SIKALCMRWYPR 210 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~--------------sl~~la~r~~p~ 210 (249)
+.++-.++..|+... .+||||+..-|+.-|+...+ .++||+ ++..|+..++..
T Consensus 280 l~dvq~~l~~~~~~~-----TILVGHSLenDL~aLKl~H~--------~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~ 346 (380)
T KOG2248|consen 280 LEDVQKELLELISKN-----TILVGHSLENDLKALKLDHP--------SVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGK 346 (380)
T ss_pred HHHHHHHHHhhcCcC-----cEEEeechhhHHHHHhhhCC--------ceeeeeEEEecCCCCccchHHHHHHHHHHHHH
Confidence 999999999999863 68999999999999997543 344443 233344444332
Q ss_pred cccCCCCCCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 211 DYRKVPSKEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 211 ~~~~~l~~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
... .....|++..||.++++|+++...+-
T Consensus 347 ~Iq---~~~~~HdS~eDA~acm~Lv~~k~~~~ 375 (380)
T KOG2248|consen 347 LIQ---EGVGGHDSVEDALACMKLVKLKIKNS 375 (380)
T ss_pred HHh---ccCCCCccHHHHHHHHHHHHHHHhcc
Confidence 221 23567999999999999999887654
No 58
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=98.57 E-value=9.6e-07 Score=73.78 Aligned_cols=137 Identities=13% Similarity=0.082 Sum_probs=88.0
Q ss_pred cCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 67 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 67 ~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
+..+++++|+||||+++..++|+.++....++. . +++..... .. .+++...
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~------~--~~~~~~~~----------------~~-----~~~~~~~ 53 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAVEPGE------A--YYIPLGHD----------------YG-----GEQLPRE 53 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEcCCCC------E--EEEecCCC----------------cc-----ccCCCHH
Confidence 456789999999999988889988886522221 1 12211100 00 1344677
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCc-cc--------C-C-
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRD-YR--------K-V- 215 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~-~~--------~-~- 215 (249)
+++.++.+|+++. ...+||||+.||+.+|.++ +..++..++|+. -+++.+.|.. .. + +
T Consensus 54 ~~~~~l~~~l~~~----~~~~v~hn~k~d~~~l~~~----gi~~~~~~~Dt~---l~a~ll~p~~~~~~l~~l~~~~l~~ 122 (193)
T cd06139 54 EVLAALKPLLEDP----SIKKVGQNLKFDLHVLANH----GIELRGPAFDTM---LASYLLNPGRRRHGLDDLAERYLGH 122 (193)
T ss_pred HHHHHHHHHHhCC----CCcEEeeccHHHHHHHHHC----CCCCCCCcccHH---HHHHHhCCCCCCCCHHHHHHHHhCC
Confidence 8899999999863 1358999999999999753 444566678883 3455555543 10 0 0
Q ss_pred --C---------------C----CCCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 216 --P---------------S----KEQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 216 --l---------------~----~~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
+ . ....|.|..|+.++..++..+.+.+-
T Consensus 123 ~~~~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 123 KTISFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred CCccHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0 01234688899999999998887764
No 59
>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=98.48 E-value=1.5e-06 Score=74.11 Aligned_cols=91 Identities=23% Similarity=0.271 Sum_probs=62.4
Q ss_pred CCcEEEEEEecC---CC-CCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC
Q 025709 68 KMPLVWIDLEMT---GL-KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 143 (249)
Q Consensus 68 ~~~~V~lDlETT---GL-~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p 143 (249)
+-+.++||+||| |+ ++..|+|+.||++..+++.... ..+.. . ..+..-.
T Consensus 2 ~l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~-------~~~~~-~-------------------~~v~~~~ 54 (195)
T cd05780 2 DLKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVIT-------WKKFD-L-------------------PFVEVVK 54 (195)
T ss_pred CceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEE-------ecCCC-C-------------------CeEEEeC
Confidence 356789999998 65 7788999999987544332110 11100 0 0112234
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccC
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 188 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 188 (249)
++.+.+..|.+++..+- +.++||||. .||++||...+..+|.
T Consensus 55 ~E~~lL~~F~~~i~~~d---pdiivgyN~~~FD~pyL~~R~~~~gi 97 (195)
T cd05780 55 TEKEMIKRFIEIVKEKD---PDVIYTYNGDNFDFPYLKKRAEKLGI 97 (195)
T ss_pred CHHHHHHHHHHHHHHcC---CCEEEecCCCCCcHHHHHHHHHHhCC
Confidence 67889999999999752 357999998 8999999988766553
No 60
>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=98.38 E-value=4.1e-07 Score=74.63 Aligned_cols=91 Identities=19% Similarity=0.145 Sum_probs=50.6
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 151 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~ 151 (249)
++||+|||||+|..+.|.-||++..++..... +...... .+..++.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~---~~~~~~~----------------------------~~~ee~~~~~ 49 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIIT---FIQWFAE----------------------------DPDEEEIILE 49 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE----EEEE-GG----------------------------GHHHHHHHHH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEE---eeHhhcc----------------------------CcHHHHHHHH
Confidence 58999999999988999999998654432110 1111110 0112334444
Q ss_pred HHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccCCCCCceeehh
Q 025709 152 VVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASLFSHVLVDVS 198 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~~~~~~iD~~ 198 (249)
+.+++.+. ..+|+||. .||++||++.+.+++.+.+...+|+.
T Consensus 50 ~~~~l~~~-----~~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~ 92 (164)
T PF13482_consen 50 FFELLDEA-----DNIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLL 92 (164)
T ss_dssp --HHHHTT-------EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHH
T ss_pred HHHHHhcC-----CeEEEEeCcccCHHHHHHHHHHcCCCcccchhhHH
Confidence 44677763 46889985 99999999999777755577899994
No 61
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=98.38 E-value=3.3e-06 Score=71.81 Aligned_cols=82 Identities=22% Similarity=0.363 Sum_probs=62.4
Q ss_pred CCcEEEEEEecC---CC-CCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC
Q 025709 68 KMPLVWIDLEMT---GL-KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 143 (249)
Q Consensus 68 ~~~~V~lDlETT---GL-~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p 143 (249)
+-+.++||+||+ |+ ++..++|+.||+...+|.... +. ....
T Consensus 2 ~l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~--------~~---------------------------~~~~ 46 (188)
T cd05781 2 DLKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEF--------IL---------------------------AEGL 46 (188)
T ss_pred CceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEE--------EE---------------------------ecCC
Confidence 457899999999 54 788999999999876655321 10 0124
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
++.+.+..|++++..+- +.+++|||+ .||++||..-+..+|
T Consensus 47 ~E~~lL~~F~~~i~~~d---Pd~i~gyN~~~FDlpyl~~Ra~~~g 88 (188)
T cd05781 47 DDRKIIREFVKYVKEYD---PDIIVGYNSNAFDWPYLVERARVLG 88 (188)
T ss_pred CHHHHHHHHHHHHHHcC---CCEEEecCCCcCcHHHHHHHHHHhC
Confidence 57889999999999863 357899998 899999998876665
No 62
>PRK05755 DNA polymerase I; Provisional
Probab=98.26 E-value=1.1e-05 Score=83.30 Aligned_cols=130 Identities=15% Similarity=0.161 Sum_probs=87.8
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
...++++|+||||+++..++|+.|++-.-++. ..+|++. ++. .+
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~--------~~~ip~~------------------~i~----------~~ 357 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAELVGLSFAVEPGE--------AAYIPLD------------------QLD----------RE 357 (880)
T ss_pred ccCeEEEEeccCCCCcccccEEEEEEEeCCCc--------EEEEecc------------------ccc----------HH
Confidence 46789999999999999999999886432221 1233220 211 15
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCccc--------C-CCC-
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYR--------K-VPS- 217 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~--------~-~l~- 217 (249)
++..|.+|+++. ..++|+||+.||+.||.++ |..++.+++||. -+++-+.|.... + +..
T Consensus 358 ~l~~l~~~L~d~----~v~kV~HNakfDl~~L~~~----gi~~~~~~~DT~---iAa~Ll~~~~~~~L~~L~~~ylg~~~ 426 (880)
T PRK05755 358 VLAALKPLLEDP----AIKKVGQNLKYDLHVLARY----GIELRGIAFDTM---LASYLLDPGRRHGLDSLAERYLGHKT 426 (880)
T ss_pred HHHHHHHHHhCC----CCcEEEeccHhHHHHHHhC----CCCcCCCcccHH---HHHHHcCCCCCCCHHHHHHHHhCCCc
Confidence 778888899873 2357999999999999853 555667789984 344555554310 0 000
Q ss_pred ------------------CCCCCcHHHHHHHHHHHHHHHHHHhcC
Q 025709 218 ------------------KEQKHRALDDIRESIMELKYYKENIFK 244 (249)
Q Consensus 218 ------------------~~~~HrAl~Da~aT~~ll~~~~~~~~~ 244 (249)
....|.|..|+..+..++..+++.+..
T Consensus 427 ~~~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 427 ISFEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred cchHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 013478999999999999999887643
No 63
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.04 E-value=2.2e-05 Score=68.87 Aligned_cols=98 Identities=19% Similarity=0.206 Sum_probs=55.9
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEE-EEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
..++++||+|||||++..+.|+=+|.- ..++. +.|++.- + .+|..+
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~---------~~Vrq~~------------------l------p~p~~E 143 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVDDT---------MHVRQHF------------------L------PAPEEE 143 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccCce---------EEEEeec------------------C------CCcchh
Confidence 577999999999999966666655544 22222 2333210 0 011111
Q ss_pred -HHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHh--ccCCCCCceeehhHHHHHHHHHC
Q 025709 147 -EAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPD--LASLFSHVLVDVSSIKALCMRWY 208 (249)
Q Consensus 147 -ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~--~~~~~~~~~iD~~sl~~la~r~~ 208 (249)
.++ ..|+..- .-..||..|. +||++|+++ +.+ +...+.+..+|. +.-+||+.
T Consensus 144 ~avl---e~fl~~~---~~~~lvsfNGkaFD~PfikR-~v~~~~el~l~~~H~DL---~h~~RRlw 199 (278)
T COG3359 144 VAVL---ENFLHDP---DFNMLVSFNGKAFDIPFIKR-MVRDRLELSLEFGHFDL---YHPSRRLW 199 (278)
T ss_pred hHHH---HHHhcCC---CcceEEEecCcccCcHHHHH-HHhcccccCccccchhh---hhhhhhhh
Confidence 122 2344331 0125787776 999999996 433 333455667887 56677765
No 64
>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=98.01 E-value=5e-05 Score=65.47 Aligned_cols=106 Identities=14% Similarity=0.155 Sum_probs=62.5
Q ss_pred CcEEEEEEecCC-----CCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC
Q 025709 69 MPLVWIDLEMTG-----LKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 143 (249)
Q Consensus 69 ~~~V~lDlETTG-----L~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p 143 (249)
-+.++||+||.+ .+|..|+||+|+++........... -++.+....+... .+- .+.|.. .+..-.
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~---~~~~~~~~~~~~~--~~~---~~~~~~--~v~~~~ 71 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNR---EIVSEDIEDFEYT--PKP---EYEGPF--KVFNEP 71 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecc---ccccccccccccc--CCC---CCCCce--EEecCC
Confidence 467899999986 3677899999998854322111100 0000000000000 000 000100 011235
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
++.+.+.+|.+|+.++- +.+++|||. .||++||.+-+..+|
T Consensus 72 ~E~~lL~~f~~~i~~~~---Pd~i~gyN~~~FD~pyl~~R~~~~~ 113 (204)
T cd05779 72 DEKALLQRFFEHIREVK---PHIIVTYNGDFFDWPFVEARAAIHG 113 (204)
T ss_pred CHHHHHHHHHHHHHHhC---CCEEEecCccccCHHHHHHHHHHhC
Confidence 78999999999999863 347899999 999999998775554
No 65
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=97.93 E-value=4.8e-05 Score=66.45 Aligned_cols=100 Identities=19% Similarity=0.242 Sum_probs=64.8
Q ss_pred ccCCcEEEEEEecCC-----CCCCCCceEEEEEEE-EcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHH
Q 025709 66 EYKMPLVWIDLEMTG-----LKIEVDRILEIACII-TDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVL 139 (249)
Q Consensus 66 ~~~~~~V~lDlETTG-----L~p~~d~IIEIgaVv-~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l 139 (249)
..+.+.++||+||+. .+|..|+|+.|++++ .++....... .-+.+.+.... + |. .+
T Consensus 4 ~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~-~~~~l~~~~~~-~-------------~~---~v 65 (230)
T cd05777 4 IAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIR-NIFTLKTCAPI-V-------------GA---QV 65 (230)
T ss_pred CCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCcee-EEEEeCCCCCC-C-------------CC---EE
Confidence 456788999999984 477889999999985 3443221111 01112221111 0 11 11
Q ss_pred hcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhc
Q 025709 140 HSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 186 (249)
Q Consensus 140 ~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 186 (249)
..-.++.+.+..|++++..+- +.+++|||+ .||+++|.+-+..+
T Consensus 66 ~~~~~E~eLL~~f~~~i~~~D---PDii~GyN~~~FDl~yL~~R~~~l 110 (230)
T cd05777 66 FSFETEEELLLAWRDFVQEVD---PDIITGYNICNFDLPYLLERAKAL 110 (230)
T ss_pred EEECCHHHHHHHHHHHHHhcC---CCEEEEecCCCCCHHHHHHHHHHh
Confidence 123578999999999999752 358999998 89999998776544
No 66
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=97.92 E-value=6.6e-05 Score=64.78 Aligned_cols=84 Identities=19% Similarity=0.301 Sum_probs=60.2
Q ss_pred ccCCcEEEEEEecCCC--------CCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHH
Q 025709 66 EYKMPLVWIDLEMTGL--------KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKK 137 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL--------~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~ 137 (249)
..+-+.+.||+||++. ++..++|+.||+...++. ..++.
T Consensus 6 ~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~--------~~~~~------------------------- 52 (207)
T cd05785 6 FDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGW--------EEVLH------------------------- 52 (207)
T ss_pred CCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCc--------eeeec-------------------------
Confidence 3467899999999653 345689999998532221 01110
Q ss_pred HHhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 138 VLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 138 ~l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
....++.+++..|++++.++- +.+|+|||+ .||+++|.+.+..++
T Consensus 53 --~~~~~E~~lL~~f~~~i~~~d---Pdii~g~N~~~FD~pyl~~R~~~~~ 98 (207)
T cd05785 53 --AEDAAEKELLEELVAIIRERD---PDVIEGHNIFRFDLPYLRRRCRRHG 98 (207)
T ss_pred --cCCCCHHHHHHHHHHHHHHhC---CCEEeccCCcccCHHHHHHHHHHhC
Confidence 013568899999999999853 358899999 999999998876654
No 67
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=97.69 E-value=0.0001 Score=65.48 Aligned_cols=171 Identities=20% Similarity=0.238 Sum_probs=99.2
Q ss_pred ccCCcEEEEEEecCCCCCCCCceEEEEEE-E----EcCcEeeeeccceEEecCCCcccccc----------hhhhhhhhh
Q 025709 66 EYKMPLVWIDLEMTGLKIEVDRILEIACI-I----TDGKLTKSVEGPDLVIHQTKECLDSM----------GEWCQNHHE 130 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL~p~~d~IIEIgaV-v----~dg~~~~~~~~~~~~I~p~~~~~~~~----------~~~~~~~h~ 130 (249)
+.-..++|+|+|+|||..-...|-|+... + .++....+.+.....++++ .+++++ .... .+
T Consensus 10 pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~-Rvl~Klsvl~~p~~v~~p~a---ee 85 (318)
T KOG4793|consen 10 PRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGS-RVLDKLSVLGGPVPVTRPIA---EE 85 (318)
T ss_pred CceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCcc-chhhhhhhccCCcCCcChhh---hh
Confidence 44578999999999998777778887754 2 3454333333333333333 222211 1111 26
Q ss_pred ccCCcHHHH--hcCCCHHH-HHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccCCCCCceeehhHHHH---H
Q 025709 131 ASGLTKKVL--HSGLTERE-AEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASLFSHVLVDVSSIKA---L 203 (249)
Q Consensus 131 ~tGIt~~~l--~~~p~~~e-a~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~---l 203 (249)
+||++...+ +....+.. +.+-+..|+...-. +.-||+||. .||+++|.+++.++|..++...+++.++-. +
T Consensus 86 itgls~~~~~l~rr~~~D~dla~LL~afls~lp~--p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~al 163 (318)
T KOG4793|consen 86 ITGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPT--PGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNAL 163 (318)
T ss_pred hcccccHHHHHHHHhhhhHHHHHHHHHHHhcCCC--CceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHH
Confidence 889987443 33344444 55555677776422 234789998 999999999999999877766665554432 2
Q ss_pred HHHHC----CC-cccC----------CC-CCCCCCcHHHHHHHHHHHHHHHHHHh
Q 025709 204 CMRWY----PR-DYRK----------VP-SKEQKHRALDDIRESIMELKYYKENI 242 (249)
Q Consensus 204 a~r~~----p~-~~~~----------~l-~~~~~HrAl~Da~aT~~ll~~~~~~~ 242 (249)
-++-. |. ...| +- .....|.|..|.-.-.-.+++..+.+
T Consensus 164 d~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~el 218 (318)
T KOG4793|consen 164 DRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINEL 218 (318)
T ss_pred hhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHH
Confidence 22211 11 1111 11 34567888887766555555544433
No 68
>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=97.63 E-value=0.00069 Score=60.37 Aligned_cols=165 Identities=19% Similarity=0.171 Sum_probs=80.8
Q ss_pred CcEEEEEEecCCCCCC---------------------CCceEEEEEEEE-cCcEeee----eccceEEecCCCcccccch
Q 025709 69 MPLVWIDLEMTGLKIE---------------------VDRILEIACIIT-DGKLTKS----VEGPDLVIHQTKECLDSMG 122 (249)
Q Consensus 69 ~~~V~lDlETTGL~p~---------------------~d~IIEIgaVv~-dg~~~~~----~~~~~~~I~p~~~~~~~~~ 122 (249)
-+||+||+|.||+... .-.|||+|..+. +...... ...+.+.+-|...... -.
T Consensus 22 ~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~-~~ 100 (262)
T PF04857_consen 22 ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFS-QA 100 (262)
T ss_dssp SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEE-EH
T ss_pred CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeecccccccee-cc
Confidence 4699999999999753 247999998866 3322211 1112222122111110 01
Q ss_pred hhhhhhhhccCCc-HHHHhcCCCHHHHHH--HHHHHHhcc--cC---CCCcEEEEecHHHHHHHHHHHHH----------
Q 025709 123 EWCQNHHEASGLT-KKVLHSGLTEREAEK--QVVEFVKKN--VG---TYTPLLAGNSVYVDFMFLKKYMP---------- 184 (249)
Q Consensus 123 ~~~~~~h~~tGIt-~~~l~~~p~~~ea~~--~~~~fl~~~--~~---~~~~~lVghn~~FD~~fL~~~~~---------- 184 (249)
..+.- -.-+|+. ++...+|.+.....+ ++.+.++-. +. ..+.++||||.-+|+.||-+.|-
T Consensus 101 ~sl~F-L~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF 179 (262)
T PF04857_consen 101 SSLQF-LRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEF 179 (262)
T ss_dssp HHHHH-HHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHHH
T ss_pred hhHHH-HHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHH
Confidence 11111 1334774 345566766544332 111333221 11 22467999999999999887651
Q ss_pred --hccCCCCCceeehhHHHH-----------HHHHHCCCc-----c-c---CC--------C-CCCCCCcHHHHHHHHHH
Q 025709 185 --DLASLFSHVLVDVSSIKA-----------LCMRWYPRD-----Y-R---KV--------P-SKEQKHRALDDIRESIM 233 (249)
Q Consensus 185 --~~~~~~~~~~iD~~sl~~-----------la~r~~p~~-----~-~---~~--------l-~~~~~HrAl~Da~aT~~ 233 (249)
.+...||. ++||..|.. ++..+.... . . .. . .....|.|=.||.+|..
T Consensus 180 ~~~~~~~FP~-i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~ 258 (262)
T PF04857_consen 180 KELLRELFPR-IYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGC 258 (262)
T ss_dssp HHHHHHHSSS-EEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHHHH
T ss_pred HHHHHHHCcc-cccHHHHHHhccccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHHHH
Confidence 12234544 889865433 111111111 0 0 00 0 23449999999999998
Q ss_pred HHH
Q 025709 234 ELK 236 (249)
Q Consensus 234 ll~ 236 (249)
++-
T Consensus 259 ~F~ 261 (262)
T PF04857_consen 259 VFI 261 (262)
T ss_dssp HHH
T ss_pred HHc
Confidence 864
No 69
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=97.61 E-value=0.00032 Score=60.46 Aligned_cols=101 Identities=16% Similarity=0.127 Sum_probs=60.6
Q ss_pred cCCcEEEEEEecCC------CCCCC--CceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHH
Q 025709 67 YKMPLVWIDLEMTG------LKIEV--DRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV 138 (249)
Q Consensus 67 ~~~~~V~lDlETTG------L~p~~--d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~ 138 (249)
++-++++||+||++ .+++. +.||+||+.-.++.... +++..+... .+... ..-+. .
T Consensus 3 P~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v------~~~~~~~~~-----~~~~~--~~~~~---~ 66 (204)
T cd05783 3 PKLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRV------LVLKREGVE-----GLEGL--LPEGA---E 66 (204)
T ss_pred CCceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEE------EEEecCCcc-----ccccc--CCCCC---e
Confidence 35688999999984 23333 78999998622232111 222211100 00000 00010 0
Q ss_pred HhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccC
Q 025709 139 LHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 188 (249)
Q Consensus 139 l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 188 (249)
+..=.++.+.+..|++|+.++ .+++|||. .||+++|.+-+..+|.
T Consensus 67 v~~~~~E~~lL~~F~~~i~~~-----~~iig~N~~~FDlpyl~~R~~~~gi 112 (204)
T cd05783 67 VEFFDSEKELIREAFKIISEY-----PIVLTFNGDNFDLPYLYNRALKLGI 112 (204)
T ss_pred EEecCCHHHHHHHHHHHHhcC-----CEEEEeCCCCcCHHHHHHHHHHhCC
Confidence 111246899999999999975 47899999 9999999988766653
No 70
>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=97.39 E-value=0.00069 Score=61.12 Aligned_cols=101 Identities=12% Similarity=0.153 Sum_probs=65.2
Q ss_pred cCCcEEEEEEecCCCC-----CCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhc
Q 025709 67 YKMPLVWIDLEMTGLK-----IEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS 141 (249)
Q Consensus 67 ~~~~~V~lDlETTGL~-----p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~ 141 (249)
.+..++.||+||.... +..|+|+.|++++.+.............+.+..... + ...+..
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~--~~~v~~ 218 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDSIE--------------D--NVEVIY 218 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCCTT--------------C--TTEEEE
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCCCC--------------C--CcEEEE
Confidence 6789999999998765 568999999988643211100011112222222110 0 111112
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhc
Q 025709 142 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 186 (249)
Q Consensus 142 ~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 186 (249)
-.++.+.+..|++++...- +-+++|||+ .||+++|..-+..+
T Consensus 219 ~~~E~~lL~~f~~~i~~~d---PDii~GyN~~~fD~~yl~~R~~~l 261 (325)
T PF03104_consen 219 FDSEKELLEAFLDIIQEYD---PDIITGYNIDGFDLPYLIERAKKL 261 (325)
T ss_dssp ESSHHHHHHHHHHHHHHHS----SEEEESSTTTTHHHHHHHHHHHT
T ss_pred ECCHHHHHHHHHHHHHhcC---CcEEEEecccCCCHHHHHHHHHHh
Confidence 2578999999999999852 358999999 79999999877655
No 71
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=97.28 E-value=0.0015 Score=55.83 Aligned_cols=89 Identities=12% Similarity=0.132 Sum_probs=57.3
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
+-+.++||+||+|.. +|..||..-...+.. +.+...... .|. .+.--+++.+
T Consensus 2 ~l~~~~fDIE~~~~~----~i~~i~~~~~~~~~i-------~~~~~~~~~--------------~~~---~v~~~~~E~~ 53 (193)
T cd05784 2 KLKVVSLDIETSMDG----ELYSIGLYGEGQERV-------LMVGDPEDD--------------APD---NIEWFADEKS 53 (193)
T ss_pred CccEEEEEeecCCCC----CEEEEEeecCCCCEE-------EEECCCCCC--------------CCC---EEEEECCHHH
Confidence 457899999999765 888888752211111 112111110 010 0111256888
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
.+..|.+++.++- +.+++|||. .||+++|..-+..++
T Consensus 54 lL~~f~~~i~~~d---PDvi~g~N~~~FD~~yl~~R~~~~~ 91 (193)
T cd05784 54 LLLALIAWFAQYD---PDIIIGWNVINFDLRLLQRRAEAHG 91 (193)
T ss_pred HHHHHHHHHHhhC---CCEEEECCCcCcCHHHHHHHHHHhC
Confidence 9999999999852 357999999 999999998775554
No 72
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.18 E-value=0.0014 Score=68.86 Aligned_cols=100 Identities=20% Similarity=0.249 Sum_probs=62.8
Q ss_pred ccCCcEEEEEEecCCC------CCCCCceEEEEEEEE-cCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHH
Q 025709 66 EYKMPLVWIDLEMTGL------KIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV 138 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL------~p~~d~IIEIgaVv~-dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~ 138 (249)
..+-+++.||+||+|. ++..|+||+||+++. .|..........+...+..++ .|. .
T Consensus 261 ~pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~c~~i--------------~g~---~ 323 (1054)
T PTZ00166 261 IAPLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECASI--------------AGA---N 323 (1054)
T ss_pred CCCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCccccC--------------CCc---e
Confidence 3577899999999864 345799999999854 333210000111111111111 121 1
Q ss_pred HhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHh
Q 025709 139 LHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPD 185 (249)
Q Consensus 139 l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~ 185 (249)
+..-.++.+.+..|.+|+...- +.+++|||+ .||+++|-.-+..
T Consensus 324 V~~f~sE~eLL~~f~~~I~~~D---PDII~GYNi~~FDlpYL~~Ra~~ 368 (1054)
T PTZ00166 324 VLSFETEKELLLAWAEFVIAVD---PDFLTGYNIINFDLPYLLNRAKA 368 (1054)
T ss_pred EEEeCCHHHHHHHHHHHHHhcC---CCEEEecCCcCCcHHHHHHHHHH
Confidence 2223578999999999999753 458999999 8999999876543
No 73
>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=97.12 E-value=0.0026 Score=55.70 Aligned_cols=107 Identities=15% Similarity=0.192 Sum_probs=64.3
Q ss_pred CCcEEEEEEecCC-----CCCCCCceEEEEEEEEcCcEeeee---ccceEEecCCCcccccchhhhhhhhhccCCcHHHH
Q 025709 68 KMPLVWIDLEMTG-----LKIEVDRILEIACIITDGKLTKSV---EGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVL 139 (249)
Q Consensus 68 ~~~~V~lDlETTG-----L~p~~d~IIEIgaVv~dg~~~~~~---~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l 139 (249)
....+.+|+|+.+ .+|..|+|+.|+.++.+....... .....++...... . ..- . ....+....+
T Consensus 3 ~l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~--~~~-~---~~~~~~~~~v 75 (231)
T cd05778 3 HLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSN-A--SNG-R---IRSGLSGIPV 75 (231)
T ss_pred ceEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccch-h--hhh-c---cccCCCCCeE
Confidence 3567899999864 367789999999886544322110 0111223322110 0 000 0 0001111223
Q ss_pred hcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHH
Q 025709 140 HSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMP 184 (249)
Q Consensus 140 ~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~ 184 (249)
.--.++.+.+.+|.+++..+- +-+++|||+ .||+++|-+-+.
T Consensus 76 ~~~~~E~~LL~~f~~~i~~~D---PDii~GyNi~~fd~~YL~~Ra~ 118 (231)
T cd05778 76 EVVESELELFEELIDLVRRFD---PDILSGYEIQRSSWGYLIERAA 118 (231)
T ss_pred EEeCCHHHHHHHHHHHHHHhC---CCEEEEeccccCcHHHHHHHHH
Confidence 334678999999999999853 458999999 999999987653
No 74
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=96.80 E-value=0.0076 Score=51.99 Aligned_cols=77 Identities=17% Similarity=0.154 Sum_probs=53.0
Q ss_pred EecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHHHHHHH
Q 025709 76 LEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQVVEF 155 (249)
Q Consensus 76 lETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~~~~f 155 (249)
.+++|+.+..++|+-||++..+..... ..+. .. ...++.+.+.+|.++
T Consensus 41 ~~~~~l~~~~~~Iv~Is~~~~~~~~~~------~~~~-~~-------------------------~~~~E~elL~~F~~~ 88 (208)
T cd05782 41 SGSDFLPLPFHKVVSISALYRDDDGGF------LKVR-TL-------------------------DGADEKELLEDFFQL 88 (208)
T ss_pred cCCCCCccccCceEEEEEEEEecCCCe------EEEe-ec-------------------------CCCCHHHHHHHHHHH
Confidence 357788888999999999865311110 0111 00 012357889999999
Q ss_pred HhcccCCCCcEEEEecH-HHHHHHHHHHHHhccC
Q 025709 156 VKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 188 (249)
Q Consensus 156 l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 188 (249)
+.++. ++|||||. .||++||...+..+|.
T Consensus 89 i~~~~----p~lv~yNg~~FDlP~L~~Ra~~~gi 118 (208)
T cd05782 89 IEKKN----PRLVSFNGRGFDLPVLHLRALIHGV 118 (208)
T ss_pred HHHhC----CEEEecCCCcCCHHHHHHHHHHhCC
Confidence 99852 47899999 9999999987655543
No 75
>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=96.78 E-value=0.045 Score=44.45 Aligned_cols=42 Identities=12% Similarity=0.171 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeeh
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDV 197 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~ 197 (249)
+...+.+++.+. ....||||+.||+.+|.+.+ +.. ...++|+
T Consensus 65 ~~~~l~~ll~~~----~i~kv~~n~~~D~~~L~~~~---~i~-~~~~~D~ 106 (176)
T PF01612_consen 65 ILDALKELLEDP----NIIKVGHNAKFDLKWLYRSF---GID-LKNVFDT 106 (176)
T ss_dssp HHHHHHHHHTTT----TSEEEESSHHHHHHHHHHHH---TS---SSEEEH
T ss_pred hHHHHHHHHhCC----CccEEEEEEechHHHHHHHh---ccc-cCCccch
Confidence 456666777752 24689999999999999872 322 2346777
No 76
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=96.63 E-value=0.0036 Score=63.66 Aligned_cols=161 Identities=17% Similarity=0.200 Sum_probs=96.6
Q ss_pred CCCcccccCCcEEEEEEecCCCCCCCCce-------------EEEEEE-EEcCcEeeeeccc-eEEecCCCcccccchhh
Q 025709 60 QTPLEFEYKMPLVWIDLEMTGLKIEVDRI-------------LEIACI-ITDGKLTKSVEGP-DLVIHQTKECLDSMGEW 124 (249)
Q Consensus 60 ~~~~~~~~~~~~V~lDlETTGL~p~~d~I-------------IEIgaV-v~dg~~~~~~~~~-~~~I~p~~~~~~~~~~~ 124 (249)
.+.++-++...+|.+|-|-.-|+++..+| ..+|-| +++|+.-..+-.| +=+|--...+ .+.
T Consensus 901 Lt~dEmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~V----vDY 976 (1118)
T KOG1275|consen 901 LTLDEMPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKV----VDY 976 (1118)
T ss_pred ccccccCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHH----HHH
Confidence 45566688899999999999888764443 134444 4444421111000 1122222233 233
Q ss_pred hhhhhhccCCcHHHHhcCC------CHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhcc-------CCCC
Q 025709 125 CQNHHEASGLTKKVLHSGL------TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLA-------SLFS 191 (249)
Q Consensus 125 ~~~~h~~tGIt~~~l~~~p------~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~-------~~~~ 191 (249)
.+ ..+||-+.+|.-.. ++.-+...+.=.+.- .+++|||...-|.+.|+-+.++-. ..++
T Consensus 977 LT---qySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~-----GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~ 1048 (1118)
T KOG1275|consen 977 LT---QYSGIKPGDLDPTTSEKRLTTLKVLYLKLRLLIQR-----GVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLG 1048 (1118)
T ss_pred HH---HhcCCCccccCCccCcceehhHHHHHHHHHHHHHc-----CcEEEcccccccceEEEEecChhhheeeeEEEecc
Confidence 33 56799998886432 344444444444432 378999999999999987653310 1122
Q ss_pred -CceeehhHHHHHHHHHCCCcccCCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 025709 192 -HVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDIRESIMELKYYKE 240 (249)
Q Consensus 192 -~~~iD~~sl~~la~r~~p~~~~~~l~~~~~HrAl~Da~aT~~ll~~~~~ 240 (249)
.+.+.. .-||+.++.... ...+|+.+.||+.+++||++|.+
T Consensus 1049 s~R~LSL---rfLa~~lLg~~I-----Q~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1049 SQRMLSL---RFLAWELLGETI-----QMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred cccEEEH---HHHHHHHhcchh-----hccccccHHHHHHHHHHHHHHHH
Confidence 245544 346666665432 46799999999999999999953
No 77
>PRK05762 DNA polymerase II; Reviewed
Probab=96.60 E-value=0.037 Score=56.82 Aligned_cols=90 Identities=11% Similarity=0.122 Sum_probs=58.6
Q ss_pred cCCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHH
Q 025709 67 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 146 (249)
Q Consensus 67 ~~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ 146 (249)
.+-+.+.||+||++. .+|+.||+.-.+... -+.+.++.... .+ .+..-+++.
T Consensus 153 p~lrvlsfDIE~~~~----~~i~sI~~~~~~~~~-------vi~ig~~~~~~---~~--------------~v~~~~sE~ 204 (786)
T PRK05762 153 PPLKVVSLDIETSNK----GELYSIGLEGCGQRP-------VIMLGPPNGEA---LD--------------FLEYVADEK 204 (786)
T ss_pred CCCeEEEEEEEEcCC----CceEEeeecCCCCCe-------EEEEECCCCCC---cc--------------eEEEcCCHH
Confidence 578899999999863 368888875111111 12222221100 00 022345789
Q ss_pred HHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 147 EAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 147 ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
+.+..|++++..+- +-+++|||+ .||+++|.+-+..+|
T Consensus 205 ~LL~~F~~~i~~~D---PDIIvGyNi~~FDlpyL~~Ra~~lg 243 (786)
T PRK05762 205 ALLEKFNAWFAEHD---PDVIIGWNVVQFDLRLLQERAERYG 243 (786)
T ss_pred HHHHHHHHHHHhcC---CCEEEEeCCCCCcHHHHHHHHHHhC
Confidence 99999999999863 358999998 899999998765543
No 78
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=96.57 E-value=0.012 Score=55.41 Aligned_cols=99 Identities=22% Similarity=0.314 Sum_probs=61.1
Q ss_pred CCcEEEEEEecCCCC-----CC--CCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHh
Q 025709 68 KMPLVWIDLEMTGLK-----IE--VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 140 (249)
Q Consensus 68 ~~~~V~lDlETTGL~-----p~--~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~ 140 (249)
+..++++|+||+... +. .++|+.|+.+..++..............+... ..|+. +.
T Consensus 2 ~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~---~~ 64 (471)
T smart00486 2 PLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKE--------------IDGVE---VY 64 (471)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCC--------------CCCCe---EE
Confidence 356889999998643 22 58999999987655432110111111222111 11211 11
Q ss_pred cCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhc
Q 025709 141 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 186 (249)
Q Consensus 141 ~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 186 (249)
.-....+.+..|.+++...- +.+++|||. .||+.+|...+..+
T Consensus 65 ~~~~E~~lL~~f~~~i~~~d---pdii~g~N~~~FD~~~i~~R~~~~ 108 (471)
T smart00486 65 EFNNEKELLKAFLEFIKKYD---PDIIYGHNISNFDLPYIISRLEKL 108 (471)
T ss_pred ecCCHHHHHHHHHHHHHHhC---CCEEEeecCCCCCHHHHHHHHHHc
Confidence 11267889999999998752 357999999 69999998876443
No 79
>PHA02528 43 DNA polymerase; Provisional
Probab=96.00 E-value=0.041 Score=57.04 Aligned_cols=103 Identities=21% Similarity=0.209 Sum_probs=60.0
Q ss_pred cCCcEEEEEEecCC----CCCC--CCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhc--cCCcHHH
Q 025709 67 YKMPLVWIDLEMTG----LKIE--VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEA--SGLTKKV 138 (249)
Q Consensus 67 ~~~~~V~lDlETTG----L~p~--~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~--tGIt~~~ 138 (249)
+.-++++||+||+. .+|. .++|+.||.--.++....+ +.+.... +|....... .-...-.
T Consensus 104 p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v-----~~~~~~~-------~~~~~~~~~~~~~~~~v~ 171 (881)
T PHA02528 104 SKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYV-----FDLGSVE-------EWDAKGDEVPQEILDKVV 171 (881)
T ss_pred CCccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEE-----EEecCcc-------cccccCCcccccccCCee
Confidence 57899999999976 4555 6799999983111111100 1111000 000000000 0000000
Q ss_pred HhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHH
Q 025709 139 LHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMP 184 (249)
Q Consensus 139 l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~ 184 (249)
+..-.++.+.+..|.+|+..+- +-+++|||+ .||+++|.+-+.
T Consensus 172 ~~~~~sE~eLL~~F~~~i~~~D---PDII~GyNi~~FDlpYL~~Ra~ 215 (881)
T PHA02528 172 YMPFDTEREMLLEYINFWEENT---PVIFTGWNVELFDVPYIINRIK 215 (881)
T ss_pred EEEcCCHHHHHHHHHHHHHHhC---CcEEEecCCccCCHHHHHHHHH
Confidence 1113578999999999998753 458999998 999999988765
No 80
>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=95.81 E-value=0.14 Score=43.41 Aligned_cols=84 Identities=13% Similarity=0.026 Sum_probs=49.4
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccC--CCCCceeehhHHHHH-----------------------HHH
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS--LFSHVLVDVSSIKAL-----------------------CMR 206 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~--~~~~~~iD~~sl~~l-----------------------a~r 206 (249)
+.+++.+- ..+-|||++.+|+.+|.+.+..... ..+..++|+..+... +..
T Consensus 74 L~~ll~d~----~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~ 149 (193)
T cd06146 74 LKRLFEDP----DVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQE 149 (193)
T ss_pred HHHHhCCC----CeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHH
Confidence 44555541 2356999999999999988654321 123568888543321 111
Q ss_pred HCCC-ccc---------CCCCCCCCCcHHHHHHHHHHHHHHHH
Q 025709 207 WYPR-DYR---------KVPSKEQKHRALDDIRESIMELKYYK 239 (249)
Q Consensus 207 ~~p~-~~~---------~~l~~~~~HrAl~Da~aT~~ll~~~~ 239 (249)
.+.. +.+ ..+...+-+=|..||..++.+++.+.
T Consensus 150 ~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 150 VLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1100 000 12344556778999999999988764
No 81
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=95.03 E-value=0.1 Score=48.59 Aligned_cols=125 Identities=17% Similarity=0.151 Sum_probs=72.9
Q ss_pred CcEEEEEEecCCCCCCCCceEEEEEE-EEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 69 MPLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 69 ~~~V~lDlETTGL~p~~d~IIEIgaV-v~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
..+++||+|+.|+.+..++ +|.| +.+|+.. .+|+|-.. +. +.++
T Consensus 17 ~~~iAiDTEf~r~~t~~p~---LcLIQi~~~e~~-------~lIdpl~~-----------------~~-----d~~~--- 61 (361)
T COG0349 17 SKAIAIDTEFMRLRTYYPR---LCLIQISDGEGA-------SLIDPLAG-----------------IL-----DLPP--- 61 (361)
T ss_pred CCceEEecccccccccCCc---eEEEEEecCCCc-------eEeccccc-----------------cc-----ccch---
Confidence 5689999999999998774 3444 4444432 45665331 11 1111
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCcccC----------C--
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRK----------V-- 215 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~~~~----------~-- 215 (249)
|...+.+- ..+=|-|.++||+.+|.+.| ...+.+++||. ++-++....... +
T Consensus 62 ----l~~Ll~d~----~v~KIfHaa~~DL~~l~~~~----g~~p~plfdTq----iAa~l~g~~~~~gl~~Lv~~ll~v~ 125 (361)
T COG0349 62 ----LVALLADP----NVVKIFHAARFDLEVLLNLF----GLLPTPLFDTQ----IAAKLAGFGTSHGLADLVEELLGVE 125 (361)
T ss_pred ----HHHHhcCC----ceeeeeccccccHHHHHHhc----CCCCCchhHHH----HHHHHhCCcccccHHHHHHHHhCCc
Confidence 23344431 12237899999999999875 24567788883 333332111000 1
Q ss_pred --------------CCCCCCCcHHHHHHHHHHHHHHHHHHhcC
Q 025709 216 --------------PSKEQKHRALDDIRESIMELKYYKENIFK 244 (249)
Q Consensus 216 --------------l~~~~~HrAl~Da~aT~~ll~~~~~~~~~ 244 (249)
+...+--=|..|+.+.+.+++.+.+.+..
T Consensus 126 ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~ 168 (361)
T COG0349 126 LDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAR 168 (361)
T ss_pred ccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12222333688999999988888776544
No 82
>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=95.02 E-value=0.65 Score=36.37 Aligned_cols=55 Identities=13% Similarity=0.149 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCc
Q 025709 146 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRD 211 (249)
Q Consensus 146 ~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~ 211 (249)
..+...+.+|+.+. ...+||||+.||+.+|.+.. ..++..++|+. -+++.+.|..
T Consensus 40 ~~~~~~l~~~l~~~----~~~~v~~~~k~d~~~L~~~~----~~~~~~~~D~~---~~ayll~~~~ 94 (155)
T cd00007 40 EEDLEALKELLEDE----DITKVGHDAKFDLVVLARDG----IELPGNIFDTM---LAAYLLNPGE 94 (155)
T ss_pred HHHHHHHHHHHcCC----CCcEEeccHHHHHHHHHHCC----CCCCCCcccHH---HHHHHhCCCC
Confidence 34566677788753 23579999999999997542 33445678873 3455556643
No 83
>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=94.77 E-value=0.28 Score=40.11 Aligned_cols=121 Identities=21% Similarity=0.164 Sum_probs=68.7
Q ss_pred CCcEEEEEEecCCCCC----CCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCC
Q 025709 68 KMPLVWIDLEMTGLKI----EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 143 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p----~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p 143 (249)
....+.||+|+++..+ .+-.+|||+. ... ..++++.. +
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~~---~~~--------~~l~~~~~------------------~--------- 58 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLAT---ESR--------CLLFQLAH------------------M--------- 58 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEec---CCc--------EEEEEhhh------------------h---------
Confidence 5789999999998865 2446667762 211 13343311 0
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCCCc------------
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRD------------ 211 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p~~------------ 211 (249)
......+.+++.+. ....|||++.+|+.+|.+.+ |..+. .++|+.. +++.+.|..
T Consensus 59 --~~~~~~l~~ll~~~----~i~kv~~~~k~D~~~L~~~~---g~~~~-~~~Dl~~---aa~ll~~~~~~~~l~~l~~~~ 125 (170)
T cd06141 59 --DKLPPSLKQLLEDP----SILKVGVGIKGDARKLARDF---GIEVR-GVVDLSH---LAKRVGPRRKLVSLARLVEEV 125 (170)
T ss_pred --hcccHHHHHHhcCC----CeeEEEeeeHHHHHHHHhHc---CCCCC-CeeeHHH---HHHHhCCCcCCccHHHHHHHH
Confidence 01123455566642 24569999999999997653 32222 2467742 222222210
Q ss_pred -----c--c---------CCCCCCCCCcHHHHHHHHHHHHHHHH
Q 025709 212 -----Y--R---------KVPSKEQKHRALDDIRESIMELKYYK 239 (249)
Q Consensus 212 -----~--~---------~~l~~~~~HrAl~Da~aT~~ll~~~~ 239 (249)
. + ..+...+-|=|..||..+.++++.++
T Consensus 126 l~~~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 126 LGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred cCcccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0 01234455778889999988887664
No 84
>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=93.09 E-value=1 Score=36.78 Aligned_cols=80 Identities=13% Similarity=0.137 Sum_probs=45.9
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhH------------HHHHHHHHCCC-ccc-----
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSS------------IKALCMRWYPR-DYR----- 213 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~s------------l~~la~r~~p~-~~~----- 213 (249)
+.+++.+. ..+.|||++..|+..|.+.+ +..+. .++|++. +..++.+++.. ..+
T Consensus 59 L~~lL~d~----~i~Kvg~~~k~D~~~L~~~~---gi~~~-~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s 130 (161)
T cd06129 59 LKMLLENP----SIVKALHGIEGDLWKLLRDF---GEKLQ-RLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCA 130 (161)
T ss_pred HHHHhCCC----CEEEEEeccHHHHHHHHHHc---CCCcc-cHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceec
Confidence 34566542 23569999999999987643 22222 2356532 12222332111 000
Q ss_pred ----CCCCCCCCCcHHHHHHHHHHHHHHHH
Q 025709 214 ----KVPSKEQKHRALDDIRESIMELKYYK 239 (249)
Q Consensus 214 ----~~l~~~~~HrAl~Da~aT~~ll~~~~ 239 (249)
..+...+-|=|..||..+.++++.++
T Consensus 131 ~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 131 DWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 12355667889999999999988765
No 85
>PRK10829 ribonuclease D; Provisional
Probab=92.70 E-value=2 Score=40.48 Aligned_cols=123 Identities=11% Similarity=0.078 Sum_probs=72.7
Q ss_pred CCcEEEEEEecCCCCCCCC--ceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCH
Q 025709 68 KMPLVWIDLEMTGLKIEVD--RILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 145 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d--~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~ 145 (249)
..++++||+|..+...... .+|||+ ++.. .++|.|-. +.+
T Consensus 21 ~~~~lalDtEf~~~~ty~~~l~LiQl~----~~~~-------~~LiD~l~------------------~~d--------- 62 (373)
T PRK10829 21 AFPAIALDTEFVRTRTYYPQLGLIQLY----DGEQ-------LSLIDPLG------------------ITD--------- 62 (373)
T ss_pred cCCeEEEecccccCccCCCceeEEEEe----cCCc-------eEEEecCC------------------ccc---------
Confidence 4678999999998876433 444554 3322 24555421 111
Q ss_pred HHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHHHHHHHHCC-C-ccc----------
Q 025709 146 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYP-R-DYR---------- 213 (249)
Q Consensus 146 ~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~~la~r~~p-~-~~~---------- 213 (249)
+.-+.+++.+. ..+-|+|++.+|+.+|.+.+ |. .+.+++||. +|.++.. . ...
T Consensus 63 ---~~~L~~ll~~~----~ivKV~H~~~~Dl~~l~~~~---g~-~p~~~fDTq----iaa~~lg~~~~~gl~~Lv~~~lg 127 (373)
T PRK10829 63 ---WSPFKALLRDP----QVTKFLHAGSEDLEVFLNAF---GE-LPQPLIDTQ----ILAAFCGRPLSCGFASMVEEYTG 127 (373)
T ss_pred ---hHHHHHHHcCC----CeEEEEeChHhHHHHHHHHc---CC-CcCCeeeHH----HHHHHcCCCccccHHHHHHHHhC
Confidence 23345566652 13448999999999997653 32 446788983 3332221 1 000
Q ss_pred --------------CCCCCCCCCcHHHHHHHHHHHHHHHHHHhc
Q 025709 214 --------------KVPSKEQKHRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 214 --------------~~l~~~~~HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
.-+....-+=|..|+.....++..+++.+-
T Consensus 128 v~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 128 VTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETE 171 (373)
T ss_pred CccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 012334556689999999999988876554
No 86
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=92.31 E-value=2.2 Score=37.22 Aligned_cols=166 Identities=19% Similarity=0.177 Sum_probs=93.5
Q ss_pred CCcEEEEEEecCCCCCC---------------------CCceEEEEEEEEcCc--Eeeee-ccceEEec---CCCccc--
Q 025709 68 KMPLVWIDLEMTGLKIE---------------------VDRILEIACIITDGK--LTKSV-EGPDLVIH---QTKECL-- 118 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~---------------------~d~IIEIgaVv~dg~--~~~~~-~~~~~~I~---p~~~~~-- 118 (249)
.-+||++|+|--|.-.. .-.+||+|.-..|.+ .-..+ ..+++-.+ +.+...
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 56899999997665311 127999999887743 32211 12222222 222211
Q ss_pred ccchhhhhhhhhccCCcHHH-HhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHh------------
Q 025709 119 DSMGEWCQNHHEASGLTKKV-LHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPD------------ 185 (249)
Q Consensus 119 ~~~~~~~~~~h~~tGIt~~~-l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~------------ 185 (249)
+.+ +.. .-+||.-+- .+.+....+..+.+..-.- +..+...+|-.+..+|..+|-+-+-.
T Consensus 103 ~SI-ElL----r~~Gidf~K~~e~GI~~~~F~ellm~sg~--v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~ 175 (239)
T KOG0304|consen 103 DSI-ELL----RRSGIDFEKHREEGIDIEEFAELLMTSGL--VLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFE 175 (239)
T ss_pred hhH-HHH----HHcCcCHHHHHHcCCCHHHHHHHHHHhhh--hccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHH
Confidence 111 222 234886433 3556666544443332211 11224678888889999999876521
Q ss_pred -ccCCCCCceeehhHHHHHHHH--HCCCccc-----CCCCCCCCCcHHHHHHHHHHHHHHHHHH
Q 025709 186 -LASLFSHVLVDVSSIKALCMR--WYPRDYR-----KVPSKEQKHRALDDIRESIMELKYYKEN 241 (249)
Q Consensus 186 -~~~~~~~~~iD~~sl~~la~r--~~p~~~~-----~~l~~~~~HrAl~Da~aT~~ll~~~~~~ 241 (249)
+..+| ..+.|+.-|++.|.. +..++.. .-.+.+.+|.|=.|+..|+..+..+++.
T Consensus 176 ~v~~~f-p~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 176 IVRQLF-PFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred HHHHHc-chhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHhc
Confidence 11233 346677666665533 2222111 1125788999999999999999888764
No 87
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=91.30 E-value=0.99 Score=46.53 Aligned_cols=97 Identities=16% Similarity=0.176 Sum_probs=62.5
Q ss_pred cccCCcEEEEEEecCCCCC-----CCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHH
Q 025709 65 FEYKMPLVWIDLEMTGLKI-----EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVL 139 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p-----~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l 139 (249)
......+++||+||.+..- ..+.++.|+.....+.... ..+.... ..|.. +
T Consensus 150 ~~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~--------~~~~~~~-------------~~~~~---v 205 (792)
T COG0417 150 VRPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI--------EVFIYTS-------------GEGFS---V 205 (792)
T ss_pred cCCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc--------ccccccC-------------CCCce---e
Confidence 4567889999999987642 3678888886643222110 0000000 00110 3
Q ss_pred hcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccC
Q 025709 140 HSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 188 (249)
Q Consensus 140 ~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 188 (249)
..-.+..+.+..|..++..+ ++.+++|||. .||+++|.+.+..++.
T Consensus 206 ~~~~~e~e~l~~~~~~i~~~---dPdVIvgyn~~~fd~pyl~~Ra~~lgi 252 (792)
T COG0417 206 EVVISEAELLERFVELIREY---DPDVIVGYNGDNFDWPYLAERAERLGI 252 (792)
T ss_pred EEecCHHHHHHHHHHHHHhc---CCCEEEeccCCcCChHHHHHHHHHhCC
Confidence 33446788999999999875 2468999999 5999999998776654
No 88
>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=91.01 E-value=0.33 Score=42.06 Aligned_cols=36 Identities=22% Similarity=0.227 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHH
Q 025709 144 TEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYM 183 (249)
Q Consensus 144 ~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~ 183 (249)
.+.+.+.+|.+++.++. +.||+||. .||+++|.+..
T Consensus 36 ~E~~lL~~F~~~~~~~~----p~LVs~NG~~FDlP~L~~Ra 72 (209)
T PF10108_consen 36 DEKELLQDFFDLVEKYN----PQLVSFNGRGFDLPVLCRRA 72 (209)
T ss_pred CHHHHHHHHHHHHHhCC----CeEEecCCccCCHHHHHHHH
Confidence 37889999999999753 56899998 99999998764
No 89
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=90.50 E-value=0.17 Score=51.65 Aligned_cols=35 Identities=17% Similarity=0.164 Sum_probs=26.6
Q ss_pred cEEEEecHHHHHHHHHHHHHhccCCCCCceeehhHHH
Q 025709 165 PLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIK 201 (249)
Q Consensus 165 ~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~sl~ 201 (249)
.++||||+.||+.-++.++.--+ -..+.+||++|.
T Consensus 242 ~liVGHNVsfDRaRirEeY~i~~--Sk~rFlDTMSlH 276 (1075)
T KOG3657|consen 242 QLIVGHNVSFDRARIREEYNING--SKIRFLDTMSLH 276 (1075)
T ss_pred ceEEeccccchHHHHHHHHhccc--cceeeeechhhh
Confidence 57899999999999998864111 235689998874
No 90
>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=90.38 E-value=13 Score=34.79 Aligned_cols=39 Identities=10% Similarity=0.180 Sum_probs=25.9
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehh
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 198 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~ 198 (249)
+.+++.+. ..+.|+|++.+|+.+|.+.+ ...+..++||.
T Consensus 62 L~~lL~d~----~i~KV~h~~k~Dl~~L~~~~----~~~~~~~fDtq 100 (367)
T TIGR01388 62 LKELLRDE----SVVKVLHAASEDLEVFLNLF----GELPQPLFDTQ 100 (367)
T ss_pred HHHHHCCC----CceEEEeecHHHHHHHHHHh----CCCCCCcccHH
Confidence 44566542 24569999999999997652 23445678883
No 91
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=89.50 E-value=0.49 Score=42.53 Aligned_cols=97 Identities=9% Similarity=0.037 Sum_probs=59.9
Q ss_pred HHHHHHHHhcccCCC-CcEEEEecH-HHHHHHHHHHHHhccCCCCCceeehhHHH---HHHHHHCCCcc-----------
Q 025709 149 EKQVVEFVKKNVGTY-TPLLAGNSV-YVDFMFLKKYMPDLASLFSHVLVDVSSIK---ALCMRWYPRDY----------- 212 (249)
Q Consensus 149 ~~~~~~fl~~~~~~~-~~~lVghn~-~FD~~fL~~~~~~~~~~~~~~~iD~~sl~---~la~r~~p~~~----------- 212 (249)
-.=+..+.+.+-+++ ....+.||. .|+..|..+.+-+++....+++.-...|+ +-+....|+..
T Consensus 182 ~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~ 261 (318)
T KOG4793|consen 182 GSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPTPKLVSSLEALATY 261 (318)
T ss_pred chHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCCCccchhHHHHHHH
Confidence 334556666643332 223345555 89999999998777654443333222233 12333445321
Q ss_pred cCCCCCCCCCcHHHHHHHHHHHHHHHHHHhcCc
Q 025709 213 RKVPSKEQKHRALDDIRESIMELKYYKENIFKT 245 (249)
Q Consensus 213 ~~~l~~~~~HrAl~Da~aT~~ll~~~~~~~~~~ 245 (249)
+...+...+|||+.|+..+-+++++|...+..+
T Consensus 262 ~~~~p~l~ahra~~Dv~~~~k~~q~~~idlla~ 294 (318)
T KOG4793|consen 262 YSLTPELDAHRALSDVLLLSKVFQKLTIDLLAS 294 (318)
T ss_pred hhcCcccchhhhccccchhhhHHHHhhhhhhhh
Confidence 113478899999999999999999998776543
No 92
>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=88.56 E-value=0.65 Score=40.63 Aligned_cols=42 Identities=19% Similarity=0.152 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhc
Q 025709 142 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 186 (249)
Q Consensus 142 ~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 186 (249)
-.++.+.+..|++++...- +-+++|||+ .||+.+|-.-+..+
T Consensus 79 ~~~E~~LL~~f~~~i~~~D---PDiivG~Ni~~fdl~~L~~R~~~l 121 (234)
T cd05776 79 FENERALLNFFLAKLQKID---PDVLVGHDLEGFDLDVLLSRIQEL 121 (234)
T ss_pred eCCHHHHHHHHHHHHhhcC---CCEEEeeccCCCCHHHHHHHHHHh
Confidence 4678999999999999752 458999999 99999998876443
No 93
>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=87.22 E-value=6.2 Score=38.01 Aligned_cols=95 Identities=12% Similarity=0.054 Sum_probs=60.5
Q ss_pred CCcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHH
Q 025709 68 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 147 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~e 147 (249)
....++||+||+ |...-.-.+|++..++.... +.|.-+... +...+.+
T Consensus 283 ~~~~~ffDiEt~---P~~~~~yL~G~~~~~~~~~~--~~~~~fla~---------------------------~~~~E~~ 330 (457)
T TIGR03491 283 APGELIFDIESD---PDENLDYLHGFLVVDKGQEN--EKYRPFLAE---------------------------DPNTEEL 330 (457)
T ss_pred CCccEEEEecCC---CCCCCceEEEEEEecCCCCC--cceeeeecC---------------------------CchHHHH
Confidence 477889999999 56667788999765432110 011111110 0123677
Q ss_pred HHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCC------CCCceeehh
Q 025709 148 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL------FSHVLVDVS 198 (249)
Q Consensus 148 a~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~------~~~~~iD~~ 198 (249)
++.+|++|+..+ +. .+++.+| .|....|++...+++.+ +-.+++|+-
T Consensus 331 ~~~~f~~~l~~~-~~--~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~ 383 (457)
T TIGR03491 331 AWQQFLQLLQSY-PD--APIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIH 383 (457)
T ss_pred HHHHHHHHHHHC-CC--CeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehH
Confidence 899999999875 22 2467777 89999999988777643 112678884
No 94
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=84.49 E-value=4.1 Score=44.54 Aligned_cols=100 Identities=17% Similarity=0.242 Sum_probs=58.3
Q ss_pred ccCCcEEEEEEecCCCCC-----CCCceEEEEEEEEcCcEeeee---------ccceEEecCCCcccccchhhhhhhhhc
Q 025709 66 EYKMPLVWIDLEMTGLKI-----EVDRILEIACIITDGKLTKSV---------EGPDLVIHQTKECLDSMGEWCQNHHEA 131 (249)
Q Consensus 66 ~~~~~~V~lDlETTGL~p-----~~d~IIEIgaVv~dg~~~~~~---------~~~~~~I~p~~~~~~~~~~~~~~~h~~ 131 (249)
..+-.+++||+|||-|.- ..|+|-=|.- .+||+.-.+. +.|+..-+|.- ...+|
T Consensus 243 radp~VlAFDIETtKlPLKFPDae~DqIMMISY-MiDGqGfLItNREiVs~DIedfEYTPKpE~-----eG~F~------ 310 (2173)
T KOG1798|consen 243 RADPRVLAFDIETTKLPLKFPDAESDQIMMISY-MIDGQGFLITNREIVSEDIEDFEYTPKPEY-----EGPFC------ 310 (2173)
T ss_pred cCCceEEEEeeecccCCCCCCCcccceEEEEEE-EecCceEEEechhhhccchhhcccCCcccc-----ccceE------
Confidence 446778899999998752 3466655553 4677653211 11211111110 01111
Q ss_pred cCCcHHHHhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 132 SGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 132 tGIt~~~l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
+-+.+.....+.+|.+-+.+. .+.++|-+|. -|||+|+.+.....|
T Consensus 311 -------v~Ne~dEv~Ll~RfFeHiq~~---kP~iivTyNGDFFDWPFve~Ra~~hG 357 (2173)
T KOG1798|consen 311 -------VFNEPDEVGLLQRFFEHIQEV---KPTIIVTYNGDFFDWPFVEARAKIHG 357 (2173)
T ss_pred -------EecCCcHHHHHHHHHHHHHhc---CCcEEEEecCccccchhhHHHHHhcC
Confidence 123466677777777777764 2457888888 679999998765443
No 95
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.70 E-value=5.7 Score=42.85 Aligned_cols=109 Identities=17% Similarity=0.120 Sum_probs=63.5
Q ss_pred CCcEEEEEEecCCCCCC--CCceEEEEEEEEcC-cEee------eeccceEEecCCCc-ccccchhhhhhhhhccCCcHH
Q 025709 68 KMPLVWIDLEMTGLKIE--VDRILEIACIITDG-KLTK------SVEGPDLVIHQTKE-CLDSMGEWCQNHHEASGLTKK 137 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~--~d~IIEIgaVv~dg-~~~~------~~~~~~~~I~p~~~-~~~~~~~~~~~~h~~tGIt~~ 137 (249)
+-.++-|++|+ +.|. .++||.|.+++... .... ....+....+|... .|. .+.. ...|+.+.
T Consensus 505 Pl~vLdFsi~S--lyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~p~---~~~~---~~~~~~~~ 576 (1172)
T TIGR00592 505 PLVVLDFSMKS--LNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPL---DLKG---EFPGKKPS 576 (1172)
T ss_pred CeEEEEeeeEE--ecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCCCCCc---hhhh---hhhccCCc
Confidence 45555556664 5554 58999999886432 1100 00112223333111 111 1111 12255555
Q ss_pred HHhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 138 VLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 138 ~l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
.+..-.+..+.+..|+.++...- +.+++|||+ .||+.+|-.-+..++
T Consensus 577 ~L~~~~sEr~lL~~fl~~~~~~D---PDii~g~n~~qfdlkvl~nR~~~l~ 624 (1172)
T TIGR00592 577 LVEDLATERALIKKFMAKVKKID---PDEIVGHDYQQRALKVLANRINDLK 624 (1172)
T ss_pred EEEEecCHHHHHHHHHHHHHhcC---CCEEEEEcccCccHHHHHHHHHHcC
Confidence 56666788999999999998642 357899999 999999988665443
No 96
>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=82.94 E-value=27 Score=29.40 Aligned_cols=28 Identities=7% Similarity=-0.044 Sum_probs=21.4
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHHhcC
Q 025709 217 SKEQKHRALDDIRESIMELKYYKENIFK 244 (249)
Q Consensus 217 ~~~~~HrAl~Da~aT~~ll~~~~~~~~~ 244 (249)
....-+=|..|+..+..++..++..+.+
T Consensus 152 t~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 152 TEDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred CHHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 3445566889999999999988887754
No 97
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=82.23 E-value=9.8 Score=38.00 Aligned_cols=130 Identities=15% Similarity=0.167 Sum_probs=74.7
Q ss_pred EEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHHH
Q 025709 72 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 151 (249)
Q Consensus 72 V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~ 151 (249)
+.+|+||+|+++....++-++...-+ +. ++|.-. | + +..-++...
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~-------~~--~yi~~~--------------~---~---------~~~~~~~~~ 69 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE-------EA--AYIPLL--------------H---G---------PEQLNVLAA 69 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc-------cc--eeEeec--------------c---c---------hhhhhhHHH
Confidence 89999999999977778777765332 11 222110 1 1 111127788
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehh-------------HHHHHHHHHCCCc-ccC---
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS-------------SIKALCMRWYPRD-YRK--- 214 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~-------------sl~~la~r~~p~~-~~~--- 214 (249)
+..|+.+.. ...||||..||..+|.+.- .. .....|++ .+..++.+++... ..+
T Consensus 70 l~~~l~~~~----~~kv~~~~K~d~~~l~~~G----i~-~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i 140 (593)
T COG0749 70 LKPLLEDEG----IKKVGQNLKYDYKVLANLG----IE-PGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDI 140 (593)
T ss_pred HHHHhhCcc----cchhccccchhHHHHHHcC----Cc-ccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHh
Confidence 888998731 3478999999999998763 11 12233332 1233556652211 000
Q ss_pred ---C---CC------CCCCCcHHHHHHHHHHHHHHHHHHhcCc
Q 025709 215 ---V---PS------KEQKHRALDDIRESIMELKYYKENIFKT 245 (249)
Q Consensus 215 ---~---l~------~~~~HrAl~Da~aT~~ll~~~~~~~~~~ 245 (249)
+ +. ....-.+..||..|.++..++.+..-++
T Consensus 141 ~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~~ 183 (593)
T COG0749 141 AGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLKT 183 (593)
T ss_pred hccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 0 00 1123445678888999888887655443
No 98
>PRK05761 DNA polymerase I; Reviewed
Probab=82.10 E-value=4 Score=42.14 Aligned_cols=41 Identities=15% Similarity=0.172 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhccC
Q 025709 143 LTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 188 (249)
Q Consensus 143 p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 188 (249)
.++.+.+.+|.+|+..+ .+.|++|. .||+++|..-+..+|.
T Consensus 208 ~~E~eLL~~f~~~i~~~-----dPdi~yN~~~FDlPYL~~Ra~~lgi 249 (787)
T PRK05761 208 DSEKELLAELFDIILEY-----PPVVTFNGDNFDLPYLYNRALKLGI 249 (787)
T ss_pred CCHHHHHHHHHHHHHhc-----CCEEEEcCCcchHHHHHHHHHHhCC
Confidence 45788999999999986 23456777 8999999988776664
No 99
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=81.70 E-value=1.9 Score=42.15 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHH
Q 025709 143 LTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMP 184 (249)
Q Consensus 143 p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~ 184 (249)
+++.+.+.+|.+|+.+.- +.+++|||+ .||+++|..-+.
T Consensus 178 ~sE~eLL~~F~~~i~~~D---PDIItGYNi~nFDlPYL~~Ra~ 217 (498)
T PHA02524 178 EDEVDLLLNYIQLWKANT---PDLVFGWNSEGFDIPYIITRIT 217 (498)
T ss_pred CCHHHHHHHHHHHHHHhC---CCEEEeCCCcccCHHHHHHHHH
Confidence 678999999999999853 458999999 999999977653
No 100
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=81.69 E-value=9.1 Score=33.66 Aligned_cols=166 Identities=18% Similarity=0.155 Sum_probs=91.9
Q ss_pred CCcEEEEEEecCCCCCC---------------------CCceEEEEEEEEcCcEee-ee-c--cceEEecCCCcccccch
Q 025709 68 KMPLVWIDLEMTGLKIE---------------------VDRILEIACIITDGKLTK-SV-E--GPDLVIHQTKECLDSMG 122 (249)
Q Consensus 68 ~~~~V~lDlETTGL~p~---------------------~d~IIEIgaVv~dg~~~~-~~-~--~~~~~I~p~~~~~~~~~ 122 (249)
.-++|.+|+|-.|.-.. -=.||++|.-+-|.+.+. .+ . .|.+-..+...+.. .
T Consensus 41 rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dmya--~ 118 (299)
T COG5228 41 RYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDMYA--T 118 (299)
T ss_pred hCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhhhcc--h
Confidence 46789999999886421 127999998876654431 11 1 24445555554321 2
Q ss_pred hhhhhhhhccCCcHHHHh-cCCCHHHHHHHHHHHHhc--ccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhH
Q 025709 123 EWCQNHHEASGLTKKVLH-SGLTEREAEKQVVEFVKK--NVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSS 199 (249)
Q Consensus 123 ~~~~~~h~~tGIt~~~l~-~~p~~~ea~~~~~~fl~~--~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~s 199 (249)
+...- -.-+||.=+..+ -+.... +|-+.+-+ .+....++++..+..+|+.+|-+.+- ..++|.+.-|.
T Consensus 119 ESieL-L~ksgIdFkkHe~~GI~v~----eF~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt--~~plP~~~EdF-- 189 (299)
T COG5228 119 ESIEL-LRKSGIDFKKHENLGIDVF----EFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILT--NDPLPNNKEDF-- 189 (299)
T ss_pred HHHHH-HHHcCCChhhHhhcCCCHH----HHHHHHhccCceeccceEEEEeecchhHHHHHHHHh--cCCCCccHHHH--
Confidence 22110 012344332222 122222 33333332 12222457888888999999987652 23444444444
Q ss_pred HHHHHHHHCCCccc-------------------C--CC-CCCCCCcHHHHHHHHHHHHHHHHHHhcCc
Q 025709 200 IKALCMRWYPRDYR-------------------K--VP-SKEQKHRALDDIRESIMELKYYKENIFKT 245 (249)
Q Consensus 200 l~~la~r~~p~~~~-------------------~--~l-~~~~~HrAl~Da~aT~~ll~~~~~~~~~~ 245 (249)
+++....+|..+. . ++ ..+..|.|-.||..|+..+-.-|..+|..
T Consensus 190 -y~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F~~ 256 (299)
T COG5228 190 -YWWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTT 256 (299)
T ss_pred -HHHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhheecc
Confidence 3333333443220 0 11 45778999999999999998888888875
No 101
>PHA03036 DNA polymerase; Provisional
Probab=80.22 E-value=8.7 Score=40.67 Aligned_cols=112 Identities=12% Similarity=0.085 Sum_probs=57.9
Q ss_pred cccCCcEEEEEEecCC--C--CCCCCceEEEEEEEEcCcEeeeeccceEEecCC----CcccccchhhhhhhhhccCCcH
Q 025709 65 FEYKMPLVWIDLEMTG--L--KIEVDRILEIACIITDGKLTKSVEGPDLVIHQT----KECLDSMGEWCQNHHEASGLTK 136 (249)
Q Consensus 65 ~~~~~~~V~lDlETTG--L--~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~----~~~~~~~~~~~~~~h~~tGIt~ 136 (249)
+.-+..|++||+|.-. - ++..+.|+.|++...+...... --++++.. .+.....-..+. ...-+.+
T Consensus 156 ~~~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~~~~~~---~~~l~n~~~~~~~~~~~~~~~~~~---~~~~~~~ 229 (1004)
T PHA03036 156 FDIPRSYLFLDIECHFDKKFPSVFINPVSHISCCYIDLSGKEK---RFTLINEDMLSEDEIEEAVKRGYY---EIESLLD 229 (1004)
T ss_pred ccCcceeEEEEEEeccCCCCCCcccCcceEEEEEEEecCCCee---EEEEeccccccccccccceeeeee---ccccccc
Confidence 5677899999999953 2 2447999999975333222100 01233321 111000000000 0001100
Q ss_pred ---HHHhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHHhc
Q 025709 137 ---KVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 186 (249)
Q Consensus 137 ---~~l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 186 (249)
...-.-.++.+ +-++..++.+.- +-+++|+|. .||++.|..-+..+
T Consensus 230 ~~~~~~~~~~sE~~-ml~~~~~i~~~d---~D~i~~yNg~nFD~~Yi~~R~~~L 279 (1004)
T PHA03036 230 MDYSKELILCSEIV-LLRIAKKLLELE---FDYVVTFNGHNFDLRYISNRLELL 279 (1004)
T ss_pred cCCceeeecCCHHH-HHHHHHHHHhcC---CCEEEeccCCCcchHHHHHHHHHh
Confidence 00011145555 447777887642 347899999 99999998765443
No 102
>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=76.96 E-value=32 Score=27.87 Aligned_cols=83 Identities=17% Similarity=0.176 Sum_probs=48.7
Q ss_pred CcEEEEEEecCCCCCCCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHH
Q 025709 69 MPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 148 (249)
Q Consensus 69 ~~~V~lDlETTGL~p~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea 148 (249)
...+.+|+|++|.++....++-|+.- .++ . .++|.... .+ .+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~--~~~-~------~~~i~~~~-----------------~~------------~~ 44 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALA--NGG-G------AYYIPLEL-----------------AL------------LD 44 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEE--eCC-c------EEEEeccc-----------------hH------------HH
Confidence 34578999999999866666544432 221 1 12333110 00 13
Q ss_pred HHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeeh
Q 025709 149 EKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDV 197 (249)
Q Consensus 149 ~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~ 197 (249)
...+.+|+.+. ....++||+.+|+.+|.+ .|..++....|+
T Consensus 45 ~~~l~~~l~~~----~~~ki~~d~K~~~~~l~~----~gi~~~~~~fDt 85 (178)
T cd06140 45 LAALKEWLEDE----KIPKVGHDAKRAYVALKR----HGIELAGVAFDT 85 (178)
T ss_pred HHHHHHHHhCC----CCceeccchhHHHHHHHH----CCCcCCCcchhH
Confidence 34456677652 134789999999999864 344444556777
No 103
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=69.33 E-value=0.75 Score=46.86 Aligned_cols=94 Identities=19% Similarity=0.329 Sum_probs=54.1
Q ss_pred cCCcEEEEEEecCCCC-----CCCCceEEEEEEE-EcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHh
Q 025709 67 YKMPLVWIDLEMTGLK-----IEVDRILEIACII-TDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 140 (249)
Q Consensus 67 ~~~~~V~lDlETTGL~-----p~~d~IIEIgaVv-~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~ 140 (249)
.+...+.||+|+.|-. |..|.||+||-++ .-|......+ --+.+++-.+ |.-..+.
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~r-nvf~l~~cap-----------------I~G~~V~ 333 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVR-NVFTLKTCAP-----------------IVGSNVH 333 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHH-hhhcccCcCC-----------------CCCceeE
Confidence 3567889999998865 4579999999663 3333221111 1112233222 2222222
Q ss_pred cCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHH
Q 025709 141 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKK 181 (249)
Q Consensus 141 ~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~ 181 (249)
.-....+++..-..|+.+- + +-+++|+|+ .||+++|-.
T Consensus 334 ~~~~e~elL~~W~~firev-D--PDvI~GYNi~nFDiPYll~ 372 (1066)
T KOG0969|consen 334 SYETEKELLESWRKFIREV-D--PDVIIGYNICNFDIPYLLN 372 (1066)
T ss_pred EeccHHHHHHHHHHHHHhc-C--CCeEecccccccccceecC
Confidence 2334555666556666652 1 357899999 999998754
No 104
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.77 E-value=5.8 Score=42.83 Aligned_cols=95 Identities=14% Similarity=0.081 Sum_probs=55.7
Q ss_pred ccCCcEEEEEEecCC---------CCCCCCceEEEEEE-EE----cCcEeeeeccceEEecCCCcccccchhhhhhhhhc
Q 025709 66 EYKMPLVWIDLEMTG---------LKIEVDRILEIACI-IT----DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEA 131 (249)
Q Consensus 66 ~~~~~~V~lDlETTG---------L~p~~d~IIEIgaV-v~----dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~ 131 (249)
..+.+.+.||+|+.+ .++..|.||+|++. +. .+....... --+...+ |. .+
T Consensus 195 ~p~~~~~sfdiE~~~~~g~~~fp~~~~~~D~ii~is~~~~~~~~~~~~~~~~~~-~~~~~~~-----------~~---~~ 259 (1172)
T TIGR00592 195 DPELKLASFDIETYFHDGKDFFPGDENPADEEIMISTTPVIAKQWDYESEPEAR-VVTWKKP-----------DK---PT 259 (1172)
T ss_pred CCcccccccccccccccccccCcccccccccccccccccccccccccCCCccch-hhhccCc-----------cc---cC
Confidence 456788899999753 45567999999974 11 111110000 0000111 11 11
Q ss_pred cCCcHHHHhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHH
Q 025709 132 SGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKK 181 (249)
Q Consensus 132 tGIt~~~l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~ 181 (249)
.| ..+..-++..+.+..+.+|+.+.- +-+++|+|+ .||+++|..
T Consensus 260 ~~---~~v~~~~~E~~~L~~f~~~i~~~d---pdii~gYNi~~FD~pyl~~ 304 (1172)
T TIGR00592 260 TG---SYVESVSEEISMIKRFWDVIDQED---TDVEITVNGDNFDLVYLAD 304 (1172)
T ss_pred CC---ccceeccchHHHHhhHHHHHhhcC---cchhcccccccCccceecC
Confidence 12 122334677888899999998742 236899999 999988866
No 105
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=50.88 E-value=1.5e+02 Score=25.42 Aligned_cols=75 Identities=19% Similarity=0.058 Sum_probs=46.3
Q ss_pred CCCceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhh-hccCCcHHHHhcCC-CHHHHHHHHHHHHhccc
Q 025709 84 EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHH-EASGLTKKVLHSGL-TEREAEKQVVEFVKKNV 160 (249)
Q Consensus 84 ~~d~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h-~~tGIt~~~l~~~p-~~~ea~~~~~~fl~~~~ 160 (249)
..--..|||++.+.-+.. +.+.|+.+|+|..-.+ +...-++.|- .-++|...-.+.+. .+..++.++.+||+..-
T Consensus 6 ~~y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~p~-G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~ 82 (213)
T PF13017_consen 6 DEYVPAEIAICKFSLKEG-IIDSFHTFINPGQIPL-GYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNK 82 (213)
T ss_pred CcEEeEEEEEEEEecCCc-cchhhhcccCCCCCCc-HHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcC
Confidence 344678999997665443 3467999999975433 2222233221 12355443333343 58899999999999763
No 106
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=50.36 E-value=56 Score=35.25 Aligned_cols=109 Identities=9% Similarity=0.095 Sum_probs=64.3
Q ss_pred cccCCcEEEEEEecCCCCCC--CCceEEEEEEEEcCcEee-------eeccceEEecCCCcccc-cchhhhhhhhhccCC
Q 025709 65 FEYKMPLVWIDLEMTGLKIE--VDRILEIACIITDGKLTK-------SVEGPDLVIHQTKECLD-SMGEWCQNHHEASGL 134 (249)
Q Consensus 65 ~~~~~~~V~lDlETTGL~p~--~d~IIEIgaVv~dg~~~~-------~~~~~~~~I~p~~~~~~-~~~~~~~~~h~~tGI 134 (249)
..++..+..+-++|+ .|+. +.+|+.|++.+....... ...-+..+++|+...++ ++.+-.+. ..++
T Consensus 525 ~~Ppl~llsL~i~T~-~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~--k~~~- 600 (1429)
T KOG0970|consen 525 PPPPLTLLSLNIRTS-MNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQ--KLSK- 600 (1429)
T ss_pred CCCCeeEEEeeeeeh-hccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHh--ccCc-
Confidence 466788999999987 4443 368998887754221111 11246778888864432 12222221 1112
Q ss_pred cHHHHhcCCCHHHHHHHHHHHHhcccCCCCcEEEEecH-HHHHHHHHHHHH
Q 025709 135 TKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMP 184 (249)
Q Consensus 135 t~~~l~~~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~-~FD~~fL~~~~~ 184 (249)
+....++...+.-|+.-+... ++-++||||+ .|++..|-..+.
T Consensus 601 ----v~~~~sErALLs~fla~~~~~---dpD~iVgHn~~~~~l~VLl~R~~ 644 (1429)
T KOG0970|consen 601 ----VVLHNSERALLSHFLAMLNKE---DPDVIVGHNIQGFYLDVLLSRLH 644 (1429)
T ss_pred ----eEEecCHHHHHHHHHHHhhcc---CCCEEEEeccccchHHHHHHHHH
Confidence 222345566677777777653 3458999995 999998865543
No 107
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=47.81 E-value=49 Score=25.99 Aligned_cols=41 Identities=12% Similarity=0.235 Sum_probs=26.6
Q ss_pred HHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehh
Q 025709 149 EKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 198 (249)
Q Consensus 149 ~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~ 198 (249)
...+.+|+.+. ....||||+.+|+.+|.+ +|..++.. +|++
T Consensus 64 ~~~l~~~l~~~----~~~kv~~d~k~~~~~L~~----~gi~~~~~-~D~~ 104 (172)
T smart00474 64 LEILKDLLEDE----TITKVGHNAKFDLHVLAR----FGIELENI-FDTM 104 (172)
T ss_pred HHHHHHHhcCC----CceEEEechHHHHHHHHH----CCCcccch-hHHH
Confidence 34455666642 245799999999999974 34444443 7873
No 108
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.35 E-value=66 Score=33.91 Aligned_cols=91 Identities=9% Similarity=0.066 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeehhH------------HHHHHHHHCCCcc
Q 025709 145 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSS------------IKALCMRWYPRDY 212 (249)
Q Consensus 145 ~~ea~~~~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~~s------------l~~la~r~~p~~~ 212 (249)
...+...+..|+.+. ....+|||+.||+.+|.++ |..+...+.||.- +..++.++++...
T Consensus 363 ~~~~~~~l~~~l~~~----~~~~v~~n~K~d~~~l~~~----gi~~~~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~ 434 (887)
T TIGR00593 363 TILTDDKFARWLLNE----QIKKIGHDAKFLMHLLKRE----GIELGGVIFDTMLAAYLLDPAQVSTLDTLARRYLVEEL 434 (887)
T ss_pred hHHHHHHHHHHHhCC----CCcEEEeeHHHHHHHHHhC----CCCCCCcchhHHHHHHHcCCCCCCCHHHHHHHHcCccc
Confidence 344566677888752 2347999999999999753 4333344566631 2223333322110
Q ss_pred -c----C--CCC-----CCCC-CcHHHHHHHHHHHHHHHHHHhc
Q 025709 213 -R----K--VPS-----KEQK-HRALDDIRESIMELKYYKENIF 243 (249)
Q Consensus 213 -~----~--~l~-----~~~~-HrAl~Da~aT~~ll~~~~~~~~ 243 (249)
. . +.. .... .-|..|+..|..|+..+.+.+-
T Consensus 435 ~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 435 ILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred ccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0 000 0001 1366788889999888877653
No 109
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=37.66 E-value=44 Score=28.91 Aligned_cols=42 Identities=17% Similarity=0.148 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHhcccCCCCcEEEEecH--HHHHHHHHHHH
Q 025709 142 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSV--YVDFMFLKKYM 183 (249)
Q Consensus 142 ~p~~~ea~~~~~~fl~~~~~~~~~~lVghn~--~FD~~fL~~~~ 183 (249)
.....||...|..||..+-...+.+|+||+= ..=+.+|++++
T Consensus 74 ~~ay~DV~~AF~~yL~~~n~GRPfILaGHSQGs~~l~~LL~e~~ 117 (207)
T PF11288_consen 74 DLAYSDVRAAFDYYLANYNNGRPFILAGHSQGSMHLLRLLKEEI 117 (207)
T ss_pred HhhHHHHHHHHHHHHHhcCCCCCEEEEEeChHHHHHHHHHHHHh
Confidence 3568999999999999875444678999965 44455666554
No 110
>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=33.98 E-value=1.2e+02 Score=23.37 Aligned_cols=38 Identities=16% Similarity=0.220 Sum_probs=24.7
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeeh
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDV 197 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~ 197 (249)
+.+++.+. ....+||++.+|+.+|.+. +..+.....|+
T Consensus 45 l~~~l~~~----~~~kv~~d~K~~~~~L~~~----~~~~~~~~~D~ 82 (150)
T cd09018 45 LKPLLEDE----KALKVGQNLKYDRGILLNY----FIELRGIAFDT 82 (150)
T ss_pred HHHHhcCC----CCceeeecHHHHHHHHHHc----CCccCCcchhH
Confidence 45566642 2357899999999998643 33334456777
No 111
>PHA02563 DNA polymerase; Provisional
Probab=31.61 E-value=48 Score=33.52 Aligned_cols=38 Identities=8% Similarity=0.107 Sum_probs=26.3
Q ss_pred HHHHHHHHhcccC-CCCcEEEEecHHHHHHHHHHHHHhc
Q 025709 149 EKQVVEFVKKNVG-TYTPLLAGNSVYVDFMFLKKYMPDL 186 (249)
Q Consensus 149 ~~~~~~fl~~~~~-~~~~~lVghn~~FD~~fL~~~~~~~ 186 (249)
+.+|+.|+....- ...+++-.||..||..||-.++.+.
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN~~FD~~Fil~~L~~~ 88 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHNLKFDGSFILKWLLRN 88 (630)
T ss_pred HHHHHHHHhhccccccceEEEEecCCccHHHHHHHHHhh
Confidence 4578888872000 0125678899999999999987653
No 112
>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=27.80 E-value=1.8e+02 Score=23.17 Aligned_cols=38 Identities=18% Similarity=0.214 Sum_probs=24.8
Q ss_pred HHHHHhcccCCCCcEEEEecHHHHHHHHHHHHHhccCCCCCceeeh
Q 025709 152 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDV 197 (249)
Q Consensus 152 ~~~fl~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iD~ 197 (249)
+..++.+. ....||||+.+|+.+|.+.+ |.. ...+.|+
T Consensus 56 l~~ll~~~----~i~kv~~d~K~~~~~L~~~~---gi~-~~~~~D~ 93 (178)
T cd06142 56 LKELLADP----NIVKVFHAAREDLELLKRDF---GIL-PQNLFDT 93 (178)
T ss_pred HHHHHcCC----CceEEEeccHHHHHHHHHHc---CCC-CCCcccH
Confidence 45566642 24579999999999987653 322 3345777
No 113
>PHA01746 hypothetical protein
Probab=27.79 E-value=65 Score=25.24 Aligned_cols=56 Identities=16% Similarity=0.285 Sum_probs=30.3
Q ss_pred ceEEEEEEEEcCcEeeeeccceEEecCCCcccccchhhhhhhhhccCCcHHHHhcCCCHHHHHHHHHHHHhc
Q 025709 87 RILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQVVEFVKK 158 (249)
Q Consensus 87 ~IIEIgaVv~dg~~~~~~~~~~~~I~p~~~~~~~~~~~~~~~h~~tGIt~~~l~~~p~~~ea~~~~~~fl~~ 158 (249)
-+++|-|+--||... |++.||... .+-+++ |||+.+-.+-..+...+...-.||.+
T Consensus 34 ivlQiNAvP~dg~vr-----~SMTiHs~n-------NfkKQI----GiTa~DAgdL~lIa~FLeKYS~~Lnk 89 (131)
T PHA01746 34 IVVQLNAVPQDGKIR-----YSMTIHSQN-------NFRKQI----GITPQDAGDLKLIAEFLEKYSDFLNE 89 (131)
T ss_pred EEEEeeccCCCCeeE-----EEEEEeccc-------chhhhc----CCCccchhhHHHHHHHHHHHHHHHHH
Confidence 456888876677664 567777543 222333 89875544333344444444444444
No 114
>PF03337 Pox_F12L: Poxvirus F12L protein; InterPro: IPR005005 The vaccinia virus F12L gene encodes a 65 kDa protein that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules [].; GO: 0016032 viral reproduction
Probab=26.22 E-value=55 Score=33.15 Aligned_cols=45 Identities=20% Similarity=0.362 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhcccC--CCCcEEEEe-cHHHHHHHHHHHHHhc
Q 025709 142 GLTEREAEKQVVEFVKKNVG--TYTPLLAGN-SVYVDFMFLKKYMPDL 186 (249)
Q Consensus 142 ~p~~~ea~~~~~~fl~~~~~--~~~~~lVgh-n~~FD~~fL~~~~~~~ 186 (249)
..+-..+..+|++||.+... ..+.+|||+ +--||.+.|++.++.-
T Consensus 251 f~s~~~li~~FL~Wl~e~~~~n~~ti~LvGy~ss~FD~pLLra~wp~~ 298 (651)
T PF03337_consen 251 FDSNKALISDFLKWLRECIMKNIRTIILVGYFSSFFDFPLLRAYWPKN 298 (651)
T ss_pred CCCchHHHHHHHHHHHHHHhccCceEEEeehhhhhhccHHHHhhcccC
Confidence 34455688999999998322 234678895 6688999999999654
No 115
>PF12083 DUF3560: Domain of unknown function (DUF3560); InterPro: IPR021944 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif.
Probab=21.17 E-value=1.8e+02 Score=23.23 Aligned_cols=27 Identities=11% Similarity=0.145 Sum_probs=19.8
Q ss_pred CCCCcEEEEecH-HHHHHHHHHHHHhcc
Q 025709 161 GTYTPLLAGNSV-YVDFMFLKKYMPDLA 187 (249)
Q Consensus 161 ~~~~~~lVghn~-~FD~~fL~~~~~~~~ 187 (249)
+.|-||||||+- .=++..+.+....++
T Consensus 40 p~GQPIlVGHHSE~R~Rr~~eR~~~~m~ 67 (126)
T PF12083_consen 40 PFGQPILVGHHSEKRHRRYRERIHNRMG 67 (126)
T ss_pred CCCCCeeccccchHHHHHHHHHHHHHHH
Confidence 345579999866 778888888765554
No 116
>COG4674 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]
Probab=20.88 E-value=1.7e+02 Score=25.78 Aligned_cols=26 Identities=42% Similarity=0.471 Sum_probs=17.3
Q ss_pred EecCCCCCCCC-----------ceEEEEEE-EEcCcEe
Q 025709 76 LEMTGLKIEVD-----------RILEIACI-ITDGKLT 101 (249)
Q Consensus 76 lETTGL~p~~d-----------~IIEIgaV-v~dg~~~ 101 (249)
++++||.+..+ +=+|||++ +.++++.
T Consensus 132 La~igL~~~~~~~A~~LSHGqKQwLEIGMll~Q~P~lL 169 (249)
T COG4674 132 LATIGLGDERDRLAALLSHGQKQWLEIGMLLAQDPKLL 169 (249)
T ss_pred HHHcccchhhhhhhhhhccchhhhhhhheeeccCCcEE
Confidence 57899987644 55788877 4455543
Done!