Query 027892
Match_columns 217
No_of_seqs 179 out of 1065
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 03:03:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027892.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027892hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05359 oligoribonuclease; Pr 100.0 3.3E-41 7.3E-46 272.0 18.9 179 36-215 2-180 (181)
2 COG1949 Orn Oligoribonuclease 100.0 1.7E-39 3.6E-44 250.5 14.7 182 34-216 3-184 (184)
3 cd06135 Orn DEDDh 3'-5' exonuc 100.0 4.3E-39 9.3E-44 258.0 17.2 172 39-210 1-172 (173)
4 KOG3242 Oligoribonuclease (3'- 100.0 6.4E-38 1.4E-42 243.8 14.9 180 35-214 24-203 (208)
5 PRK09146 DNA polymerase III su 100.0 3.2E-33 6.9E-38 234.4 20.3 169 29-213 39-230 (239)
6 PRK05711 DNA polymerase III su 100.0 2.4E-32 5.2E-37 229.0 18.4 156 36-209 3-175 (240)
7 PRK09145 DNA polymerase III su 100.0 4.3E-32 9.4E-37 222.4 18.5 161 35-208 27-199 (202)
8 TIGR01406 dnaQ_proteo DNA poly 100.0 6.7E-32 1.5E-36 224.7 18.2 154 38-209 1-171 (225)
9 PRK07740 hypothetical protein; 100.0 2.3E-31 5E-36 224.0 19.8 162 35-213 57-229 (244)
10 PRK07942 DNA polymerase III su 100.0 4.6E-31 1E-35 220.7 18.7 170 33-211 2-181 (232)
11 TIGR00573 dnaq exonuclease, DN 100.0 6.5E-31 1.4E-35 217.8 18.7 161 35-211 5-178 (217)
12 PRK08517 DNA polymerase III su 100.0 8.9E-31 1.9E-35 221.7 19.6 159 33-210 64-231 (257)
13 PRK06310 DNA polymerase III su 100.0 7.8E-31 1.7E-35 221.5 19.0 159 35-210 5-174 (250)
14 cd06131 DNA_pol_III_epsilon_Ec 100.0 1.2E-30 2.6E-35 207.1 17.5 151 39-206 1-166 (167)
15 PRK06063 DNA polymerase III su 100.0 2.4E-30 5.2E-35 224.9 18.9 160 34-212 12-181 (313)
16 PRK06807 DNA polymerase III su 100.0 4.1E-30 9E-35 223.1 19.3 157 35-210 6-172 (313)
17 cd06134 RNaseT DEDDh 3'-5' exo 100.0 3.2E-30 7E-35 209.4 17.3 164 37-210 5-189 (189)
18 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 9E-31 2E-35 210.5 13.9 155 39-205 1-176 (177)
19 PRK05168 ribonuclease T; Provi 100.0 4.2E-30 9.1E-35 212.1 18.2 166 34-210 14-201 (211)
20 PRK06309 DNA polymerase III su 100.0 4.8E-30 1E-34 214.6 18.3 154 37-210 2-166 (232)
21 TIGR01298 RNaseT ribonuclease 100.0 4.1E-30 9E-35 210.5 17.4 168 34-211 5-193 (200)
22 smart00479 EXOIII exonuclease 100.0 8.2E-29 1.8E-33 195.8 18.7 156 38-211 1-168 (169)
23 cd06138 ExoI_N N-terminal DEDD 100.0 2.7E-29 5.8E-34 202.9 15.7 155 40-204 1-183 (183)
24 cd06130 DNA_pol_III_epsilon_li 100.0 1.2E-28 2.6E-33 193.1 16.5 145 39-204 1-155 (156)
25 PRK07246 bifunctional ATP-depe 100.0 1.1E-28 2.3E-33 237.7 19.1 158 35-212 5-172 (820)
26 PRK07883 hypothetical protein; 100.0 1.8E-28 3.8E-33 227.5 19.1 160 34-211 12-183 (557)
27 PRK07748 sporulation inhibitor 100.0 1.8E-28 4E-33 201.7 17.0 160 35-209 2-179 (207)
28 COG2176 PolC DNA polymerase II 100.0 8.4E-30 1.8E-34 242.8 10.0 157 35-210 419-586 (1444)
29 PRK05601 DNA polymerase III su 100.0 3.2E-28 6.8E-33 212.4 18.5 154 34-206 43-245 (377)
30 PRK06195 DNA polymerase III su 100.0 4.1E-28 8.9E-33 210.8 18.5 153 37-210 1-164 (309)
31 PRK08074 bifunctional ATP-depe 100.0 8.9E-28 1.9E-32 234.4 19.8 158 36-212 2-171 (928)
32 PRK07247 DNA polymerase III su 100.0 4.5E-28 9.8E-33 197.5 14.9 153 36-210 4-169 (195)
33 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 9.5E-29 2.1E-33 195.9 10.2 136 40-203 1-160 (161)
34 cd06127 DEDDh DEDDh 3'-5' exon 100.0 1.1E-27 2.5E-32 185.8 16.0 147 40-203 1-158 (159)
35 TIGR01405 polC_Gram_pos DNA po 100.0 1.4E-27 3E-32 235.4 19.5 161 35-213 188-358 (1213)
36 cd06149 ISG20 DEDDh 3'-5' exon 100.0 2.6E-28 5.7E-33 192.7 11.3 140 40-204 1-157 (157)
37 TIGR01407 dinG_rel DnaQ family 100.0 1.6E-27 3.4E-32 231.2 18.9 155 38-211 1-166 (850)
38 PRK06722 exonuclease; Provisio 100.0 1.9E-27 4.1E-32 202.8 16.5 155 35-207 3-178 (281)
39 cd06133 ERI-1_3'hExo_like DEDD 100.0 3.5E-27 7.6E-32 188.1 17.0 154 39-206 1-175 (176)
40 PRK07983 exodeoxyribonuclease 99.9 5.9E-27 1.3E-31 194.1 16.1 138 39-209 2-153 (219)
41 cd06145 REX1_like DEDDh 3'-5' 99.9 1.7E-27 3.6E-32 186.8 12.0 136 40-204 1-150 (150)
42 PRK11779 sbcB exonuclease I; P 99.9 2.9E-26 6.2E-31 208.2 17.7 166 35-209 4-197 (476)
43 PRK09182 DNA polymerase III su 99.9 4.8E-26 1E-30 196.1 17.2 155 33-209 33-200 (294)
44 cd06144 REX4_like DEDDh 3'-5' 99.9 7.7E-27 1.7E-31 183.3 10.1 142 40-204 1-152 (152)
45 COG0847 DnaQ DNA polymerase II 99.9 6.6E-25 1.4E-29 184.2 17.9 156 37-209 13-181 (243)
46 PF00929 RNase_T: Exonuclease; 99.9 3.1E-26 6.7E-31 178.1 1.6 154 40-203 1-164 (164)
47 PTZ00315 2'-phosphotransferase 99.9 2.4E-23 5.1E-28 191.0 19.0 166 36-209 55-254 (582)
48 PRK00448 polC DNA polymerase I 99.9 1.9E-23 4.2E-28 208.5 16.0 157 36-211 418-585 (1437)
49 COG2925 SbcB Exonuclease I [DN 99.8 7.2E-18 1.6E-22 146.1 11.5 166 35-209 7-200 (475)
50 KOG2249 3'-5' exonuclease [Rep 99.7 3.4E-16 7.3E-21 130.1 13.1 147 38-212 106-268 (280)
51 cd06143 PAN2_exo DEDDh 3'-5' e 99.6 1.3E-15 2.8E-20 121.2 7.1 141 38-204 6-174 (174)
52 COG5018 KapD Inhibitor of the 99.6 1.3E-14 2.8E-19 113.3 8.5 165 37-208 4-183 (210)
53 KOG0542 Predicted exonuclease 99.5 5.1E-13 1.1E-17 110.5 11.7 168 35-208 54-240 (280)
54 cd05160 DEDDy_DNA_polB_exo DED 99.4 6E-12 1.3E-16 102.5 10.6 98 39-156 1-104 (199)
55 KOG2248 3'-5' exonuclease [Rep 99.3 3.5E-11 7.6E-16 106.6 12.7 148 35-211 214-376 (380)
56 cd06125 DnaQ_like_exo DnaQ-lik 99.3 5E-11 1.1E-15 86.5 10.8 91 40-202 1-94 (96)
57 PHA02570 dexA exonuclease; Pro 99.2 3.2E-10 7E-15 92.9 13.1 160 40-209 4-198 (220)
58 cd06139 DNA_polA_I_Ecoli_like_ 98.7 3.6E-07 7.7E-12 73.3 11.4 138 35-212 3-172 (193)
59 PF13482 RNase_H_2: RNase_H su 98.5 1.1E-07 2.5E-12 74.7 5.1 91 40-166 1-92 (164)
60 cd05780 DNA_polB_Kod1_like_exo 98.5 6.3E-07 1.4E-11 73.0 8.7 90 37-156 3-97 (195)
61 PRK05755 DNA polymerase I; Pro 98.5 1.9E-06 4.2E-11 84.8 12.3 130 36-212 314-471 (880)
62 cd05781 DNA_polB_B3_exo DEDDy 98.4 2.4E-06 5.1E-11 69.4 10.3 81 37-155 3-88 (188)
63 COG3359 Predicted exonuclease 98.3 2.8E-06 6.2E-11 70.7 7.5 29 34-62 95-123 (278)
64 KOG4793 Three prime repair exo 98.2 6.5E-06 1.4E-10 69.3 8.0 172 31-208 7-216 (318)
65 cd05779 DNA_polB_epsilon_exo D 98.0 4.4E-05 9.6E-10 62.8 9.9 106 37-155 2-113 (204)
66 cd05777 DNA_polB_delta_exo DED 98.0 3E-05 6.5E-10 64.8 8.7 100 34-154 4-110 (230)
67 cd05785 DNA_polB_like2_exo Unc 98.0 3.7E-05 8.1E-10 63.3 8.8 83 35-155 7-98 (207)
68 cd05783 DNA_polB_B1_exo DEDDy 97.7 0.00023 4.9E-09 58.5 8.7 41 111-156 71-112 (204)
69 PF04857 CAF1: CAF1 family rib 97.7 0.00026 5.7E-09 60.3 9.2 165 36-203 21-260 (262)
70 KOG1275 PAB-dependent poly(A) 97.5 0.00027 5.9E-09 68.1 7.7 158 28-208 901-1090(1118)
71 PF03104 DNA_pol_B_exo1: DNA p 97.5 0.00037 8.1E-09 60.3 8.0 100 35-154 155-261 (325)
72 cd05784 DNA_polB_II_exo DEDDy 97.5 0.0006 1.3E-08 55.5 8.4 89 36-155 2-91 (193)
73 PF01612 DNA_pol_A_exo1: 3'-5' 97.5 0.0069 1.5E-07 47.3 14.2 42 116-165 65-106 (176)
74 PTZ00166 DNA polymerase delta 97.4 0.00079 1.7E-08 67.6 9.0 97 35-151 262-366 (1054)
75 cd05778 DNA_polB_zeta_exo inac 97.3 0.0015 3.3E-08 54.7 8.9 105 37-151 4-117 (231)
76 cd05782 DNA_polB_like1_exo Unc 97.1 0.0043 9.4E-08 51.1 9.0 78 43-156 40-118 (208)
77 smart00486 POLBc DNA polymeras 96.9 0.005 1.1E-07 55.8 8.9 98 36-153 2-107 (471)
78 cd06146 mut-7_like_exo DEDDy 3 96.4 0.067 1.5E-06 43.4 11.0 134 35-207 20-192 (193)
79 PHA02528 43 DNA polymerase; Pr 96.4 0.015 3.3E-07 57.4 8.4 105 35-152 104-215 (881)
80 COG0349 Rnd Ribonuclease D [Tr 96.1 0.033 7.3E-07 49.4 8.6 133 35-214 15-170 (361)
81 PRK05762 DNA polymerase II; Re 95.8 0.038 8.2E-07 54.2 8.0 90 35-155 153-243 (786)
82 PF10108 DNA_pol_B_exo2: Predi 95.7 0.045 9.7E-07 45.1 7.0 36 112-151 36-72 (209)
83 cd00007 35EXOc 3'-5' exonuclea 95.5 0.24 5.2E-06 37.3 10.2 54 114-178 40-93 (155)
84 cd06141 WRN_exo DEDDy 3'-5' ex 95.4 0.18 4E-06 39.5 9.6 124 36-207 17-169 (170)
85 PRK10829 ribonuclease D; Provi 94.8 0.48 1E-05 42.5 11.4 126 35-212 20-172 (373)
86 KOG0304 mRNA deadenylase subun 94.7 0.32 6.8E-06 40.3 9.0 168 35-209 22-238 (239)
87 cd06129 RNaseD_like DEDDy 3'-5 94.5 0.44 9.5E-06 37.2 9.3 125 36-207 12-160 (161)
88 COG5228 POP2 mRNA deadenylase 94.4 0.29 6.4E-06 40.6 8.1 167 35-213 40-256 (299)
89 TIGR01388 rnd ribonuclease D. 93.9 3.3 7.2E-05 37.0 14.8 83 35-166 16-100 (367)
90 KOG1798 DNA polymerase epsilon 93.1 0.59 1.3E-05 48.3 9.2 102 32-155 241-357 (2173)
91 COG0417 PolB DNA polymerase el 92.1 0.85 1.8E-05 45.0 8.9 96 34-156 151-252 (792)
92 cd05776 DNA_polB_alpha_exo ina 91.2 0.36 7.9E-06 40.3 4.7 41 110-153 79-120 (234)
93 TIGR03491 RecB family nuclease 91.0 2.4 5.1E-05 39.1 10.2 95 37-167 284-384 (457)
94 cd06148 Egl_like_exo DEDDy 3'- 90.3 6.2 0.00014 31.9 11.1 27 186-212 153-179 (197)
95 KOG3657 Mitochondrial DNA poly 89.7 0.24 5.3E-06 48.2 2.6 35 133-169 242-276 (1075)
96 KOG0969 DNA polymerase delta, 88.8 0.062 1.3E-06 51.8 -2.0 93 35-148 272-371 (1066)
97 KOG4793 Three prime repair exo 87.0 1 2.2E-05 38.6 4.3 100 112-211 177-292 (318)
98 cd06140 DNA_polA_I_Bacillus_li 85.4 9.7 0.00021 29.7 9.1 84 37-166 3-86 (178)
99 TIGR00592 pol2 DNA polymerase 85.2 4.3 9.3E-05 41.9 8.6 109 37-154 506-623 (1172)
100 PHA02563 DNA polymerase; Provi 84.5 3.7 8.1E-05 39.4 7.3 37 118-154 51-88 (630)
101 PHA02524 43A DNA polymerase su 83.9 1.6 3.6E-05 40.6 4.6 39 110-151 177-216 (498)
102 PRK05761 DNA polymerase I; Rev 83.8 3.4 7.4E-05 40.8 6.9 41 111-156 208-249 (787)
103 PHA03036 DNA polymerase; Provi 80.4 8.1 0.00018 39.1 8.1 111 32-152 155-277 (1004)
104 COG0749 PolA DNA polymerase I 77.6 5.2 0.00011 38.0 5.6 73 40-151 25-97 (593)
105 TIGR00593 pola DNA polymerase 72.2 19 0.00041 36.2 8.2 91 113-211 363-478 (887)
106 PF13017 Maelstrom: piRNA path 67.4 15 0.00033 30.2 5.6 73 53-127 7-81 (213)
107 KOG0970 DNA polymerase alpha, 66.1 22 0.00049 36.4 7.1 108 34-152 526-644 (1429)
108 cd06142 RNaseD_exo DEDDy 3'-5' 64.6 22 0.00047 27.4 5.8 39 120-166 56-94 (178)
109 smart00474 35EXOc 3'-5' exonuc 60.8 21 0.00046 27.0 5.0 40 118-166 65-104 (172)
110 PF11074 DUF2779: Domain of un 60.6 61 0.0013 24.6 7.3 36 112-151 56-91 (130)
111 TIGR00592 pol2 DNA polymerase 54.0 8.7 0.00019 39.7 2.2 37 110-149 267-304 (1172)
112 PF12083 DUF3560: Domain of un 45.2 46 0.001 25.2 4.4 28 128-155 39-67 (126)
113 cd09018 DEDDy_polA_RNaseD_like 38.7 87 0.0019 23.1 5.2 39 120-166 45-83 (150)
114 COG4674 Uncharacterized ABC-ty 35.4 65 0.0014 26.9 4.1 25 44-68 132-168 (249)
115 KOG2549 Transcription initiati 29.1 2.2E+02 0.0047 27.2 6.9 79 109-198 233-319 (576)
116 PF03337 Pox_F12L: Poxvirus F1 26.0 68 0.0015 31.0 3.2 43 112-154 253-298 (651)
117 PHA01746 hypothetical protein 22.7 95 0.0021 23.0 2.7 57 55-127 34-90 (131)
No 1
>PRK05359 oligoribonuclease; Provisional
Probab=100.00 E-value=3.3e-41 Score=271.96 Aligned_cols=179 Identities=48% Similarity=0.711 Sum_probs=160.7
Q ss_pred CCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHH
Q 027892 36 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 115 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e 115 (217)
..+|||+|+|||||+|.+|+|||||||+++++...+.+.|+.+|+|+..++..++.+++.+|.+||||+++++++|++.+
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 46899999999999999999999999988887666667899999999877666678888888889999999999999999
Q ss_pred HHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcccCCCCCCCCCChHHH
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDD 195 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~~~l~~~~~H~Al~D 195 (217)
++.+|++|++++++++.+++||||+.||..||++++++++.+++++.+|++++++++|+|+|.. .++++....|||++|
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 9999999998766554467899999999999999999999899999999988888999999975 346777889999999
Q ss_pred HHHHHHHHHHHHHHhcccCC
Q 027892 196 IRESIMELKYYKENIFKTNL 215 (217)
Q Consensus 196 a~at~~ll~~~~~~~~~~~~ 215 (217)
|+++++++++|++.+++.++
T Consensus 161 ~~~s~~~~~~~~~~~~~~~~ 180 (181)
T PRK05359 161 IRESIAELKYYREHFFKLAP 180 (181)
T ss_pred HHHHHHHHHHHHHHhccCCC
Confidence 99999999999999999876
No 2
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=100.00 E-value=1.7e-39 Score=250.45 Aligned_cols=182 Identities=48% Similarity=0.703 Sum_probs=173.6
Q ss_pred cCCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 34 EYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
....++|++|+|+|||||.+|+|||||++++|+++..+.+.+...|+.+......+.+|++.+|.-+|+++...+...+.
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 45789999999999999999999999999999999999999999999999888999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcccCCCCCCCCCChH
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRAL 193 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~~~l~~~~~H~Al 193 (217)
.+|-.+.++||+.|+|++.++++|+++.-|++||.++||++..+||+|.+|++++++||+||.|..... +.....|+||
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 999999999999999999889999999999999999999999999999999999999999999987665 8889999999
Q ss_pred HHHHHHHHHHHHHHHHhcccCCC
Q 027892 194 DDIRESIMELKYYKENIFKTNLK 216 (217)
Q Consensus 194 ~Da~at~~ll~~~~~~~~~~~~~ 216 (217)
+|++..++-|+|||++++++.++
T Consensus 162 ~DI~ESI~EL~~YR~~f~~~~~~ 184 (184)
T COG1949 162 DDIRESIAELRYYREHFLKPAPG 184 (184)
T ss_pred HHHHHHHHHHHHHHHHhccCCCC
Confidence 99999999999999999998764
No 3
>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=4.3e-39 Score=258.04 Aligned_cols=172 Identities=61% Similarity=0.941 Sum_probs=152.0
Q ss_pred EEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHH
Q 027892 39 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEK 118 (217)
Q Consensus 39 ~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~ 118 (217)
++++|+||||++|.+++|||||||.+++....+.+.|+.+|+|...++..+++|+..+|.+|||+++++.++|++.+++.
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 58999999999999999999999987776555567899999999877666667888777889999999999999999999
Q ss_pred HHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcccCCCCCCCCCChHHHHHH
Q 027892 119 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDIRE 198 (217)
Q Consensus 119 ~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~~~l~~~~~H~Al~Da~a 198 (217)
+|.+|++++...+..++||||++||+.||++++.+++.+++++.+|+.++.+++++++|...+.+++...+||||+||++
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 99999987543334578999999999999999998888888899999888889999999876667778899999999999
Q ss_pred HHHHHHHHHHHh
Q 027892 199 SIMELKYYKENI 210 (217)
Q Consensus 199 t~~ll~~~~~~~ 210 (217)
|+.+|++|++.+
T Consensus 161 ~~~~~~~~~~~~ 172 (173)
T cd06135 161 SIAELKYYRENI 172 (173)
T ss_pred HHHHHHHHHHHh
Confidence 999999999876
No 4
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=100.00 E-value=6.4e-38 Score=243.80 Aligned_cols=180 Identities=61% Similarity=0.970 Sum_probs=173.3
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
...++|++|||+|||+..+|+|+|||+|++||++..+.+.++..|+.++++.+.+.+||..||..+|+|+..++...+++
T Consensus 24 l~q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl~ 103 (208)
T KOG3242|consen 24 LKQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITLA 103 (208)
T ss_pred ccCceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccHH
Confidence 67899999999999999999999999999999999888899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcccCCCCCCCCCChHH
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALD 194 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~~~l~~~~~H~Al~ 194 (217)
+|-.++++|++.+++++.++|.|+++.-|+.||.++||.+-..+++|++|+++++++++||+|....+.+.....|||++
T Consensus 104 ~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL~~Rw~P~~~~~aPkK~~~HrAld 183 (208)
T KOG3242|consen 104 DAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKELARRWYPDIKARAPKKKATHRALD 183 (208)
T ss_pred HHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHHHHHhCchhhccCcccccccchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999998887888899999999
Q ss_pred HHHHHHHHHHHHHHHhcccC
Q 027892 195 DIRESIMELKYYKENIFKTN 214 (217)
Q Consensus 195 Da~at~~ll~~~~~~~~~~~ 214 (217)
|++..++-|++|++.+|+..
T Consensus 184 DI~ESI~ELq~Yr~nifkk~ 203 (208)
T KOG3242|consen 184 DIRESIKELQYYRENIFKKS 203 (208)
T ss_pred HHHHHHHHHHHHHHHhccCc
Confidence 99999999999999999865
No 5
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=3.2e-33 Score=234.43 Aligned_cols=169 Identities=17% Similarity=0.169 Sum_probs=138.0
Q ss_pred CCccccCCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 29 TPLEFEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 29 ~~~~~~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
....+....+|+++|+||||++|.+|+|||||+|.+++......+.|+.+|+|+.++++. +. .+||||++++.
T Consensus 39 ~~~~~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~----~~---~IhGIt~e~l~ 111 (239)
T PRK09146 39 SPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEE----SV---VIHGITHSELQ 111 (239)
T ss_pred CCCCCcccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChh----hh---hhcCCCHHHHh
Confidence 334355778999999999999999999999999965554433456789999999877542 33 67799999999
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhh-hcCCCCceeehHHHHHHHHHhCCCc--------
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDL-ASLFSHVLVDVSSIKALCMRWYPRD-------- 179 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~-~~~~~~~~iDt~~l~~la~~~~p~~-------- 179 (217)
++|++.+++.+|.+|+++ .++||||+.||+.||++++.++ +..++++++||. ++++++.|..
T Consensus 112 ~ap~~~evl~~l~~~~~~------~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl---~Lar~l~~~~~~~~~~~~ 182 (239)
T PRK09146 112 DAPDLERILDELLEALAG------KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTM---EIEARIQRKQAGGLWNRL 182 (239)
T ss_pred CCCCHHHHHHHHHHHhCC------CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechH---HHHHHHcccccccccchh
Confidence 999999999999999987 4689999999999999999764 445677899998 5566554321
Q ss_pred -----c---------cCCCCCCCCCChHHHHHHHHHHHHHHHHHhccc
Q 027892 180 -----Y---------RKVPSKEQKHRALDDIRESIMELKYYKENIFKT 213 (217)
Q Consensus 180 -----~---------~~~l~~~~~H~Al~Da~at~~ll~~~~~~~~~~ 213 (217)
. .++++..++|||++||.+|++|+..+.+.++..
T Consensus 183 ~~~~~~~~~L~~l~~~~gl~~~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 183 KGKKPESIRLADSRLRYGLPAYSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred ccCCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 1 135788899999999999999999999988865
No 6
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=2.4e-32 Score=228.99 Aligned_cols=156 Identities=19% Similarity=0.191 Sum_probs=127.6
Q ss_pred CCCEEEEEecCCCCCCC-CCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 36 KMPLVWIDLEMTGLKIE-VDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~-~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
.+++|+||+||||++|. +|+|||||+| +.++.. .++.|+.+|+|..++++ .+. .+||||++++.++|.+
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~--~~~~f~~~i~P~~~i~~----~a~---~VHGIT~e~l~~~p~f 73 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINRRL--TGRNFHVYIKPDRLVDP----EAL---AVHGITDEFLADKPTF 73 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEE--eccEEEEEECcCCcCCH----HHh---hhcCCCHHHHcCCCCH
Confidence 46899999999999997 8999999999 455433 35679999999887754 344 6779999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCC-----CceeehHHHHHHHHHhCCCccc-------
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-----HVLVDVSSIKALCMRWYPRDYR------- 181 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-----~~~iDt~~l~~la~~~~p~~~~------- 181 (217)
.+++.+|.+|+++ .++||||+.||+.||++++.+++..++ ..++||. .++|+.+|....
T Consensus 74 ~ev~~~f~~fi~~------~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl---~lar~~~p~~~~~L~aL~~ 144 (240)
T PRK05711 74 AEVADEFLDFIRG------AELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTL---AMARRMFPGKRNSLDALCK 144 (240)
T ss_pred HHHHHHHHHHhCC------CEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHH---HHHHHHcCCCCCCHHHHHH
Confidence 9999999999988 458999999999999999988874443 4689997 677887776432
Q ss_pred -CCCCC--CCCCChHHHHHHHHHHHHHHHHH
Q 027892 182 -KVPSK--EQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 182 -~~l~~--~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
++++. ...|+|+.||++|++|+..+...
T Consensus 145 ~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 145 RYGIDNSHRTLHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred HCCCCCCCCCCCCHHHHHHHHHHHHHHHHCc
Confidence 34544 35699999999999999888644
No 7
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=4.3e-32 Score=222.41 Aligned_cols=161 Identities=22% Similarity=0.261 Sum_probs=130.7
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
.+.+||++|+||||++|..++|||||+|.++++.....+.|+.+|+|+..++ ++++ .+||||++++.++|++.
T Consensus 27 ~~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~----~~~~---~ihGIt~~~l~~~~~~~ 99 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLS----AESI---KIHRLRHQDLEDGLSEE 99 (202)
T ss_pred CCCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCC----HhHh---hhcCcCHHHHhcCCCHH
Confidence 4579999999999999999999999999776655444567999999987653 4445 67799999999999999
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhh-hhcCCCCceeehHHHHH-HHHHhCCC-cc---------cC
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPD-LASLFSHVLVDVSSIKA-LCMRWYPR-DY---------RK 182 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~-~~~~~~~~~iDt~~l~~-la~~~~p~-~~---------~~ 182 (217)
+++++|.+|+++ .++||||+.||+.||++++.+ .+.+++.+.+|+..++. ...+..|. .. .+
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 999999999987 358999999999999999865 46678888999986642 12222332 11 13
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHH
Q 027892 183 VPSKEQKHRALDDIRESIMELKYYKE 208 (217)
Q Consensus 183 ~l~~~~~H~Al~Da~at~~ll~~~~~ 208 (217)
+++..++|+|++||.+|++|+..+++
T Consensus 174 gi~~~~~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 174 DLPVLGRHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHh
Confidence 67778899999999999999998865
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=100.00 E-value=6.7e-32 Score=224.72 Aligned_cols=154 Identities=18% Similarity=0.215 Sum_probs=125.7
Q ss_pred CEEEEEecCCCCCCCC-CcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHH
Q 027892 38 PLVWIDLEMTGLKIEV-DRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 115 (217)
Q Consensus 38 ~~v~lD~ETTGl~p~~-d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e 115 (217)
++|++|+||||++|.+ ++|||||+| +.++.. .++.|+.+|+|..++++ .++ .+||||++++.++|++.+
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--TGDNFHVYVNPERDMPA----EAA---KVHGITDEFLADKPKFKE 71 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcE--ecceEEEEECcCCCCCH----HHH---hccCCCHHHHhCCCCHHH
Confidence 5899999999999975 899999999 555432 35679999999987754 344 677999999999999999
Q ss_pred HHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc--C-CC--CceeehHHHHHHHHHhCCCccc--------C
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS--L-FS--HVLVDVSSIKALCMRWYPRDYR--------K 182 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~--~-~~--~~~iDt~~l~~la~~~~p~~~~--------~ 182 (217)
++.+|.+|+++ .++||||+.||+.||++++.+++. . ++ ++++||. .++++++|.... +
T Consensus 72 v~~~f~~fi~~------~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl---~lar~~~p~~~~~L~~L~~~~ 142 (225)
T TIGR01406 72 IADEFLDFIGG------SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTL---AMARERFPGQRNSLDALCKRF 142 (225)
T ss_pred HHHHHHHHhCC------CEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHH---HHHHHHcCCCCCCHHHHHHhc
Confidence 99999999988 468999999999999999988873 2 22 5799997 677887775432 3
Q ss_pred CCCC--CCCCChHHHHHHHHHHHHHHHHH
Q 027892 183 VPSK--EQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 183 ~l~~--~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
+++. ...|+|+.||.+|++|+..+...
T Consensus 143 gi~~~~r~~H~Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 143 KVDNSHRTLHGALLDAHLLAEVYLALTGG 171 (225)
T ss_pred CCCCCCCCCcCHHHHHHHHHHHHHHHHcC
Confidence 4543 45799999999999999988654
No 9
>PRK07740 hypothetical protein; Provisional
Probab=100.00 E-value=2.3e-31 Score=223.98 Aligned_cols=162 Identities=19% Similarity=0.183 Sum_probs=132.4
Q ss_pred CCCCEEEEEecCCCCCCCC-CcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEV-DRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~-d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
...+||+||+||||++|.. ++|||||||.++++.. ..+.|+.+|+|..++++ .+. .+||||++++.++|++
T Consensus 57 ~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i-~~~~f~~lv~P~~~i~~----~~~---~ltGIt~e~l~~ap~~ 128 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEV-ETDTFYSLVKPKRPIPE----HIL---ELTGITAEDVAFAPPL 128 (244)
T ss_pred cCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEE-EEEEEEEEeCcCCCCCh----hhe---eccCCCHHHHhCCCCH
Confidence 5668999999999999986 8999999996655543 24568999999987654 333 7889999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhh-hhcCCCCceeehHHHHHHHHHhCCCcc---------cCC
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPD-LASLFSHVLVDVSSIKALCMRWYPRDY---------RKV 183 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~-~~~~~~~~~iDt~~l~~la~~~~p~~~---------~~~ 183 (217)
.+++.+|.+|+++ .++||||+.||+.||++++.+ .+.+++.+++||. .+++.+.|... .++
T Consensus 129 ~evl~~f~~fi~~------~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~---~l~r~l~~~~~~~sL~~l~~~~g 199 (244)
T PRK07740 129 AEVLHRFYAFIGA------GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTM---FLTKLLAHERDFPTLDDALAYYG 199 (244)
T ss_pred HHHHHHHHHHhCC------CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechH---HHHHHHcCCCCCCCHHHHHHHCC
Confidence 9999999999987 469999999999999998744 4567778899998 44555555432 136
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHhccc
Q 027892 184 PSKEQKHRALDDIRESIMELKYYKENIFKT 213 (217)
Q Consensus 184 l~~~~~H~Al~Da~at~~ll~~~~~~~~~~ 213 (217)
++...+|+|++||++|++|+..+.+.+...
T Consensus 200 i~~~~~H~Al~Da~ata~l~~~ll~~~~~~ 229 (244)
T PRK07740 200 IPIPRRHHALGDALMTAKLWAILLVEAQQR 229 (244)
T ss_pred cCCCCCCCcHHHHHHHHHHHHHHHHHHHHc
Confidence 777889999999999999999987766543
No 10
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=4.6e-31 Score=220.69 Aligned_cols=170 Identities=16% Similarity=0.109 Sum_probs=129.2
Q ss_pred ccCCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhc-CC
Q 027892 33 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS-GL 111 (217)
Q Consensus 33 ~~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~-~~ 111 (217)
++...+|++||+||||++|.+++|||||+|.++.++.. .+.|+++|+|..++++ .++ .+||||++++.+ ++
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-VESREWLADPGVEIPE----EAS---AVHGITTEYARAHGR 73 (232)
T ss_pred CcccCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCcc-ccceEEEECCCCCCCH----HHH---HHhCCCHHHHHhhCC
Confidence 36778999999999999999999999999966632222 2458899999887754 334 677999999965 88
Q ss_pred CHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcC--CCCceeehHHHHHHHHHhCCCcc-------cC
Q 027892 112 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL--FSHVLVDVSSIKALCMRWYPRDY-------RK 182 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~--~~~~~iDt~~l~~la~~~~p~~~-------~~ 182 (217)
++.+++.+|.+++.+....+ .++||||+.||+.||++++.+.+.. .+.+++|+..+.+...++.+... .+
T Consensus 74 ~~~~vl~e~~~~l~~~~~~~-~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~ 152 (232)
T PRK07942 74 PAAEVLAEIADALREAWARG-VPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHY 152 (232)
T ss_pred CHHHHHHHHHHHHHHHhhcC-CEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHc
Confidence 89999999999986533222 3589999999999999999888743 34678999844332222211111 24
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHhc
Q 027892 183 VPSKEQKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 183 ~l~~~~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
+++..++|+|++||.+|++|+..+.+.+.
T Consensus 153 gi~~~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 153 GVRLDNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 67888999999999999999999876553
No 11
>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=99.97 E-value=6.5e-31 Score=217.76 Aligned_cols=161 Identities=16% Similarity=0.108 Sum_probs=128.5
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEE-ECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACII-TDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~-~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
....||++|+||||++|..+ |||||+|. .++.. +.+.|+.+|+|..++++ .+. .+||||++++.++|++
T Consensus 5 ~~~~fvv~D~ETTGl~~~~~-IIeIgav~v~~~~~--~~~~f~~li~P~~~i~~----~a~---~ihGIt~e~l~~~p~~ 74 (217)
T TIGR00573 5 VLDTETTGDNETTGLYAGHD-IIEIGAVEIINRRI--TGNKFHTYIKPDRPIDP----DAI---KIHGITDDMLKDKPDF 74 (217)
T ss_pred EecCEEEEEecCCCCCCCCC-EEEEEEEEEECCCE--eeeEEEEEECcCCCCCH----HHH---hhcCCCHHHHcCCCCH
Confidence 45789999999999999888 99999995 65543 23578999999977653 333 6789999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc--CCCCceeehHHHHHHHHHhCCCcc--------cCC
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS--LFSHVLVDVSSIKALCMRWYPRDY--------RKV 183 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~--~~~~~~iDt~~l~~la~~~~p~~~--------~~~ 183 (217)
.+++++|.+|+++ .++||||+.||+.||++++.+++. +.+.+++|+..+.+..+...|... .++
T Consensus 75 ~ev~~~~~~~~~~------~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~g 148 (217)
T TIGR00573 75 KEIAEDFADYIRG------AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYE 148 (217)
T ss_pred HHHHHHHHHHhCC------CEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHcC
Confidence 9999999999987 368999999999999999987753 345678999865555544444221 135
Q ss_pred CCCC--CCCChHHHHHHHHHHHHHHHHHhc
Q 027892 184 PSKE--QKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 184 l~~~--~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
++.. .+|+|++||++|++|++.+.+..-
T Consensus 149 l~~~~~~~H~Al~DA~~ta~l~~~l~~~~~ 178 (217)
T TIGR00573 149 ITNSHRALHGALADAFILAKLYLVMTGKQT 178 (217)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHHHHhcch
Confidence 5544 799999999999999999977653
No 12
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=8.9e-31 Score=221.66 Aligned_cols=159 Identities=16% Similarity=0.201 Sum_probs=129.9
Q ss_pred ccCCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCC
Q 027892 33 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 112 (217)
Q Consensus 33 ~~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~ 112 (217)
.+....||++|+||||++|..++|||||||.+++.. . .++|+.+|+|+ .+++ .++ ++||||++++.++|+
T Consensus 64 ~~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~-i-~~~f~~~v~p~-~ip~----~~~---~itGIt~e~l~~ap~ 133 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGE-I-IDRFESFVKAK-EVPE----YIT---ELTGITYEDLENAPS 133 (257)
T ss_pred CCCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCE-E-EEEEEEEECCC-CCCh----hhh---hhcCcCHHHHcCCCC
Confidence 457789999999999999999999999999554332 2 24689999996 4543 334 678999999999999
Q ss_pred HHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc-CCCCceeehHHHHHHHHHhCCCccc--------CC
Q 027892 113 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDYR--------KV 183 (217)
Q Consensus 113 ~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iDt~~l~~la~~~~p~~~~--------~~ 183 (217)
+.+|+.+|.+|+++ .++||||++||..||++++.+.+. ++.++.+||. .+++++.+.... .+
T Consensus 134 ~~evl~~f~~fl~~------~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl---~la~~~~~~~~~~L~~L~~~lg 204 (257)
T PRK08517 134 LKEVLEEFRLFLGD------SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTI---DLAKRTIESPRYGLSFLKELLG 204 (257)
T ss_pred HHHHHHHHHHHHCC------CeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehH---HHHHHHccCCCCCHHHHHHHcC
Confidence 99999999999987 469999999999999999988874 4667889997 566666543221 25
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 184 PSKEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 184 l~~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
++...+|||++||.+|++|+..+...+
T Consensus 205 i~~~~~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 205 IEIEVHHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred cCCCCCCChHHHHHHHHHHHHHHHHHh
Confidence 677799999999999999999987654
No 13
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=7.8e-31 Score=221.51 Aligned_cols=159 Identities=21% Similarity=0.273 Sum_probs=128.9
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
..++||+||+||||++|.+|+|||||+|.++++.. .+.|+.+|+|+.+++.. +. .+||||+++++++|++.
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~--~~~~~~li~P~~~I~~~----a~---~ihgIt~e~v~~~p~~~ 75 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEV--IDSVEFLINPERVVSAE----SQ---RIHHISDAMLRDKPKIA 75 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeE--EEEEEEEECcCCCCCHh----hh---hccCcCHHHHhCCCCHH
Confidence 34789999999999999999999999996654422 34688999999887643 33 67799999999999999
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCC---CCceeehHHHHHHHHHhCCCcc--------cCC
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF---SHVLVDVSSIKALCMRWYPRDY--------RKV 183 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~---~~~~iDt~~l~~la~~~~p~~~--------~~~ 183 (217)
+++.+|.+|+++. .++||||++||++||++++.+.+.++ +++++||. ++++++.+... .++
T Consensus 76 ev~~~~~~fl~~~-----~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl---~lar~~~~~~~~~L~~l~~~~g 147 (250)
T PRK06310 76 EVFPQIKGFFKEG-----DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTL---RLAKEYGDSPNNSLEALAVHFN 147 (250)
T ss_pred HHHHHHHHHhCCC-----CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehH---HHHHhcccCCCCCHHHHHHHCC
Confidence 9999999999762 46999999999999999998887544 36799997 56666532110 236
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 184 PSKEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 184 l~~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
++..++|||++||.+|++|++.+.+.+
T Consensus 148 ~~~~~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 148 VPYDGNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CCCCCCcChHHHHHHHHHHHHHHHHhc
Confidence 777889999999999999999987653
No 14
>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=99.97 E-value=1.2e-30 Score=207.09 Aligned_cols=151 Identities=21% Similarity=0.205 Sum_probs=119.7
Q ss_pred EEEEEecCCCCCC-CCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHH
Q 027892 39 LVWIDLEMTGLKI-EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 117 (217)
Q Consensus 39 ~v~lD~ETTGl~p-~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~ 117 (217)
||++|+||||++| .+++|||||+|.+++... ..+.|+.+|+|..+++ +.++ ++||||++++.++|++.+++
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~-~~~~~~~~v~P~~~i~----~~~~---~ihGIt~e~l~~~~~~~~v~ 72 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRL-TGNTFHVYINPERDIP----EEAF---KVHGITDEFLADKPKFAEIA 72 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcE-eccEEEEEECCCCCCC----HHHH---HHhCCCHHHHhcCCCHHHHH
Confidence 6899999999999 679999999995544322 3456889999987654 4445 67799999999999999999
Q ss_pred HHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc----CCCCceeehHHHHHHHHHhCCCcc--------cCCCC
Q 027892 118 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS----LFSHVLVDVSSIKALCMRWYPRDY--------RKVPS 185 (217)
Q Consensus 118 ~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~----~~~~~~iDt~~l~~la~~~~p~~~--------~~~l~ 185 (217)
.+|.+|+++ .++||||+.||+.||++++.+.+. ..+..++||. +++++.+|... .++++
T Consensus 73 ~~l~~~l~~------~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~---~~~~~~~~~~~~~L~~l~~~~~i~ 143 (167)
T cd06131 73 DEFLDFIRG------AELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTL---ALARKKFPGKPNSLDALCKRFGID 143 (167)
T ss_pred HHHHHHHCC------CeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhH---HHHHHHcCCCCCCHHHHHHHCCCC
Confidence 999999987 358999999999999999987642 2346789997 56666665322 13455
Q ss_pred C--CCCCChHHHHHHHHHHHHHH
Q 027892 186 K--EQKHRALDDIRESIMELKYY 206 (217)
Q Consensus 186 ~--~~~H~Al~Da~at~~ll~~~ 206 (217)
. ..+|+|++||++|++|+..+
T Consensus 144 ~~~~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 144 NSHRTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCCCCChHHHHHHHHHHHHHh
Confidence 4 36899999999999999764
No 15
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=2.4e-30 Score=224.85 Aligned_cols=160 Identities=18% Similarity=0.157 Sum_probs=130.8
Q ss_pred cCCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 34 EYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
..+.+||+||+||||++|.+++|||||+|.++.+... .+.|+.+|+|.... ..+ .+||||++++.++|++
T Consensus 12 ~~~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i-~~~~~~lv~P~~~~------~~~---~IhGIt~e~l~~ap~f 81 (313)
T PRK06063 12 HYPRGWAVVDVETSGFRPGQARIISLAVLGLDADGNV-EQSVVTLLNPGVDP------GPT---HVHGLTAEMLEGQPQF 81 (313)
T ss_pred CCCCCEEEEEEECCCCCCCCCEEEEEEEEEEECCcee-eeEEEEEECcCCCC------CCe---ecCCCCHHHHhCCCCH
Confidence 4678999999999999999999999999966543332 35689999997532 112 5779999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCC-CceeehHHHHHHHHHhCCCccc---------CC
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRWYPRDYR---------KV 183 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-~~~iDt~~l~~la~~~~p~~~~---------~~ 183 (217)
.+++.+|.+|+++ .++||||+.||+.||++++.+++..++ ..++||. ++++++.+...+ ++
T Consensus 82 ~ev~~~l~~~l~~------~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl---~lar~~~~~~~~~kL~~l~~~~g 152 (313)
T PRK06063 82 ADIAGEVAELLRG------RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTV---ELARRLGLGLPNLRLETLAAHWG 152 (313)
T ss_pred HHHHHHHHHHcCC------CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehH---HHHHHhccCCCCCCHHHHHHHcC
Confidence 9999999999988 369999999999999999988886554 3589997 677777654433 35
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 184 PSKEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 184 l~~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
++..++|||++||.+|++|+..+.+.+..
T Consensus 153 i~~~~~H~Al~DA~ata~l~~~ll~~~~~ 181 (313)
T PRK06063 153 VPQQRPHDALDDARVLAGILRPSLERARE 181 (313)
T ss_pred CCCCCCCCcHHHHHHHHHHHHHHHHHHHh
Confidence 67789999999999999999988766543
No 16
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=4.1e-30 Score=223.11 Aligned_cols=157 Identities=18% Similarity=0.186 Sum_probs=130.0
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
.+.+||+||+||||++|..++|||||||.+++.. +.+.|+.+|+|..++++ .++ .+||||++++.++|++.
T Consensus 6 ~~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~--i~~~f~~lVkP~~~I~~----~a~---~ihGIT~e~l~~~~~~~ 76 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHE--LVDQFVSYVNPERPIPD----RIT---SLTGITNYRVSDAPTIE 76 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEECCE--EEEEEEEEECcCCCCCH----hhh---ccCCCCHHHHhCCCCHH
Confidence 6789999999999999999999999999554332 23568999999987754 344 67899999999999999
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcC-CCCceeehHHHHHHHHHhCCCccc---------CCC
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYR---------KVP 184 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~-~~~~~iDt~~l~~la~~~~p~~~~---------~~l 184 (217)
+++.+|.+|+++. ++||||+.||+.||++++.++|.+ ...+++||. .+++.++|.... .++
T Consensus 77 evl~~f~~fl~~~------~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl---~la~~~~~~~~~~kL~~L~~~lgi 147 (313)
T PRK06807 77 EVLPLFLAFLHTN------VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTV---FLAKKYMKHAPNHKLETLKRMLGI 147 (313)
T ss_pred HHHHHHHHHHcCC------eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHH---HHHHHHhCCCCCCCHHHHHHHcCC
Confidence 9999999999873 589999999999999999888863 445799997 556666665433 245
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 185 SKEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 185 ~~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
+. ++|||++||++|++|++.+....
T Consensus 148 ~~-~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 148 RL-SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CC-CCcChHHHHHHHHHHHHHHHHhh
Confidence 66 89999999999999999887665
No 17
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.97 E-value=3.2e-30 Score=209.37 Aligned_cols=164 Identities=19% Similarity=0.176 Sum_probs=123.3
Q ss_pred CCEEEEEecCCCCCCCCCcEEEEEEEEE-CC-ce-eeeecCCceeecCC--ccchhhhhhHHhhhhhhcCCcHHH-HhcC
Q 027892 37 MPLVWIDLEMTGLKIEVDRILEIACIIT-DG-KL-TKSVEGPDLVIHQT--KECLDSMGEWCQNHHEASGLTKKV-LHSG 110 (217)
Q Consensus 37 ~~~v~lD~ETTGl~p~~d~IieIgav~~-d~-~~-~~~~~~~~~li~p~--~~i~~~~~~~~~~~h~itGIt~~~-l~~~ 110 (217)
-..|++|+||||++|.+|+|||||||.+ ++ +. ....+.|+++++|+ .++++ .+. .+||||+++ ++++
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~----~~~---~ihGIt~~~~~~~~ 77 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDP----AAL---EFNGIDPFHPFRFA 77 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCH----HHH---hhcCCCchhhhccc
Confidence 4578999999999999999999999944 22 22 12345799999994 45543 333 678999876 6788
Q ss_pred CCHHHHHHHHHHHHhhccCC---CCceEEEecHHHhHHHHHhHhhhhhc---CC-CCceeehHHHHHHHHHhCCCcc---
Q 027892 111 LTEREAEKQVVEFVKKNVGT---YTPLLAGNSVYVDFMFLKKYMPDLAS---LF-SHVLVDVSSIKALCMRWYPRDY--- 180 (217)
Q Consensus 111 ~~~~e~~~~~~~~l~~~~~~---~~~~lVghn~~FD~~fL~~~~~~~~~---~~-~~~~iDt~~l~~la~~~~p~~~--- 180 (217)
+..++++.+|.+++.+.... +..++||||+.||+.||++++.+++. ++ +.+++||. .+++..+|...
T Consensus 78 ~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~---~la~~~~~~~~L~~ 154 (189)
T cd06134 78 VDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTA---TLAGLAYGQTVLAK 154 (189)
T ss_pred cchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHH---HHHHHHhCCCcHHH
Confidence 88888888888888754311 12479999999999999999988775 23 34689997 55666666432
Q ss_pred ---cCCCC--CCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 181 ---RKVPS--KEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 181 ---~~~l~--~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
.++++ ..++|+|++||++|++|+..+.+.|
T Consensus 155 l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 155 ACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred HHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 24565 3579999999999999999987654
No 18
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.97 E-value=9e-31 Score=210.54 Aligned_cols=155 Identities=16% Similarity=0.156 Sum_probs=116.8
Q ss_pred EEEEEecCCCCC-CCCCcEEEEEEEEECCceee-----------eecCCceeecCCccchhhhhhHHhhhhhhcCCcHHH
Q 027892 39 LVWIDLEMTGLK-IEVDRILEIACIITDGKLTK-----------SVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV 106 (217)
Q Consensus 39 ~v~lD~ETTGl~-p~~d~IieIgav~~d~~~~~-----------~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~ 106 (217)
|++||+|||||+ +.+|+|||||||.+++.... +.++|+++|+|..++++.+ + .+||||+++
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a----~---~IhGIt~e~ 73 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGA----S---EITGLSNDL 73 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhH----H---HHhCcCHHH
Confidence 689999999999 68899999999955433211 1246899999998876433 3 678999999
Q ss_pred HhcCCCHHH-HHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhcCCC--CceeehHHHHHHHHHhCCCcc--
Q 027892 107 LHSGLTERE-AEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASLFS--HVLVDVSSIKALCMRWYPRDY-- 180 (217)
Q Consensus 107 l~~~~~~~e-~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~~~--~~~iDt~~l~~la~~~~p~~~-- 180 (217)
+.++|++.+ +.+.+.+|++... +..++||||+ +||++||++++.+++..++ ..++||. .++++..|++.
T Consensus 74 l~~~~~~~~~~~~~l~~f~~~~~--~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl---~l~r~~~~~L~~l 148 (177)
T cd06136 74 LEHKAPFDSDTANLIKLFLRRQP--KPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSL---PAFRELDQSLGSL 148 (177)
T ss_pred HhcCCCccHHHHHHHHHHHHhcC--CCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeH---HHHhhhHhhHHHH
Confidence 999887664 5666667775421 1247999998 8999999999988876543 4568987 45555555332
Q ss_pred ---cCCCCCCCCCChHHHHHHHHHHHHH
Q 027892 181 ---RKVPSKEQKHRALDDIRESIMELKY 205 (217)
Q Consensus 181 ---~~~l~~~~~H~Al~Da~at~~ll~~ 205 (217)
.++++..++|||++||.+|++++.+
T Consensus 149 ~~~~~~~~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 149 YKRLFGQEPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHhCCCcccccchHHHHHHHHHHHhh
Confidence 1467888999999999999998864
No 19
>PRK05168 ribonuclease T; Provisional
Probab=99.97 E-value=4.2e-30 Score=212.06 Aligned_cols=166 Identities=19% Similarity=0.193 Sum_probs=127.2
Q ss_pred cCCCCEEEEEecCCCCCCCCCcEEEEEEEEEC----CceeeeecCCceeecCC--ccchhhhhhHHhhhhhhcCCcHHH-
Q 027892 34 EYKMPLVWIDLEMTGLKIEVDRILEIACIITD----GKLTKSVEGPDLVIHQT--KECLDSMGEWCQNHHEASGLTKKV- 106 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d----~~~~~~~~~~~~li~p~--~~i~~~~~~~~~~~h~itGIt~~~- 106 (217)
.....+|++|+||||++|.+|+|||||+|.+. +.. ...+.|+.+|+|. .+++ +.++ .+||||+++
T Consensus 14 ~~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i-~~~~~f~~lv~P~~~~~i~----~~~~---~ihGIt~e~~ 85 (211)
T PRK05168 14 FRGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWL-YPDETLHFHVEPFEGANLE----PEAL---AFNGIDPDNP 85 (211)
T ss_pred hcCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcE-eccceEEEEECCCCCCCCC----HHHH---hhcCCCchhh
Confidence 45678999999999999999999999999432 322 2346799999994 4454 3444 678999875
Q ss_pred HhcCCCHHHHHHHHHHHHhhccCC---CCceEEEecHHHhHHHHHhHhhhhhc---CC-CCceeehHHHHHHHHHhCCCc
Q 027892 107 LHSGLTEREAEKQVVEFVKKNVGT---YTPLLAGNSVYVDFMFLKKYMPDLAS---LF-SHVLVDVSSIKALCMRWYPRD 179 (217)
Q Consensus 107 l~~~~~~~e~~~~~~~~l~~~~~~---~~~~lVghn~~FD~~fL~~~~~~~~~---~~-~~~~iDt~~l~~la~~~~p~~ 179 (217)
+++++++.+++.++.+|+.+.... +..++||||+.||+.||++++.+++. ++ +++++||. ++++++++..
T Consensus 86 ~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~---~lar~~~~~~ 162 (211)
T PRK05168 86 LRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTA---TLSGLALGQT 162 (211)
T ss_pred hhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHH---HHHHHHcCCC
Confidence 889999999999999999753211 12579999999999999999988763 22 35789998 5666666543
Q ss_pred c------cCCCC--CCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 180 Y------RKVPS--KEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 180 ~------~~~l~--~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
. .++++ ...+|+|++||.+|++|+..+.+.+
T Consensus 163 ~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 163 VLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred CHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 2 13554 3579999999999999999987765
No 20
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=4.8e-30 Score=214.56 Aligned_cols=154 Identities=22% Similarity=0.263 Sum_probs=126.2
Q ss_pred CCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHH
Q 027892 37 MPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 116 (217)
Q Consensus 37 ~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~ 116 (217)
.++|+||+||||+++.+|+|||||++ ++.. .+.|+.+++|..++++. +. .+||||+++++++|++.++
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---SESFQTLVNPEIPIPAE----AS---KIHGITTDEVADAPKFPEA 69 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEE--cCcc---ccEEEEEeCCCCCCChh----HH---hhcCCCHHHHhCCCCHHHH
Confidence 36899999999999999999999995 3222 24588999999887543 33 6789999999999999999
Q ss_pred HHHHHHHHhhccCCCCceEEEec-HHHhHHHHHhHhhhhhcC-CCCceeehHHHHHHHHHhCCCccc---------CCCC
Q 027892 117 EKQVVEFVKKNVGTYTPLLAGNS-VYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYR---------KVPS 185 (217)
Q Consensus 117 ~~~~~~~l~~~~~~~~~~lVghn-~~FD~~fL~~~~~~~~~~-~~~~~iDt~~l~~la~~~~p~~~~---------~~l~ 185 (217)
+++|.+|+++. .++|||| ++||++||++++.+.+.. ..++++||. ++++++.|.... ++++
T Consensus 70 ~~~~~~fi~~~-----~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~---~l~~~~~~~~~~~~L~~l~~~~~~~ 141 (232)
T PRK06309 70 YQKFIEFCGTD-----NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSL---KWAQKYRPDLPKHNLQYLRQVYGFE 141 (232)
T ss_pred HHHHHHHHcCC-----CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHH---HHHHHHcCCCCCCCHHHHHHHcCCC
Confidence 99999999852 4699999 589999999999888754 346899997 667777665432 3567
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 186 KEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 186 ~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
..++|||++||.+|++|++.+.+.+
T Consensus 142 ~~~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 142 ENQAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 7889999999999999999987543
No 21
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.97 E-value=4.1e-30 Score=210.47 Aligned_cols=168 Identities=20% Similarity=0.180 Sum_probs=126.0
Q ss_pred cCCCCEEEEEecCCCCCCCCCcEEEEEEEEE--CCcee-eeecCCceeecCC--ccchhhhhhHHhhhhhhcCCcHH-HH
Q 027892 34 EYKMPLVWIDLEMTGLKIEVDRILEIACIIT--DGKLT-KSVEGPDLVIHQT--KECLDSMGEWCQNHHEASGLTKK-VL 107 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~~d~IieIgav~~--d~~~~-~~~~~~~~li~p~--~~i~~~~~~~~~~~h~itGIt~~-~l 107 (217)
+....++++|+||||++|.+|+|||||+|.+ +++.. ...+.|+.+++|. .+++. .+. .+||||++ ++
T Consensus 5 ~~~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~----~a~---~ihGIt~~~~~ 77 (200)
T TIGR01298 5 FRGYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQP----EAL---EFTGIDLDHPL 77 (200)
T ss_pred hcCCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCH----HHH---HccCCChhhhh
Confidence 4567899999999999999999999999943 22222 2245689999984 45543 233 67899975 68
Q ss_pred hcCCCHHHHHHHHHHHHhhccC---CCCceEEEecHHHhHHHHHhHhhhhhcC---C-CCceeehHHHHHHHHHhCCCcc
Q 027892 108 HSGLTEREAEKQVVEFVKKNVG---TYTPLLAGNSVYVDFMFLKKYMPDLASL---F-SHVLVDVSSIKALCMRWYPRDY 180 (217)
Q Consensus 108 ~~~~~~~e~~~~~~~~l~~~~~---~~~~~lVghn~~FD~~fL~~~~~~~~~~---~-~~~~iDt~~l~~la~~~~p~~~ 180 (217)
.+++++++++.++.+|+.+... .+..++||||++||..||++++.+++.. + +..++||. ++++..+|...
T Consensus 78 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl---~lar~~~~~~~ 154 (200)
T TIGR01298 78 RGAVSEYEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTA---TLAGLAYGQTV 154 (200)
T ss_pred hcCcchHHHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHH---HHHHHHcCccc
Confidence 9999999999999999853321 0125799999999999999999887642 2 34689998 56666665432
Q ss_pred ------cCCCC--CCCCCChHHHHHHHHHHHHHHHHHhc
Q 027892 181 ------RKVPS--KEQKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 181 ------~~~l~--~~~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
.++++ ..++|||++||.+|++|+..+.+.+-
T Consensus 155 L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 155 LAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred HHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 23555 35899999999999999999877653
No 22
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.97 E-value=8.2e-29 Score=195.76 Aligned_cols=156 Identities=29% Similarity=0.359 Sum_probs=124.8
Q ss_pred CEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHH
Q 027892 38 PLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 117 (217)
Q Consensus 38 ~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~ 117 (217)
.||++|+||||+++..++|||||+|.++++. +.+.|+.+|+|..++ +++++ .+||||++++.+++++.+++
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 4899999999999999999999999766553 345689999997655 34555 67799999999999999999
Q ss_pred HHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhcC--CCCceeehHHHHHHHHHhCCCcc--------cCCCCC
Q 027892 118 KQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASL--FSHVLVDVSSIKALCMRWYPRDY--------RKVPSK 186 (217)
Q Consensus 118 ~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~--~~~~~iDt~~l~~la~~~~p~~~--------~~~l~~ 186 (217)
.+|.+|+++. ++|+||. .||+.||++++.+.+.. ...+++|+. .+++...+... .++++.
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 4667776 99999999999887753 335689997 45555554321 134555
Q ss_pred CCC-CChHHHHHHHHHHHHHHHHHhc
Q 027892 187 EQK-HRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 187 ~~~-H~Al~Da~at~~ll~~~~~~~~ 211 (217)
.++ |+|++||++|++|++.+++.++
T Consensus 143 ~~~~H~A~~Da~~t~~l~~~~~~~~~ 168 (169)
T smart00479 143 IGRAHRALDDARATAKLFKKLVERLL 168 (169)
T ss_pred CCCCcCcHHHHHHHHHHHHHHHHHhh
Confidence 555 9999999999999999988775
No 23
>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=99.97 E-value=2.7e-29 Score=202.95 Aligned_cols=155 Identities=21% Similarity=0.242 Sum_probs=117.7
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhc-CCCHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS-GLTEREAEK 118 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~-~~~~~e~~~ 118 (217)
+++|+||||++|.+|+|||||+|.++++...+ +.|+.+++|....+. .+.+. .+||||++++.+ +|++.+++.
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~-~~~~~~v~p~~~~~~--~~~a~---~ihGIt~e~l~~~~~~~~~~l~ 74 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEI-EPFNIFCRLPPDVLP--SPEAL---IVTGITPQQLLKEGLSEYEFIA 74 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCc-cceeEEEeCCCCCCC--CHHHH---HHhCCCHHHHHhcCCCHHHHHH
Confidence 48999999999999999999999777654444 678999998753211 22233 567999999998 899999999
Q ss_pred HHHHHHhhccCCCCceEEEec-HHHhHHHHHhHhhhhhc-CC------CCceeehHHHHHHHHHhCCC----------cc
Q 027892 119 QVVEFVKKNVGTYTPLLAGNS-VYVDFMFLKKYMPDLAS-LF------SHVLVDVSSIKALCMRWYPR----------DY 180 (217)
Q Consensus 119 ~~~~~l~~~~~~~~~~lVghn-~~FD~~fL~~~~~~~~~-~~------~~~~iDt~~l~~la~~~~p~----------~~ 180 (217)
+|.+|+++. ..++|||| +.||..||++++.+.+. ++ ++..+|+..+.++.+.+.|. ..
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 999999631 13588986 89999999999977653 22 23468988666555443331 11
Q ss_pred c---------CCCCCCCCCChHHHHHHHHHHHH
Q 027892 181 R---------KVPSKEQKHRALDDIRESIMELK 204 (217)
Q Consensus 181 ~---------~~l~~~~~H~Al~Da~at~~ll~ 204 (217)
+ ++++..++|||++||++|++|++
T Consensus 151 ~~~L~~l~~~~gi~~~~~H~Al~Da~~ta~l~~ 183 (183)
T cd06138 151 SFKLEDLAQANGIEHSNAHDALSDVEATIALAK 183 (183)
T ss_pred chhHHHHHHHCCCCccccccHHHHHHHHHHHhC
Confidence 1 35778899999999999999874
No 24
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.96 E-value=1.2e-28 Score=193.07 Aligned_cols=145 Identities=17% Similarity=0.100 Sum_probs=116.5
Q ss_pred EEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHH
Q 027892 39 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEK 118 (217)
Q Consensus 39 ~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~ 118 (217)
||++|+||||.+ .++|||||+|.+++... .++|+.+|+|+.++++ .++ .+||||++++.+++++.++++
T Consensus 1 ~v~~D~Ettg~~--~~~ii~ig~v~~~~~~~--~~~~~~~i~p~~~~~~----~~~---~i~GIt~e~l~~~~~~~~v~~ 69 (156)
T cd06130 1 FVAIDFETANAD--RASACSIGLVKVRDGQI--VDTFYTLIRPPTRFDP----FNI---AIHGITPEDVADAPTFPEVWP 69 (156)
T ss_pred CEEEEEeCCCCC--CCceEEEEEEEEECCEE--EEEEEEEeCcCCCCCh----hhc---cccCcCHHHHhcCCCHHHHHH
Confidence 689999999976 58999999995544322 3468999999986643 334 678999999999999999999
Q ss_pred HHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcC-CCCceeehHHHHHHHHHhCCCccc---------CCCCCCC
Q 027892 119 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYR---------KVPSKEQ 188 (217)
Q Consensus 119 ~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~-~~~~~iDt~~l~~la~~~~p~~~~---------~~l~~~~ 188 (217)
+|.+|+++ .++||||++||+.||++++.+.|.. .+.+.+|+. .+++..++.... .+++..
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 4699999999999999999888753 456799997 455555554322 256666
Q ss_pred CCChHHHHHHHHHHHH
Q 027892 189 KHRALDDIRESIMELK 204 (217)
Q Consensus 189 ~H~Al~Da~at~~ll~ 204 (217)
+|+|++||++|++|+-
T Consensus 140 ~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 140 HHDALEDARACAEILL 155 (156)
T ss_pred CcCchHHHHHHHHHHh
Confidence 9999999999999874
No 25
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.1e-28 Score=237.67 Aligned_cols=158 Identities=15% Similarity=0.185 Sum_probs=133.0
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEE-ECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACII-TDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~-~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
...+||++|+||||+++ +|+|||||||. .++.. .+.|+.+|+|..++++. ++ .+||||++++.++|++
T Consensus 5 ~~~~~vvvD~ETTGl~~-~d~IIeIgaV~v~~g~i---~~~f~~lv~P~~~i~~~----~~---~ltGIt~e~l~~ap~~ 73 (820)
T PRK07246 5 KLRKYAVVDLEATGAGP-NASIIQVGIVIIEGGEI---IDSYTTDVNPHEPLDEH----IK---HLTGITDQQLAQAPDF 73 (820)
T ss_pred cCCCEEEEEEecCCcCC-CCeEEEEEEEEEECCEE---EEEEEEEeCcCCCCCHh----Hh---hcCCCCHHHHhcCCCH
Confidence 45789999999999997 59999999994 44433 34689999999887643 33 7889999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcccC---------CC
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRK---------VP 184 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~~---------~l 184 (217)
++++++|.+|+++ .++||||+.||+.||++++.+.+..+.++.+||. ++++.++|...++ ++
T Consensus 74 ~ev~~~~~~~l~~------~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~---~la~~~~p~~~~~~L~~L~~~lgl 144 (820)
T PRK07246 74 SQVARHIYDLIED------CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTV---ELAQVFFPTLEKYSLSHLSRELNI 144 (820)
T ss_pred HHHHHHHHHHhCC------CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHH---HHHHHHhCCCCCCCHHHHHHHcCC
Confidence 9999999999988 4699999999999999998777766677889997 6778888865443 56
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 185 SKEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 185 ~~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
+..++|||++||++|++|+..+.+.+..
T Consensus 145 ~~~~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 145 DLADAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 7788999999999999999998877643
No 26
>PRK07883 hypothetical protein; Validated
Probab=99.96 E-value=1.8e-28 Score=227.47 Aligned_cols=160 Identities=20% Similarity=0.198 Sum_probs=132.4
Q ss_pred cCCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 34 EYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
.....||+||+||||++|..++|||||||.+++... + +.|+.+|+|..++++. ++ .+||||++++.++|++
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~i-v-~~f~~lV~P~~~i~~~----~~---~itGIt~e~l~~ap~~ 82 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEV-L-GEFATLVNPGRPIPPF----IT---VLTGITTAMVAGAPPI 82 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEE-E-EEEEEEECCCCCCChh----HH---hhcCCCHHHHhCCCCH
Confidence 456899999999999999999999999996544322 2 3589999998877543 33 7889999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCC-CceeehHHHHHHHHHhCC--Cccc---------
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRWYP--RDYR--------- 181 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-~~~iDt~~l~~la~~~~p--~~~~--------- 181 (217)
.+++.+|.+|+++ .++||||+.||+.||++++.+.|.+++ +.++||. .+++++.| ....
T Consensus 83 ~evl~~f~~fl~~------~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl---~lar~l~~~~~~~~~~L~~L~~~ 153 (557)
T PRK07883 83 EEVLPAFLEFARG------AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTV---RLARRVLPRDEAPNVRLSTLARL 153 (557)
T ss_pred HHHHHHHHHHhcC------CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecH---HHHHHhcccCCCCCCCHHHHHHH
Confidence 9999999999987 468999999999999999998886554 5789997 56677665 2222
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHHhc
Q 027892 182 KVPSKEQKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 182 ~~l~~~~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
.+++..++|+|++||.+|++|+..+.+.+.
T Consensus 154 ~gi~~~~~H~Al~DA~ata~l~~~l~~~~~ 183 (557)
T PRK07883 154 FGATTTPTHRALDDARATVDVLHGLIERLG 183 (557)
T ss_pred CCcccCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 256778899999999999999999877764
No 27
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.96 E-value=1.8e-28 Score=201.71 Aligned_cols=160 Identities=17% Similarity=0.193 Sum_probs=119.9
Q ss_pred CCCCEEEEEecCCCCCCC------CCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 35 YKMPLVWIDLEMTGLKIE------VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~------~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
.+.+||+||+||||+++. .++|||||||.+++.. +.+.|+.+|+|... +.+++.++ ++||||++++.
T Consensus 2 ~~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~--i~~~f~~lV~P~~~--~~i~~~~~---~ltGIt~~~l~ 74 (207)
T PRK07748 2 DEQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCE--VEDTFSSYVKPKTF--PSLTERCK---SFLGITQEDVD 74 (207)
T ss_pred CcceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCc--ChhhhcceECCCcc--CccChhhh---hhcCcCHHHHc
Confidence 356899999999998753 3799999999554432 23579999999862 11234455 77899999999
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCC--CceeehHHHHHHHHHhCCCcc------
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS--HVLVDVSSIKALCMRWYPRDY------ 180 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~--~~~iDt~~l~~la~~~~p~~~------ 180 (217)
++|++.+++++|.+|+++. ..+++||..||+.||++++.+.+..++ ..++|+. .+.+++++...
T Consensus 75 ~ap~~~evl~~f~~~~~~~-----~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~---~~~~~~~~~~~~~~L~~ 146 (207)
T PRK07748 75 KGISFEELVEKLAEYDKRC-----KPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLS---LEYKKFFGERNQTGLWK 146 (207)
T ss_pred cCCCHHHHHHHHHHHhCcC-----CeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHH---HHHHHHhCcCCCCCHHH
Confidence 9999999999999999872 124445679999999999988775433 4578876 33344443221
Q ss_pred ---cCCCCC-CCCCChHHHHHHHHHHHHHHHHH
Q 027892 181 ---RKVPSK-EQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 181 ---~~~l~~-~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
.++++. ..+|||++||++|++|++.+.+.
T Consensus 147 ~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 147 AIEEYGKEGTGKHHCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred HHHHcCCCCCCCCcChHHHHHHHHHHHHHHHhC
Confidence 235664 46899999999999999998766
No 28
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.96 E-value=8.4e-30 Score=242.77 Aligned_cols=157 Identities=21% Similarity=0.317 Sum_probs=138.7
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
....|||||+|||||+|..++||||||+ +.+|+.. +.|+.+|+|.++++..+ + ++||||++||.+++++
T Consensus 419 ~datyVVfDiETTGLs~~~d~iIE~aAvKikng~iI---d~f~~Fi~P~~pl~~~~----t---elTgITdeml~~a~~i 488 (1444)
T COG2176 419 DDATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRII---DKFQFFIKPGRPLSATI----T---ELTGITDEMLENAPEI 488 (1444)
T ss_pred ccccEEEEEeecCCcCcccchhhhheeeeeeCCcch---HHHHHhcCCCCcCchhh----h---hccccCHHHHcCCccH
Confidence 4567999999999999999999999999 6666653 46899999999986543 3 8999999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhh-cCCCCceeehHHHHHHHHHhCCCcccCC---------
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLA-SLFSHVLVDVSSIKALCMRWYPRDYRKV--------- 183 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~-~~~~~~~iDt~~l~~la~~~~p~~~~~~--------- 183 (217)
++|+.+|.+|+++ +++|+||++||..||+..+.+++ .++.+++|||+ +++|.++|.+.+++
T Consensus 489 ~~vL~kf~~~~~d------~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL---~lar~L~P~~ksh~Lg~l~kk~~ 559 (1444)
T COG2176 489 EEVLEKFREFIGD------SILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTL---ELARALNPEFKSHRLGTLCKKLG 559 (1444)
T ss_pred HHHHHHHHHHhcC------cEEEeccCccchhHHHHHHHHhCCccccCchhhHH---HHHHHhChhhhhcchHHHHHHhC
Confidence 9999999999999 68999999999999999998776 47788999998 88999999887663
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 184 PSKEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 184 l~~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
+....+|||..|+.||+.|+..+.+.+
T Consensus 560 v~le~hHRA~yDaeat~~vf~~f~~~~ 586 (1444)
T COG2176 560 VELERHHRADYDAEATAKVFFVFLKDL 586 (1444)
T ss_pred ccHHHhhhhhhhHHHHHHHHHHHHHHH
Confidence 466889999999999999999887764
No 29
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=3.2e-28 Score=212.41 Aligned_cols=154 Identities=14% Similarity=0.063 Sum_probs=124.6
Q ss_pred cCCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 34 EYKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
+...+||+||+|||||+|..|+|||||||.+..+.. +.+.|+.+|+|+....+ . .+||||+++++++|.|
T Consensus 43 ~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~-ive~f~tLVnP~~~~~p--~-------~LHGIT~e~La~AP~f 112 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGE-EVEHFHAVLNPGEDPGP--F-------HLHGLSAEEFAQGKRF 112 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCE-EEEEEEEEECcCCCCCC--c-------cccCCCHHHHhcCCCH
Confidence 455789999999999999999999999995432222 23569999999875321 1 4779999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhh----------------------------hcCCCCceeeh
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDL----------------------------ASLFSHVLVDV 165 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~----------------------------~~~~~~~~iDt 165 (217)
.+++++|.+|+++ .+|||||+.||+.||.+++.+. +.+.+..++||
T Consensus 113 ~eVl~el~~fL~g------~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDT 186 (377)
T PRK05601 113 SQILKPLDRLIDG------RTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDT 186 (377)
T ss_pred HHHHHHHHHHhCC------CEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEh
Confidence 9999999999998 4699999999999999987553 12455679999
Q ss_pred HHHHHHHHHhCCCcccC---------CCCC----------CCCCChH--HHHHHHHHHHHHH
Q 027892 166 SSIKALCMRWYPRDYRK---------VPSK----------EQKHRAL--DDIRESIMELKYY 206 (217)
Q Consensus 166 ~~l~~la~~~~p~~~~~---------~l~~----------~~~H~Al--~Da~at~~ll~~~ 206 (217)
+ +++|+.+|.+.++ +++. ...|+|| +|++.+++|+...
T Consensus 187 L---~LARrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 187 L---ATARRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred H---HHHHHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 7 7889888876543 4454 6778998 6999999999775
No 30
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4.1e-28 Score=210.79 Aligned_cols=153 Identities=15% Similarity=0.168 Sum_probs=122.8
Q ss_pred CCEEEEEecCCCCCCCCCcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHH
Q 027892 37 MPLVWIDLEMTGLKIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 115 (217)
Q Consensus 37 ~~~v~lD~ETTGl~p~~d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e 115 (217)
++||+||+||||. .+|+|||||+|.+ ++... +.|+++|+|.... +.+.++ .+||||+++++++|++.+
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 4799999999985 5689999999954 44332 4589999997521 122333 678999999999999999
Q ss_pred HHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCC-CceeehHHHHHHHHHhCCCcccC---------CCC
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRWYPRDYRK---------VPS 185 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~-~~~iDt~~l~~la~~~~p~~~~~---------~l~ 185 (217)
++.+|.+|+++ .++||||++||+.||++++.+++.+++ .+++||. +++++++|...++ +++
T Consensus 70 v~~~~~~fl~~------~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~---~lar~l~~~~~~~~L~~L~~~~gi~ 140 (309)
T PRK06195 70 IWEKIKHYFNN------NLVIAHNASFDISVLRKTLELYNIPMPSFEYICTM---KLAKNFYSNIDNARLNTVNNFLGYE 140 (309)
T ss_pred HHHHHHHHhCC------CEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHH---HHHHHHcCCCCcCCHHHHHHHcCCC
Confidence 99999999987 469999999999999999988876543 5799997 6778887765433 445
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 186 KEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 186 ~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
..+|||++||++|++|+..+.+.+
T Consensus 141 -~~~H~Al~DA~ata~l~~~l~~~~ 164 (309)
T PRK06195 141 -FKHHDALADAMACSNILLNISKEL 164 (309)
T ss_pred -CcccCCHHHHHHHHHHHHHHHHHh
Confidence 369999999999999998887654
No 31
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=8.9e-28 Score=234.36 Aligned_cols=158 Identities=18% Similarity=0.256 Sum_probs=133.2
Q ss_pred CCCEEEEEecCCCCCCCC-CcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 36 KMPLVWIDLEMTGLKIEV-DRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~~-d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
..+||++|+||||++|.. ++|||||+|.+ ++.. .+.|+.+|+|..++++. +. .+||||++++.++|++
T Consensus 2 ~~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i---~~~f~~~v~P~~~i~~~----~~---~ltGIt~~~l~~ap~f 71 (928)
T PRK08074 2 SKRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEI---LERFSSFVNPERPIPPF----IT---ELTGISEEMVKQAPLF 71 (928)
T ss_pred CCCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEE---EEEEEEEECcCCCCCHH----Hh---hcCCCCHHHHhcCCCH
Confidence 468999999999999875 89999999954 4433 34689999999887653 33 7889999999999999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc-CCCCceeehHHHHHHHHHhCCCcccC---------C
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDYRK---------V 183 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iDt~~l~~la~~~~p~~~~~---------~ 183 (217)
.+++.+|.+|+++ .++||||+.||++||++++.+.|. +++.+++||. ++++..+|...++ +
T Consensus 72 ~ev~~~l~~~l~~------~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~---~la~~~~p~~~~~~L~~l~~~l~ 142 (928)
T PRK08074 72 EDVAPEIVELLEG------AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTV---ELARILLPTAESYKLRDLSEELG 142 (928)
T ss_pred HHHHHHHHHHhCC------CeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHH---HHHHHhcCCCCCCCHHHHHHhCC
Confidence 9999999999987 469999999999999999988875 3556899997 6777778865543 4
Q ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 184 PSKEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 184 l~~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
++..++|||++||.+|++|+..+.+.+..
T Consensus 143 i~~~~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 143 LEHDQPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred CCCCCCCChHHHHHHHHHHHHHHHHHHHh
Confidence 67889999999999999999999887653
No 32
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4.5e-28 Score=197.46 Aligned_cols=153 Identities=18% Similarity=0.140 Sum_probs=114.2
Q ss_pred CCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHH
Q 027892 36 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 115 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e 115 (217)
..+||++|+||||+++ +++|||||||.+++... .+.|+.+|+|..+++... + .+||||+++++++|++.+
T Consensus 4 ~~~~vvlD~EtTGl~~-~~eIIeIgaV~v~~g~~--~~~f~~lv~P~~~i~~~~----~---~lhGIt~~~v~~ap~~~e 73 (195)
T PRK07247 4 LETYIAFDLEFNTVNG-VSHIIQVSAVKYDDHKE--VDSFDSYVYTDVPLQSFI----N---GLTGITADKIADAPKVEE 73 (195)
T ss_pred CCeEEEEEeeCCCCCC-CCeEEEEEEEEEECCEE--EEEEEEEECCCCCCCccc----e---ecCCCCHHHHhCCCCHHH
Confidence 3589999999999985 68999999995443322 235889999988775433 3 788999999999999999
Q ss_pred HHHHHHHHHhhccCCCCceEEEecHH-HhHHHHHhHhhhhhcCCC-CceeehHHHHHHHHHh--CCCccc---------C
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSVY-VDFMFLKKYMPDLASLFS-HVLVDVSSIKALCMRW--YPRDYR---------K 182 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~~-FD~~fL~~~~~~~~~~~~-~~~iDt~~l~~la~~~--~p~~~~---------~ 182 (217)
++++|.+|+++ .++||||+. ||+.||++.. ..+. ...+|+.... +.++. .|...+ .
T Consensus 74 vl~~f~~f~~~------~~lVaHNa~~fD~~fL~~~g----~~~~~~~~idt~~~~-~~~~~~~~~~~~~~~L~~La~~~ 142 (195)
T PRK07247 74 VLAAFKEFVGE------LPLIGYNAQKSDLPILAENG----LDLSDQYQVDLYDEA-FERRSSDLNGIANLKLQTVADFL 142 (195)
T ss_pred HHHHHHHHHCC------CeEEEEeCcHhHHHHHHHcC----CCcCCCceeehHHHH-HHhhccccCCCCCCCHHHHHHhc
Confidence 99999999988 358999996 8999998642 2222 2356765221 23332 233332 2
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 027892 183 VPSKEQKHRALDDIRESIMELKYYKENI 210 (217)
Q Consensus 183 ~l~~~~~H~Al~Da~at~~ll~~~~~~~ 210 (217)
+++. .+|||++||++|+++++.+.+..
T Consensus 143 gi~~-~~HrAl~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 143 GIKG-RGHNSLEDARMTARVYESFLESD 169 (195)
T ss_pred CCCC-CCcCCHHHHHHHHHHHHHHHhhc
Confidence 4564 68999999999999999887653
No 33
>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=99.96 E-value=9.5e-29 Score=195.89 Aligned_cols=136 Identities=20% Similarity=0.216 Sum_probs=107.1
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCC------
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT------ 112 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~------ 112 (217)
|++|+||||++|..++|||||+|.+ ++... |+.+|+|+.+++++. + .+||||+++++++|+
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-----IDSLVRPSVRVTDWR----T---RFSGVTPADLEEAAKAGKTIF 68 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEE-----EeccccCCCCCCccc----e---eccCCCHHHHhhhhhcCCccc
Confidence 5899999999999999999999955 55542 567999998776433 3 778999999998874
Q ss_pred -HHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCc---cc-------
Q 027892 113 -EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRD---YR------- 181 (217)
Q Consensus 113 -~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~---~~------- 181 (217)
+++++++|.+|+++. .+|||||+.||+.||+.. +.+++||. .+++++.|.. .+
T Consensus 69 ~~~~~~~~~~~~i~~~-----~vlVgHn~~fD~~fL~~~--------~~~~iDT~---~l~~~~~~~~~~~~~~~L~~L~ 132 (161)
T cd06137 69 GWEAARAALWKFIDPD-----TILVGHSLQNDLDALRMI--------HTRVVDTA---ILTREAVKGPLAKRQWSLRTLC 132 (161)
T ss_pred cHHHHHHHHHHhcCCC-----cEEEeccHHHHHHHHhCc--------CCCeeEeh---hhhhhccCCCcCCCCccHHHHH
Confidence 458999999999862 469999999999999862 45789998 5666665543 11
Q ss_pred ---CCCCC---CCCCChHHHHHHHHHHH
Q 027892 182 ---KVPSK---EQKHRALDDIRESIMEL 203 (217)
Q Consensus 182 ---~~l~~---~~~H~Al~Da~at~~ll 203 (217)
++++. ..+|+|++||++|++|+
T Consensus 133 ~~~~~~~~~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 133 RDFLGLKIQGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred HHHCCchhcCCCCCCCcHHHHHHHHHHh
Confidence 23332 56899999999999986
No 34
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.96 E-value=1.1e-27 Score=185.79 Aligned_cols=147 Identities=26% Similarity=0.323 Sum_probs=119.3
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 119 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~~ 119 (217)
|++|+||||++|..++|||||++.++.+.. ..+.|+.+|+|+..+.+ .++ .++||+++++.+++++.+++.+
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~-~~~~~~~~i~p~~~~~~----~~~---~~~gi~~~~~~~~~~~~~~~~~ 72 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIE-IVERFETLVNPGRPIPP----EAT---AIHGITDEMLADAPPFEEVLPE 72 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcC-hhhhhheeeCcCCcCCH----hhe---eccCCCHHHHhcCCCHHHHHHH
Confidence 589999999999999999999997766532 34568999999876643 333 5689999999999999999999
Q ss_pred HHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhh-cCCCCceeehHHHHHHHHHhCCCcc----------cCCCCCCC
Q 027892 120 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLA-SLFSHVLVDVSSIKALCMRWYPRDY----------RKVPSKEQ 188 (217)
Q Consensus 120 ~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~-~~~~~~~iDt~~l~~la~~~~p~~~----------~~~l~~~~ 188 (217)
|.+|+++ .++||||+.||..||++.+.+++ .+++.+++|+.. +.+.+++... ..+.+...
T Consensus 73 ~~~~l~~------~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~---~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 143 (159)
T cd06127 73 FLEFLGG------RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLR---LARRLLPGLRSHRLGLLLAERYGIPLEG 143 (159)
T ss_pred HHHHHCC------CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHH---HHHHHcCCCCcCchHHHHHHHcCCCCCC
Confidence 9999987 46999999999999999998776 356678999984 4444443221 12456789
Q ss_pred CCChHHHHHHHHHHH
Q 027892 189 KHRALDDIRESIMEL 203 (217)
Q Consensus 189 ~H~Al~Da~at~~ll 203 (217)
+|+|++||++|++++
T Consensus 144 ~H~Al~Da~~t~~l~ 158 (159)
T cd06127 144 AHRALADALATAELL 158 (159)
T ss_pred CCCcHHHHHHHHHHh
Confidence 999999999999987
No 35
>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=99.95 E-value=1.4e-27 Score=235.41 Aligned_cols=161 Identities=19% Similarity=0.257 Sum_probs=134.4
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
...+||+||+||||++|..++|||||||.+++.. . .+.|+.+|+|..++++ .++ ++||||++++.++|++.
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~-i-id~f~~~V~P~~~I~~----~~~---~ltGIT~e~L~~ap~~~ 258 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGR-I-IDKFQFFIKPHEPLSA----FVT---ELTGITQDMLENAPEIE 258 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCe-E-EEEEEEEECCCCCCCH----HHH---HHhCCCHHHHhCCCCHH
Confidence 3569999999999999999999999999544332 2 2468999999987754 333 78899999999999999
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc-CCCCceeehHHHHHHHHHhCCCccc---------CCC
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDYR---------KVP 184 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iDt~~l~~la~~~~p~~~~---------~~l 184 (217)
+++++|.+|+++ .++||||+.||+.||++.+.+++. +++++++||+ .+++.+.|.... .++
T Consensus 259 evl~~f~~fl~~------~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl---~lar~l~p~~k~~kL~~Lak~lgi 329 (1213)
T TIGR01405 259 EVLEKFKEFFKD------SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTL---ELARALNPEYKSHRLGNICKKLGV 329 (1213)
T ss_pred HHHHHHHHHhCC------CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHH---HHHHHHhccCCCCCHHHHHHHcCC
Confidence 999999999988 469999999999999999988874 4677899997 567777765543 256
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhccc
Q 027892 185 SKEQKHRALDDIRESIMELKYYKENIFKT 213 (217)
Q Consensus 185 ~~~~~H~Al~Da~at~~ll~~~~~~~~~~ 213 (217)
+..++|||++||.+|++++..+.+.+...
T Consensus 330 ~~~~~HrAl~DA~aTa~I~~~ll~~l~~~ 358 (1213)
T TIGR01405 330 DLDDHHRADYDAEATAKVFKVMVEQLKEK 358 (1213)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHHHHHHc
Confidence 77789999999999999999998776543
No 36
>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=99.95 E-value=2.6e-28 Score=192.65 Aligned_cols=140 Identities=24% Similarity=0.300 Sum_probs=108.8
Q ss_pred EEEEecCCCCCCC--CCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHH
Q 027892 40 VWIDLEMTGLKIE--VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 117 (217)
Q Consensus 40 v~lD~ETTGl~p~--~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~ 117 (217)
|++|+||||++|. .++|++||+|..+|... |+.+|+|..++++. .+ .+||||+++++++|++++++
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~-----~~~lv~P~~~i~~~----~~---~i~GIt~~~l~~a~~~~~v~ 68 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVL-----YDKYIRPEGPVTDY----RT---RWSGIRRQHLVNATPFAVAQ 68 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEE-----EEEeECCCCccCcc----ce---ECCCCCHHHHhcCCCHHHHH
Confidence 5899999999997 47888888886566542 67899999887543 33 67899999999999999999
Q ss_pred HHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHh--CCCcccC------------C
Q 027892 118 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRW--YPRDYRK------------V 183 (217)
Q Consensus 118 ~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~--~p~~~~~------------~ 183 (217)
++|.+|+++ .++||||+.||+.||+... .+..++||..+. +.++. +|...++ +
T Consensus 69 ~~l~~~l~~------~vlV~Hn~~~D~~~l~~~~------~~~~~~Dt~~l~-~~~~~~~~p~~~~~~L~~L~~~~~~~~ 135 (157)
T cd06149 69 KEILKILKG------KVVVGHAIHNDFKALKYFH------PKHMTRDTSTIP-LLNRKAGFPENCRVSLKVLAKRLLHRD 135 (157)
T ss_pred HHHHHHcCC------CEEEEeCcHHHHHHhcccC------CCcCEEECcccc-cchhhcCCcccCChhHHHHHHHHcChh
Confidence 999999988 4799999999999999652 234578887553 33332 5543322 2
Q ss_pred CCC-CCCCChHHHHHHHHHHHH
Q 027892 184 PSK-EQKHRALDDIRESIMELK 204 (217)
Q Consensus 184 l~~-~~~H~Al~Da~at~~ll~ 204 (217)
++. ..+|||++||++|++|+|
T Consensus 136 i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 136 IQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred hcCCCCCcCcHHHHHHHHHHhC
Confidence 343 568999999999999985
No 37
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.95 E-value=1.6e-27 Score=231.16 Aligned_cols=155 Identities=20% Similarity=0.333 Sum_probs=130.6
Q ss_pred CEEEEEecCCCCCCCCCcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHH
Q 027892 38 PLVWIDLEMTGLKIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 116 (217)
Q Consensus 38 ~~v~lD~ETTGl~p~~d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~ 116 (217)
+||++|+||||++|..++|||||+|.+ ++.. .+.|+.+|+|..++++.+ + .+||||++++.++|.++++
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i---~~~f~~~v~P~~~i~~~~----~---~ltGIt~e~l~~ap~~~ev 70 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEI---VDTFHTDVNPNEPIPPFI----Q---ELTGISDNMLQQAPYFSQV 70 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEE---EEEEEEEeCCCCCCChhh----h---hhcCcCHHHHhCCCCHHHH
Confidence 489999999999999999999999955 4432 246899999998776433 3 7889999999999999999
Q ss_pred HHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcC-CCCceeehHHHHHHHHHhCCCcccC---------CCCC
Q 027892 117 EKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL-FSHVLVDVSSIKALCMRWYPRDYRK---------VPSK 186 (217)
Q Consensus 117 ~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~-~~~~~iDt~~l~~la~~~~p~~~~~---------~l~~ 186 (217)
+.+|.+|+++ .++||||+.||+.||++++.+.|.+ ++.+.+||. .+++.++|...++ +++.
T Consensus 71 ~~~l~~~l~~------~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~---~l~~~~~p~~~~~~L~~l~~~~gi~~ 141 (850)
T TIGR01407 71 AQEIYDLLED------GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTV---ELAQIFFPTEESYQLSELSEALGLTH 141 (850)
T ss_pred HHHHHHHhCC------CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHH---HHHHHhcCCCCCCCHHHHHHHCCCCC
Confidence 9999999987 4699999999999999999888754 677899997 5667777754433 5677
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHhc
Q 027892 187 EQKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 187 ~~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
.++|||++||.+|++|+..+.+.+-
T Consensus 142 ~~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 142 ENPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999977653
No 38
>PRK06722 exonuclease; Provisional
Probab=99.95 E-value=1.9e-27 Score=202.85 Aligned_cols=155 Identities=14% Similarity=0.103 Sum_probs=117.1
Q ss_pred CCCCEEEEEecCCCCCCC----CCcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhc
Q 027892 35 YKMPLVWIDLEMTGLKIE----VDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS 109 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~----~d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~ 109 (217)
+...|||||+|||| +|. .++|||||||.+ ++.+.. .+.|+.+|+|..+++ .+++ .+||||++|+.+
T Consensus 3 ~~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~I-vd~F~sLV~P~~~I~----~~i~---~LTGIT~emV~~ 73 (281)
T PRK06722 3 NATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKV-IGEFSELVKPGARLT----RHTT---KLTGITKKDLIG 73 (281)
T ss_pred CCCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeE-EeeEEEEECCCCcCC----HhHh---hhcCCCHHHHcC
Confidence 45789999999995 443 389999999954 454333 356999999997764 4455 788999999999
Q ss_pred CCCHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCC----CceeehHHHHHHHHHhCCCc------
Q 027892 110 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFS----HVLVDVSSIKALCMRWYPRD------ 179 (217)
Q Consensus 110 ~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~----~~~iDt~~l~~la~~~~p~~------ 179 (217)
+|++.+++.+|.+|+++. + +|+||+.||+.||++++.+.|...+ .+++|+. ++++..++..
T Consensus 74 AP~f~eVl~ef~~fig~~-----~-lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~---~la~~~~~~l~~~~~s 144 (281)
T PRK06722 74 VEKFPQIIEKFIQFIGED-----S-IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQ---KFVFQAYEELFEHTPS 144 (281)
T ss_pred CCCHHHHHHHHHHHHCCC-----c-EEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHH---HHHHHHhhhhccCCCC
Confidence 999999999999999873 3 5677789999999999988775433 2357776 3333322221
Q ss_pred -c----cCCCCC-CCCCChHHHHHHHHHHHHHHH
Q 027892 180 -Y----RKVPSK-EQKHRALDDIRESIMELKYYK 207 (217)
Q Consensus 180 -~----~~~l~~-~~~H~Al~Da~at~~ll~~~~ 207 (217)
. ..+++. +.+|||++||.+|++|+..+.
T Consensus 145 L~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 145 LQSAVEQLGLIWEGKQHRALADAENTANILLKAY 178 (281)
T ss_pred HHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHh
Confidence 1 235664 569999999999999998775
No 39
>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=99.95 E-value=3.5e-27 Score=188.07 Aligned_cols=154 Identities=21% Similarity=0.214 Sum_probs=118.5
Q ss_pred EEEEEecCCCCCCCC-----CcEEEEEEEEECCceeeeecCCceeecCCc--cchhhhhhHHhhhhhhcCCcHHHHhcCC
Q 027892 39 LVWIDLEMTGLKIEV-----DRILEIACIITDGKLTKSVEGPDLVIHQTK--ECLDSMGEWCQNHHEASGLTKKVLHSGL 111 (217)
Q Consensus 39 ~v~lD~ETTGl~p~~-----d~IieIgav~~d~~~~~~~~~~~~li~p~~--~i~~~~~~~~~~~h~itGIt~~~l~~~~ 111 (217)
||++|+||||+++.+ ++|||||||.++++.....+.|+.+|+|.. .+ ++++. .+||||++++.++|
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i----~~~~~---~i~gIt~e~l~~~~ 73 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKL----SDFCT---ELTGITQEDVDNAP 73 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCch----hHHHH---HhcCcCHHHHhcCC
Confidence 689999999999875 999999999776655434567999999987 44 34445 67899999999999
Q ss_pred CHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc----CCCCceeehHHHHHHHHHhCCCcc-------
Q 027892 112 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS----LFSHVLVDVSSIKALCMRWYPRDY------- 180 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~----~~~~~~iDt~~l~~la~~~~p~~~------- 180 (217)
++.+|+.+|.+|+++.. + .+++||..||..+|.+++.+.+. ++..+++|+..+. ++..+...
T Consensus 74 ~~~~vl~~~~~~l~~~~---~-~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~---~~~~~~~~~~~L~~l 146 (176)
T cd06133 74 SFPEVLKEFLEWLGKNG---K-YAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEF---AKFYGLKKRTGLSKA 146 (176)
T ss_pred CHHHHHHHHHHHHHhCC---C-eEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHH---HHHhCCCCCCCHHHH
Confidence 99999999999999831 1 34555669999998888765542 3556799998544 44444321
Q ss_pred --cCCCCCC-CCCChHHHHHHHHHHHHHH
Q 027892 181 --RKVPSKE-QKHRALDDIRESIMELKYY 206 (217)
Q Consensus 181 --~~~l~~~-~~H~Al~Da~at~~ll~~~ 206 (217)
.++++.. ..|+|++||++|+++++.+
T Consensus 147 ~~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 147 LEYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred HHHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 1356655 8999999999999999875
No 40
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.95 E-value=5.9e-27 Score=194.10 Aligned_cols=138 Identities=18% Similarity=0.147 Sum_probs=110.2
Q ss_pred EEEEEecCCCCCCCCCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHH
Q 027892 39 LVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAE 117 (217)
Q Consensus 39 ~v~lD~ETTGl~p~~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~ 117 (217)
+++||+||||+++ +|||||+| +.++... +.|+.+++|..+++. .+. .+||||++++.++|++.+++
T Consensus 2 ~~vlD~ETTGl~~---~IieIg~v~v~~~~i~---~~~~~lv~P~~~i~~----~~~---~ihgIt~e~v~~ap~~~ev~ 68 (219)
T PRK07983 2 LRVIDTETCGLQG---GIVEIASVDVIDGKIV---NPMSHLVRPDRPISP----QAM---AIHRITEAMVADKPWIEDVI 68 (219)
T ss_pred eEEEEEECCCCCC---CCEEEEEEEEECCEEE---EEEEEEECcCCCCCH----HHh---hcCCCCHHHHcCCCCHHHHH
Confidence 7899999999985 49999999 6665542 468899999988754 333 67899999999999999998
Q ss_pred HHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcccC--------CCC----
Q 027892 118 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRK--------VPS---- 185 (217)
Q Consensus 118 ~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~~--------~l~---- 185 (217)
.+| +++ .++||||+.||++||.. +..+++||. +++|+++|+.... ++.
T Consensus 69 ~~~---~~~------~~lVaHNa~FD~~~L~~--------~~~~~idTl---~lar~l~p~~~~~l~~L~~~~~l~~~~~ 128 (219)
T PRK07983 69 PHY---YGS------EWYVAHNASFDRRVLPE--------MPGEWICTM---KLARRLWPGIKYSNMALYKSRKLNVQTP 128 (219)
T ss_pred HHH---cCC------CEEEEeCcHhhHHHHhC--------cCCCcEeHH---HHHHHHccCCCCCHHHHHHHcCCCCCCC
Confidence 874 444 47999999999999964 346789997 7888888875421 222
Q ss_pred -CCCCCChHHHHHHHHHHHHHHHHH
Q 027892 186 -KEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 186 -~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
..++|||++||.+|++|+..+.+.
T Consensus 129 ~~~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 129 PGLHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 257999999999999999998754
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=99.95 E-value=1.7e-27 Score=186.76 Aligned_cols=136 Identities=21% Similarity=0.270 Sum_probs=106.4
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCC-CHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL-TEREAEK 118 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~-~~~e~~~ 118 (217)
+++||||||+++. ++|++||++..++.. .|+.+|+|..++++.+ + ++||||++|+.++| +++++++
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-----VLDELVKPDGEIVDYN----T---RFSGITEEMLENVTTTLEDVQK 67 (150)
T ss_pred CEEeeeeeeecCC-CEEEEEEEEeCCCCE-----EEEEeECCCCccchhc----c---CcCCCCHHHhccCCCCHHHHHH
Confidence 5899999999976 999999999555543 2778999998876543 3 78899999999985 9999999
Q ss_pred HHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcccC----------C--CCC
Q 027892 119 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYRK----------V--PSK 186 (217)
Q Consensus 119 ~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~~----------~--l~~ 186 (217)
+|.+|+++. .+|||||+.||+.||+. .+++++||. .+++++.+...++ + +..
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 245689997 4555544432211 1 222
Q ss_pred -CCCCChHHHHHHHHHHHH
Q 027892 187 -EQKHRALDDIRESIMELK 204 (217)
Q Consensus 187 -~~~H~Al~Da~at~~ll~ 204 (217)
..+|||++||++|++|++
T Consensus 132 ~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 132 GEGGHDSVEDARAALELVK 150 (150)
T ss_pred CCCCCCcHHHHHHHHHHhC
Confidence 578999999999999874
No 42
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.94 E-value=2.9e-26 Score=208.15 Aligned_cols=166 Identities=19% Similarity=0.193 Sum_probs=123.6
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh-cCCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH-SGLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~-~~~~~ 113 (217)
+..+|||+|+||||++|.+|+|||||+|.++++...+.+.++.+++|....+. ...+. .+||||++++. .+.+.
T Consensus 4 ~~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp--~p~a~---~IhGIT~e~l~~~g~~e 78 (476)
T PRK11779 4 MQPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLP--SPEAV---LITGITPQEALEKGLPE 78 (476)
T ss_pred CCCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCC--CHHHH---HHhCCCHHHHHhcCCCH
Confidence 56789999999999999999999999997776654555678999999864321 11223 67799999985 46679
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEec-HHHhHHHHHhHhhhhh-c----CC--CCceeehHHHHHHHHHhCCCc------
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNS-VYVDFMFLKKYMPDLA-S----LF--SHVLVDVSSIKALCMRWYPRD------ 179 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn-~~FD~~fL~~~~~~~~-~----~~--~~~~iDt~~l~~la~~~~p~~------ 179 (217)
.+++.+|.+|+.. ++ .++|||| ++||..||+..+.+.. . .+ ++..+|+..+.++++.+.|+.
T Consensus 79 ~e~~~~i~~~l~~---~~-~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~ 154 (476)
T PRK11779 79 AEFAARIHAEFSQ---PG-TCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPEN 154 (476)
T ss_pred HHHHHHHHHHHhc---CC-CEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCccc
Confidence 9999999999962 12 3589997 7999999999873321 1 11 233456665556666544321
Q ss_pred ----c---------cCCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 027892 180 ----Y---------RKVPSKEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 180 ----~---------~~~l~~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
. .++++..++|||++||.+|++|++.+++.
T Consensus 155 ~~g~~s~rLe~L~~~~gI~~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 155 EDGLPSFKLEHLTKANGIEHENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred ccCCCCCcHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHh
Confidence 1 13678899999999999999999999876
No 43
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=4.8e-26 Score=196.07 Aligned_cols=155 Identities=18% Similarity=0.174 Sum_probs=110.3
Q ss_pred ccCCCCEEEEEecCCCCCCCCCcEEEEEEEEEC----CceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 33 FEYKMPLVWIDLEMTGLKIEVDRILEIACIITD----GKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 33 ~~~~~~~v~lD~ETTGl~p~~d~IieIgav~~d----~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
......+|++|+||||++|.+|+|||||+|.++ |.+..+.+.|+.+++|..++++. ++ .+||||++|+.
T Consensus 33 ~~~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~----~t---~IhGIt~e~v~ 105 (294)
T PRK09182 33 GEFVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPE----IT---RLTGITDEMVA 105 (294)
T ss_pred CCCCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHH----HH---HhcCCCHHHHh
Confidence 345678999999999999999999999999543 44333446789999999877543 33 77899999999
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCccc-------
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYR------- 181 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~------- 181 (217)
+++...+ ++.+|++.. .++||||+.||+.||++.++.+.. ..+.|+.....+. .+...+
T Consensus 106 ~~~~~~~---~l~~fl~~~-----~vlVAHNA~FD~~fL~~~~~~~~~---~~~~ct~~~i~~~---~~~~~~~kL~~La 171 (294)
T PRK09182 106 GQTIDPA---AVDALIAPA-----DLIIAHNAGFDRPFLERFSPVFAT---KPWACSVSEIDWS---ARGFEGTKLGYLA 171 (294)
T ss_pred cCCCcHH---HHHHHhcCC-----CEEEEeCHHHHHHHHHHHHHhccC---CcccccHHHHhhc---cccCCCCCHHHHH
Confidence 9876544 456666652 478999999999999998755431 2234543211111 111111
Q ss_pred --CCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 027892 182 --KVPSKEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 182 --~~l~~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
++ ...++|||++||.+|++|+..+...
T Consensus 172 ~~~g-~~~~aHrAl~Da~Ata~ll~~~l~~ 200 (294)
T PRK09182 172 GQAG-FFHEGHRAVDDCQALLELLARPLPE 200 (294)
T ss_pred HHcC-CCCCCcChHHHHHHHHHHHHHHHhh
Confidence 24 4568999999999999999976543
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=99.94 E-value=7.7e-27 Score=183.27 Aligned_cols=142 Identities=22% Similarity=0.262 Sum_probs=101.2
Q ss_pred EEEEecCCCCCCCCCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEK 118 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~ 118 (217)
|++|+||||++|. ++++||+.| +++.+...+ |+.+|+|+.+++. +++ .+||||+++++++|++.+++.
T Consensus 1 v~lD~EttGl~~~-~~~~~i~~v~~v~~~~~~~---~~~~v~P~~~i~~----~~~---~ihGIt~~~v~~a~~~~~~~~ 69 (152)
T cd06144 1 VALDCEMVGVGPD-GSESALARVSIVNEDGNVV---YDTYVKPQEPVTD----YRT---AVSGIRPEHLKDAPDFEEVQK 69 (152)
T ss_pred CEEEEEeecccCC-CCEEEEEEEEEEeCCCCEE---EEEEECCCCCCCc----ccc---cCCCCCHHHHcCCCCHHHHHH
Confidence 5899999999986 467777766 444433322 6889999877653 333 678999999999999999999
Q ss_pred HHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHh-CCCcc-----c--CCCCC-CCC
Q 027892 119 QVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRW-YPRDY-----R--KVPSK-EQK 189 (217)
Q Consensus 119 ~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~-~p~~~-----~--~~l~~-~~~ 189 (217)
+|.+|+++ .++||||+.||++||+...+ .+.++|+..+..+...+ .+... . .+++. ..+
T Consensus 70 ~l~~~l~~------~vlVgHn~~fD~~~L~~~~~------~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~ 137 (152)
T cd06144 70 KVAELLKG------RILVGHALKNDLKVLKLDHP------KKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGE 137 (152)
T ss_pred HHHHHhCC------CEEEEcCcHHHHHHhcCcCC------CccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCC
Confidence 99999987 46899999999999985322 23467776432111111 01100 0 13332 468
Q ss_pred CChHHHHHHHHHHHH
Q 027892 190 HRALDDIRESIMELK 204 (217)
Q Consensus 190 H~Al~Da~at~~ll~ 204 (217)
|||++||++|++|++
T Consensus 138 H~Al~DA~at~~l~~ 152 (152)
T cd06144 138 HSSVEDARAAMRLYR 152 (152)
T ss_pred cCcHHHHHHHHHHhC
Confidence 999999999999875
No 45
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.93 E-value=6.6e-25 Score=184.22 Aligned_cols=156 Identities=24% Similarity=0.290 Sum_probs=129.0
Q ss_pred CCEEEEEecCCCCCCCCCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHH
Q 027892 37 MPLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 115 (217)
Q Consensus 37 ~~~v~lD~ETTGl~p~~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e 115 (217)
.++++||+||||+++.+++|||||+| +.++... ...|+.+++|..++++.. . .++|||.+++.++|.+.+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~--~~~~~~~v~P~~~i~~~~----~---~i~git~e~l~~~p~~~~ 83 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIV--ERSFHTLVNPERPIPPEI----F---KIHGITDEMLADAPKFAE 83 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeee--cceeEEEECCCCCCChhh----h---hhcCCCHHHHhcCCCHHH
Confidence 68999999999999999999999999 6666543 234889999977765433 2 678999999999999999
Q ss_pred HHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCC-CCceeehHHHHHHHHHhCCCccc---------CCCC
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF-SHVLVDVSSIKALCMRWYPRDYR---------KVPS 185 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~-~~~~iDt~~l~~la~~~~p~~~~---------~~l~ 185 (217)
++++|.+|+++. .++||||+.||..||+.++...+... ...++|+. .++++..|+... .++.
T Consensus 84 v~~~~~~~i~~~-----~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~---~~~r~~~~~~~~~~L~~l~~~~gi~ 155 (243)
T COG0847 84 VLPEFLDFIGGL-----RLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTL---ALARRHFPGFDRSSLDALAERLGID 155 (243)
T ss_pred HHHHHHHHHCCC-----CeEEEEchhhcHHHHHHHHHHcCCCcccCceehHH---HHHHHHcCCCccchHHHHHHHcCCC
Confidence 999999999983 36999999999999999998877543 45688997 678888887432 2455
Q ss_pred --CCCCCChHHHHHHHHHHHHHHHHH
Q 027892 186 --KEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 186 --~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
....|+|+.||.++++++..+...
T Consensus 156 ~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 156 RNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred cCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 568899999999999998888764
No 46
>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=99.92 E-value=3.1e-26 Score=178.09 Aligned_cols=154 Identities=24% Similarity=0.311 Sum_probs=112.2
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 119 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~~ 119 (217)
|+||+||||+++..++|||||+|..++......+.|+.+|+|... ..++++++ .+||||.+++.+++++.+++.+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~--~~i~~~~~---~~~gIt~~~l~~~~~~~~~~~~ 75 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEP--PKISPWAT---KVHGITQEDLEDAPSFEEALDE 75 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSH--CSSEHHHH---HHHHHCHHHHHCHCEHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeeccccccc--ccCCHHHe---eecCCcccccccCCcHHHHHHh
Confidence 689999999999899999999995554432223458899999876 12356666 6679999999999999999999
Q ss_pred HHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhh-hcCCC--CceeehHHHHHHHHHhCC--Ccc----cCCCCCCC-C
Q 027892 120 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDL-ASLFS--HVLVDVSSIKALCMRWYP--RDY----RKVPSKEQ-K 189 (217)
Q Consensus 120 ~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~-~~~~~--~~~iDt~~l~~la~~~~p--~~~----~~~l~~~~-~ 189 (217)
|.+|+++. .++||||+.||..++.+.+.+. +.+++ ..++|+..+......-.+ .+. .++++... +
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 4799999999999999888665 33333 345666533222211111 111 12444444 7
Q ss_pred CChHHHHHHHHHHH
Q 027892 190 HRALDDIRESIMEL 203 (217)
Q Consensus 190 H~Al~Da~at~~ll 203 (217)
|+|++||++|++||
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 47
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.91 E-value=2.4e-23 Score=190.96 Aligned_cols=166 Identities=14% Similarity=0.124 Sum_probs=121.6
Q ss_pred CCCEEEEEecCCCCCCC---CCcEEEEEEEEEC-CceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCC
Q 027892 36 KMPLVWIDLEMTGLKIE---VDRILEIACIITD-GKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 111 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~---~d~IieIgav~~d-~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~ 111 (217)
-..|||||+||||+++. .++|||||||+++ .+..+ .+.|+.+|+|... +.++++++ ++||||++++.++|
T Consensus 55 ~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~I-i~~F~~yVkP~~~--p~Ls~fct---~LTGITqe~V~~Ap 128 (582)
T PTZ00315 55 FDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATP-VAEFQRYVRPVKN--PVLSRFCT---ELTGITQSMVSRAD 128 (582)
T ss_pred CCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEE-EEEEEEEECCCCC--CCCChhHh---hhcCcCHHHHhcCC
Confidence 37899999999999874 4899999999764 23222 2469999999752 12356677 78899999999999
Q ss_pred CHHHHHHHHHHHHhhcc----CCCCceEEEecHHHhH-HHHHhHhhh---hhcCCCC-ceeehHHHHHHHHHhCCCc---
Q 027892 112 TEREAEKQVVEFVKKNV----GTYTPLLAGNSVYVDF-MFLKKYMPD---LASLFSH-VLVDVSSIKALCMRWYPRD--- 179 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~----~~~~~~lVghn~~FD~-~fL~~~~~~---~~~~~~~-~~iDt~~l~~la~~~~p~~--- 179 (217)
+|.+++.+|.+|+++.. ++....+|+||..||+ .||.+++.. .+.++.. .++|+.. .+++..+|+.
T Consensus 129 ~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~--~lar~l~p~~~~~ 206 (582)
T PTZ00315 129 PFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKK--YMSQLGFGNGSGC 206 (582)
T ss_pred CHHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHH--HHHHHhCcccccc
Confidence 99999999999998752 1112358899999998 599988863 3444433 4666531 3555555521
Q ss_pred --------ccC---------CCC-CCCCCChHHHHHHHHHHHHHHHHH
Q 027892 180 --------YRK---------VPS-KEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 180 --------~~~---------~l~-~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
..+ +++ .+.+|||++||++|++|+..+.+.
T Consensus 207 ~~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~ 254 (582)
T PTZ00315 207 GGGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRR 254 (582)
T ss_pred ccccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHc
Confidence 111 344 456899999999999999988654
No 48
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.90 E-value=1.9e-23 Score=208.50 Aligned_cols=157 Identities=20% Similarity=0.289 Sum_probs=131.7
Q ss_pred CCCEEEEEecCCCCCCCCCcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 36 KMPLVWIDLEMTGLKIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~~d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
..++|++|+||||+++..++|||||++.+ +|.. .+.|+.+|+|..++++ .++ .+||||++++.+++++.
T Consensus 418 ~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~i---ie~F~~~V~P~~~I~~----~~~---~LTGIT~e~L~~aps~~ 487 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEI---IDKFEFFIKPGHPLSA----FTT---ELTGITDDMVKDAPSIE 487 (1437)
T ss_pred cCcEEEEEhhhcCCCCchhhhheeeeEEEeCCeE---eeeEEEEECCCCCCCH----HHH---HHhCCCHHHHcCCCCHH
Confidence 46799999999999999999999999954 4433 2569999999987754 334 78899999999999999
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc-CCCCceeehHHHHHHHHHhCCCccc---------CCC
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS-LFSHVLVDVSSIKALCMRWYPRDYR---------KVP 184 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~-~~~~~~iDt~~l~~la~~~~p~~~~---------~~l 184 (217)
+++++|.+|+++ .++||||+.||..||++.+.++|. ++....+|+. ++++.+.|.... .++
T Consensus 488 EaL~~f~~figg------~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTL---elar~l~p~~k~~kL~~LAk~lGL 558 (1437)
T PRK00448 488 EVLPKFKEFCGD------SILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTL---ELSRFLYPELKSHRLNTLAKKFGV 558 (1437)
T ss_pred HHHHHHHHHhCC------CEEEEeCccccHHHHHHHHHHcCCccccccceeHH---HHHHHHcCccccccHHHHHHHcCC
Confidence 999999999988 469999999999999999998875 4667899997 566777765432 356
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHHHhc
Q 027892 185 SKEQKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 185 ~~~~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
+...+|||++||.+|++|+..+.+.+.
T Consensus 559 ~~~~~HrAl~DA~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 559 ELEHHHRADYDAEATAYLLIKFLKDLK 585 (1437)
T ss_pred CCCCCcChHHHHHHHHHHHHHHHHHHH
Confidence 778899999999999999999977654
No 49
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.75 E-value=7.2e-18 Score=146.11 Aligned_cols=166 Identities=16% Similarity=0.171 Sum_probs=131.1
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHH-hcCCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVL-HSGLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l-~~~~~~ 113 (217)
...+|.+.|.||.|.+|..|++.|+|+|.+|.+.+++++....+++|.....+. ++.+ -+||||++.. ++|.+.
T Consensus 7 ~~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~-P~a~----LITGITPQ~~~~~G~~E 81 (475)
T COG2925 7 KQPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQ-PGAV----LITGITPQEAREKGINE 81 (475)
T ss_pred CCCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCC-CCce----eeecCCHHHHHhcCCCh
Confidence 557899999999999999999999999999999999999889999998765442 1222 5889998765 678889
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEe-cHHHhHHHHHhHhhh-hhc----CC--CCceeehHHHHHHHHHhCCCccc----
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGN-SVYVDFMFLKKYMPD-LAS----LF--SHVLVDVSSIKALCMRWYPRDYR---- 181 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVgh-n~~FD~~fL~~~~~~-~~~----~~--~~~~iDt~~l~~la~~~~p~~~~---- 181 (217)
.+.+.++...+.. |+++ ++|+ |++||-.+-+.-|-| +-. .| .+..+|.+-+++.+..+.|+...
T Consensus 82 ~~F~~~I~~~ls~---P~Tc-v~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n 157 (475)
T COG2925 82 AAFAARIHAELTQ---PNTC-VLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPEN 157 (475)
T ss_pred HHHHHHHHHHhCC---CCee-eecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcC
Confidence 9999888877765 5556 5675 579999988877632 211 12 24567777777888888886542
Q ss_pred ---------------CCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 027892 182 ---------------KVPSKEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 182 ---------------~~l~~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
+++.+.++|+||+|++||+++.|..++.
T Consensus 158 ~dG~pSFkLEhLt~ANgieH~nAHdAmsDVyATIamAklvk~~ 200 (475)
T COG2925 158 DDGLPSFKLEHLTKANGIEHSNAHDAMSDVYATIAMAKLVKTA 200 (475)
T ss_pred CCCCcchhhHHHhhccccccchhhHHHHHHHHHHHHHHHHHhh
Confidence 2578999999999999999999998875
No 50
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.69 E-value=3.4e-16 Score=130.12 Aligned_cols=147 Identities=24% Similarity=0.284 Sum_probs=107.6
Q ss_pred CEEEEEecCCCCCCCCCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHH
Q 027892 38 PLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 116 (217)
Q Consensus 38 ~~v~lD~ETTGl~p~~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~ 116 (217)
++|++|||+.|..|+. +.=.+|-| +++..+.++ |+.+|+|..++.+ |-+ .++||+++.+.++++|+.|
T Consensus 106 r~vAmDCEMVG~Gp~G-~~s~lARvSIVN~~G~Vv---yDkyVkP~~~VtD----yRT---~vSGIrpehm~~A~pf~~a 174 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDG-RESLLARVSIVNYHGHVV---YDKYVKPTEPVTD----YRT---RVSGIRPEHMRDAMPFKVA 174 (280)
T ss_pred eEEEEeeeEeccCCCc-cceeeeEEEEeeccCcEe---eeeecCCCccccc----cee---eecccCHHHhccCccHHHH
Confidence 6999999999999862 22334444 455444444 5679999998854 444 7889999999999999999
Q ss_pred HHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH---------------HHHHHHHHhCCCccc
Q 027892 117 EKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS---------------SIKALCMRWYPRDYR 181 (217)
Q Consensus 117 ~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~---------------~l~~la~~~~p~~~~ 181 (217)
-.+++++|.++ +||||.+..|+..|.-..++- .+.||+ +|..|++.++...
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------ILVGHALHNDLQALKLEHPRS------MIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKD-- 240 (280)
T ss_pred HHHHHHHHhCC------EEeccccccHHHHHhhhCchh------hhcccccCchHHHHhhccCCccHHHHHHHHhchh--
Confidence 99999999994 699999999999998765432 133443 2333444433221
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 182 KVPSKEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 182 ~~l~~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
+. ...|+..+||+||++||+..+..|.+
T Consensus 241 --IQ-~GeHsSvEDA~AtM~LY~~vk~qwe~ 268 (280)
T KOG2249|consen 241 --IQ-VGEHSSVEDARATMELYKRVKVQWEK 268 (280)
T ss_pred --hh-ccccCcHHHHHHHHHHHHHHHHHHHH
Confidence 22 33499999999999999998877654
No 51
>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=99.61 E-value=1.3e-15 Score=121.16 Aligned_cols=141 Identities=16% Similarity=0.204 Sum_probs=94.3
Q ss_pred CEEEEEecCCCCCCCC-CcE-----EEEEEE-EEC----CceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHH
Q 027892 38 PLVWIDLEMTGLKIEV-DRI-----LEIACI-ITD----GKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV 106 (217)
Q Consensus 38 ~~v~lD~ETTGl~p~~-d~I-----ieIgav-~~d----~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~ 106 (217)
.||.+|.|++++.++. ..+ .|+|-| ++| ..+.++ +..+|+|..++.++. + .++|||+++
T Consensus 6 e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vl---lD~~VkP~~~V~DYr----T---~~SGIt~~~ 75 (174)
T cd06143 6 EFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPF---IDDYISTTEPVVDYL----T---RFSGIKPGD 75 (174)
T ss_pred eEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEE---EeeeECCCCCccCcC----c---cccccCHHH
Confidence 3455555555544443 322 367766 666 333443 457999998886544 4 788999999
Q ss_pred HhcCC------CHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHH----------
Q 027892 107 LHSGL------TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKA---------- 170 (217)
Q Consensus 107 l~~~~------~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~---------- 170 (217)
+.+++ +++++..++.+++... .+||||.+..|+..|+-..+ +..++||+.++.
T Consensus 76 L~~a~~~~~~~t~~~v~~~l~~li~~~-----tILVGHsL~nDL~aL~l~hp------~~~viDTa~l~~~~~~r~~sLk 144 (174)
T cd06143 76 LDPKTSSKNLTTLKSAYLKLRLLVDLG-----CIFVGHGLAKDFRVINIQVP------KEQVIDTVELFHLPGQRKLSLR 144 (174)
T ss_pred cCccccccccCCHHHHHHHHHHHcCCC-----CEEEeccchhHHHHhcCcCC------CcceEEcHHhccCCCCCChhHH
Confidence 98764 6899999999988642 57999999999999985321 235788864432
Q ss_pred -HHHHhCCCcccCCCCCCCCCChHHHHHHHHHHHH
Q 027892 171 -LCMRWYPRDYRKVPSKEQKHRALDDIRESIMELK 204 (217)
Q Consensus 171 -la~~~~p~~~~~~l~~~~~H~Al~Da~at~~ll~ 204 (217)
|++.++.. .+. ...|++++||+||++||+
T Consensus 145 ~La~~~L~~----~IQ-~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 145 FLAWYLLGE----KIQ-SETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHHHHcCC----ccc-CCCcCcHHHHHHHHHHhC
Confidence 22222211 122 369999999999999984
No 52
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.56 E-value=1.3e-14 Score=113.31 Aligned_cols=165 Identities=18% Similarity=0.109 Sum_probs=118.9
Q ss_pred CCEEEEEecCCCC----CCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCC
Q 027892 37 MPLVWIDLEMTGL----KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 112 (217)
Q Consensus 37 ~~~v~lD~ETTGl----~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~ 112 (217)
..++++|+|.|-- .+...+||||+|.+++.-...+.+.|+.+|+|.+. +.++..|. .+|||++..+.++|-
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 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKF--PKLTKRCK---SLTKITQKQVDEAPI 78 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccC--chHHHHHH---Hhhhhhhhhccccch
Confidence 4688999999933 34568999999985432222223469999999864 35678888 889999999999999
Q ss_pred HHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc---CCCCceeehHHHHHHHHHhCCCcc-------cC
Q 027892 113 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS---LFSHVLVDVSSIKALCMRWYPRDY-------RK 182 (217)
Q Consensus 113 ~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~---~~~~~~iDt~~l~~la~~~~p~~~-------~~ 182 (217)
+..++++|..||..+.|+..+. ++....+|...|++.....+. ++..+.+|+..-++-.++ .|..- .+
T Consensus 79 fs~v~E~f~r~L~~h~Pr~~~~-wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~-~pr~tgln~ale~~ 156 (210)
T COG5018 79 FSMVFEDFIRKLNEHDPRKNST-WATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFG-DPRLTGLNKALEEY 156 (210)
T ss_pred HHHHHHHHHHHHHhcCcccCCc-cccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhc-CCccccHHHHHHHh
Confidence 9999999999999986654443 344569999999988755543 234468898744432222 22211 12
Q ss_pred CC-CCCCCCChHHHHHHHHHHHHHHHH
Q 027892 183 VP-SKEQKHRALDDIRESIMELKYYKE 208 (217)
Q Consensus 183 ~l-~~~~~H~Al~Da~at~~ll~~~~~ 208 (217)
|. ..+..|||++||+.+.++++...+
T Consensus 157 G~sf~G~~HraldDArn~~rl~klv~~ 183 (210)
T COG5018 157 GDSFTGTHHRALDDARNAYRLFKLVEQ 183 (210)
T ss_pred ccccCCchhhhHHHHHHHHHHHHHHcc
Confidence 33 467899999999999999998743
No 53
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.47 E-value=5.1e-13 Score=110.51 Aligned_cols=168 Identities=12% Similarity=0.141 Sum_probs=118.9
Q ss_pred CCCCEEEEEecCCCCCCC----CCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhc
Q 027892 35 YKMPLVWIDLEMTGLKIE----VDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS 109 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~----~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~ 109 (217)
.-..++++|+|+|--+.. ..+|||+.+| ....+...+.+.|+.+|+|... +.++++|+ .+|||.++.+..
T Consensus 54 ~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~n--p~LS~fC~---~lTgI~Q~tVD~ 128 (280)
T KOG0542|consen 54 PFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVEN--PRLSDFCT---SLTGIQQETVDE 128 (280)
T ss_pred ccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccC--chHHHHHH---HhhCchHhhhcc
Confidence 446789999999954432 4799999999 4444444445479999999753 35689998 899999999999
Q ss_pred CCCHHHHHHHHHHHHhhc--cCC-CCceEEEecHHHhH-HHHHhHhhhhhcCCC---CceeehHHHHHHHHHh-CCCcc-
Q 027892 110 GLTEREAEKQVVEFVKKN--VGT-YTPLLAGNSVYVDF-MFLKKYMPDLASLFS---HVLVDVSSIKALCMRW-YPRDY- 180 (217)
Q Consensus 110 ~~~~~e~~~~~~~~l~~~--~~~-~~~~lVghn~~FD~-~fL~~~~~~~~~~~~---~~~iDt~~l~~la~~~-~p~~~- 180 (217)
+|+|.+|+.+|..|+... .+. +..-+|... +-|+ .||..++..-+...| +.+||+...++.-.+. .+...
T Consensus 129 a~~f~~vl~~f~~Wlr~~~~~~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it 207 (280)
T KOG0542|consen 129 APTFPQVLSEFDSWLRKDSLGDKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNIT 207 (280)
T ss_pred CCCHHHHHHHHHHHHHHhhcccccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHH
Confidence 999999999999999864 223 444456533 6665 477777754443333 3689998655433332 22211
Q ss_pred ----cCCC-CCCCCCChHHHHHHHHHHHHHHHH
Q 027892 181 ----RKVP-SKEQKHRALDDIRESIMELKYYKE 208 (217)
Q Consensus 181 ----~~~l-~~~~~H~Al~Da~at~~ll~~~~~ 208 (217)
.+++ -.+.+|++++||+.++++++.+.+
T Consensus 208 ~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~ 240 (280)
T KOG0542|consen 208 GMLEHYGLQFEGRAHSGIDDARNIARIAQKMIR 240 (280)
T ss_pred HHHHHhCCcccCCcccCchhHHHHHHHHHHHHh
Confidence 2344 457899999999999999887643
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=99.36 E-value=6e-12 Score=102.50 Aligned_cols=98 Identities=19% Similarity=0.187 Sum_probs=72.5
Q ss_pred EEEEEecCCCC----CCCCCcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 39 LVWIDLEMTGL----KIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 39 ~v~lD~ETTGl----~p~~d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
.++||+||||+ ++..|+|++||++.. +|.... +.....+.. . ...|++..++...++.
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~----~~~~~~~~~---~----------~~~~i~~~~v~~~~~E 63 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVV----FLLKTSTVG---D----------DIEFIDGIEVEYFADE 63 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceee----EEEeecccC---C----------cCCCCCCceEEEeCCH
Confidence 36899999999 888999999999854 655432 111111111 1 1116777778888999
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhc
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 156 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 156 (217)
.+++.+|.++++++- +.++||||+ .||++||...+..++.
T Consensus 64 ~~lL~~f~~~i~~~d---pdiivg~N~~~FD~~~L~~R~~~~~~ 104 (199)
T cd05160 64 KELLKRFFDIIREYD---PDILTGYNIDDFDLPYLLKRAEALGI 104 (199)
T ss_pred HHHHHHHHHHHHhcC---CCEEEEeccCCCcHHHHHHHHHHhCC
Confidence 999999999999852 247999999 8999999988776664
No 55
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.30 E-value=3.5e-11 Score=106.63 Aligned_cols=148 Identities=20% Similarity=0.252 Sum_probs=108.7
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhc-CCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHS-GLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~-~~~~ 113 (217)
...+.+++|||+....-. -++..+++|-.++.. + +..+|+|..+|.++.+ .++|||++++.+ ...+
T Consensus 214 ~~~~i~AlDCEm~~te~g-~el~RVt~VD~~~~v--i---~D~fVkP~~~VvDy~T-------~~SGIT~~~~e~~t~tl 280 (380)
T KOG2248|consen 214 KSPNIFALDCEMVVTENG-LELTRVTAVDRDGKV--I---LDTFVKPNKPVVDYNT-------RYSGITEEDLENSTITL 280 (380)
T ss_pred CCCCeEEEEeeeeeeccc-eeeEEeeeeeccCcE--E---eEEeecCCCccccccc-------ccccccHHHHhcCccCH
Confidence 557899999999988755 667777776555543 3 4579999999976654 678999999975 5689
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHH--------------HHHHHhCCCc
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIK--------------ALCMRWYPRD 179 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~--------------~la~~~~p~~ 179 (217)
.++-.+++.|+... .++|||+..-|+..|+.. |..++||..++ .++..++...
T Consensus 281 ~dvq~~l~~~~~~~-----TILVGHSLenDL~aLKl~--------H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~ 347 (380)
T KOG2248|consen 281 EDVQKELLELISKN-----TILVGHSLENDLKALKLD--------HPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKL 347 (380)
T ss_pred HHHHHHHHhhcCcC-----cEEEeechhhHHHHHhhh--------CCceeeeeEEEecCCCCccchHHHHHHHHHHHHHH
Confidence 99999999988763 689999999999999963 45567775222 1222222111
Q ss_pred ccCCCCCCCCCChHHHHHHHHHHHHHHHHHhc
Q 027892 180 YRKVPSKEQKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 180 ~~~~l~~~~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
.. .....|++..||.++++|+++..+...
T Consensus 348 Iq---~~~~~HdS~eDA~acm~Lv~~k~~~~~ 376 (380)
T KOG2248|consen 348 IQ---EGVGGHDSVEDALACMKLVKLKIKNSE 376 (380)
T ss_pred Hh---ccCCCCccHHHHHHHHHHHHHHHhccc
Confidence 11 235679999999999999998866543
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=99.29 E-value=5e-11 Score=86.49 Aligned_cols=91 Identities=23% Similarity=0.339 Sum_probs=66.1
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 119 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~~ 119 (217)
+++|+||||+++..++|++|+....++.. . ++. +
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~-~-------~~~--------------------~------------------ 34 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPED-T-------AVI--------------------D------------------ 34 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCC-E-------EEe--------------------h------------------
Confidence 47999999999999999999986432111 0 000 1
Q ss_pred HHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcC---CCCceeehHHHHHHHHHhCCCcccCCCCCCCCCChHHHH
Q 027892 120 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL---FSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDI 196 (217)
Q Consensus 120 ~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~---~~~~~iDt~~l~~la~~~~p~~~~~~l~~~~~H~Al~Da 196 (217)
|.+|+++.. ..++||||++||++||++++.+.+.. ++.+++||..+ |++||
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 777787631 13689999999999999999887643 34679999732 89999
Q ss_pred HHHHHH
Q 027892 197 RESIME 202 (217)
Q Consensus 197 ~at~~l 202 (217)
+.+..+
T Consensus 89 ~~~~~~ 94 (96)
T cd06125 89 ENTLQI 94 (96)
T ss_pred HHHHHh
Confidence 877654
No 57
>PHA02570 dexA exonuclease; Provisional
Probab=99.21 E-value=3.2e-10 Score=92.87 Aligned_cols=160 Identities=16% Similarity=0.190 Sum_probs=106.1
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecC------------Cccch--hhhhhHHhhhhhhcCCcHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQ------------TKECL--DSMGEWCQNHHEASGLTKK 105 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p------------~~~i~--~~~~~~~~~~h~itGIt~~ 105 (217)
+++|+||.|..|+ ..|++||||.++.... ....|+.+|.. ....+ ..+.||..+ ++|
T Consensus 4 lMIDlETmG~~p~-AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQ-------S~E 74 (220)
T PHA02570 4 FIIDFETFGNTPD-GAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQ-------SPE 74 (220)
T ss_pred EEEEeeccCCCCC-ceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhC-------CHH
Confidence 5899999999975 8999999998886544 34556665542 10111 234455432 222
Q ss_pred HH---h---cCCCHHHHHHHHHHHHhhcc-CCCCceEEEecHHHhHHHHHhHhhhh----h--cCCCCc---eeehHHHH
Q 027892 106 VL---H---SGLTEREAEKQVVEFVKKNV-GTYTPLLAGNSVYVDFMFLKKYMPDL----A--SLFSHV---LVDVSSIK 169 (217)
Q Consensus 106 ~l---~---~~~~~~e~~~~~~~~l~~~~-~~~~~~lVghn~~FD~~fL~~~~~~~----~--~~~~~~---~iDt~~l~ 169 (217)
.. . +..++.+++.+|.+||..+. ......++|...+||..+|+..+.+. + .+.|+. ..|+.++.
T Consensus 75 AR~~L~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~i 154 (220)
T PHA02570 75 ARKNLKPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAI 154 (220)
T ss_pred HHHhccCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHHHHHHHhcccCcCcCCCeeecCccchHHHH
Confidence 22 1 23679999999999999764 23335688999999999999998776 4 344443 56887765
Q ss_pred HH---HHH--hCCCcccCCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 027892 170 AL---CMR--WYPRDYRKVPSKEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 170 ~l---a~~--~~p~~~~~~l~~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
+. .|- ..| +.+..++.-.+|+|+.||.--+..|.|-++.
T Consensus 155 e~~~l~r~~~~cp-~~~g~l~gfv~H~sihDcakd~lml~y~~ry 198 (220)
T PHA02570 155 EATLLTRGMTTCP-LPKGTLDGFVAHDSIHDCAKDILMLIYAKRY 198 (220)
T ss_pred hhhhccCCcccCC-CcCccccchhhcccHHHHHHHHHHHHHHHHH
Confidence 42 111 111 1223356668999999999888888776654
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=98.66 E-value=3.6e-07 Score=73.34 Aligned_cols=138 Identities=13% Similarity=0.080 Sum_probs=87.2
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
....++++|+||||+++..++|+.++....++. .+ ++..... . + .+++...
T Consensus 3 ~~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~------~~--~~~~~~~-------------~---~-----~~~~~~~ 53 (193)
T cd06139 3 EKAKVFAFDTETTSLDPMQAELVGISFAVEPGE------AY--YIPLGHD-------------Y---G-----GEQLPRE 53 (193)
T ss_pred ccCCeEEEEeecCCCCcCCCeEEEEEEEcCCCC------EE--EEecCCC-------------c---c-----ccCCCHH
Confidence 356789999999999988888988886422221 11 2211100 0 0 1345677
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCc-ccC---------C-
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRD-YRK---------V- 183 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~-~~~---------~- 183 (217)
+++.++.+++++. ...+||||+.||+.+|.+. |..++..++||.. +++...|.. ... +
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----GIELRGPAFDTML---ASYLLNPGRRRHGLDDLAERYLGH 122 (193)
T ss_pred HHHHHHHHHHhCC----CCcEEeeccHHHHHHHHHC----CCCCCCCcccHHH---HHHHhCCCCCCCCHHHHHHHHhCC
Confidence 8888999999863 1358999999999999753 4445556788863 334444432 100 0
Q ss_pred --C---------------C----CCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 184 --P---------------S----KEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 184 --l---------------~----~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
+ . ....|.|..|+.++.+++..+.+.+-.
T Consensus 123 ~~~~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 123 KTISFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CCccHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 0 0 012345888999999999998877654
No 59
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.54 E-value=1.1e-07 Score=74.71 Aligned_cols=91 Identities=19% Similarity=0.145 Sum_probs=50.1
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 119 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~~ 119 (217)
++||+|||||+|..+.|.-||++..+++.... +..+.... +..++.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~---~~~~~~~~----------------------------~~ee~~~~~ 49 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIIT---FIQWFAED----------------------------PDEEEIILE 49 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE----EEEE-GGG----------------------------HHHHHHHHH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEE---eeHhhccC----------------------------cHHHHHHHH
Confidence 58999999999988999999998554432110 11111110 112233334
Q ss_pred HHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 120 VVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 120 ~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
+.+++.+. ..+|+||. .||.++|++.+.+++.+.+...+|+.
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 33667663 45889985 99999999998777755577899997
No 60
>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=98.50 E-value=6.3e-07 Score=73.00 Aligned_cols=90 Identities=23% Similarity=0.262 Sum_probs=60.5
Q ss_pred CCEEEEEecCC---CC-CCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCC
Q 027892 37 MPLVWIDLEMT---GL-KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 112 (217)
Q Consensus 37 ~~~v~lD~ETT---Gl-~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~ 112 (217)
-++++||+||| |+ ++..|+|++||.+..+++... ..++... ..+..-.+
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~-------~~~~~~~--------------------~~v~~~~~ 55 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVI-------TWKKFDL--------------------PFVEVVKT 55 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEE-------EecCCCC--------------------CeEEEeCC
Confidence 46889999998 65 778899999998653332111 0111000 01112246
Q ss_pred HHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhc
Q 027892 113 EREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 156 (217)
Q Consensus 113 ~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 156 (217)
..+.+.+|.+++..+- +.++||||. .||+++|..-+..+|.
T Consensus 56 E~~lL~~F~~~i~~~d---pdiivgyN~~~FD~pyL~~R~~~~gi 97 (195)
T cd05780 56 EKEMIKRFIEIVKEKD---PDVIYTYNGDNFDFPYLKKRAEKLGI 97 (195)
T ss_pred HHHHHHHHHHHHHHcC---CCEEEecCCCCCcHHHHHHHHHHhCC
Confidence 7889999999998742 246999998 7999999987765553
No 61
>PRK05755 DNA polymerase I; Provisional
Probab=98.45 E-value=1.9e-06 Score=84.79 Aligned_cols=130 Identities=15% Similarity=0.155 Sum_probs=86.4
Q ss_pred CCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHH
Q 027892 36 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 115 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e 115 (217)
...++++|+||||+++..++|+.|++-..++. ..+|.+. ++. .+
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 46789999999999999999999886333221 1223211 221 15
Q ss_pred HHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCcc-c-------C-CCC-
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDY-R-------K-VPS- 185 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~-~-------~-~l~- 185 (217)
++..|.+|+++. ..++|+||+.||+.+|.+. |..++.+++||.. +++.+.|... . + +..
T Consensus 358 ~l~~l~~~L~d~----~v~kV~HNakfDl~~L~~~----gi~~~~~~~DT~i---Aa~Ll~~~~~~~L~~L~~~ylg~~~ 426 (880)
T PRK05755 358 VLAALKPLLEDP----AIKKVGQNLKYDLHVLARY----GIELRGIAFDTML---ASYLLDPGRRHGLDSLAERYLGHKT 426 (880)
T ss_pred HHHHHHHHHhCC----CCcEEEeccHhHHHHHHhC----CCCcCCCcccHHH---HHHHcCCCCCCCHHHHHHHHhCCCc
Confidence 677888899873 1347999999999999853 5555567889963 3333444321 0 0 000
Q ss_pred ------------------CCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 186 ------------------KEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 186 ------------------~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
....|.|..|+.++.+|+..+++.+-.
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 62
>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=98.43 E-value=2.4e-06 Score=69.35 Aligned_cols=81 Identities=21% Similarity=0.342 Sum_probs=60.2
Q ss_pred CCEEEEEecCC---CC-CCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCC
Q 027892 37 MPLVWIDLEMT---GL-KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 112 (217)
Q Consensus 37 ~~~v~lD~ETT---Gl-~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~ 112 (217)
-+.++||+||+ |+ ++..++|+.||+...++....+ . .+..+
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~--------~---------------------------~~~~~ 47 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFI--------L---------------------------AEGLD 47 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEE--------E---------------------------ecCCC
Confidence 46889999999 54 7788999999987655542210 0 01246
Q ss_pred HHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhh
Q 027892 113 EREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 155 (217)
Q Consensus 113 ~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 155 (217)
..+.+..|.+++..+- +.+++|||. .||+++|..-...+|
T Consensus 48 E~~lL~~F~~~i~~~d---Pd~i~gyN~~~FDlpyl~~Ra~~~g 88 (188)
T cd05781 48 DRKIIREFVKYVKEYD---PDIIVGYNSNAFDWPYLVERARVLG 88 (188)
T ss_pred HHHHHHHHHHHHHHcC---CCEEEecCCCcCcHHHHHHHHHHhC
Confidence 7889999999999852 246899997 799999988766555
No 63
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.28 E-value=2.8e-06 Score=70.65 Aligned_cols=29 Identities=21% Similarity=0.221 Sum_probs=23.2
Q ss_pred cCCCCEEEEEecCCCCCCCCCcEEEEEEE
Q 027892 34 EYKMPLVWIDLEMTGLKIEVDRILEIACI 62 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~~d~IieIgav 62 (217)
...+++++||+|||||++..+.|+=+|.-
T Consensus 95 ~~~e~~~FFDiETTGL~~ag~~I~~~g~a 123 (278)
T COG3359 95 YEAEDVAFFDIETTGLDRAGNTITLVGGA 123 (278)
T ss_pred ccccceEEEeeeccccCCCCCeEEEEEEE
Confidence 34678999999999999976777666654
No 64
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=98.20 E-value=6.5e-06 Score=69.31 Aligned_cols=172 Identities=19% Similarity=0.192 Sum_probs=97.7
Q ss_pred ccccCCCCEEEEEecCCCCCCCCCcEEEEEEE-E----ECCceeeeecCCceeecCCccchhhh----------hhHHhh
Q 027892 31 LEFEYKMPLVWIDLEMTGLKIEVDRILEIACI-I----TDGKLTKSVEGPDLVIHQTKECLDSM----------GEWCQN 95 (217)
Q Consensus 31 ~~~~~~~~~v~lD~ETTGl~p~~d~IieIgav-~----~d~~~~~~~~~~~~li~p~~~i~~~~----------~~~~~~ 95 (217)
.++..-..|+|+|+|+|||......|-|++.. + .++....+.+.-...+.+. .+.++. ....
T Consensus 7 se~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~-Rvl~Klsvl~~p~~v~~p~a-- 83 (318)
T KOG4793|consen 7 SEVPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGS-RVLDKLSVLGGPVPVTRPIA-- 83 (318)
T ss_pred CcCCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCcc-chhhhhhhccCCcCCcChhh--
Confidence 33445688999999999998777888888865 2 2333222222211222211 111110 0111
Q ss_pred hhhhcCCcHHHHh--cCCCHH-HHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhcCCCCce--eehHHHH
Q 027892 96 HHEASGLTKKVLH--SGLTER-EAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASLFSHVL--VDVSSIK 169 (217)
Q Consensus 96 ~h~itGIt~~~l~--~~~~~~-e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~~~~~~--iDt~~l~ 169 (217)
.++||++.+-+. ....++ ++.+-+..|+.....++ + +|+||- .||+++|.+++..+|...+... +|+....
T Consensus 84 -eeitgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~-C-LVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~ 160 (318)
T KOG4793|consen 84 -EEITGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPG-C-LVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPAL 160 (318)
T ss_pred -hhhcccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCc-e-EEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHH
Confidence 278899885442 222343 45555677777654333 4 899997 8999999999999997666554 4554322
Q ss_pred -HHHHHhCC----C-cccC-----------CCCCCCCCChHHHHHHHHHHHHHHHH
Q 027892 170 -ALCMRWYP----R-DYRK-----------VPSKEQKHRALDDIRESIMELKYYKE 208 (217)
Q Consensus 170 -~la~~~~p----~-~~~~-----------~l~~~~~H~Al~Da~at~~ll~~~~~ 208 (217)
.+-++-.+ . ...+ .-.....|.|.+|.-...-.+++-.+
T Consensus 161 ~ald~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ 216 (318)
T KOG4793|consen 161 NALDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRIN 216 (318)
T ss_pred HHHhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHH
Confidence 23232211 1 1111 11456789998887765554444433
No 65
>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=98.04 E-value=4.4e-05 Score=62.76 Aligned_cols=106 Identities=14% Similarity=0.162 Sum_probs=60.9
Q ss_pred CCEEEEEecCCC-----CCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCC
Q 027892 37 MPLVWIDLEMTG-----LKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 111 (217)
Q Consensus 37 ~~~v~lD~ETTG-----l~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~ 111 (217)
-++++||+||.+ .+|..|.||+|+.+........... .++.+......... +- .+.|. -.+..-.
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~---~~~~~~~~~~~~~~--~~---~~~~~--~~v~~~~ 71 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNR---EIVSEDIEDFEYTP--KP---EYEGP--FKVFNEP 71 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecc---cccccccccccccC--CC---CCCCc--eEEecCC
Confidence 367899999986 3677899999998754322111100 01000000000000 00 00010 0011235
Q ss_pred CHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhh
Q 027892 112 TEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 155 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 155 (217)
+..+.+.+|.+|+..+- +-+++|||. .||+++|.+-...+|
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 78999999999999853 246899998 899999987665544
No 66
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=98.02 E-value=3e-05 Score=64.78 Aligned_cols=100 Identities=19% Similarity=0.258 Sum_probs=63.2
Q ss_pred cCCCCEEEEEecCCC-----CCCCCCcEEEEEEEE-ECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHH
Q 027892 34 EYKMPLVWIDLEMTG-----LKIEVDRILEIACII-TDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVL 107 (217)
Q Consensus 34 ~~~~~~v~lD~ETTG-----l~p~~d~IieIgav~-~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l 107 (217)
+.+-+.+++|+||+. .+|..|+|+.||++. .++....... .-..+.+...++ |. .+
T Consensus 4 ~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~-~~~~l~~~~~~~--------------~~---~v 65 (230)
T cd05777 4 IAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIR-NIFTLKTCAPIV--------------GA---QV 65 (230)
T ss_pred CCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCcee-EEEEeCCCCCCC--------------CC---EE
Confidence 345788999999984 367789999999984 3443221111 001122211110 11 11
Q ss_pred hcCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhh
Q 027892 108 HSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 154 (217)
Q Consensus 108 ~~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 154 (217)
..-.+..+.+..|.+++...- +.+++|||+ .||+++|.+-+..+
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 122578899999999998742 247999998 89999997765443
No 67
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.00 E-value=3.7e-05 Score=63.30 Aligned_cols=83 Identities=19% Similarity=0.309 Sum_probs=58.1
Q ss_pred CCCCEEEEEecCCCC--------CCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHH
Q 027892 35 YKMPLVWIDLEMTGL--------KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKV 106 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl--------~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~ 106 (217)
.+-++++||+||++. ++..+.|+.||....++. . ..+.
T Consensus 7 ~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~-~-------~~~~-------------------------- 52 (207)
T cd05785 7 DDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGW-E-------EVLH-------------------------- 52 (207)
T ss_pred CCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCc-e-------eeec--------------------------
Confidence 456899999999753 345689999997422211 0 0000
Q ss_pred HhcCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhh
Q 027892 107 LHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 155 (217)
Q Consensus 107 l~~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 155 (217)
....+..+++.+|++++..+- +.+|+|||+ .||+++|.+.+..+|
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 013578889999999999852 246899999 999999998776554
No 68
>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=97.71 E-value=0.00023 Score=58.55 Aligned_cols=41 Identities=15% Similarity=0.220 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhc
Q 027892 111 LTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 156 (217)
Q Consensus 111 ~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 156 (217)
.+..+++.+|.+++.++ ++++|||. .||+++|.+-...+|.
T Consensus 71 ~~E~~lL~~F~~~i~~~-----~~iig~N~~~FDlpyl~~R~~~~gi 112 (204)
T cd05783 71 DSEKELIREAFKIISEY-----PIVLTFNGDNFDLPYLYNRALKLGI 112 (204)
T ss_pred CCHHHHHHHHHHHHhcC-----CEEEEeCCCCcCHHHHHHHHHHhCC
Confidence 47899999999999975 46899998 8999999987766654
No 69
>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=97.69 E-value=0.00026 Score=60.27 Aligned_cols=165 Identities=18% Similarity=0.152 Sum_probs=80.7
Q ss_pred CCCEEEEEecCCCCCCC---------------------CCcEEEEEEEEE-CCceeee----ecCCceeecCCccchhhh
Q 027892 36 KMPLVWIDLEMTGLKIE---------------------VDRILEIACIIT-DGKLTKS----VEGPDLVIHQTKECLDSM 89 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~---------------------~d~IieIgav~~-d~~~~~~----~~~~~~li~p~~~i~~~~ 89 (217)
.-.||+||+|.||+... .-.|||+|..+. +.+.... ...|...+-|.......
T Consensus 21 ~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~- 99 (262)
T PF04857_consen 21 KADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQ- 99 (262)
T ss_dssp HSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEE-
T ss_pred hCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceec-
Confidence 35699999999999753 246999999866 3332211 11122332232211000
Q ss_pred hhHHhhhhhhcCCc-HHHHhcCCCHHHHHH--HHHHHHhhc--cC---CCCceEEEecHHHhHHHHHhHhh---------
Q 027892 90 GEWCQNHHEASGLT-KKVLHSGLTEREAEK--QVVEFVKKN--VG---TYTPLLAGNSVYVDFMFLKKYMP--------- 152 (217)
Q Consensus 90 ~~~~~~~h~itGIt-~~~l~~~~~~~e~~~--~~~~~l~~~--~~---~~~~~lVghn~~FD~~fL~~~~~--------- 152 (217)
.+++.-. .-+|+. ++...+|.+.....+ ++.+.++-. +. ..+.+|||||.-+|+-+|-+.+-
T Consensus 100 ~~sl~FL-~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~e 178 (262)
T PF04857_consen 100 ASSLQFL-RKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEE 178 (262)
T ss_dssp HHHHHHH-HHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHH
T ss_pred chhHHHH-HHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHH
Confidence 1111111 345776 455566765443332 111222211 10 12356999999999999987651
Q ss_pred ---hhhcCCCCceeehHHHHHH-----------HHHhCCCc-----cc----CC---------CCCCCCCChHHHHHHHH
Q 027892 153 ---DLASLFSHVLVDVSSIKAL-----------CMRWYPRD-----YR----KV---------PSKEQKHRALDDIRESI 200 (217)
Q Consensus 153 ---~~~~~~~~~~iDt~~l~~l-----------a~~~~p~~-----~~----~~---------l~~~~~H~Al~Da~at~ 200 (217)
.+...||. ++||..|+.. +..+.... .. .+ ......|.|=.||.+|+
T Consensus 179 F~~~~~~~FP~-i~DtK~la~~~~~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg 257 (262)
T PF04857_consen 179 FKELLRELFPR-IYDTKYLAEECPGKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTG 257 (262)
T ss_dssp HHHHHHHHSSS-EEEHHHHHTSTTTS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHHH
T ss_pred HHHHHHHHCcc-cccHHHHHHhccccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHHH
Confidence 12233543 8899754421 11111100 00 00 12344999999999999
Q ss_pred HHH
Q 027892 201 MEL 203 (217)
Q Consensus 201 ~ll 203 (217)
.++
T Consensus 258 ~~F 260 (262)
T PF04857_consen 258 CVF 260 (262)
T ss_dssp HHH
T ss_pred HHH
Confidence 876
No 70
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=97.54 E-value=0.00027 Score=68.11 Aligned_cols=158 Identities=19% Similarity=0.217 Sum_probs=99.6
Q ss_pred CCCccccCCCCEEEEEecCCCCCCCCCcE-------------EEEEEE-EECCceeeeecCC-ceeecCCccchhhhhhH
Q 027892 28 QTPLEFEYKMPLVWIDLEMTGLKIEVDRI-------------LEIACI-ITDGKLTKSVEGP-DLVIHQTKECLDSMGEW 92 (217)
Q Consensus 28 ~~~~~~~~~~~~v~lD~ETTGl~p~~d~I-------------ieIgav-~~d~~~~~~~~~~-~~li~p~~~i~~~~~~~ 92 (217)
.+..+-+....+|.+|-|=.-|.++..+| ..+|-| +++|++...+-.| .-+|-.++.+.++++
T Consensus 901 Lt~dEmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLT-- 978 (1118)
T KOG1275|consen 901 LTLDEMPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLT-- 978 (1118)
T ss_pred ccccccCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHH--
Confidence 34444567789999999988887664443 256666 5555532111111 123444445555554
Q ss_pred HhhhhhhcCCcHHHHhcC------CCHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 93 CQNHHEASGLTKKVLHSG------LTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 93 ~~~~h~itGIt~~~l~~~------~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
+.+||-+.+|... .+++.+..++.=.+.- | +++|||....|++.|+-.-++ ..++||.
T Consensus 979 -----qySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~----G-viFVGHGL~nDFrvINi~Vp~------~QiiDTv 1042 (1118)
T KOG1275|consen 979 -----QYSGIKPGDLDPTTSEKRLTTLKVLYLKLRLLIQR----G-VIFVGHGLQNDFRVINIHVPE------EQIIDTV 1042 (1118)
T ss_pred -----HhcCCCccccCCccCcceehhHHHHHHHHHHHHHc----C-cEEEcccccccceEEEEecCh------hhheeee
Confidence 6789999888532 3577777777655553 2 689999999999988754321 2244544
Q ss_pred HHH-----------HHHHHhCCCcccCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 027892 167 SIK-----------ALCMRWYPRDYRKVPSKEQKHRALDDIRESIMELKYYKE 208 (217)
Q Consensus 167 ~l~-----------~la~~~~p~~~~~~l~~~~~H~Al~Da~at~~ll~~~~~ 208 (217)
.++ -||..++... ....+|+..+||+.+++||+.|.+
T Consensus 1043 ~lf~~~s~R~LSLrfLa~~lLg~~-----IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1043 TLFRLGSQRMLSLRFLAWELLGET-----IQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred EEEecccccEEEHHHHHHHHhcch-----hhccccccHHHHHHHHHHHHHHHH
Confidence 322 2333333322 357799999999999999999965
No 71
>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=97.52 E-value=0.00037 Score=60.33 Aligned_cols=100 Identities=12% Similarity=0.146 Sum_probs=63.8
Q ss_pred CCCCEEEEEecCCCCC-----CCCCcEEEEEEEEECCc-eeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 35 YKMPLVWIDLEMTGLK-----IEVDRILEIACIITDGK-LTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~-----p~~d~IieIgav~~d~~-~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
.+-++++||+||...+ +..|+|+.|++++.+.. ...... ....+.+..... + ...+.
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~-~~~~~~~~~~~~--------------~--~~~v~ 217 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRR-KVFTLGSCDSIE--------------D--NVEVI 217 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEE-EEEECSCSCCTT--------------C--TTEEE
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCce-EEEEecCCCCCC--------------C--CcEEE
Confidence 5689999999998665 56899999998754321 111111 111222222110 0 11112
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhh
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 154 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 154 (217)
.-.+..+.+..|++++... +| -+++|||+ .||+++|..-+..+
T Consensus 218 ~~~~E~~lL~~f~~~i~~~-dP--Dii~GyN~~~fD~~yl~~R~~~l 261 (325)
T PF03104_consen 218 YFDSEKELLEAFLDIIQEY-DP--DIITGYNIDGFDLPYLIERAKKL 261 (325)
T ss_dssp EESSHHHHHHHHHHHHHHH-S---SEEEESSTTTTHHHHHHHHHHHT
T ss_pred EECCHHHHHHHHHHHHHhc-CC--cEEEEecccCCCHHHHHHHHHHh
Confidence 2257899999999999885 22 47999999 79999998766554
No 72
>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=97.50 E-value=0.0006 Score=55.54 Aligned_cols=89 Identities=12% Similarity=0.132 Sum_probs=55.6
Q ss_pred CCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHH
Q 027892 36 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTERE 115 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e 115 (217)
+-++++||+||+|.. +|..||..-...+.. ..+...... .|. .+.--++..+
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 357899999999754 888888632111111 111111110 010 0111246788
Q ss_pred HHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhh
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 155 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 155 (217)
.+..|.+++...- +.+++|||. .||+++|..-+..++
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 9999999998852 247999998 899999988765544
No 73
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=97.49 E-value=0.0069 Score=47.35 Aligned_cols=42 Identities=12% Similarity=0.171 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeeh
Q 027892 116 AEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDV 165 (217)
Q Consensus 116 ~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt 165 (217)
+...+.+++.+. ....||||+.||..+|.+.+ +.. ..+++|+
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 556677778762 24689999999999999862 332 2346777
No 74
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.37 E-value=0.00079 Score=67.61 Aligned_cols=97 Identities=21% Similarity=0.280 Sum_probs=60.3
Q ss_pred CCCCEEEEEecCCCC------CCCCCcEEEEEEEEE-CCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHH
Q 027892 35 YKMPLVWIDLEMTGL------KIEVDRILEIACIIT-DGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVL 107 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl------~p~~d~IieIgav~~-d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l 107 (217)
.+-++++||+||+|. +|..|.||+||.++. .|.........-....+..++ .|. .+
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~c~~i--------------~g~---~V 324 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKECASI--------------AGA---NV 324 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCccccC--------------CCc---eE
Confidence 567899999999864 345799999999843 333210000111111111111 121 11
Q ss_pred hcCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHh
Q 027892 108 HSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYM 151 (217)
Q Consensus 108 ~~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~ 151 (217)
..-.+..+.+..|.+|+... + +.+++|||+ .||+++|..-+
T Consensus 325 ~~f~sE~eLL~~f~~~I~~~-D--PDII~GYNi~~FDlpYL~~Ra 366 (1054)
T PTZ00166 325 LSFETEKELLLAWAEFVIAV-D--PDFLTGYNIINFDLPYLLNRA 366 (1054)
T ss_pred EEeCCHHHHHHHHHHHHHhc-C--CCEEEecCCcCCcHHHHHHHH
Confidence 22357889999999999875 2 347999998 79999997654
No 75
>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=97.32 E-value=0.0015 Score=54.66 Aligned_cols=105 Identities=16% Similarity=0.224 Sum_probs=62.1
Q ss_pred CCEEEEEecCCC-----CCCCCCcEEEEEEEEECCceeeee---cCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 37 MPLVWIDLEMTG-----LKIEVDRILEIACIITDGKLTKSV---EGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 37 ~~~v~lD~ETTG-----l~p~~d~IieIgav~~d~~~~~~~---~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
.+++.+|+|+.+ .+|..|.|++|+.++.+....... .....++.+....... . . ....+....+.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~---~---~~~~~~~~~v~ 76 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASN-G---R---IRSGLSGIPVE 76 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhh-h---c---cccCCCCCeEE
Confidence 467899999874 356789999999986543322110 0011222222210000 0 0 00112222233
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHh
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYM 151 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~ 151 (217)
.-++..+.+.+|.+++...- +-+++|||+ .||+++|-+-+
T Consensus 77 ~~~~E~~LL~~f~~~i~~~D---PDii~GyNi~~fd~~YL~~Ra 117 (231)
T cd05778 77 VVESELELFEELIDLVRRFD---PDILSGYEIQRSSWGYLIERA 117 (231)
T ss_pred EeCCHHHHHHHHHHHHHHhC---CCEEEEeccccCcHHHHHHHH
Confidence 34688999999999998852 247999999 89999997654
No 76
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=97.07 E-value=0.0043 Score=51.07 Aligned_cols=78 Identities=15% Similarity=0.128 Sum_probs=52.8
Q ss_pred EecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHHHHHH
Q 027892 43 DLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQVVE 122 (217)
Q Consensus 43 D~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~~~~~ 122 (217)
..+++|+.+..++|+-||++..++.... + .+. .. ...+..+++.+|.+
T Consensus 40 ~~~~~~l~~~~~~Iv~Is~~~~~~~~~~----~--~~~-~~-------------------------~~~~E~elL~~F~~ 87 (208)
T cd05782 40 KSGSDFLPLPFHKVVSISALYRDDDGGF----L--KVR-TL-------------------------DGADEKELLEDFFQ 87 (208)
T ss_pred hcCCCCCccccCceEEEEEEEEecCCCe----E--EEe-ec-------------------------CCCCHHHHHHHHHH
Confidence 3467889888999999999865211110 0 111 00 01234778999999
Q ss_pred HHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhc
Q 027892 123 FVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 156 (217)
Q Consensus 123 ~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 156 (217)
++..+- ++|||||. .||+++|.+-+..+|.
T Consensus 88 ~i~~~~----p~lv~yNg~~FDlP~L~~Ra~~~gi 118 (208)
T cd05782 88 LIEKKN----PRLVSFNGRGFDLPVLHLRALIHGV 118 (208)
T ss_pred HHHHhC----CEEEecCCCcCCHHHHHHHHHHhCC
Confidence 999852 56899998 8999999987655443
No 77
>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=96.92 E-value=0.005 Score=55.76 Aligned_cols=98 Identities=21% Similarity=0.303 Sum_probs=59.8
Q ss_pred CCCEEEEEecCCCCC-----CC--CCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 36 KMPLVWIDLEMTGLK-----IE--VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~-----p~--~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
+..++++|+||+... +. .+.|++|+.+..++..............+... +.|+. +.
T Consensus 2 ~~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~---~~ 64 (471)
T smart00486 2 PLKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKE--------------IDGVE---VY 64 (471)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCC--------------CCCCe---EE
Confidence 356889999998542 22 58999999986554432111111112222221 11211 11
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhh
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPD 153 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~ 153 (217)
.-....+.+.+|.+++...- +.+++|||. .||+++|...+..
T Consensus 65 ~~~~E~~lL~~f~~~i~~~d---pdii~g~N~~~FD~~~i~~R~~~ 107 (471)
T smart00486 65 EFNNEKELLKAFLEFIKKYD---PDIIYGHNISNFDLPYIISRLEK 107 (471)
T ss_pred ecCCHHHHHHHHHHHHHHhC---CCEEEeecCCCCCHHHHHHHHHH
Confidence 11267889999999998742 246999998 6999999876543
No 78
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=96.36 E-value=0.067 Score=43.37 Aligned_cols=134 Identities=13% Similarity=0.050 Sum_probs=74.1
Q ss_pred CCCCEEEEEecCCCCCC----CCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcC
Q 027892 35 YKMPLVWIDLEMTGLKI----EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSG 110 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p----~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~ 110 (217)
....+|.||+|+++... .+-.+|||+. .+. ..++++... .+ .
T Consensus 20 ~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat---~~~--------~~lid~~~~---------------~~-~------- 65 (193)
T cd06146 20 EAGRVVGIDSEWKPSFLGDSDPRVAILQLAT---EDE--------VFLLDLLAL---------------EN-L------- 65 (193)
T ss_pred ccCCEEEEECccCCCccCCCCCCceEEEEec---CCC--------EEEEEchhc---------------cc-c-------
Confidence 46789999999986653 2456777772 221 123332210 01 0
Q ss_pred CCHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhc--CCCCceeehHHHHHHHHHhCC---------Cc
Q 027892 111 LTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLAS--LFSHVLVDVSSIKALCMRWYP---------RD 179 (217)
Q Consensus 111 ~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~--~~~~~~iDt~~l~~la~~~~p---------~~ 179 (217)
.-+...+.+.+++.+. ..+-|||++.+|..+|.+.+...+. ..+..++|+..+........+ ..
T Consensus 66 -~~~~~~~~L~~ll~d~----~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~ 140 (193)
T cd06146 66 -ESEDWDRLLKRLFEDP----DVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKT 140 (193)
T ss_pred -chHHHHHHHHHHhCCC----CeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCccc
Confidence 0111223355566652 1346999999999999987643221 123568898743322111000 00
Q ss_pred c---------------c---------CCCCCCCCCChHHHHHHHHHHHHHHH
Q 027892 180 Y---------------R---------KVPSKEQKHRALDDIRESIMELKYYK 207 (217)
Q Consensus 180 ~---------------~---------~~l~~~~~H~Al~Da~at~~ll~~~~ 207 (217)
. + ..+...+-+=|..||.++.+++..+.
T Consensus 141 ~sL~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 141 KGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred CCHHHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0 01344556678999999999888764
No 79
>PHA02528 43 DNA polymerase; Provisional
Probab=96.35 E-value=0.015 Score=57.45 Aligned_cols=105 Identities=22% Similarity=0.179 Sum_probs=58.5
Q ss_pred CCCCEEEEEecCCC----CCCC--CCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 35 YKMPLVWIDLEMTG----LKIE--VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 35 ~~~~~v~lD~ETTG----l~p~--~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
..-++++||+||+. .+|. .+.|++||.- +..... +..+.-+....+....+.. ...-...-...
T Consensus 104 p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~--~~~~~~----~~v~~~~~~~~~~~~~~~~----~~~~~~~v~~~ 173 (881)
T PHA02528 104 SKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHY--DSIDDR----FYVFDLGSVEEWDAKGDEV----PQEILDKVVYM 173 (881)
T ss_pred CCccEEEEEEEECCCCCCCCcccCCCcEEEEEEe--cCCCCE----EEEEEecCcccccccCCcc----cccccCCeeEE
Confidence 46799999999986 4555 6799999973 222111 1111111000000000000 00000000011
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhh
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMP 152 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~ 152 (217)
.-.+..+.+..|.+|+..+- +.+++|||+ .||+++|.+-+.
T Consensus 174 ~~~sE~eLL~~F~~~i~~~D---PDII~GyNi~~FDlpYL~~Ra~ 215 (881)
T PHA02528 174 PFDTEREMLLEYINFWEENT---PVIFTGWNVELFDVPYIINRIK 215 (881)
T ss_pred EcCCHHHHHHHHHHHHHHhC---CcEEEecCCccCCHHHHHHHHH
Confidence 13578999999999998742 347999998 899999977654
No 80
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.14 E-value=0.033 Score=49.36 Aligned_cols=133 Identities=16% Similarity=0.101 Sum_probs=77.8
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
....++++|+|+.|+.+.++ ++|.| +.+++.. .+|+|-..+ . +.++
T Consensus 15 ~~~~~iAiDTEf~r~~t~~p---~LcLIQi~~~e~~-------~lIdpl~~~-----------------~-----d~~~- 61 (361)
T COG0349 15 RGSKAIAIDTEFMRLRTYYP---RLCLIQISDGEGA-------SLIDPLAGI-----------------L-----DLPP- 61 (361)
T ss_pred cCCCceEEecccccccccCC---ceEEEEEecCCCc-------eEecccccc-----------------c-----ccch-
Confidence 44678999999999999887 45666 5566542 467764321 1 1122
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHH------------HhCC-Ccc
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCM------------RWYP-RDY 180 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~------------~~~p-~~~ 180 (217)
|...+.+- . .+=|-|+++||+.+|.+.+. ..+.+++||....++++ .+.. ++.
T Consensus 62 ------l~~Ll~d~---~-v~KIfHaa~~DL~~l~~~~g----~~p~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ld 127 (361)
T COG0349 62 ------LVALLADP---N-VVKIFHAARFDLEVLLNLFG----LLPTPLFDTQIAAKLAGFGTSHGLADLVEELLGVELD 127 (361)
T ss_pred ------HHHHhcCC---c-eeeeeccccccHHHHHHhcC----CCCCchhHHHHHHHHhCCcccccHHHHHHHHhCCccc
Confidence 33344441 1 22367999999999998752 24667888853222221 1110 000
Q ss_pred c-C--------CCCCCCCCChHHHHHHHHHHHHHHHHHhcccC
Q 027892 181 R-K--------VPSKEQKHRALDDIRESIMELKYYKENIFKTN 214 (217)
Q Consensus 181 ~-~--------~l~~~~~H~Al~Da~at~~ll~~~~~~~~~~~ 214 (217)
+ + -+...+--=|..|+....++++.+.+.+...+
T Consensus 128 K~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~ 170 (361)
T COG0349 128 KSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREG 170 (361)
T ss_pred ccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 0 0 02222233378899999999988887765544
No 81
>PRK05762 DNA polymerase II; Reviewed
Probab=95.75 E-value=0.038 Score=54.19 Aligned_cols=90 Identities=11% Similarity=0.122 Sum_probs=57.0
Q ss_pred CCCCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHH
Q 027892 35 YKMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTER 114 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~ 114 (217)
.+-+.++||+||++- .+|.+||..-.+.. . -..+.+....+ . +.+..-++..
T Consensus 153 p~lrvlsfDIE~~~~----~~i~sI~~~~~~~~-~------vi~ig~~~~~~---~--------------~~v~~~~sE~ 204 (786)
T PRK05762 153 PPLKVVSLDIETSNK----GELYSIGLEGCGQR-P------VIMLGPPNGEA---L--------------DFLEYVADEK 204 (786)
T ss_pred CCCeEEEEEEEEcCC----CceEEeeecCCCCC-e------EEEEECCCCCC---c--------------ceEEEcCCHH
Confidence 467899999999863 36888886411111 1 11222221100 0 0122345788
Q ss_pred HHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhh
Q 027892 115 EAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLA 155 (217)
Q Consensus 115 e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 155 (217)
+.+..|++++..+- +-+++|||+ .||+++|.+-+..+|
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 99999999999852 247999998 799999987664443
No 82
>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=95.67 E-value=0.045 Score=45.14 Aligned_cols=36 Identities=22% Similarity=0.227 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHh
Q 027892 112 TEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYM 151 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~ 151 (217)
...+.+.+|.++++.+. +.||+||. .||+++|.+-.
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 37788999999998753 56999997 89999998653
No 83
>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=95.48 E-value=0.24 Score=37.32 Aligned_cols=54 Identities=13% Similarity=0.135 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCC
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPR 178 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~ 178 (217)
..+.+.+.+|+.+. ....||||+.||..+|.+.. ...+..++||. -+++.+.|.
T Consensus 40 ~~~~~~l~~~l~~~----~~~~v~~~~k~d~~~L~~~~----~~~~~~~~D~~---~~ayll~~~ 93 (155)
T cd00007 40 EEDLEALKELLEDE----DITKVGHDAKFDLVVLARDG----IELPGNIFDTM---LAAYLLNPG 93 (155)
T ss_pred HHHHHHHHHHHcCC----CCcEEeccHHHHHHHHHHCC----CCCCCCcccHH---HHHHHhCCC
Confidence 34566677888763 13489999999999997643 22344578885 334444553
No 84
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=95.43 E-value=0.18 Score=39.48 Aligned_cols=124 Identities=19% Similarity=0.120 Sum_probs=69.5
Q ss_pred CCCEEEEEecCCCCCC----CCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCC
Q 027892 36 KMPLVWIDLEMTGLKI----EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGL 111 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p----~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~ 111 (217)
....+.||+|+++..+ .+-.+|||+ .++. ..++++.. +
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~---~~~~--------~~l~~~~~------------------~--------- 58 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLA---TESR--------CLLFQLAH------------------M--------- 58 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEe---cCCc--------EEEEEhhh------------------h---------
Confidence 6789999999998865 345677777 2221 12344321 0
Q ss_pred CHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHH-------------HHHHhCC-
Q 027892 112 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKA-------------LCMRWYP- 177 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~-------------la~~~~p- 177 (217)
......+.+++.+. ....|||++.+|+.+|.+.+ |..+. .++|+..+.. ++..++.
T Consensus 59 --~~~~~~l~~ll~~~----~i~kv~~~~k~D~~~L~~~~---g~~~~-~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~ 128 (170)
T cd06141 59 --DKLPPSLKQLLEDP----SILKVGVGIKGDARKLARDF---GIEVR-GVVDLSHLAKRVGPRRKLVSLARLVEEVLGL 128 (170)
T ss_pred --hcccHHHHHHhcCC----CeeEEEeeeHHHHHHHHhHc---CCCCC-CeeeHHHHHHHhCCCcCCccHHHHHHHHcCc
Confidence 00112455667652 13569999999999997543 22222 3477753221 2222111
Q ss_pred Ccc--c---------CCCCCCCCCChHHHHHHHHHHHHHHH
Q 027892 178 RDY--R---------KVPSKEQKHRALDDIRESIMELKYYK 207 (217)
Q Consensus 178 ~~~--~---------~~l~~~~~H~Al~Da~at~~ll~~~~ 207 (217)
.+. + ..+...+-|=|..||..+.+++..++
T Consensus 129 ~~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 129 PLSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred ccCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 000 0 01334455678999999998887664
No 85
>PRK10829 ribonuclease D; Provisional
Probab=94.83 E-value=0.48 Score=42.53 Aligned_cols=126 Identities=12% Similarity=0.038 Sum_probs=74.3
Q ss_pred CCCCEEEEEecCCCCCCCCC--cEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCC
Q 027892 35 YKMPLVWIDLEMTGLKIEVD--RILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 112 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d--~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~ 112 (217)
...++++||+|..+...... .+|||+ ++.. .++|.|-. +.+
T Consensus 20 ~~~~~lalDtEf~~~~ty~~~l~LiQl~----~~~~-------~~LiD~l~------------------~~d-------- 62 (373)
T PRK10829 20 RAFPAIALDTEFVRTRTYYPQLGLIQLY----DGEQ-------LSLIDPLG------------------ITD-------- 62 (373)
T ss_pred hcCCeEEEecccccCccCCCceeEEEEe----cCCc-------eEEEecCC------------------ccc--------
Confidence 45678999999998876533 344444 3332 13566531 110
Q ss_pred HHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhC-C-Cccc---------
Q 027892 113 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWY-P-RDYR--------- 181 (217)
Q Consensus 113 ~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~-p-~~~~--------- 181 (217)
+..+.+.+.+. ..+-|+|++++|+.+|.+.+ |. .+..++||.... +... + ....
T Consensus 63 ----~~~L~~ll~~~----~ivKV~H~~~~Dl~~l~~~~---g~-~p~~~fDTqiaa---~~lg~~~~~gl~~Lv~~~lg 127 (373)
T PRK10829 63 ----WSPFKALLRDP----QVTKFLHAGSEDLEVFLNAF---GE-LPQPLIDTQILA---AFCGRPLSCGFASMVEEYTG 127 (373)
T ss_pred ----hHHHHHHHcCC----CeEEEEeChHhHHHHHHHHc---CC-CcCCeeeHHHHH---HHcCCCccccHHHHHHHHhC
Confidence 12355567663 13348999999999997644 32 345688995322 1111 1 1100
Q ss_pred ------C--------CCCCCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 182 ------K--------VPSKEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 182 ------~--------~l~~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
+ -++..+-+=|..|+....+++..+++.+..
T Consensus 128 v~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 128 VTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred CccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 133445566899999999999888776543
No 86
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=94.72 E-value=0.32 Score=40.27 Aligned_cols=168 Identities=16% Similarity=0.135 Sum_probs=93.1
Q ss_pred CCCCEEEEEecCCCCCCC---------------------CCcEEEEEEEEECCcee--e----eecCCcee-ecCCccch
Q 027892 35 YKMPLVWIDLEMTGLKIE---------------------VDRILEIACIITDGKLT--K----SVEGPDLV-IHQTKECL 86 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~---------------------~d~IieIgav~~d~~~~--~----~~~~~~~l-i~p~~~i~ 86 (217)
..-+||++|+|=-|.-.. .-.+||+|.-..|.++. . +++ |+.. .++.+..-
T Consensus 22 ~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWq-fNF~dF~~~~D~~ 100 (239)
T KOG0304|consen 22 KDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQ-FNFSDFNLEKDMY 100 (239)
T ss_pred HhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCCCCCceeE-EecccCCchhhcc
Confidence 456899999997664311 12699999987764332 1 221 3322 33332221
Q ss_pred hhhhhHHhhhhhhcCCcHHH-HhcCCCHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhh------------
Q 027892 87 DSMGEWCQNHHEASGLTKKV-LHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPD------------ 153 (217)
Q Consensus 87 ~~~~~~~~~~h~itGIt~~~-l~~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~------------ 153 (217)
..+++.-. +-+||.=+- ...|...++..+.+..-.- +-.+...+|-.+.+||+..|-+-+..
T Consensus 101 --a~~SIElL-r~~Gidf~K~~e~GI~~~~F~ellm~sg~--v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~ 175 (239)
T KOG0304|consen 101 --AQDSIELL-RRSGIDFEKHREEGIDIEEFAELLMTSGL--VLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFE 175 (239)
T ss_pred --chhhHHHH-HHcCcCHHHHHHcCCCHHHHHHHHHHhhh--hccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHH
Confidence 11221111 445887443 3567766654444432211 11223568999999999999776521
Q ss_pred -hhcCCCCceeehHHHHHHHHH--hCCCccc-----CCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 027892 154 -LASLFSHVLVDVSSIKALCMR--WYPRDYR-----KVPSKEQKHRALDDIRESIMELKYYKEN 209 (217)
Q Consensus 154 -~~~~~~~~~iDt~~l~~la~~--~~p~~~~-----~~l~~~~~H~Al~Da~at~~ll~~~~~~ 209 (217)
+...+ ..+.|+..+++.+.. ...++.. .-...+.+|.|=+|+..|+..+.-+++.
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 11123 346787766655533 1111100 0124678999999999999988877653
No 87
>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=94.47 E-value=0.44 Score=37.23 Aligned_cols=125 Identities=10% Similarity=0.067 Sum_probs=68.9
Q ss_pred CCCEEEEEecCCCCCCC--CCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCH
Q 027892 36 KMPLVWIDLEMTGLKIE--VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTE 113 (217)
Q Consensus 36 ~~~~v~lD~ETTGl~p~--~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~ 113 (217)
...++.||+|+...... +-.+|||+. ++.. ..++++... +-
T Consensus 12 ~~~~ig~D~E~~~~~~~~~~~~liQl~~---~~~~-------~~l~d~~~~----------------~~----------- 54 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYYGEVALIQLCV---SEEK-------CYLFDPLSL----------------SV----------- 54 (161)
T ss_pred CCCEEEEECCccCCCCCCCceEEEEEEE---CCCC-------EEEEecccC----------------cc-----------
Confidence 57899999999987643 344666662 3121 134443210 00
Q ss_pred HHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHH------------HHHHHhCC-Ccc
Q 027892 114 REAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIK------------ALCMRWYP-RDY 180 (217)
Q Consensus 114 ~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~------------~la~~~~p-~~~ 180 (217)
..+.+.+++.+. ..+.|||++..|...|.+.+ +..+. .++|+.... .++.+++. .+.
T Consensus 55 --~~~~L~~lL~d~----~i~Kvg~~~k~D~~~L~~~~---gi~~~-~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~ 124 (161)
T cd06129 55 --DWQGLKMLLENP----SIVKALHGIEGDLWKLLRDF---GEKLQ-RLFDTTIAANLKGLPERWSLASLVEHFLGKTLD 124 (161)
T ss_pred --CHHHHHHHhCCC----CEEEEEeccHHHHHHHHHHc---CCCcc-cHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCC
Confidence 112344566652 13469999999999997632 22221 235664221 22222211 000
Q ss_pred c---------CCCCCCCCCChHHHHHHHHHHHHHHH
Q 027892 181 R---------KVPSKEQKHRALDDIRESIMELKYYK 207 (217)
Q Consensus 181 ~---------~~l~~~~~H~Al~Da~at~~ll~~~~ 207 (217)
+ ..+...+-|=|..||.++.++++.++
T Consensus 125 K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 125 KSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred ccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 01445567779999999999888765
No 88
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=94.36 E-value=0.29 Score=40.58 Aligned_cols=167 Identities=19% Similarity=0.164 Sum_probs=94.5
Q ss_pred CCCCEEEEEecCCCCCCC---------------------CCcEEEEEEEEECCceeeeec----CCceeecCCccchhhh
Q 027892 35 YKMPLVWIDLEMTGLKIE---------------------VDRILEIACIITDGKLTKSVE----GPDLVIHQTKECLDSM 89 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~---------------------~d~IieIgav~~d~~~~~~~~----~~~~li~p~~~i~~~~ 89 (217)
...++|.+|+|-.|.-.. .=.|||+|.-.-|.++...-. .|++-..+.+++- .
T Consensus 40 ~rYn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~dmy--a 117 (299)
T COG5228 40 SRYNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKKDMY--A 117 (299)
T ss_pred HhCCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchhhhc--c
Confidence 356899999999886432 126999998866654432111 3566666665442 1
Q ss_pred hhHHhhhhhhcCCcHHHH-hcCCCHHHHHHHHHHHHhh--ccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 90 GEWCQNHHEASGLTKKVL-HSGLTEREAEKQVVEFVKK--NVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 90 ~~~~~~~h~itGIt~~~l-~~~~~~~e~~~~~~~~l~~--~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
++++.-. .-.||.=+.. .-|....| |-+.+-+ .+....+++|.++..||+.+|-+.+.. .++|.+.=|..
T Consensus 118 ~ESieLL-~ksgIdFkkHe~~GI~v~e----F~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt~--~plP~~~EdFy 190 (299)
T COG5228 118 TESIELL-RKSGIDFKKHENLGIDVFE----FSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTN--DPLPNNKEDFY 190 (299)
T ss_pred hHHHHHH-HHcCCChhhHhhcCCCHHH----HHHHHhccCceeccceEEEEeecchhHHHHHHHHhc--CCCCccHHHHH
Confidence 2222111 2346653322 23444443 4444432 222223568899999999999887632 23343333322
Q ss_pred HHHHHHHHhCCCccc-------------------C--C-CCCCCCCChHHHHHHHHHHHHHHHHHhccc
Q 027892 167 SIKALCMRWYPRDYR-------------------K--V-PSKEQKHRALDDIRESIMELKYYKENIFKT 213 (217)
Q Consensus 167 ~l~~la~~~~p~~~~-------------------~--~-l~~~~~H~Al~Da~at~~ll~~~~~~~~~~ 213 (217)
.+...++|+.+. . + ...+..|.|-.||..|+..+-..|..+|.+
T Consensus 191 ---~~l~~yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F~~ 256 (299)
T COG5228 191 ---WWLHQYFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTT 256 (299)
T ss_pred ---HHHHHHCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhheecc
Confidence 222223333221 0 1 246778999999999999888778877754
No 89
>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=93.91 E-value=3.3 Score=37.03 Aligned_cols=83 Identities=14% Similarity=0.179 Sum_probs=49.0
Q ss_pred CCCCEEEEEecCCCCCCCCC--cEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCC
Q 027892 35 YKMPLVWIDLEMTGLKIEVD--RILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLT 112 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~p~~d--~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~ 112 (217)
....+++||+|..+...... .+|||+ .++.. ++|.|-.. + .
T Consensus 16 ~~~~~ia~DtE~~~~~~y~~~l~LiQia----~~~~~-------~liD~~~~----------------~----------~ 58 (367)
T TIGR01388 16 RTFPFVALDTEFVRERTFWPQLGLIQVA----DGEQL-------ALIDPLVI----------------I----------D 58 (367)
T ss_pred hcCCEEEEeccccCCCCCCCcceEEEEe----eCCeE-------EEEeCCCc----------------c----------c
Confidence 34689999999998875443 345554 33321 35554210 0 0
Q ss_pred HHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 113 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 113 ~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
+..+.+++.+. ..+.|+|++.+|+.+|.+.+ ...+..++||.
T Consensus 59 ----~~~L~~lL~d~----~i~KV~h~~k~Dl~~L~~~~----~~~~~~~fDtq 100 (367)
T TIGR01388 59 ----WSPLKELLRDE----SVVKVLHAASEDLEVFLNLF----GELPQPLFDTQ 100 (367)
T ss_pred ----HHHHHHHHCCC----CceEEEeecHHHHHHHHHHh----CCCCCCcccHH
Confidence 12344566652 13469999999999997643 22345578885
No 90
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=93.11 E-value=0.59 Score=48.29 Aligned_cols=102 Identities=15% Similarity=0.134 Sum_probs=61.3
Q ss_pred cccCCCCEEEEEecCCCCC-----CCCCcEEEEEEEEECCceeeeec---------CCceeecCCccchhhhhhHHhhhh
Q 027892 32 EFEYKMPLVWIDLEMTGLK-----IEVDRILEIACIITDGKLTKSVE---------GPDLVIHQTKECLDSMGEWCQNHH 97 (217)
Q Consensus 32 ~~~~~~~~v~lD~ETTGl~-----p~~d~IieIgav~~d~~~~~~~~---------~~~~li~p~~~i~~~~~~~~~~~h 97 (217)
.+...-++++||+|||-|. ...|+|.-|+- .+||++-.+.. .|+.--+|+- ...+
T Consensus 241 i~radp~VlAFDIETtKlPLKFPDae~DqIMMISY-MiDGqGfLItNREiVs~DIedfEYTPKpE~-----eG~F----- 309 (2173)
T KOG1798|consen 241 IERADPRVLAFDIETTKLPLKFPDAESDQIMMISY-MIDGQGFLITNREIVSEDIEDFEYTPKPEY-----EGPF----- 309 (2173)
T ss_pred cccCCceEEEEeeecccCCCCCCCcccceEEEEEE-EecCceEEEechhhhccchhhcccCCcccc-----ccce-----
Confidence 3446678999999999874 23577777765 55776532211 1211111110 0000
Q ss_pred hhcCCcHHHHhcCCCHHHHHHHHHHHHhhccCCCCceEEEecHH-HhHHHHHhHhhhhh
Q 027892 98 EASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVY-VDFMFLKKYMPDLA 155 (217)
Q Consensus 98 ~itGIt~~~l~~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~~-FD~~fL~~~~~~~~ 155 (217)
.+-+-+.....+.+|.+-+.+.- +.++|-+|.. ||++|+++-....|
T Consensus 310 --------~v~Ne~dEv~Ll~RfFeHiq~~k---P~iivTyNGDFFDWPFve~Ra~~hG 357 (2173)
T KOG1798|consen 310 --------CVFNEPDEVGLLQRFFEHIQEVK---PTIIVTYNGDFFDWPFVEARAKIHG 357 (2173)
T ss_pred --------EEecCCcHHHHHHHHHHHHHhcC---CcEEEEecCccccchhhHHHHHhcC
Confidence 01234567778888888887742 3468889985 79999998765444
No 91
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=92.07 E-value=0.85 Score=44.95 Aligned_cols=96 Identities=17% Similarity=0.184 Sum_probs=60.5
Q ss_pred cCCCCEEEEEecCCCCC---C--CCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 34 EYKMPLVWIDLEMTGLK---I--EVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~---p--~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
....+++++|+||.+.. + ..+.++.|+.....+.... ..+... ...|.. +.
T Consensus 151 ~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~--------~~~~~~-------------~~~~~~---v~ 206 (792)
T COG0417 151 RPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI--------EVFIYT-------------SGEGFS---VE 206 (792)
T ss_pred CCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc--------cccccc-------------CCCCce---eE
Confidence 35678999999998654 2 2677888886543222110 000000 000111 23
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhc
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 156 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 156 (217)
...+..+++.+|.+++...- +.+++|||. .||+++|..-+..+|.
T Consensus 207 ~~~~e~e~l~~~~~~i~~~d---PdVIvgyn~~~fd~pyl~~Ra~~lgi 252 (792)
T COG0417 207 VVISEAELLERFVELIREYD---PDVIVGYNGDNFDWPYLAERAERLGI 252 (792)
T ss_pred EecCHHHHHHHHHHHHHhcC---CCEEEeccCCcCChHHHHHHHHHhCC
Confidence 33467889999999998752 357999999 5999999988766654
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=91.23 E-value=0.36 Score=40.32 Aligned_cols=41 Identities=17% Similarity=0.148 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhh
Q 027892 110 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPD 153 (217)
Q Consensus 110 ~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~ 153 (217)
-.+..+.+..|++++... +| -+++|||+ .||+++|-.-+..
T Consensus 79 ~~~E~~LL~~f~~~i~~~-DP--DiivG~Ni~~fdl~~L~~R~~~ 120 (234)
T cd05776 79 FENERALLNFFLAKLQKI-DP--DVLVGHDLEGFDLDVLLSRIQE 120 (234)
T ss_pred eCCHHHHHHHHHHHHhhc-CC--CEEEeeccCCCCHHHHHHHHHH
Confidence 357899999999999884 33 47999999 8999999776533
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=90.99 E-value=2.4 Score=39.05 Aligned_cols=95 Identities=12% Similarity=0.051 Sum_probs=60.1
Q ss_pred CCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHH
Q 027892 37 MPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 116 (217)
Q Consensus 37 ~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~ 116 (217)
...++||+||+ |...-.-.+|++..++.... +.|..+... +.....++
T Consensus 284 ~~~~ffDiEt~---P~~~~~yL~G~~~~~~~~~~--~~~~~fla~---------------------------~~~~E~~~ 331 (457)
T TIGR03491 284 PGELIFDIESD---PDENLDYLHGFLVVDKGQEN--EKYRPFLAE---------------------------DPNTEELA 331 (457)
T ss_pred CccEEEEecCC---CCCCCceEEEEEEecCCCCC--cceeeeecC---------------------------CchHHHHH
Confidence 66789999999 55566788898755432110 112111111 11236678
Q ss_pred HHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcC------CCCceeehHH
Q 027892 117 EKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL------FSHVLVDVSS 167 (217)
Q Consensus 117 ~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~------~~~~~iDt~~ 167 (217)
+.+|.+|+..+ + + ..|+++| .|....|++...+++.+ +..+++|+..
T Consensus 332 ~~~f~~~l~~~-~-~-~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~ 384 (457)
T TIGR03491 332 WQQFLQLLQSY-P-D-APIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHT 384 (457)
T ss_pred HHHHHHHHHHC-C-C-CeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHH
Confidence 88999999875 2 2 2478888 99999999887766533 1126788863
No 94
>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=90.30 E-value=6.2 Score=31.86 Aligned_cols=27 Identities=7% Similarity=-0.064 Sum_probs=20.4
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHhcc
Q 027892 186 KEQKHRALDDIRESIMELKYYKENIFK 212 (217)
Q Consensus 186 ~~~~H~Al~Da~at~~ll~~~~~~~~~ 212 (217)
..+-.=|..||..+.+|+..++..+..
T Consensus 153 ~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 153 EDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 344455889999999999888877643
No 95
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=89.71 E-value=0.24 Score=48.15 Aligned_cols=35 Identities=17% Similarity=0.206 Sum_probs=26.4
Q ss_pred ceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHHH
Q 027892 133 PLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSIK 169 (217)
Q Consensus 133 ~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l~ 169 (217)
.++||||++||+.-++.++. +. .-..+++||.+|.
T Consensus 242 ~liVGHNVsfDRaRirEeY~-i~-~Sk~rFlDTMSlH 276 (1075)
T KOG3657|consen 242 QLIVGHNVSFDRARIREEYN-IN-GSKIRFLDTMSLH 276 (1075)
T ss_pred ceEEeccccchHHHHHHHHh-cc-ccceeeeechhhh
Confidence 47999999999999998763 11 1245789998764
No 96
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=88.85 E-value=0.062 Score=51.76 Aligned_cols=93 Identities=20% Similarity=0.333 Sum_probs=57.4
Q ss_pred CCCCEEEEEecCCCCC-----CCCCcEEEEEEE-EECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 35 YKMPLVWIDLEMTGLK-----IEVDRILEIACI-ITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 35 ~~~~~v~lD~ETTGl~-----p~~d~IieIgav-~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
.+-+...+|+|+.|-. |..|.|||||-+ ...|......+ --..+++-. ||...++.
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~r-nvf~l~~ca-----------------pI~G~~V~ 333 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVR-NVFTLKTCA-----------------PIVGSNVH 333 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHH-hhhcccCcC-----------------CCCCceeE
Confidence 4568889999999865 346899999976 33443322111 011122222 33333333
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHH
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLK 148 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~ 148 (217)
.-...+++++....|+.. ++| .+++|+|+ .||++.|-
T Consensus 334 ~~~~e~elL~~W~~fire-vDP--DvI~GYNi~nFDiPYll 371 (1066)
T KOG0969|consen 334 SYETEKELLESWRKFIRE-VDP--DVIIGYNICNFDIPYLL 371 (1066)
T ss_pred EeccHHHHHHHHHHHHHh-cCC--CeEecccccccccceec
Confidence 334567777777778876 333 36899999 89998764
No 97
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=86.99 E-value=1 Score=38.57 Aligned_cols=100 Identities=10% Similarity=0.034 Sum_probs=61.2
Q ss_pred CHHHHHHHHHHHHhhccCCC-CceEEEecH-HHhHHHHHhHhhhhhcCC--CCceeehHHHH-HHHHHhCCCcc--c---
Q 027892 112 TEREAEKQVVEFVKKNVGTY-TPLLAGNSV-YVDFMFLKKYMPDLASLF--SHVLVDVSSIK-ALCMRWYPRDY--R--- 181 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~~~-~~~lVghn~-~FD~~fL~~~~~~~~~~~--~~~~iDt~~l~-~la~~~~p~~~--~--- 181 (217)
.-++...-|..+.+.+.+++ ....+.||. .|+..|..+++-+++... ++..++.+-+. +-+....|.-. +
T Consensus 177 ~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~p~~vs~le 256 (318)
T KOG4793|consen 177 RMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPTPKLVSSLE 256 (318)
T ss_pred cccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCCCccchhHH
Confidence 34444455667777654443 233455665 899999999997776432 34455543110 11222334211 1
Q ss_pred ------CCCCCCCCCChHHHHHHHHHHHHHHHHHhc
Q 027892 182 ------KVPSKEQKHRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 182 ------~~l~~~~~H~Al~Da~at~~ll~~~~~~~~ 211 (217)
...+...+|||+.|+..+-++.+.+...+-
T Consensus 257 ~Lat~~~~~p~l~ahra~~Dv~~~~k~~q~~~idll 292 (318)
T KOG4793|consen 257 ALATYYSLTPELDAHRALSDVLLLSKVFQKLTIDLL 292 (318)
T ss_pred HHHHHhhcCcccchhhhccccchhhhHHHHhhhhhh
Confidence 125788999999999999999999876653
No 98
>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=85.38 E-value=9.7 Score=29.66 Aligned_cols=84 Identities=17% Similarity=0.165 Sum_probs=49.1
Q ss_pred CCEEEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHH
Q 027892 37 MPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREA 116 (217)
Q Consensus 37 ~~~v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~ 116 (217)
.+.+.+|+|++|.++.+.+++-|+. ..++ . .++|.+.. .+ .+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l--~~~~-~------~~~i~~~~-----------------~~------------~~ 44 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLAL--ANGG-G------AYYIPLEL-----------------AL------------LD 44 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEE--EeCC-c------EEEEeccc-----------------hH------------HH
Confidence 4567899999999986666654443 2221 1 12333110 00 13
Q ss_pred HHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 117 EKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 117 ~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
...+.+++.+. + ...++||+.+|..+|.+ .|..++....||.
T Consensus 45 ~~~l~~~l~~~---~-~~ki~~d~K~~~~~l~~----~gi~~~~~~fDt~ 86 (178)
T cd06140 45 LAALKEWLEDE---K-IPKVGHDAKRAYVALKR----HGIELAGVAFDTM 86 (178)
T ss_pred HHHHHHHHhCC---C-CceeccchhHHHHHHHH----CCCcCCCcchhHH
Confidence 34466677652 1 34789999999999864 2433444457774
No 99
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.23 E-value=4.3 Score=41.89 Aligned_cols=109 Identities=17% Similarity=0.122 Sum_probs=61.4
Q ss_pred CCEEEEEecCCCCCCCCCcEEEEEEEEECC-cee-----e-eecCCceeecCCc-cchhhhhhHHhhhhhhcCCcHHHHh
Q 027892 37 MPLVWIDLEMTGLKIEVDRILEIACIITDG-KLT-----K-SVEGPDLVIHQTK-ECLDSMGEWCQNHHEASGLTKKVLH 108 (217)
Q Consensus 37 ~~~v~lD~ETTGl~p~~d~IieIgav~~d~-~~~-----~-~~~~~~~li~p~~-~i~~~~~~~~~~~h~itGIt~~~l~ 108 (217)
-.++.|++|+.-.+...+++|.|++++... ... . ....+....+|.. ..|... .. ...|+.+..+.
T Consensus 506 l~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~p~~~---~~---~~~~~~~~~L~ 579 (1172)
T TIGR00592 506 LVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDL---KG---EFPGKKPSLVE 579 (1172)
T ss_pred eEEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCCCCCchh---hh---hhhccCCcEEE
Confidence 344444555433333458999999885432 110 0 0011223334421 122111 11 12255555566
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhh
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDL 154 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~ 154 (217)
.-.+..+.+..|+.++... + +.+++|||+ .||+.+|-.-+..+
T Consensus 580 ~~~sEr~lL~~fl~~~~~~-D--PDii~g~n~~qfdlkvl~nR~~~l 623 (1172)
T TIGR00592 580 DLATERALIKKFMAKVKKI-D--PDEIVGHDYQQRALKVLANRINDL 623 (1172)
T ss_pred EecCHHHHHHHHHHHHHhc-C--CCEEEEEcccCccHHHHHHHHHHc
Confidence 6678888999999999853 2 346899998 89999998765444
No 100
>PHA02563 DNA polymerase; Provisional
Probab=84.46 E-value=3.7 Score=39.40 Aligned_cols=37 Identities=8% Similarity=0.147 Sum_probs=25.1
Q ss_pred HHHHHHHhhccCC-CCceEEEecHHHhHHHHHhHhhhh
Q 027892 118 KQVVEFVKKNVGT-YTPLLAGNSVYVDFMFLKKYMPDL 154 (217)
Q Consensus 118 ~~~~~~l~~~~~~-~~~~lVghn~~FD~~fL~~~~~~~ 154 (217)
.+|++|+.....+ ...++-.||..||-.||-.++.+.
T Consensus 51 ~~f~~~i~~~~~k~~~~~vYfHN~~FD~~Fil~~L~~~ 88 (630)
T PHA02563 51 DEFLQWIEDTTYKETECIIYFHNLKFDGSFILKWLLRN 88 (630)
T ss_pred HHHHHHHhhccccccceEEEEecCCccHHHHHHHHHhh
Confidence 3677888721000 125677899999999999987543
No 101
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=83.92 E-value=1.6 Score=40.58 Aligned_cols=39 Identities=15% Similarity=0.108 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHh
Q 027892 110 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYM 151 (217)
Q Consensus 110 ~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~ 151 (217)
-++..+.+.+|.+|+.+.- +.+++|||+ .||+++|..-.
T Consensus 177 f~sE~eLL~~F~~~i~~~D---PDIItGYNi~nFDlPYL~~Ra 216 (498)
T PHA02524 177 FEDEVDLLLNYIQLWKANT---PDLVFGWNSEGFDIPYIITRI 216 (498)
T ss_pred eCCHHHHHHHHHHHHHHhC---CCEEEeCCCcccCHHHHHHHH
Confidence 3589999999999998852 357999998 89999987654
No 102
>PRK05761 DNA polymerase I; Reviewed
Probab=83.78 E-value=3.4 Score=40.78 Aligned_cols=41 Identities=15% Similarity=0.172 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhc
Q 027892 111 LTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLAS 156 (217)
Q Consensus 111 ~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~ 156 (217)
.+..+++.+|.+|+..+ .+.|++|. .||+++|..-...+|.
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 35778999999999986 23566887 8999999887766664
No 103
>PHA03036 DNA polymerase; Provisional
Probab=80.42 E-value=8.1 Score=39.05 Aligned_cols=111 Identities=11% Similarity=0.081 Sum_probs=57.8
Q ss_pred cccCCCCEEEEEecCCC--C--CCCCCcEEEEEEEEECCceeeeecCCceeecCCc----cchhhhhhHHhhhhhhcCCc
Q 027892 32 EFEYKMPLVWIDLEMTG--L--KIEVDRILEIACIITDGKLTKSVEGPDLVIHQTK----ECLDSMGEWCQNHHEASGLT 103 (217)
Q Consensus 32 ~~~~~~~~v~lD~ETTG--l--~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~----~i~~~~~~~~~~~h~itGIt 103 (217)
.+..+..+++||+|.-. - +|..+.|++|+....+...... --++++..- +..+.....+. ...-+.
T Consensus 155 ~~~~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~~~~~~---~~~l~n~~~~~~~~~~~~~~~~~~---~~~~~~ 228 (1004)
T PHA03036 155 RFDIPRSYLFLDIECHFDKKFPSVFINPVSHISCCYIDLSGKEK---RFTLINEDMLSEDEIEEAVKRGYY---EIESLL 228 (1004)
T ss_pred CccCcceeEEEEEEeccCCCCCCcccCcceEEEEEEEecCCCee---EEEEeccccccccccccceeeeee---cccccc
Confidence 35788899999999963 2 2346899999975333222110 113444321 11110000000 000110
Q ss_pred H---HHHhcCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhh
Q 027892 104 K---KVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMP 152 (217)
Q Consensus 104 ~---~~l~~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~ 152 (217)
+ ...-.-++..+ +-++.+++...- .-+++|+|. .||++.|..-+.
T Consensus 229 ~~~~~~~~~~~sE~~-ml~~~~~i~~~d---~D~i~~yNg~nFD~~Yi~~R~~ 277 (1004)
T PHA03036 229 DMDYSKELILCSEIV-LLRIAKKLLELE---FDYVVTFNGHNFDLRYISNRLE 277 (1004)
T ss_pred ccCCceeeecCCHHH-HHHHHHHHHhcC---CCEEEeccCCCcchHHHHHHHH
Confidence 0 00001135555 447788887642 246899998 899998876543
No 104
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=77.64 E-value=5.2 Score=38.04 Aligned_cols=73 Identities=12% Similarity=0.165 Sum_probs=48.3
Q ss_pred EEEEecCCCCCCCCCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHHH
Q 027892 40 VWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQ 119 (217)
Q Consensus 40 v~lD~ETTGl~p~~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~~ 119 (217)
+.+|+||+|+++....++.++....+ . .+ +|.-.. + ++ --++...
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~---~----~~--yi~~~~-----------------~--~~-------~~~~~~~ 69 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE---E----AA--YIPLLH-----------------G--PE-------QLNVLAA 69 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc---c----ce--eEeecc-----------------c--hh-------hhhhHHH
Confidence 89999999999987888777754332 1 11 111100 1 11 1116778
Q ss_pred HHHHHhhccCCCCceEEEecHHHhHHHHHhHh
Q 027892 120 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYM 151 (217)
Q Consensus 120 ~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~ 151 (217)
+..|+.+. + ...||||..||..+|.+..
T Consensus 70 l~~~l~~~---~-~~kv~~~~K~d~~~l~~~G 97 (593)
T COG0749 70 LKPLLEDE---G-IKKVGQNLKYDYKVLANLG 97 (593)
T ss_pred HHHHhhCc---c-cchhccccchhHHHHHHcC
Confidence 88899873 1 2379999999999998764
No 105
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.20 E-value=19 Score=36.19 Aligned_cols=91 Identities=10% Similarity=0.066 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehHHH------------HHHHHHhCCCc-
Q 027892 113 EREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSSI------------KALCMRWYPRD- 179 (217)
Q Consensus 113 ~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~~l------------~~la~~~~p~~- 179 (217)
...+...+..|+.+. ....||||+.||+.+|.+. |..+...+.||... ..++.+++...
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 344566677888762 1347999999999999753 33333345676422 12333332210
Q ss_pred cc------CCCC-----CCCC-CChHHHHHHHHHHHHHHHHHhc
Q 027892 180 YR------KVPS-----KEQK-HRALDDIRESIMELKYYKENIF 211 (217)
Q Consensus 180 ~~------~~l~-----~~~~-H~Al~Da~at~~ll~~~~~~~~ 211 (217)
.. .+.. .... .-|..|+..|.+|+..+.+.+-
T Consensus 435 ~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 435 ILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred ccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 00 0000 0011 1367788899999988877764
No 106
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=67.37 E-value=15 Score=30.19 Aligned_cols=73 Identities=19% Similarity=0.046 Sum_probs=43.6
Q ss_pred CCcEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhh-hhcCCcHHHHhcCC-CHHHHHHHHHHHHhhc
Q 027892 53 VDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHH-EASGLTKKVLHSGL-TEREAEKQVVEFVKKN 127 (217)
Q Consensus 53 ~d~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h-~itGIt~~~l~~~~-~~~e~~~~~~~~l~~~ 127 (217)
..-..|||++.+.-+.. +.+.|+.+|+|.+..... ..-++.|. .-++|..+-.+.+. .+..++.++.+||+..
T Consensus 7 ~y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~p~G~-~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~ 81 (213)
T PF13017_consen 7 EYVPAEIAICKFSLKEG-IIDSFHTFINPGQIPLGY-RYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPN 81 (213)
T ss_pred cEEeEEEEEEEEecCCc-cchhhhcccCCCCCCcHH-HHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhc
Confidence 34578999996543332 345699999998643321 11122221 22344433223333 6999999999999875
No 107
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=66.12 E-value=22 Score=36.38 Aligned_cols=108 Identities=9% Similarity=0.130 Sum_probs=62.2
Q ss_pred cCCCCEEEEEecCCCCCCC--CCcEEEEEEEEECCc-ee------eeecCCceeecCCccchh-hhhhHHhhhhhhcCCc
Q 027892 34 EYKMPLVWIDLEMTGLKIE--VDRILEIACIITDGK-LT------KSVEGPDLVIHQTKECLD-SMGEWCQNHHEASGLT 103 (217)
Q Consensus 34 ~~~~~~v~lD~ETTGl~p~--~d~IieIgav~~d~~-~~------~~~~~~~~li~p~~~i~~-~~~~~~~~~h~itGIt 103 (217)
..+..+..+-++|+ .++. +.+|+.|++.+.... +. .....|..+++|+....+ .+.+.+.. ..++
T Consensus 526 ~Ppl~llsL~i~T~-~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~--k~~~-- 600 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTS-MNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQ--KLSK-- 600 (1429)
T ss_pred CCCeeEEEeeeeeh-hccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHh--ccCc--
Confidence 46678889999998 3443 478999988743211 10 112347889999864332 22211111 1111
Q ss_pred HHHHhcCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhh
Q 027892 104 KKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMP 152 (217)
Q Consensus 104 ~~~l~~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~ 152 (217)
+.-.-+....+.-|+.-+... + +.++||||+ .|++..|-..+.
T Consensus 601 ---v~~~~sErALLs~fla~~~~~-d--pD~iVgHn~~~~~l~VLl~R~~ 644 (1429)
T KOG0970|consen 601 ---VVLHNSERALLSHFLAMLNKE-D--PDVIVGHNIQGFYLDVLLSRLH 644 (1429)
T ss_pred ---eEEecCHHHHHHHHHHHhhcc-C--CCEEEEeccccchHHHHHHHHH
Confidence 111224555666676666652 2 346999995 999999965543
No 108
>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=64.59 E-value=22 Score=27.44 Aligned_cols=39 Identities=18% Similarity=0.210 Sum_probs=25.3
Q ss_pred HHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 120 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 120 ~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
+.+++.+. ....||||+.+|...|.+.+ |.. ...+.|+.
T Consensus 56 l~~ll~~~----~i~kv~~d~K~~~~~L~~~~---gi~-~~~~~D~~ 94 (178)
T cd06142 56 LKELLADP----NIVKVFHAAREDLELLKRDF---GIL-PQNLFDTQ 94 (178)
T ss_pred HHHHHcCC----CceEEEeccHHHHHHHHHHc---CCC-CCCcccHH
Confidence 55567652 13579999999999987543 322 33457775
No 109
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=60.84 E-value=21 Score=27.00 Aligned_cols=40 Identities=13% Similarity=0.262 Sum_probs=26.3
Q ss_pred HHHHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 118 KQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 118 ~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
..+.+|+.+. ....||||+.+|..+|++ .|..++. .+|+.
T Consensus 65 ~~l~~~l~~~----~~~kv~~d~k~~~~~L~~----~gi~~~~-~~D~~ 104 (172)
T smart00474 65 EILKDLLEDE----TITKVGHNAKFDLHVLAR----FGIELEN-IFDTM 104 (172)
T ss_pred HHHHHHhcCC----CceEEEechHHHHHHHHH----CCCcccc-hhHHH
Confidence 4455667652 135799999999999974 3443443 37875
No 110
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=60.61 E-value=61 Score=24.56 Aligned_cols=36 Identities=11% Similarity=0.031 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHHhhccCCCCceEEEecHHHhHHHHHhHh
Q 027892 112 TEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYM 151 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~ 151 (217)
+-.+.+..+++-++... ..+|.+|.+|....|+...
T Consensus 56 Pr~~~~~~L~~~i~~~~----g~ivvyN~sfE~~rL~ela 91 (130)
T PF11074_consen 56 PRRELIEALIKAIGSIY----GSIVVYNKSFEKTRLKELA 91 (130)
T ss_pred chHHHHHHHHHHhhhhc----CeEEEechHHHHHHHHHHH
Confidence 45556777777777631 2478899999999888753
No 111
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=54.03 E-value=8.7 Score=39.71 Aligned_cols=37 Identities=14% Similarity=0.129 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHh
Q 027892 110 GLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKK 149 (217)
Q Consensus 110 ~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~ 149 (217)
-++..+.+..|.+++.+. ++ -+++|+|+ .||++.+..
T Consensus 267 ~~~E~~~L~~f~~~i~~~-dp--dii~gYNi~~FD~pyl~~ 304 (1172)
T TIGR00592 267 VSEEISMIKRFWDVIDQE-DT--DVEITVNGDNFDLVYLAD 304 (1172)
T ss_pred ccchHHHHhhHHHHHhhc-Cc--chhcccccccCccceecC
Confidence 356788888888888763 22 35899998 899987765
No 112
>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=45.18 E-value=46 Score=25.20 Aligned_cols=28 Identities=11% Similarity=0.177 Sum_probs=20.1
Q ss_pred cCCCCceEEEecH-HHhHHHHHhHhhhhh
Q 027892 128 VGTYTPLLAGNSV-YVDFMFLKKYMPDLA 155 (217)
Q Consensus 128 ~~~~~~~lVghn~-~FD~~fL~~~~~~~~ 155 (217)
+|.|-||||||+. .=|...+.+....++
T Consensus 39 ip~GQPIlVGHHSE~R~Rr~~eR~~~~m~ 67 (126)
T PF12083_consen 39 IPFGQPILVGHHSEKRHRRYRERIHNRMG 67 (126)
T ss_pred cCCCCCeeccccchHHHHHHHHHHHHHHH
Confidence 4556689999886 678888887655443
No 113
>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=38.70 E-value=87 Score=23.09 Aligned_cols=39 Identities=15% Similarity=0.203 Sum_probs=24.7
Q ss_pred HHHHHhhccCCCCceEEEecHHHhHHHHHhHhhhhhcCCCCceeehH
Q 027892 120 VVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVS 166 (217)
Q Consensus 120 ~~~~l~~~~~~~~~~lVghn~~FD~~fL~~~~~~~~~~~~~~~iDt~ 166 (217)
+.+++.+. ....+|||+.+|..+|.+. +........|+.
T Consensus 45 l~~~l~~~----~~~kv~~d~K~~~~~L~~~----~~~~~~~~~D~~ 83 (150)
T cd09018 45 LKPLLEDE----KALKVGQNLKYDRGILLNY----FIELRGIAFDTM 83 (150)
T ss_pred HHHHhcCC----CCceeeecHHHHHHHHHHc----CCccCCcchhHH
Confidence 55566652 1347899999999998653 222334457775
No 114
>COG4674 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]
Probab=35.39 E-value=65 Score=26.85 Aligned_cols=25 Identities=44% Similarity=0.508 Sum_probs=16.8
Q ss_pred ecCCCCCCCCC-----------cEEEEEEE-EECCce
Q 027892 44 LEMTGLKIEVD-----------RILEIACI-ITDGKL 68 (217)
Q Consensus 44 ~ETTGl~p~~d-----------~IieIgav-~~d~~~ 68 (217)
++++||.+..+ +=+|||++ ..+++.
T Consensus 132 La~igL~~~~~~~A~~LSHGqKQwLEIGMll~Q~P~l 168 (249)
T COG4674 132 LATIGLGDERDRLAALLSHGQKQWLEIGMLLAQDPKL 168 (249)
T ss_pred HHHcccchhhhhhhhhhccchhhhhhhheeeccCCcE
Confidence 57888886643 45788888 445554
No 115
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=29.15 E-value=2.2e+02 Score=27.15 Aligned_cols=79 Identities=15% Similarity=0.153 Sum_probs=44.8
Q ss_pred cCCCHHHHHHHHHHHHhhccCCCCceEEEecH-HHhHHHHHhHhhhhhcCCCCceeehHHHHHHHHHhCCCccc------
Q 027892 109 SGLTEREAEKQVVEFVKKNVGTYTPLLAGNSV-YVDFMFLKKYMPDLASLFSHVLVDVSSIKALCMRWYPRDYR------ 181 (217)
Q Consensus 109 ~~~~~~e~~~~~~~~l~~~~~~~~~~lVghn~-~FD~~fL~~~~~~~~~~~~~~~iDt~~l~~la~~~~p~~~~------ 181 (217)
..+.+.+.++.|..||.+-+ --|+ --|+..|-..+.-...-++++.|++- .....+.|.+..
T Consensus 233 TDsGL~~LlPyFv~fIae~v--------s~ni~~~nL~lL~~lm~m~rSLl~Np~i~le---pYlh~L~PSvlTCvVsk~ 301 (576)
T KOG2549|consen 233 TDSGLQQLLPYFVTFIAEGV--------SVNIVQNNLELLIYLMRMVRSLLDNPNIFLE---PYLHQLVPSVLTCVVSKN 301 (576)
T ss_pred cCccHHHHHHHHHHHHhhhe--------eeccccccHHHHHHHHHHHHHHhcCCccchh---hHHHHHhhHHHHhhhhhh
Confidence 45689999999999998832 1222 33455555444332223455555543 222333343221
Q ss_pred -CCCCCCCCCChHHHHHH
Q 027892 182 -KVPSKEQKHRALDDIRE 198 (217)
Q Consensus 182 -~~l~~~~~H~Al~Da~a 198 (217)
...+..+.|.||-|--|
T Consensus 302 l~~~p~~dnhwaLRDfAA 319 (576)
T KOG2549|consen 302 LCLRPELDNHWALRDFAA 319 (576)
T ss_pred ccCCccccchHHHHHHHH
Confidence 12467889999999765
No 116
>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=26.03 E-value=68 Score=31.02 Aligned_cols=43 Identities=21% Similarity=0.450 Sum_probs=30.9
Q ss_pred CHHHHHHHHHHHHhhccC--CCCceEEEe-cHHHhHHHHHhHhhhh
Q 027892 112 TEREAEKQVVEFVKKNVG--TYTPLLAGN-SVYVDFMFLKKYMPDL 154 (217)
Q Consensus 112 ~~~e~~~~~~~~l~~~~~--~~~~~lVgh-n~~FD~~fL~~~~~~~ 154 (217)
+-..+..+|++||.+... ..+.+|||+ +-=||.+.|++.++.-
T Consensus 253 s~~~li~~FL~Wl~e~~~~n~~ti~LvGy~ss~FD~pLLra~wp~~ 298 (651)
T PF03337_consen 253 SNKALISDFLKWLRECIMKNIRTIILVGYFSSFFDFPLLRAYWPKN 298 (651)
T ss_pred CchHHHHHHHHHHHHHHhccCceEEEeehhhhhhccHHHHhhcccC
Confidence 445588899999987221 123578995 5568999999998643
No 117
>PHA01746 hypothetical protein
Probab=22.71 E-value=95 Score=23.03 Aligned_cols=57 Identities=16% Similarity=0.246 Sum_probs=32.2
Q ss_pred cEEEEEEEEECCceeeeecCCceeecCCccchhhhhhHHhhhhhhcCCcHHHHhcCCCHHHHHHHHHHHHhhc
Q 027892 55 RILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHEASGLTKKVLHSGLTEREAEKQVVEFVKKN 127 (217)
Q Consensus 55 ~IieIgav~~d~~~~~~~~~~~~li~p~~~i~~~~~~~~~~~h~itGIt~~~l~~~~~~~e~~~~~~~~l~~~ 127 (217)
-+++|-|+.-||... |+.-|+..... -..+ |||+++-.+-.-+++.+...-.||..+
T Consensus 34 ivlQiNAvP~dg~vr-----~SMTiHs~nNf-------kKQI----GiTa~DAgdL~lIa~FLeKYS~~LnkY 90 (131)
T PHA01746 34 IVVQLNAVPQDGKIR-----YSMTIHSQNNF-------RKQI----GITPQDAGDLKLIAEFLEKYSDFLNEY 90 (131)
T ss_pred EEEEeeccCCCCeeE-----EEEEEecccch-------hhhc----CCCccchhhHHHHHHHHHHHHHHHHHH
Confidence 357788876666653 44556654322 1222 899866544444555566666666654
Done!