Query psy17350
Match_columns 528
No_of_seqs 378 out of 1811
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 20:04:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17350.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17350hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 2.6E-39 5.7E-44 306.5 14.6 147 365-515 1-174 (174)
2 KOG2248|consensus 100.0 1.1E-38 2.4E-43 333.8 16.2 168 358-526 212-380 (380)
3 KOG2249|consensus 100.0 1.6E-37 3.4E-42 307.0 13.4 152 362-517 105-262 (280)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 1.2E-35 2.7E-40 275.1 15.8 150 365-515 1-150 (150)
5 cd06149 ISG20 DEDDh 3'-5' exon 100.0 3.8E-34 8.3E-39 267.2 15.5 149 365-515 1-157 (157)
6 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 4.8E-34 1E-38 267.0 14.0 150 365-515 1-161 (161)
7 cd06144 REX4_like DEDDh 3'-5' 100.0 1.2E-30 2.7E-35 241.6 15.1 147 365-515 1-152 (152)
8 KOG2249|consensus 99.9 2.4E-28 5.1E-33 242.0 5.6 110 3-119 153-268 (280)
9 cd06143 PAN2_exo DEDDh 3'-5' e 99.9 8.9E-28 1.9E-32 227.9 6.6 103 3-111 64-174 (174)
10 PRK07247 DNA polymerase III su 99.9 5.9E-25 1.3E-29 212.7 17.5 153 362-522 5-170 (195)
11 PRK07740 hypothetical protein; 99.9 1.4E-24 3E-29 216.7 16.5 159 361-525 58-230 (244)
12 PRK05711 DNA polymerase III su 99.9 4.2E-24 9.1E-29 212.9 16.6 160 362-526 4-181 (240)
13 PRK09146 DNA polymerase III su 99.9 6.8E-24 1.5E-28 211.2 17.1 155 361-521 46-227 (239)
14 PRK06310 DNA polymerase III su 99.9 7.5E-24 1.6E-28 212.1 17.1 155 360-520 5-173 (250)
15 cd06130 DNA_pol_III_epsilon_li 99.9 7.1E-24 1.5E-28 194.1 15.4 143 364-515 1-155 (156)
16 TIGR01406 dnaQ_proteo DNA poly 99.9 7.7E-24 1.7E-28 208.9 16.3 153 363-520 1-171 (225)
17 smart00479 EXOIII exonuclease 99.9 6.7E-24 1.4E-28 195.4 14.4 153 363-521 1-167 (169)
18 PRK09145 DNA polymerase III su 99.9 1E-23 2.2E-28 203.8 16.4 153 361-519 28-199 (202)
19 PRK06063 DNA polymerase III su 99.9 1.2E-23 2.6E-28 216.9 17.6 155 360-522 13-180 (313)
20 PRK06807 DNA polymerase III su 99.9 2E-23 4.3E-28 215.4 17.7 154 361-521 7-172 (313)
21 PRK06309 DNA polymerase III su 99.9 1.1E-23 2.4E-28 208.4 14.6 153 363-520 3-165 (232)
22 PRK08517 DNA polymerase III su 99.9 5.6E-23 1.2E-27 206.7 18.6 186 322-522 35-232 (257)
23 PRK07942 DNA polymerase III su 99.9 1.7E-23 3.7E-28 207.2 13.8 158 361-522 5-181 (232)
24 TIGR00573 dnaq exonuclease, DN 99.9 3.5E-23 7.5E-28 202.6 15.7 159 362-525 7-181 (217)
25 cd06131 DNA_pol_III_epsilon_Ec 99.9 4.5E-23 9.7E-28 191.9 15.5 149 364-517 1-166 (167)
26 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 1.6E-23 3.4E-28 199.1 11.5 144 364-516 1-176 (177)
27 PRK07983 exodeoxyribonuclease 99.9 7.4E-23 1.6E-27 201.4 16.3 147 364-520 2-153 (219)
28 PRK07748 sporulation inhibitor 99.9 8.4E-23 1.8E-27 198.4 13.9 159 362-524 4-183 (207)
29 PRK06195 DNA polymerase III su 99.9 2.2E-22 4.9E-27 207.0 17.6 150 363-521 2-164 (309)
30 KOG2248|consensus 99.9 9.9E-24 2.1E-28 221.5 5.7 116 3-121 261-379 (380)
31 PRK07246 bifunctional ATP-depe 99.9 2.4E-22 5.1E-27 230.1 16.9 157 361-524 6-173 (820)
32 PRK07883 hypothetical protein; 99.9 4.3E-22 9.3E-27 219.5 16.7 161 360-526 13-187 (557)
33 TIGR01298 RNaseT ribonuclease 99.9 3.9E-22 8.4E-27 193.3 13.6 158 362-525 8-196 (200)
34 cd06134 RNaseT DEDDh 3'-5' exo 99.9 1.5E-21 3.3E-26 187.4 14.7 153 362-520 5-188 (189)
35 PRK05168 ribonuclease T; Provi 99.9 1.5E-21 3.3E-26 190.6 14.4 159 362-526 17-206 (211)
36 TIGR01407 dinG_rel DnaQ family 99.9 1.8E-21 3.9E-26 223.9 17.3 153 363-521 1-165 (850)
37 cd06127 DEDDh DEDDh 3'-5' exon 99.9 2.8E-21 6E-26 173.6 13.7 144 365-514 1-158 (159)
38 PRK08074 bifunctional ATP-depe 99.9 2.5E-21 5.3E-26 224.5 17.0 156 362-523 3-171 (928)
39 PRK05601 DNA polymerase III su 99.9 7E-21 1.5E-25 198.7 17.0 152 361-517 45-245 (377)
40 COG2176 PolC DNA polymerase II 99.9 2.1E-22 4.5E-27 228.4 5.9 160 361-526 420-591 (1444)
41 TIGR01405 polC_Gram_pos DNA po 99.9 3.7E-21 8E-26 226.1 16.3 161 360-526 188-360 (1213)
42 PRK06722 exonuclease; Provisio 99.9 5.1E-21 1.1E-25 194.6 15.0 154 361-520 4-180 (281)
43 cd06133 ERI-1_3'hExo_like DEDD 99.9 3.4E-21 7.5E-26 179.4 11.6 149 364-517 1-175 (176)
44 cd06138 ExoI_N N-terminal DEDD 99.8 7.8E-21 1.7E-25 181.2 10.0 146 365-514 1-182 (183)
45 COG0847 DnaQ DNA polymerase II 99.8 5.4E-20 1.2E-24 181.4 16.3 156 362-520 13-181 (243)
46 PF00929 RNase_T: Exonuclease; 99.8 4.1E-22 8.9E-27 179.1 0.2 146 365-514 1-164 (164)
47 PRK09182 DNA polymerase III su 99.8 7.2E-20 1.6E-24 187.5 14.6 151 361-520 36-200 (294)
48 PRK11779 sbcB exonuclease I; P 99.8 3.7E-18 8.1E-23 184.8 13.6 158 361-522 5-199 (476)
49 PTZ00315 2'-phosphotransferase 99.8 1.2E-17 2.7E-22 182.8 16.1 160 362-525 56-259 (582)
50 PRK00448 polC DNA polymerase I 99.7 5.3E-18 1.2E-22 201.9 13.8 160 361-526 418-589 (1437)
51 PRK05359 oligoribonuclease; Pr 99.7 5E-18 1.1E-22 162.5 10.9 147 362-520 3-174 (181)
52 cd06135 Orn DEDDh 3'-5' exonuc 99.7 3.1E-18 6.7E-23 162.3 8.3 142 364-519 1-170 (173)
53 KOG1275|consensus 99.7 2.9E-18 6.4E-23 190.7 6.3 160 356-519 904-1090(1118)
54 KOG1275|consensus 99.7 4.3E-18 9.3E-23 189.4 7.1 130 5-150 978-1116(1118)
55 cd06149 ISG20 DEDDh 3'-5' exon 99.6 3.1E-15 6.7E-20 139.9 6.1 104 3-111 46-157 (157)
56 cd06145 REX1_like DEDDh 3'-5' 99.5 1.5E-14 3.3E-19 134.2 6.6 105 4-111 44-150 (150)
57 cd06137 DEDDh_RNase DEDDh 3'-5 99.5 3.5E-14 7.6E-19 133.0 6.3 107 3-111 45-161 (161)
58 cd06144 REX4_like DEDDh 3'-5' 99.1 8.1E-11 1.8E-15 109.3 6.5 101 4-111 47-152 (152)
59 cd05160 DEDDy_DNA_polB_exo DED 98.9 2.7E-08 5.8E-13 95.5 13.3 123 364-494 1-163 (199)
60 KOG3242|consensus 98.7 1E-08 2.2E-13 97.4 5.3 144 362-520 26-198 (208)
61 COG1949 Orn Oligoribonuclease 98.7 1.5E-08 3.2E-13 95.5 6.1 148 361-523 5-180 (184)
62 cd06139 DNA_polA_I_Ecoli_like_ 98.6 5.2E-07 1.1E-11 85.0 12.7 142 361-520 4-169 (193)
63 COG5018 KapD Inhibitor of the 98.6 2.1E-08 4.6E-13 94.9 1.7 159 363-525 5-189 (210)
64 KOG0542|consensus 98.5 1.8E-07 4E-12 93.5 6.3 158 364-526 58-247 (280)
65 PF01612 DNA_pol_A_exo1: 3'-5' 98.4 1.8E-06 3.8E-11 79.7 10.7 133 362-519 20-173 (176)
66 COG2925 SbcB Exonuclease I [DN 98.4 1.8E-06 3.9E-11 90.7 9.9 159 360-522 7-202 (475)
67 cd06146 mut-7_like_exo DEDDy 3 98.3 3.9E-06 8.5E-11 81.2 11.5 134 360-518 20-192 (193)
68 PRK05755 DNA polymerase I; Pro 98.1 1.6E-05 3.4E-10 93.2 11.7 134 361-520 314-468 (880)
69 cd06130 DNA_pol_III_epsilon_li 98.0 4.5E-06 9.8E-11 76.4 4.3 98 4-111 47-155 (156)
70 cd06125 DnaQ_like_exo DnaQ-lik 98.0 2.5E-05 5.3E-10 67.6 8.4 58 365-458 1-61 (96)
71 smart00479 EXOIII exonuclease 98.0 3.2E-06 6.9E-11 77.8 2.9 105 5-117 51-167 (169)
72 cd06141 WRN_exo DEDDy 3'-5' ex 98.0 4.5E-05 9.7E-10 71.3 9.9 128 361-517 17-168 (170)
73 cd00007 35EXOc 3'-5' exonuclea 97.9 0.00034 7.3E-09 62.7 13.3 130 364-519 2-153 (155)
74 cd06129 RNaseD_like DEDDy 3'-5 97.8 0.00012 2.6E-09 68.6 9.8 127 361-517 12-159 (161)
75 cd05780 DNA_polB_Kod1_like_exo 97.8 0.0002 4.3E-09 69.3 11.1 117 361-494 2-156 (195)
76 PRK07740 hypothetical protein; 97.7 4.5E-05 9.7E-10 76.7 4.6 104 4-116 111-225 (244)
77 cd06127 DEDDh DEDDh 3'-5' exon 97.5 0.00014 3E-09 65.2 4.9 99 5-111 50-159 (159)
78 PF00929 RNase_T: Exonuclease; 97.4 5.5E-06 1.2E-10 74.3 -4.8 100 4-110 52-164 (164)
79 PF04857 CAF1: CAF1 family rib 97.4 0.0012 2.7E-08 66.9 11.3 150 361-515 21-261 (262)
80 PRK09145 DNA polymerase III su 97.3 0.00026 5.6E-09 68.7 4.8 101 5-114 82-198 (202)
81 PRK10829 ribonuclease D; Provi 97.3 0.0027 5.8E-08 68.0 12.3 129 360-519 20-168 (373)
82 cd05781 DNA_polB_B3_exo DEDDy 97.2 0.0029 6.2E-08 61.3 11.1 129 362-516 3-187 (188)
83 PRK07247 DNA polymerase III su 97.2 0.00066 1.4E-08 66.3 6.6 104 4-117 54-169 (195)
84 cd06134 RNaseT DEDDh 3'-5' exo 97.2 0.00079 1.7E-08 65.0 6.8 109 4-117 62-189 (189)
85 TIGR00573 dnaq exonuclease, DN 97.2 0.00035 7.5E-09 68.8 4.0 110 4-120 57-180 (217)
86 PRK06310 DNA polymerase III su 97.1 0.00046 1E-08 69.7 4.8 104 4-116 57-173 (250)
87 PRK06807 DNA polymerase III su 97.1 0.00057 1.2E-08 71.4 4.9 102 5-116 59-171 (313)
88 cd05779 DNA_polB_epsilon_exo D 97.1 0.011 2.4E-07 58.1 13.7 150 362-514 2-203 (204)
89 cd05784 DNA_polB_II_exo DEDDy 97.1 0.008 1.7E-07 58.6 12.2 116 361-493 2-153 (193)
90 PF13482 RNase_H_2: RNase_H su 97.0 0.0012 2.6E-08 61.2 5.7 106 365-495 1-117 (164)
91 smart00474 35EXOc 3'-5' exonuc 97.0 0.019 4E-07 52.4 13.5 88 432-519 65-169 (172)
92 cd06133 ERI-1_3'hExo_like DEDD 97.0 0.00063 1.4E-08 63.3 3.6 102 5-112 59-174 (176)
93 PRK06063 DNA polymerase III su 96.9 0.001 2.2E-08 69.5 5.0 104 4-116 64-178 (313)
94 cd06142 RNaseD_exo DEDDy 3'-5' 96.9 0.015 3.3E-07 54.0 12.4 129 362-519 12-158 (178)
95 cd06136 TREX1_2 DEDDh 3'-5' ex 96.8 0.0012 2.5E-08 63.1 4.1 100 4-113 63-177 (177)
96 cd05777 DNA_polB_delta_exo DED 96.8 0.026 5.6E-07 56.1 13.5 145 361-517 6-223 (230)
97 PRK06309 DNA polymerase III su 96.8 0.0016 3.4E-08 64.9 4.8 105 4-116 49-165 (232)
98 cd05785 DNA_polB_like2_exo Unc 96.7 0.0083 1.8E-07 59.0 9.5 73 360-456 7-90 (207)
99 PRK07246 bifunctional ATP-depe 96.7 0.0017 3.6E-08 75.9 5.1 103 5-116 57-169 (820)
100 cd06148 Egl_like_exo DEDDy 3'- 96.7 0.0045 9.7E-08 60.1 7.2 88 433-520 56-176 (197)
101 TIGR01388 rnd ribonuclease D. 96.7 0.021 4.6E-07 60.9 12.6 128 361-519 17-164 (367)
102 COG0349 Rnd Ribonuclease D [Tr 96.5 0.023 5E-07 60.4 11.7 120 361-507 16-143 (361)
103 PRK07942 DNA polymerase III su 96.5 0.0034 7.4E-08 62.7 5.3 112 5-121 58-184 (232)
104 TIGR01298 RNaseT ribonuclease 96.5 0.0039 8.5E-08 60.8 5.5 109 5-118 66-193 (200)
105 PRK07748 sporulation inhibitor 96.5 0.0045 9.9E-08 60.4 5.9 111 4-121 62-184 (207)
106 PRK07883 hypothetical protein; 96.5 0.0029 6.4E-08 70.9 5.2 109 4-121 65-186 (557)
107 PRK06195 DNA polymerase III su 96.5 0.0037 8E-08 65.0 5.6 103 4-116 50-163 (309)
108 TIGR01407 dinG_rel DnaQ family 96.5 0.0025 5.4E-08 74.7 4.8 103 5-116 51-164 (850)
109 cd05783 DNA_polB_B1_exo DEDDy 96.5 0.037 8E-07 54.4 12.1 127 361-493 4-170 (204)
110 PRK08517 DNA polymerase III su 96.4 0.0045 9.8E-08 63.0 5.0 103 5-117 118-231 (257)
111 TIGR01405 polC_Gram_pos DNA po 96.3 0.0024 5.3E-08 77.1 3.5 104 4-116 240-354 (1213)
112 PRK08074 bifunctional ATP-depe 96.0 0.0071 1.5E-07 71.7 4.8 102 5-117 55-169 (928)
113 PRK07983 exodeoxyribonuclease 95.8 0.012 2.5E-07 58.6 4.8 103 4-116 47-153 (219)
114 PRK05711 DNA polymerase III su 95.8 0.0097 2.1E-07 60.0 4.2 103 5-115 57-174 (240)
115 cd06131 DNA_pol_III_epsilon_Ec 95.8 0.0095 2.1E-07 55.4 3.9 100 5-112 52-165 (167)
116 PRK11779 sbcB exonuclease I; P 95.7 0.0092 2E-07 65.8 3.9 108 4-117 60-198 (476)
117 TIGR01406 dnaQ_proteo DNA poly 95.6 0.014 3.1E-07 58.0 4.8 103 5-115 53-170 (225)
118 PRK05168 ribonuclease T; Provi 95.6 0.015 3.3E-07 57.2 4.9 107 5-116 75-200 (211)
119 cd06138 ExoI_N N-terminal DEDD 95.5 0.012 2.6E-07 56.3 3.7 101 5-111 52-183 (183)
120 PRK09146 DNA polymerase III su 95.3 0.02 4.2E-07 57.7 4.5 104 4-116 99-226 (239)
121 cd06140 DNA_polA_I_Bacillus_li 95.3 0.35 7.5E-06 45.3 12.5 105 363-494 4-113 (178)
122 COG0847 DnaQ DNA polymerase II 95.2 0.029 6.3E-07 55.5 5.2 108 3-116 63-181 (243)
123 PRK05762 DNA polymerase II; Re 95.1 0.19 4E-06 58.9 12.3 138 360-516 153-347 (786)
124 COG0749 PolA DNA polymerase I 94.9 0.089 1.9E-06 59.4 8.4 133 365-521 25-180 (593)
125 PRK06722 exonuclease; Provisio 94.6 0.04 8.6E-07 57.0 4.5 104 4-115 60-179 (281)
126 cd06146 mut-7_like_exo DEDDy 3 94.3 0.066 1.4E-06 51.9 5.1 86 27-112 70-190 (193)
127 PRK00448 polC DNA polymerase I 94.3 0.06 1.3E-06 66.4 5.8 102 5-115 470-582 (1437)
128 cd05778 DNA_polB_zeta_exo inac 93.7 1.2 2.6E-05 44.5 12.9 154 362-520 4-222 (231)
129 PRK05601 DNA polymerase III su 93.1 0.27 5.8E-06 52.8 7.4 103 5-113 96-245 (377)
130 cd05776 DNA_polB_alpha_exo ina 93.0 0.44 9.4E-06 47.7 8.5 130 363-494 4-187 (234)
131 cd06135 Orn DEDDh 3'-5' exonuc 92.9 0.14 2.9E-06 48.8 4.6 92 7-115 61-170 (173)
132 PF01612 DNA_pol_A_exo1: 3'-5' 92.6 0.11 2.4E-06 47.7 3.5 87 27-114 65-172 (176)
133 PF03104 DNA_pol_B_exo1: DNA p 92.6 0.28 6E-06 50.1 6.6 86 360-456 155-254 (325)
134 cd06147 Rrp6p_like_exo DEDDy 3 92.5 0.94 2E-05 43.4 9.7 103 363-494 25-132 (192)
135 cd09018 DEDDy_polA_RNaseD_like 92.2 1.2 2.6E-05 40.0 9.5 61 434-494 45-110 (150)
136 PTZ00166 DNA polymerase delta 92.1 1.6 3.4E-05 53.0 13.0 147 360-517 262-482 (1054)
137 PRK09182 DNA polymerase III su 92.1 0.15 3.2E-06 53.0 4.0 101 4-116 93-200 (294)
138 cd06141 WRN_exo DEDDy 3'-5' ex 91.8 0.29 6.4E-06 45.6 5.3 63 29-91 63-131 (170)
139 cd06129 RNaseD_like DEDDy 3'-5 90.4 0.27 5.8E-06 46.0 3.5 83 29-112 57-158 (161)
140 cd05782 DNA_polB_like1_exo Unc 90.3 0.32 6.8E-06 48.0 4.1 64 428-493 79-169 (208)
141 PRK05359 oligoribonuclease; Pr 89.9 0.65 1.4E-05 44.8 5.8 93 7-116 65-174 (181)
142 PF10108 DNA_pol_B_exo2: Predi 89.5 4.9 0.00011 40.1 11.7 91 427-519 37-171 (209)
143 TIGR00593 pola DNA polymerase 89.3 1.1 2.4E-05 53.3 8.2 93 427-520 363-476 (887)
144 TIGR00592 pol2 DNA polymerase 88.0 7.3 0.00016 48.0 14.1 129 363-493 507-682 (1172)
145 PHA02528 43 DNA polymerase; Pr 86.9 3.3 7.1E-05 49.4 10.0 153 360-516 104-323 (881)
146 cd00007 35EXOc 3'-5' exonuclea 84.6 1 2.2E-05 40.1 3.4 66 26-91 41-112 (155)
147 smart00474 35EXOc 3'-5' exonuc 83.9 1.7 3.8E-05 39.4 4.8 62 28-91 64-132 (172)
148 smart00486 POLBc DNA polymeras 83.4 2 4.3E-05 45.8 5.7 144 362-517 3-220 (471)
149 cd06139 DNA_polA_I_Ecoli_like_ 82.4 1.8 3.9E-05 40.6 4.4 92 24-115 52-168 (193)
150 KOG4793|consensus 82.0 0.8 1.7E-05 47.2 1.9 162 358-521 9-218 (318)
151 PHA02570 dexA exonuclease; Pro 81.0 1.7 3.8E-05 43.5 3.8 92 365-457 4-124 (220)
152 KOG0969|consensus 79.7 0.92 2E-05 52.5 1.6 148 361-519 273-478 (1066)
153 cd06142 RNaseD_exo DEDDy 3'-5' 79.3 3.5 7.5E-05 38.2 5.1 63 27-90 52-120 (178)
154 PRK05761 DNA polymerase I; Rev 78.0 8.2 0.00018 45.6 8.7 90 425-514 208-334 (787)
155 PTZ00315 2'-phosphotransferase 77.7 4 8.8E-05 46.4 5.8 114 4-123 113-261 (582)
156 COG2176 PolC DNA polymerase II 76.8 2 4.4E-05 52.0 3.3 104 4-116 471-585 (1444)
157 COG0417 PolB DNA polymerase el 76.8 32 0.0007 40.7 13.1 123 358-494 150-309 (792)
158 PRK10829 ribonuclease D; Provi 76.1 5.7 0.00012 42.9 6.2 134 29-171 64-219 (373)
159 KOG0304|consensus 69.1 15 0.00033 37.0 6.9 105 411-518 109-236 (239)
160 TIGR01388 rnd ribonuclease D. 64.6 12 0.00027 40.1 5.7 63 29-92 60-128 (367)
161 COG2925 SbcB Exonuclease I [DN 61.1 11 0.00024 40.9 4.5 109 4-118 63-202 (475)
162 cd06128 DNA_polA_exo DEDDy 3'- 61.1 14 0.00031 33.5 4.8 60 434-493 45-109 (151)
163 PHA02524 43A DNA polymerase su 54.0 47 0.001 37.4 8.0 128 361-494 105-288 (498)
164 cd06148 Egl_like_exo DEDDy 3'- 52.4 14 0.00031 35.8 3.3 63 28-90 54-129 (197)
165 COG3359 Predicted exonuclease 50.4 60 0.0013 33.6 7.4 113 361-496 97-221 (278)
166 TIGR03491 RecB family nuclease 49.9 1.3E+02 0.0028 33.2 10.7 54 440-495 343-411 (457)
167 PRK05755 DNA polymerase I; Pro 49.6 20 0.00044 42.7 4.7 89 27-116 358-468 (880)
168 KOG0970|consensus 48.4 44 0.00095 41.0 6.9 91 359-456 526-639 (1429)
169 KOG1798|consensus 42.8 2.5E+02 0.0055 36.0 12.0 149 360-518 244-451 (2173)
170 KOG2613|consensus 41.2 94 0.002 34.3 7.6 126 360-522 311-446 (502)
171 COG5018 KapD Inhibitor of the 38.9 32 0.00069 33.7 3.3 55 60-117 131-185 (210)
172 PF00843 Arena_nucleocap: Aren 38.3 30 0.00065 38.3 3.3 138 363-509 373-526 (533)
173 cd09018 DEDDy_polA_RNaseD_like 35.7 21 0.00046 31.8 1.6 61 30-90 44-110 (150)
174 KOG3657|consensus 29.8 33 0.00071 40.8 2.1 31 439-469 239-275 (1075)
175 PF13017 Maelstrom: piRNA path 25.4 86 0.0019 31.1 4.0 65 377-441 6-81 (213)
176 PF11906 DUF3426: Protein of u 23.9 2.8E+02 0.0061 25.3 6.9 61 359-419 64-126 (149)
177 cd06140 DNA_polA_I_Bacillus_li 22.5 70 0.0015 29.7 2.6 63 28-90 45-113 (178)
178 COG0349 Rnd Ribonuclease D [Tr 22.0 1.3E+02 0.0027 32.7 4.6 78 31-109 62-152 (361)
No 1
>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=100.00 E-value=2.6e-39 Score=306.49 Aligned_cols=147 Identities=32% Similarity=0.468 Sum_probs=134.5
Q ss_pred EEEeeceecCCC--------CcC--------cEEEEEEEE----eCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccC
Q psy17350 365 YGLDCEMCKTSN--------DQN--------ELTRVTLVD----EQENVVYESLVKPYNPITNYLTAYSGITRALLAPVA 424 (528)
Q Consensus 365 vALDcEmtgt~~--------g~~--------eLirIs~Vd----~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~ 424 (528)
+||||||+++++ |+. +|+||++|| ++|+++||+||+|..+|.||+|+|||||+++|+++.
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 589999998877 433 799999999 699999999999999999999999999999999863
Q ss_pred -----CCHHHHHHHHHhcCCCCcEEEEcCchhhHHHHcccCC--CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCC
Q psy17350 425 -----TRLEHVQKILSELLPPDAILVGQSLNCDLHALKMMHP--YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQ 497 (528)
Q Consensus 425 -----p~l~dV~~~L~~~i~~d~ILVGHnL~fDL~~L~~~hp--~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~ 497 (528)
.++++++.++.+++++++|||||++++||++|++.|| .+|||+.+|+.+. .++++|+.||+.|||++||.+
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~--~r~~sLk~La~~~L~~~IQ~~ 158 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPG--QRKLSLRFLAWYLLGEKIQSE 158 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCC--CCChhHHHHHHHHcCCcccCC
Confidence 4799999999999988999999999999999999988 6999999997643 358999999999999999985
Q ss_pred CCCCChHHHHHHHHHHHH
Q psy17350 498 DGGHCSKEDAIAALRLVK 515 (528)
Q Consensus 498 ~~~HdAlEDA~AT~eL~~ 515 (528)
+|||+|||+|||+||+
T Consensus 159 --~HdSvEDArAam~Ly~ 174 (174)
T cd06143 159 --THDSIEDARTALKLYR 174 (174)
T ss_pred --CcCcHHHHHHHHHHhC
Confidence 8999999999999984
No 2
>KOG2248|consensus
Probab=100.00 E-value=1.1e-38 Score=333.83 Aligned_cols=168 Identities=46% Similarity=0.669 Sum_probs=160.1
Q ss_pred CCCCCCeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 358 VTPTSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 358 ~~~~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
+....+++|||||||.+..| .|++||++||.+++++||+||+|..+|.||+|+|||||++|+++++.+++|||.+|++|
T Consensus 212 v~~~~~i~AlDCEm~~te~g-~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~ 290 (380)
T KOG2248|consen 212 VSKSPNIFALDCEMVVTENG-LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLEL 290 (380)
T ss_pred CCCCCCeEEEEeeeeeeccc-eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHhh
Confidence 56678999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHcccCCCEeeehhhchhcCCC-CCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMMHPYVIDTSVIFNTTGIR-THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKL 516 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~hp~vIDTs~L~~~~~~~-~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~ 516 (528)
++.++|||||++++||++|++.||.+|||+.+|.+..++ .++.+|++||+.|||+.||++..+|+|.|||+|||+|+++
T Consensus 291 ~~~~TILVGHSLenDL~aLKl~H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~ 370 (380)
T KOG2248|consen 291 ISKNTILVGHSLENDLKALKLDHPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHDSVEDALACMKLVKL 370 (380)
T ss_pred cCcCcEEEeechhhHHHHHhhhCCceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999987765 6788999999999999999655689999999999999999
Q ss_pred HHHcCCcCCC
Q psy17350 517 KLSKGDLIGL 526 (528)
Q Consensus 517 ~L~~g~~fg~ 526 (528)
+++++..||.
T Consensus 371 k~~~~~~~g~ 380 (380)
T KOG2248|consen 371 KIKNSESQGS 380 (380)
T ss_pred HHhcccccCC
Confidence 9999999984
No 3
>KOG2249|consensus
Probab=100.00 E-value=1.6e-37 Score=306.96 Aligned_cols=152 Identities=39% Similarity=0.537 Sum_probs=141.3
Q ss_pred CCeEEEeeceecCCCC--cCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC
Q psy17350 362 SPLYGLDCEMCKTSND--QNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP 439 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g--~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~ 439 (528)
.++|||||||+|++++ .+.++||||||+.|.|+||+||||..+|+||+|++|||+++.+.+| .+|+.||.++.+||.
T Consensus 105 ~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A-~pf~~aQ~ev~klL~ 183 (280)
T KOG2249|consen 105 TRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDA-MPFKVAQKEVLKLLK 183 (280)
T ss_pred ceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccC-ccHHHHHHHHHHHHh
Confidence 3799999999999985 6789999999999999999999999999999999999999999995 999999999999998
Q ss_pred CCcEEEEcCchhhHHHHcccCCC--EeeehhhchhcC--CCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHH
Q psy17350 440 PDAILVGQSLNCDLHALKMMHPY--VIDTSVIFNTTG--IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515 (528)
Q Consensus 440 ~d~ILVGHnL~fDL~~L~~~hp~--vIDTs~L~~~~~--~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~ 515 (528)
++|||||.|.+||.+|++.||+ +.||+.+.+... .....+||+.|++.+||++||.| .|+|+|||+|||+||+
T Consensus 184 -gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~G--eHsSvEDA~AtM~LY~ 260 (280)
T KOG2249|consen 184 -GRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVG--EHSSVEDARATMELYK 260 (280)
T ss_pred -CCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhcc--ccCcHHHHHHHHHHHH
Confidence 9999999999999999999995 899999876544 34567999999999999999997 5999999999999998
Q ss_pred HH
Q psy17350 516 LK 517 (528)
Q Consensus 516 ~~ 517 (528)
+.
T Consensus 261 ~v 262 (280)
T KOG2249|consen 261 RV 262 (280)
T ss_pred HH
Confidence 54
No 4
>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=100.00 E-value=1.2e-35 Score=275.05 Aligned_cols=150 Identities=55% Similarity=0.805 Sum_probs=137.6
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCCCcEE
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDAIL 444 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d~IL 444 (528)
|||||||+|+..| +||++|++|+.+|+++|++||+|..+|++++|++||||++||+++.|++++|++++.+|++++++|
T Consensus 1 ~~iD~E~~g~~~g-~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~~~~vl 79 (150)
T cd06145 1 FALDCEMCYTTDG-LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79 (150)
T ss_pred CEEeeeeeeecCC-CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhCCCCEE
Confidence 6899999999998 999999999999999999999999999999999999999999996459999999999999768999
Q ss_pred EEcCchhhHHHHcccCCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHH
Q psy17350 445 VGQSLNCDLHALKMMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515 (528)
Q Consensus 445 VGHnL~fDL~~L~~~hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~ 515 (528)
||||+.||+++|+..+++++||..+++...++..+++|+.||++|+++.++.+..+|+|++||+||++||+
T Consensus 80 VgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred EEcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 99999999999999999999999998765444457899999999999988753348999999999999984
No 5
>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=100.00 E-value=3.8e-34 Score=267.17 Aligned_cols=149 Identities=36% Similarity=0.540 Sum_probs=133.8
Q ss_pred EEEeeceecCCCC--cCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCCCc
Q psy17350 365 YGLDCEMCKTSND--QNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDA 442 (528)
Q Consensus 365 vALDcEmtgt~~g--~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d~ 442 (528)
+||||||||++++ .++|++|++|+++|+++|++||+|..+|+++++++||||++||+++ |++++|+++|.+|++ ++
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a-~~~~~v~~~l~~~l~-~~ 78 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNA-TPFAVAQKEILKILK-GK 78 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcC-CCHHHHHHHHHHHcC-CC
Confidence 6899999999986 5899999999999999999999999999999999999999999995 999999999999998 99
Q ss_pred EEEEcCchhhHHHHcccCCC--Eeeehhhch--hc--CCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHH
Q psy17350 443 ILVGQSLNCDLHALKMMHPY--VIDTSVIFN--TT--GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515 (528)
Q Consensus 443 ILVGHnL~fDL~~L~~~hp~--vIDTs~L~~--~~--~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~ 515 (528)
||||||+.||+++|++.|+. ++||+.++. .. .+...+++|+.||++|+|..||.+..+|+|++||+||++||+
T Consensus 79 vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 79 VVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred EEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 99999999999999999875 899987632 21 122356899999999999999875457999999999999985
No 6
>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=100.00 E-value=4.8e-34 Score=266.99 Aligned_cols=150 Identities=38% Similarity=0.577 Sum_probs=135.0
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEe-CCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCC-------HHHHHHHHHh
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDE-QENVVYESLVKPYNPITNYLTAYSGITRALLAPVATR-------LEHVQKILSE 436 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~-------l~dV~~~L~~ 436 (528)
|||||||||+++..++|++|++|+. +|+++|++||+|..+|+++++++||||++||+++ |+ +++++++|.+
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a-~~~~~~~~~~~~~~~~~~~ 79 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEA-AKAGKTIFGWEAARAALWK 79 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhh-hhcCCccccHHHHHHHHHH
Confidence 6899999999987799999999999 8999999999999999999999999999999985 53 5699999999
Q ss_pred cCCCCcEEEEcCchhhHHHHcccCCCEeeehhhchhcCCCC---CCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHH
Q psy17350 437 LLPPDAILVGQSLNCDLHALKMMHPYVIDTSVIFNTTGIRT---HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRL 513 (528)
Q Consensus 437 ~i~~d~ILVGHnL~fDL~~L~~~hp~vIDTs~L~~~~~~~~---~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL 513 (528)
|++.+++|||||+.||+++|+..+++++||..|++...+.. .+++|+.||++|+|++++.+..+|+|++||+||++|
T Consensus 80 ~i~~~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l 159 (161)
T cd06137 80 FIDPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREV 159 (161)
T ss_pred hcCCCcEEEeccHHHHHHHHhCcCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHH
Confidence 99834999999999999999999999999999998654332 479999999999999997633579999999999999
Q ss_pred HH
Q psy17350 514 VK 515 (528)
Q Consensus 514 ~~ 515 (528)
|+
T Consensus 160 ~~ 161 (161)
T cd06137 160 VL 161 (161)
T ss_pred hC
Confidence 83
No 7
>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=99.97 E-value=1.2e-30 Score=241.64 Aligned_cols=147 Identities=46% Similarity=0.666 Sum_probs=130.5
Q ss_pred EEEeeceecCCCC--cCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCCCc
Q psy17350 365 YGLDCEMCKTSND--QNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDA 442 (528)
Q Consensus 365 vALDcEmtgt~~g--~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d~ 442 (528)
|+|||||||+++. ..+|++|++|+.+|+++|++||+|..+++++++++||||++||++ +|++.+++++|.+|++ ++
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~-a~~~~~~~~~l~~~l~-~~ 78 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKD-APDFEEVQKKVAELLK-GR 78 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcC-CCCHHHHHHHHHHHhC-CC
Confidence 5899999999986 368889999999999999999999999999999999999999999 5999999999999998 89
Q ss_pred EEEEcCchhhHHHHcccCC--CEeeehhhchhcCCC-CCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHH
Q psy17350 443 ILVGQSLNCDLHALKMMHP--YVIDTSVIFNTTGIR-THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 515 (528)
Q Consensus 443 ILVGHnL~fDL~~L~~~hp--~vIDTs~L~~~~~~~-~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~ 515 (528)
+|||||+.||+++|++.++ .++||..+....... ..+++|+.||++|||++++.+ +|+|++||+||++||+
T Consensus 79 vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~--~H~Al~DA~at~~l~~ 152 (152)
T cd06144 79 ILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG--EHSSVEDARAAMRLYR 152 (152)
T ss_pred EEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCC--CcCcHHHHHHHHHHhC
Confidence 9999999999999998876 489998875433221 357999999998899998643 7999999999999984
No 8
>KOG2249|consensus
Probab=99.94 E-value=2.4e-28 Score=241.98 Aligned_cols=110 Identities=26% Similarity=0.256 Sum_probs=98.6
Q ss_pred ccceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCC--cEeecccccCCCC--CCCCCc
Q psy17350 3 LSLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHP--YVIDTSVIFNTTG--IRTHKP 76 (528)
Q Consensus 3 ~~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp--~i~DTa~~~~~~~--~~~~~~ 76 (528)
..|+||||||+ +|.+|++ |+.||+++.+++. ++|||||+|+|| ||++.|| .|||||.+.|+.+ ....++
T Consensus 153 yRT~vSGIrpe-hm~~A~p--f~~aQ~ev~klL~--gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tp 227 (280)
T KOG2249|consen 153 YRTRVSGIRPE-HMRDAMP--FKVAQKEVLKLLK--GRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATP 227 (280)
T ss_pred ceeeecccCHH-HhccCcc--HHHHHHHHHHHHh--CCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCc
Confidence 46899999999 5677765 6679999999999 599999999999 9999999 4999999999976 457899
Q ss_pred cHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCCC
Q psy17350 77 KLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDL 119 (528)
Q Consensus 77 SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~~ 119 (528)
|||.|++.+||++||.| .|||||||+|||+||+....+|+.
T Consensus 228 SLK~Lt~~~Lg~~IQ~G--eHsSvEDA~AtM~LY~~vk~qwe~ 268 (280)
T KOG2249|consen 228 SLKKLTEALLGKDIQVG--EHSSVEDARATMELYKRVKVQWEK 268 (280)
T ss_pred cHHHHHHHHhchhhhcc--ccCcHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999 699999999999999987766544
No 9
>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=99.94 E-value=8.9e-28 Score=227.94 Aligned_cols=103 Identities=26% Similarity=0.275 Sum_probs=89.5
Q ss_pred ccceeeccCCCCCCchhhh----hhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCC--cEeecccccCCCCCCCC
Q psy17350 3 LSLEVLGLNPGGVLLNAYF----KMNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHP--YVIDTSVIFNTTGIRTH 74 (528)
Q Consensus 3 ~~~~vSGI~p~~~~~~a~~----~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp--~i~DTa~~~~~~~~~~~ 74 (528)
+.|+||||+|+++ .+++. ..++.+|++|.+++.. ++|||||+|+|| ||+|.|| .|||||.+|+++.+ +
T Consensus 64 YrT~~SGIt~~~L-~~a~~~~~~~t~~~v~~~l~~li~~-~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~~--r 139 (174)
T cd06143 64 YLTRFSGIKPGDL-DPKTSSKNLTTLKSAYLKLRLLVDL-GCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPGQ--R 139 (174)
T ss_pred cCccccccCHHHc-CccccccccCCHHHHHHHHHHHcCC-CCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCCC--C
Confidence 4689999999965 44432 2466799999988753 799999999999 9999999 69999999998754 4
Q ss_pred CccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 75 KPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 75 ~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
++|||.||+.+||++||++ ||||+|||+|||+|||
T Consensus 140 ~~sLk~La~~~L~~~IQ~~--~HdSvEDArAam~Ly~ 174 (174)
T cd06143 140 KLSLRFLAWYLLGEKIQSE--THDSIEDARTALKLYR 174 (174)
T ss_pred ChhHHHHHHHHcCCcccCC--CcCcHHHHHHHHHHhC
Confidence 8999999999999999997 9999999999999995
No 10
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=5.9e-25 Score=212.74 Aligned_cols=153 Identities=22% Similarity=0.287 Sum_probs=127.5
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEe-CCcE--EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcC
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDE-QENV--VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELL 438 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~v--i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i 438 (528)
..|+++||||||.++. ++|++|++|.. +|++ .|++||+|..+|+++++++||||++||+++ |++.+|+++|.+|+
T Consensus 5 ~~~vvlD~EtTGl~~~-~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~a-p~~~evl~~f~~f~ 82 (195)
T PRK07247 5 ETYIAFDLEFNTVNGV-SHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADA-PKVEEVLAAFKEFV 82 (195)
T ss_pred CeEEEEEeeCCCCCCC-CeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCC-CCHHHHHHHHHHHH
Confidence 4799999999999764 89999999998 5554 499999999999999999999999999995 99999999999999
Q ss_pred CCCcEEEEcCch-hhHHHHcccC-----CCEeeehhhc-hhc---CCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH
Q psy17350 439 PPDAILVGQSLN-CDLHALKMMH-----PYVIDTSVIF-NTT---GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI 508 (528)
Q Consensus 439 ~~d~ILVGHnL~-fDL~~L~~~h-----p~vIDTs~L~-~~~---~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~ 508 (528)
+ +.++||||+. ||+.+|+... ++.+||.... ... .....+++|..||+. +|++.+ +|+|++||+
T Consensus 83 ~-~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~-~gi~~~----~HrAl~DA~ 156 (195)
T PRK07247 83 G-ELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADF-LGIKGR----GHNSLEDAR 156 (195)
T ss_pred C-CCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHh-cCCCCC----CcCCHHHHH
Confidence 8 9999999997 8999997532 3467875432 111 112346899999985 688742 699999999
Q ss_pred HHHHHHHHHHHcCC
Q psy17350 509 AALRLVKLKLSKGD 522 (528)
Q Consensus 509 AT~eL~~~~L~~g~ 522 (528)
+|+.||+++++++.
T Consensus 157 ~ta~v~~~ll~~~~ 170 (195)
T PRK07247 157 MTARVYESFLESDQ 170 (195)
T ss_pred HHHHHHHHHHhhcc
Confidence 99999999988764
No 11
>PRK07740 hypothetical protein; Provisional
Probab=99.92 E-value=1.4e-24 Score=216.66 Aligned_cols=159 Identities=25% Similarity=0.291 Sum_probs=135.4
Q ss_pred CCCeEEEeeceecCCCCc-CcEEEEEEEEeCCcEE----EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHH
Q psy17350 361 TSPLYGLDCEMCKTSNDQ-NELTRVTLVDEQENVV----YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILS 435 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~-~eLirIs~Vd~~G~vi----~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~ 435 (528)
+.++++|||||||.++.. ++|++|++|..++..+ |+++|+|..+|+++.+++||||+++|++ +|++.||..+|.
T Consensus 58 ~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~-ap~~~evl~~f~ 136 (244)
T PRK07740 58 DLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAF-APPLAEVLHRFY 136 (244)
T ss_pred CCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhC-CCCHHHHHHHHH
Confidence 468999999999999865 7999999999855544 7889999999999999999999999999 599999999999
Q ss_pred hcCCCCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHH
Q psy17350 436 ELLPPDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKED 506 (528)
Q Consensus 436 ~~i~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlED 506 (528)
+|++ +.+|||||+.||+.+|+.. ..+++||..+++........++|..||.. +|++... .|+|++|
T Consensus 137 ~fi~-~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~-~gi~~~~---~H~Al~D 211 (244)
T PRK07740 137 AFIG-AGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAY-YGIPIPR---RHHALGD 211 (244)
T ss_pred HHhC-CCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHH-CCcCCCC---CCCcHHH
Confidence 9998 8999999999999998632 13699999998754433457899999975 7888763 6999999
Q ss_pred HHHHHHHHHHHHHcCCcCC
Q psy17350 507 AIAALRLVKLKLSKGDLIG 525 (528)
Q Consensus 507 A~AT~eL~~~~L~~g~~fg 525 (528)
|+||++||.+.+..-...|
T Consensus 212 a~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 212 ALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred HHHHHHHHHHHHHHHHHcC
Confidence 9999999999886644433
No 12
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.91 E-value=4.2e-24 Score=212.92 Aligned_cols=160 Identities=17% Similarity=0.153 Sum_probs=133.7
Q ss_pred CCeEEEeeceecCCCC-cCcEEEEEEEEe-CCcE---EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 362 SPLYGLDCEMCKTSND-QNELTRVTLVDE-QENV---VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g-~~eLirIs~Vd~-~G~v---i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
.++++||+||||+++. .++|++|++|.. ++.+ .|+.||+|..+|+...+++||||++||++ +|+|++|.++|.+
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~-~p~f~ev~~~f~~ 82 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLAD-KPTFAEVADEFLD 82 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcC-CCCHHHHHHHHHH
Confidence 5799999999999985 689999999987 4443 38899999999999999999999999999 5999999999999
Q ss_pred cCCCCcEEEEcCchhhHHHHccc-------C------CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCCh
Q psy17350 437 LLPPDAILVGQSLNCDLHALKMM-------H------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCS 503 (528)
Q Consensus 437 ~i~~d~ILVGHnL~fDL~~L~~~-------h------p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdA 503 (528)
|++ +.+|||||+.||+.+|+.. . ..++||..+.+... +..+++|..||++ +|++... ...|+|
T Consensus 83 fi~-~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~-p~~~~~L~aL~~~-~gi~~~~-r~~H~A 158 (240)
T PRK05711 83 FIR-GAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMF-PGKRNSLDALCKR-YGIDNSH-RTLHGA 158 (240)
T ss_pred HhC-CCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHc-CCCCCCHHHHHHH-CCCCCCC-CCCCCH
Confidence 998 8999999999999999632 1 24899998876543 2346799999996 5876532 246999
Q ss_pred HHHHHHHHHHHHHHHHcCCcCCC
Q psy17350 504 KEDAIAALRLVKLKLSKGDLIGL 526 (528)
Q Consensus 504 lEDA~AT~eL~~~~L~~g~~fg~ 526 (528)
+.||++|++||..+......|+.
T Consensus 159 L~DA~~~A~v~~~l~~~~~~l~~ 181 (240)
T PRK05711 159 LLDAEILAEVYLAMTGGQTSLGF 181 (240)
T ss_pred HHHHHHHHHHHHHHHCccccccc
Confidence 99999999999988766555543
No 13
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=6.8e-24 Score=211.23 Aligned_cols=155 Identities=24% Similarity=0.264 Sum_probs=131.1
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeC-CcE----EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHH
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQ-ENV----VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILS 435 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~-G~v----i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~ 435 (528)
..+|++||+||||+++..++|++|++|..+ |.+ .|++||+|..+|+...+++||||++||++ +|++.+|+.+|.
T Consensus 46 ~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~-ap~~~evl~~l~ 124 (239)
T PRK09146 46 EVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQD-APDLERILDELL 124 (239)
T ss_pred cCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhC-CCCHHHHHHHHH
Confidence 468999999999999988999999999984 433 37899999999999999999999999999 599999999999
Q ss_pred hcCCCCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCC-------------CCCCCCHHHHHHHhhCCc
Q psy17350 436 ELLPPDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGI-------------RTHKPKLKMLTSHFLGLD 493 (528)
Q Consensus 436 ~~i~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~-------------~~~k~sLk~La~~~Lg~~ 493 (528)
++++ +.++||||+.||+++|+.. ...+|||..+++.... ....++|..||+. +|++
T Consensus 125 ~~~~-~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~-~gl~ 202 (239)
T PRK09146 125 EALA-GKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLR-YGLP 202 (239)
T ss_pred HHhC-CCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHH-cCCC
Confidence 9998 8999999999999999642 1258999998764211 0145789999996 5777
Q ss_pred ccCCCCCCChHHHHHHHHHHHHHHHHcC
Q psy17350 494 IQNQDGGHCSKEDAIAALRLVKLKLSKG 521 (528)
Q Consensus 494 Iq~~~~~HdAlEDA~AT~eL~~~~L~~g 521 (528)
.. .+|+|++||+||++||...+++.
T Consensus 203 ~~---~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 203 AY---SPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred CC---CCCCcHHHHHHHHHHHHHHHHHH
Confidence 53 37999999999999999988654
No 14
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=7.5e-24 Score=212.05 Aligned_cols=155 Identities=19% Similarity=0.290 Sum_probs=132.6
Q ss_pred CCCCeEEEeeceecCCCCcCcEEEEEEEEeCCcE---EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 360 PTSPLYGLDCEMCKTSNDQNELTRVTLVDEQENV---VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~v---i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
+..++|+|||||||+++..++|++|++|+..+.. .|+.+|+|..+|+...+.+||||++||+++ |++.+|.+++.+
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~-p~~~ev~~~~~~ 83 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDK-PKIAEVFPQIKG 83 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCC-CCHHHHHHHHHH
Confidence 3468999999999999888999999999985443 388899999999999999999999999995 999999999999
Q ss_pred cCCCCcEEEEcCchhhHHHHccc-----------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHH
Q psy17350 437 LLPPDAILVGQSLNCDLHALKMM-----------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKE 505 (528)
Q Consensus 437 ~i~~d~ILVGHnL~fDL~~L~~~-----------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlE 505 (528)
|++.+.+|||||+.||+.+|+.. +..+|||..+++... ...+++|..||+. +|++... +|+|++
T Consensus 84 fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~-~~~~~~L~~l~~~-~g~~~~~---aH~Al~ 158 (250)
T PRK06310 84 FFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYG-DSPNNSLEALAVH-FNVPYDG---NHRAMK 158 (250)
T ss_pred HhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcc-cCCCCCHHHHHHH-CCCCCCC---CcChHH
Confidence 99855999999999999999642 235899999887532 2235899999986 5887643 799999
Q ss_pred HHHHHHHHHHHHHHc
Q psy17350 506 DAIAALRLVKLKLSK 520 (528)
Q Consensus 506 DA~AT~eL~~~~L~~ 520 (528)
||+||++||+..+++
T Consensus 159 Da~at~~vl~~l~~~ 173 (250)
T PRK06310 159 DVEINIKVFKHLCKR 173 (250)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999988764
No 15
>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=99.91 E-value=7.1e-24 Score=194.05 Aligned_cols=143 Identities=20% Similarity=0.296 Sum_probs=122.6
Q ss_pred eEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 364 LYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 364 ~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
||+|||||+|.. .++|++|++|.. .|+++ |+.||+|..+++.+.+++||||+++|+++ +++.+|+++|.++++
T Consensus 1 ~v~~D~Ettg~~--~~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~-~~~~~v~~~l~~~l~- 76 (156)
T cd06130 1 FVAIDFETANAD--RASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADA-PTFPEVWPEIKPFLG- 76 (156)
T ss_pred CEEEEEeCCCCC--CCceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcC-CCHHHHHHHHHHHhC-
Confidence 689999999866 468999999998 55553 78999999999999999999999999994 889999999999998
Q ss_pred CcEEEEcCchhhHHHHccc-------CC--CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHH
Q psy17350 441 DAILVGQSLNCDLHALKMM-------HP--YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAAL 511 (528)
Q Consensus 441 d~ILVGHnL~fDL~~L~~~-------hp--~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~ 511 (528)
+.++||||+.||+.+|+.. .+ ..+||..+++........++|..||+. +|++.+ +|+|++||+||+
T Consensus 77 ~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~~~-~g~~~~----~H~Al~Da~~ta 151 (156)
T cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEH-LGIELN----HHDALEDARACA 151 (156)
T ss_pred CCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHHHH-cCCCcc----CcCchHHHHHHH
Confidence 8999999999999999532 12 589999988764333456899999986 688875 599999999999
Q ss_pred HHHH
Q psy17350 512 RLVK 515 (528)
Q Consensus 512 eL~~ 515 (528)
+||.
T Consensus 152 ~l~~ 155 (156)
T cd06130 152 EILL 155 (156)
T ss_pred HHHh
Confidence 9985
No 16
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.91 E-value=7.7e-24 Score=208.91 Aligned_cols=153 Identities=16% Similarity=0.136 Sum_probs=129.1
Q ss_pred CeEEEeeceecCCCCc-CcEEEEEEEEe-CCcE---EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 363 PLYGLDCEMCKTSNDQ-NELTRVTLVDE-QENV---VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~-~eLirIs~Vd~-~G~v---i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
++++||+||||+++.. ++|++|++|.. ++.. .|+.||+|..+|+...+++||||++||+++ |+|++|+.+|.+|
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~-p~f~ev~~~f~~f 79 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADK-PKFKEIADEFLDF 79 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCC-CCHHHHHHHHHHH
Confidence 4799999999999864 79999999976 4333 389999999999999999999999999995 9999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHccc-----------C--CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMM-----------H--PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSK 504 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~-----------h--p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAl 504 (528)
++ +.+|||||+.||+.+|+.. . ..++||..+++... +..+++|..||++ +|++... ...|+|+
T Consensus 80 i~-~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~-p~~~~~L~~L~~~-~gi~~~~-r~~H~Al 155 (225)
T TIGR01406 80 IG-GSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERF-PGQRNSLDALCKR-FKVDNSH-RTLHGAL 155 (225)
T ss_pred hC-CCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHc-CCCCCCHHHHHHh-cCCCCCC-CCCcCHH
Confidence 98 8999999999999999632 1 25899999887543 3457899999997 5777543 2479999
Q ss_pred HHHHHHHHHHHHHHHc
Q psy17350 505 EDAIAALRLVKLKLSK 520 (528)
Q Consensus 505 EDA~AT~eL~~~~L~~ 520 (528)
+||++|++||..+...
T Consensus 156 ~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 156 LDAHLLAEVYLALTGG 171 (225)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999999999876654
No 17
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.91 E-value=6.7e-24 Score=195.40 Aligned_cols=153 Identities=35% Similarity=0.485 Sum_probs=129.8
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEeCC-c--EEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDEQE-N--VVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP 439 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~~G-~--vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~ 439 (528)
.+++|||||+|.+++.++|++|++|..++ . ..|+.+|+|..+|+++.+++||||++++++ ++++.+|+.+|.++++
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~-~~~~~~~~~~~~~~l~ 79 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDD-APTFEEVLEELLEFLK 79 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhC-CCCHHHHHHHHHHHhc
Confidence 37999999999999889999999999844 2 359999999999999999999999999999 6999999999999998
Q ss_pred CCcEEEEcCc-hhhHHHHcccCC----------CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH
Q psy17350 440 PDAILVGQSL-NCDLHALKMMHP----------YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI 508 (528)
Q Consensus 440 ~d~ILVGHnL-~fDL~~L~~~hp----------~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~ 508 (528)
+.++||||. .||+.+|+..+. +++||..+++...+ ...++|..||+. +|.+... ..|+|++||+
T Consensus 80 -~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~-~~~~~L~~l~~~-~~~~~~~--~~H~A~~Da~ 154 (169)
T smart00479 80 -GKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNP-GRKYSLKKLAER-LGLEVIG--RAHRALDDAR 154 (169)
T ss_pred -CCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCC-CCCCCHHHHHHH-CCCCCCC--CCcCcHHHHH
Confidence 778888887 999999975321 37999998875443 237999999986 5777543 2599999999
Q ss_pred HHHHHHHHHHHcC
Q psy17350 509 AALRLVKLKLSKG 521 (528)
Q Consensus 509 AT~eL~~~~L~~g 521 (528)
+|++||+++++.+
T Consensus 155 ~t~~l~~~~~~~~ 167 (169)
T smart00479 155 ATAKLFKKLVERL 167 (169)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999887654
No 18
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=1e-23 Score=203.76 Aligned_cols=153 Identities=20% Similarity=0.251 Sum_probs=127.9
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeCCc-EE----EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHH
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQEN-VV----YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILS 435 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~-vi----~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~ 435 (528)
..++|+|||||||+++..++|++|++|..++. ++ |+.+|+|..+++.+.+++||||++||++ ++++.+|+++|.
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~-~~~~~~vl~~~~ 106 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLED-GLSEEEALRQLL 106 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhc-CCCHHHHHHHHH
Confidence 45899999999999987799999999998544 32 7899999999999999999999999999 599999999999
Q ss_pred hcCCCCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhc---C--CCCCCCCHHHHHHHhhCCcccCCCCCC
Q psy17350 436 ELLPPDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTT---G--IRTHKPKLKMLTSHFLGLDIQNQDGGH 501 (528)
Q Consensus 436 ~~i~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~---~--~~~~k~sLk~La~~~Lg~~Iq~~~~~H 501 (528)
++++ +.++||||+.||+.+|+.. ...++|++.++... . ....+++|..||+. +|++.. +.|
T Consensus 107 ~~i~-~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~---~~H 181 (202)
T PRK09145 107 AFIG-NRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKH-LDLPVL---GRH 181 (202)
T ss_pred HHHc-CCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHH-cCCCCC---CCC
Confidence 9998 8999999999999999632 12489998876421 1 11235899999986 688764 379
Q ss_pred ChHHHHHHHHHHHHHHHH
Q psy17350 502 CSKEDAIAALRLVKLKLS 519 (528)
Q Consensus 502 dAlEDA~AT~eL~~~~L~ 519 (528)
+|++||+||++||.+..+
T Consensus 182 ~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 182 DALNDAIMAALIFLRLRK 199 (202)
T ss_pred CcHHHHHHHHHHHHHHHh
Confidence 999999999999986543
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.91 E-value=1.2e-23 Score=216.90 Aligned_cols=155 Identities=19% Similarity=0.209 Sum_probs=131.3
Q ss_pred CCCCeEEEeeceecCCCCcCcEEEEEEEEe--CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHH
Q psy17350 360 PTSPLYGLDCEMCKTSNDQNELTRVTLVDE--QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILS 435 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g~~eLirIs~Vd~--~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~ 435 (528)
...+|++||+||||.+++.++|++|++|.. +|+++ |.+||+|..+ ...+.+||||++||+++ |+|.+++++|.
T Consensus 13 ~~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~--~~~~~IhGIt~e~l~~a-p~f~ev~~~l~ 89 (313)
T PRK06063 13 YPRGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGVD--PGPTHVHGLTAEMLEGQ-PQFADIAGEVA 89 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCCC--CCCeecCCCCHHHHhCC-CCHHHHHHHHH
Confidence 356899999999999998899999999976 57665 8899999853 46799999999999995 99999999999
Q ss_pred hcCCCCcEEEEcCchhhHHHHcccC---------CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHH
Q psy17350 436 ELLPPDAILVGQSLNCDLHALKMMH---------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKED 506 (528)
Q Consensus 436 ~~i~~d~ILVGHnL~fDL~~L~~~h---------p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlED 506 (528)
+|++ +.+|||||+.||+++|+... ..++||..+++.......+++|..||++ +|++.. .+|+|++|
T Consensus 90 ~~l~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~-~gi~~~---~~H~Al~D 164 (313)
T PRK06063 90 ELLR-GRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAH-WGVPQQ---RPHDALDD 164 (313)
T ss_pred HHcC-CCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHH-cCCCCC---CCCCcHHH
Confidence 9998 89999999999999996421 2489999998764444457899999985 688754 37999999
Q ss_pred HHHHHHHHHHHHHcCC
Q psy17350 507 AIAALRLVKLKLSKGD 522 (528)
Q Consensus 507 A~AT~eL~~~~L~~g~ 522 (528)
|+||++||...+++..
T Consensus 165 A~ata~l~~~ll~~~~ 180 (313)
T PRK06063 165 ARVLAGILRPSLERAR 180 (313)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999988876643
No 20
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=2e-23 Score=215.39 Aligned_cols=154 Identities=22% Similarity=0.299 Sum_probs=132.9
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
..+||+||+||||+++..++|++|++|.. +|+++ |+++|+|..+|+.+.+++||||++||+++ +++.+|+++|.+|
T Consensus 7 ~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~-~~~~evl~~f~~f 85 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDA-PTIEEVLPLFLAF 85 (313)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCC-CCHHHHHHHHHHH
Confidence 35899999999999988889999999998 56554 88899999999999999999999999995 9999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHccc-------C--CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMM-------H--PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI 508 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~-------h--p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~ 508 (528)
++ +.+|||||+.||+.+|+.. . ..++||..+++...+....++|..||+. +|++. . +|+|+.||+
T Consensus 86 l~-~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~-lgi~~-~---~H~Al~DA~ 159 (313)
T PRK06807 86 LH-TNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRM-LGIRL-S---SHNAFDDCI 159 (313)
T ss_pred Hc-CCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHH-cCCCC-C---CcChHHHHH
Confidence 98 8899999999999999642 1 2589999987654333346799999975 78887 3 799999999
Q ss_pred HHHHHHHHHHHcC
Q psy17350 509 AALRLVKLKLSKG 521 (528)
Q Consensus 509 AT~eL~~~~L~~g 521 (528)
+|++||+.++...
T Consensus 160 ~ta~l~~~l~~~~ 172 (313)
T PRK06807 160 TCAAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999887654
No 21
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=1.1e-23 Score=208.36 Aligned_cols=153 Identities=20% Similarity=0.248 Sum_probs=131.1
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCCCc
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDA 442 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d~ 442 (528)
++++||+||||+++..++|++|++|+......|+.+|+|..+|+...+.+||||++||+++ |++.+|.+++.+|++.+.
T Consensus 3 ~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~-p~f~ev~~~~~~fi~~~~ 81 (232)
T PRK06309 3 ALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADA-PKFPEAYQKFIEFCGTDN 81 (232)
T ss_pred cEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCC-CCHHHHHHHHHHHHcCCC
Confidence 5899999999999888999999999764455799999999999999999999999999995 999999999999998668
Q ss_pred EEEEcCc-hhhHHHHcccC---------CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHH
Q psy17350 443 ILVGQSL-NCDLHALKMMH---------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALR 512 (528)
Q Consensus 443 ILVGHnL-~fDL~~L~~~h---------p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~e 512 (528)
+|||||. .||+.+|+... ..++||..+++...+...+++|..||+.| |++.. .+|+|++||.||++
T Consensus 82 ~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~~~~-~~~~~---~aH~Al~Da~~t~~ 157 (232)
T PRK06309 82 ILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVY-GFEEN---QAHRALDDVITLHR 157 (232)
T ss_pred EEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHHHHc-CCCCC---CCCCcHHHHHHHHH
Confidence 9999994 89999996421 25899999887544333467999999864 77654 37999999999999
Q ss_pred HHHHHHHc
Q psy17350 513 LVKLKLSK 520 (528)
Q Consensus 513 L~~~~L~~ 520 (528)
||...+++
T Consensus 158 vl~~l~~~ 165 (232)
T PRK06309 158 VFSALVGD 165 (232)
T ss_pred HHHHHHHH
Confidence 99988754
No 22
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.90 E-value=5.6e-23 Score=206.74 Aligned_cols=186 Identities=20% Similarity=0.272 Sum_probs=148.5
Q ss_pred ccCHHhHhhcCCCCCCCCcccccccCceeCccccccCCCCCCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEE
Q psy17350 322 LLSALQMIEEDYPIPLRGELSAKFSKYINTKEVYAEVTPTSPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESL 398 (528)
Q Consensus 322 ~l~~~~l~~~~yp~p~~g~~~~~~~~~v~T~~~~~~~~~~~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~L 398 (528)
-...+.+...|+|+-... ++.+..+....+. ....|+++|+||+|..++.++|++|++|.. +|+++ |+++
T Consensus 35 ~~~~~~~~~~g~~~~~~~------~~~~~l~~~~~~~-~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~ 107 (257)
T PRK08517 35 DIDLELLKALGLPLVENK------ENLITLKTRFTPI-KDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESF 107 (257)
T ss_pred HHHHHHHHHCCCceEEcC------CCeEEeccCCCCC-CCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEE
Confidence 344566777888884322 2333333333443 346899999999999998789999999998 66664 8899
Q ss_pred EcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCCCcEEEEcCchhhHHHHccc---------CCCEeeehhh
Q psy17350 399 VKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDAILVGQSLNCDLHALKMM---------HPYVIDTSVI 469 (528)
Q Consensus 399 VkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L 469 (528)
|+|. +|+.+.+++||||++|+++ +|++.+|+.+|.++++ +.++||||+.||+++|+.. +++.+||..+
T Consensus 108 v~p~-~ip~~~~~itGIt~e~l~~-ap~~~evl~~f~~fl~-~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~l 184 (257)
T PRK08517 108 VKAK-EVPEYITELTGITYEDLEN-APSLKEVLEEFRLFLG-DSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDL 184 (257)
T ss_pred ECCC-CCChhhhhhcCcCHHHHcC-CCCHHHHHHHHHHHHC-CCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHH
Confidence 9997 8999999999999999999 4999999999999998 8999999999999999642 2357999888
Q ss_pred chhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHHHHHHcCC
Q psy17350 470 FNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGD 522 (528)
Q Consensus 470 ~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g~ 522 (528)
++... +..+++|..||+ ++|++.. .+|+|+.||+||++||..++.+.+
T Consensus 185 a~~~~-~~~~~~L~~L~~-~lgi~~~---~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 185 AKRTI-ESPRYGLSFLKE-LLGIEIE---VHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred HHHHc-cCCCCCHHHHHH-HcCcCCC---CCCChHHHHHHHHHHHHHHHHHhH
Confidence 76432 235789999998 4788864 379999999999999999987654
No 23
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.90 E-value=1.7e-23 Score=207.20 Aligned_cols=158 Identities=25% Similarity=0.243 Sum_probs=129.1
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeC--CcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQ--ENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~--G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
..+|++||+||||+++..++|++|++|..+ |+++ ++.||+|..+|+...+.+||||++|+.+.++++.++..++..
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~ 84 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIAD 84 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHH
Confidence 358999999999999988999999999874 7765 789999999999999999999999998756778888877777
Q ss_pred cC----CCCcEEEEcCchhhHHHHcccC----------CCEeeehhhchhcCC-CCCCCCHHHHHHHhhCCcccCCCCCC
Q psy17350 437 LL----PPDAILVGQSLNCDLHALKMMH----------PYVIDTSVIFNTTGI-RTHKPKLKMLTSHFLGLDIQNQDGGH 501 (528)
Q Consensus 437 ~i----~~d~ILVGHnL~fDL~~L~~~h----------p~vIDTs~L~~~~~~-~~~k~sLk~La~~~Lg~~Iq~~~~~H 501 (528)
++ ..+.+|||||+.||+++|+... ..++||..+.+.... ...+++|..||++ +|++... +|
T Consensus 85 ~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~-~gi~~~~---aH 160 (232)
T PRK07942 85 ALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEH-YGVRLDN---AH 160 (232)
T ss_pred HHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHH-cCCCCCC---CC
Confidence 65 2489999999999999996431 247999887653211 1235799999986 6887653 79
Q ss_pred ChHHHHHHHHHHHHHHHHcCC
Q psy17350 502 CSKEDAIAALRLVKLKLSKGD 522 (528)
Q Consensus 502 dAlEDA~AT~eL~~~~L~~g~ 522 (528)
+|++||+||++||..++++-+
T Consensus 161 ~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 161 EATADALAAARVAWALARRFP 181 (232)
T ss_pred ChHHHHHHHHHHHHHHHHHHH
Confidence 999999999999998877554
No 24
>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=99.90 E-value=3.5e-23 Score=202.64 Aligned_cols=159 Identities=18% Similarity=0.204 Sum_probs=132.5
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEe-CCcE---EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDE-QENV---VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~v---i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
..||++|+||||.+++.+ |++|++|.. ++.. .|++||+|..+++...+.+||||++||.++ |++.+|+++|.+|
T Consensus 7 ~~fvv~D~ETTGl~~~~~-IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~-p~~~ev~~~~~~~ 84 (217)
T TIGR00573 7 DTETTGDNETTGLYAGHD-IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDK-PDFKEIAEDFADY 84 (217)
T ss_pred cCEEEEEecCCCCCCCCC-EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCC-CCHHHHHHHHHHH
Confidence 579999999999998866 999999984 5543 488999999999999999999999999995 9999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHcccC----------CCEeeehhhchh--cCCCCCCCCHHHHHHHhhCCcccCCCCCCChHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMMH----------PYVIDTSVIFNT--TGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKE 505 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~h----------p~vIDTs~L~~~--~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlE 505 (528)
++ +.++||||+.||+.+|+... .+++||..+++. +..+..+++|..||+. +|++... ...|+|++
T Consensus 85 ~~-~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~-~gl~~~~-~~~H~Al~ 161 (217)
T TIGR00573 85 IR-GAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKR-YEITNSH-RALHGALA 161 (217)
T ss_pred hC-CCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCC-cccCCHHH
Confidence 98 89999999999999996431 247898776543 2223456899999986 5877542 13799999
Q ss_pred HHHHHHHHHHHHHHcCCcCC
Q psy17350 506 DAIAALRLVKLKLSKGDLIG 525 (528)
Q Consensus 506 DA~AT~eL~~~~L~~g~~fg 525 (528)
||++|++||+..+.+....+
T Consensus 162 DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 162 DAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred HHHHHHHHHHHHHhcchhhc
Confidence 99999999999988876655
No 25
>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=99.90 E-value=4.5e-23 Score=191.87 Aligned_cols=149 Identities=18% Similarity=0.177 Sum_probs=124.5
Q ss_pred eEEEeeceecCCC-CcCcEEEEEEEEe-CCcE---EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcC
Q psy17350 364 LYGLDCEMCKTSN-DQNELTRVTLVDE-QENV---VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELL 438 (528)
Q Consensus 364 ~vALDcEmtgt~~-g~~eLirIs~Vd~-~G~v---i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i 438 (528)
+++||+||||.++ ..++|++|++|.. ++.+ -|+.+|+|..++++..+++||||+++++++ +++++|+++|.+|+
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~-~~~~~v~~~l~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADK-PKFAEIADEFLDFI 79 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcC-CCHHHHHHHHHHHH
Confidence 5899999999998 5689999999976 4443 478999999999999999999999999994 89999999999999
Q ss_pred CCCcEEEEcCchhhHHHHccc-----------C-CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHH
Q psy17350 439 PPDAILVGQSLNCDLHALKMM-----------H-PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKED 506 (528)
Q Consensus 439 ~~d~ILVGHnL~fDL~~L~~~-----------h-p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlED 506 (528)
+ +.++||||+.||+.+|+.. . ..++||..+++... +...++|..||+. +|++... ...|+|+.|
T Consensus 80 ~-~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~-~~~~~~L~~l~~~-~~i~~~~-~~~H~Al~D 155 (167)
T cd06131 80 R-GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKF-PGKPNSLDALCKR-FGIDNSH-RTLHGALLD 155 (167)
T ss_pred C-CCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHc-CCCCCCHHHHHHH-CCCCCCC-CCCCChHHH
Confidence 8 8899999999999999632 1 14799998876533 2346799999986 5877642 237999999
Q ss_pred HHHHHHHHHHH
Q psy17350 507 AIAALRLVKLK 517 (528)
Q Consensus 507 A~AT~eL~~~~ 517 (528)
|++|++||.++
T Consensus 156 a~~~a~l~~~l 166 (167)
T cd06131 156 AELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHHh
Confidence 99999999753
No 26
>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=99.90 E-value=1.6e-23 Score=199.10 Aligned_cols=144 Identities=20% Similarity=0.285 Sum_probs=117.2
Q ss_pred eEEEeeceecCC-CCcCcEEEEEEEEeCCc--------------E--EEEEEEcCCCCCCCCceeecCCChhhhcccCCC
Q psy17350 364 LYGLDCEMCKTS-NDQNELTRVTLVDEQEN--------------V--VYESLVKPYNPITNYLTAYSGITRALLAPVATR 426 (528)
Q Consensus 364 ~vALDcEmtgt~-~g~~eLirIs~Vd~~G~--------------v--i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~ 426 (528)
|++||+||||++ +..++|++|++|...+. + -|++||+|..+|+...+++||||++|+.++ |+
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~-~~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHK-AP 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcC-CC
Confidence 689999999999 56799999999987432 2 278999999999999999999999999995 66
Q ss_pred HH-HHHHHHHhcC---CCCcEEEEcCc-hhhHHHHcccC----------CCEeeehhhchhcCCCCCCCCHHHHHHHhhC
Q psy17350 427 LE-HVQKILSELL---PPDAILVGQSL-NCDLHALKMMH----------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLG 491 (528)
Q Consensus 427 l~-dV~~~L~~~i---~~d~ILVGHnL-~fDL~~L~~~h----------p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg 491 (528)
+. ++++.+.+|+ +.+.+|||||+ .||+++|+... ..++||..+++... ++|..||++++|
T Consensus 80 ~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~-----~~L~~l~~~~~~ 154 (177)
T cd06136 80 FDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD-----QSLGSLYKRLFG 154 (177)
T ss_pred ccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-----hhHHHHHHHHhC
Confidence 65 3556565554 43569999998 89999995321 24799999987532 299999998788
Q ss_pred CcccCCCCCCChHHHHHHHHHHHHH
Q psy17350 492 LDIQNQDGGHCSKEDAIAALRLVKL 516 (528)
Q Consensus 492 ~~Iq~~~~~HdAlEDA~AT~eL~~~ 516 (528)
++... +|+|+.||.||+++|.+
T Consensus 155 ~~~~~---~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 155 QEPKN---SHTAEGDVLALLKCALH 176 (177)
T ss_pred CCccc---ccchHHHHHHHHHHHhh
Confidence 88754 79999999999999975
No 27
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.90 E-value=7.4e-23 Score=201.41 Aligned_cols=147 Identities=22% Similarity=0.165 Sum_probs=124.4
Q ss_pred eEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 364 LYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 364 ~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
+++||+||||+++ .|++|++|+. +|+++ |++||+|..+|+...+.+||||++||+++ |++.+|+++ |++
T Consensus 2 ~~vlD~ETTGl~~---~IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~a-p~~~ev~~~---~~~- 73 (219)
T PRK07983 2 LRVIDTETCGLQG---GIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADK-PWIEDVIPH---YYG- 73 (219)
T ss_pred eEEEEEECCCCCC---CCEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCC-CCHHHHHHH---HcC-
Confidence 6899999999863 4999999987 66765 89999999999999999999999999995 999999887 465
Q ss_pred CcEEEEcCchhhHHHHcccCCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCccc--CCCCCCChHHHHHHHHHHHHHHH
Q psy17350 441 DAILVGQSLNCDLHALKMMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQ--NQDGGHCSKEDAIAALRLVKLKL 518 (528)
Q Consensus 441 d~ILVGHnL~fDL~~L~~~hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq--~~~~~HdAlEDA~AT~eL~~~~L 518 (528)
+.+|||||+.||+++|.....++|||..+++...+. .+++|..||.. +|++.. .+..+|+|+.||++|++||.+.+
T Consensus 74 ~~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~-~~~~l~~L~~~-~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~ 151 (219)
T PRK07983 74 SEWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPG-IKYSNMALYKS-RKLNVQTPPGLHHHRALYDCYITAALLIDIM 151 (219)
T ss_pred CCEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccC-CCCCHHHHHHH-cCCCCCCCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 899999999999999987777899999998764433 34899999985 677642 11248999999999999999988
Q ss_pred Hc
Q psy17350 519 SK 520 (528)
Q Consensus 519 ~~ 520 (528)
+.
T Consensus 152 ~~ 153 (219)
T PRK07983 152 NT 153 (219)
T ss_pred HH
Confidence 53
No 28
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.89 E-value=8.4e-23 Score=198.45 Aligned_cols=159 Identities=21% Similarity=0.232 Sum_probs=125.8
Q ss_pred CCeEEEeeceecCCCC------cCcEEEEEEEEe-CCcEE--EEEEEcCCC--CCCCCceeecCCChhhhcccCCCHHHH
Q psy17350 362 SPLYGLDCEMCKTSND------QNELTRVTLVDE-QENVV--YESLVKPYN--PITNYLTAYSGITRALLAPVATRLEHV 430 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g------~~eLirIs~Vd~-~G~vi--~d~LVkP~~--~I~dy~T~isGIT~e~L~~a~p~l~dV 430 (528)
.+|++||+||||.+.+ .+||++|++|.. +|+++ |++||+|.. +++.+++++||||++||++ +|++++|
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~-ap~~~ev 82 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDK-GISFEEL 82 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHcc-CCCHHHH
Confidence 4799999999997643 369999999997 55543 999999987 6899999999999999999 5999999
Q ss_pred HHHHHhcCCCCcEEEEcCchhhHHHHccc-------CC---CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCC
Q psy17350 431 QKILSELLPPDAILVGQSLNCDLHALKMM-------HP---YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGG 500 (528)
Q Consensus 431 ~~~L~~~i~~d~ILVGHnL~fDL~~L~~~-------hp---~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~ 500 (528)
+++|.+|++....+|.|+..||+++|+.. .| +++|+..+++........++|..+|+. +|++... .+
T Consensus 83 l~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~-~gi~~~~--~~ 159 (207)
T PRK07748 83 VEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEE-YGKEGTG--KH 159 (207)
T ss_pred HHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHH-cCCCCCC--CC
Confidence 99999999832444445579999999532 12 478888777643333345899999986 6887532 37
Q ss_pred CChHHHHHHHHHHHHHHHHcCCcC
Q psy17350 501 HCSKEDAIAALRLVKLKLSKGDLI 524 (528)
Q Consensus 501 HdAlEDA~AT~eL~~~~L~~g~~f 524 (528)
|+|++||++|++||.++++++-.+
T Consensus 160 H~Al~DA~~ta~l~~~l~~~~~~~ 183 (207)
T PRK07748 160 HCALDDAMTTYNIFKLVEKDKEYL 183 (207)
T ss_pred cChHHHHHHHHHHHHHHHhCccee
Confidence 999999999999999888776433
No 29
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.89 E-value=2.2e-22 Score=206.96 Aligned_cols=150 Identities=14% Similarity=0.206 Sum_probs=126.9
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCC-CCCCCceeecCCChhhhcccCCCHHHHHHHHHhcC
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYN-PITNYLTAYSGITRALLAPVATRLEHVQKILSELL 438 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~-~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i 438 (528)
+|++||+||||. ..++|++|++|.. +|+++ |++||+|.. .+++..+++||||++||+++ |+|.+|+++|.+|+
T Consensus 2 ~~vviD~ETTg~--~~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~a-p~f~ev~~~~~~fl 78 (309)
T PRK06195 2 NFVAIDFETANE--KRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDE-LEFDKIWEKIKHYF 78 (309)
T ss_pred cEEEEEEeCCCC--CCCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCC-CCHHHHHHHHHHHh
Confidence 689999999975 3479999999998 66665 889999985 57788999999999999995 99999999999999
Q ss_pred CCCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHH
Q psy17350 439 PPDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIA 509 (528)
Q Consensus 439 ~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~A 509 (528)
+ +.+|||||+.||+++|+.. ...++||..+++...+....++|..||+. +|++.+ +|+|++||+|
T Consensus 79 ~-~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~-~gi~~~----~H~Al~DA~a 152 (309)
T PRK06195 79 N-NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNF-LGYEFK----HHDALADAMA 152 (309)
T ss_pred C-CCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHH-cCCCCc----ccCCHHHHHH
Confidence 8 8999999999999999642 12589999988754333357899999996 687742 6999999999
Q ss_pred HHHHHHHHHHcC
Q psy17350 510 ALRLVKLKLSKG 521 (528)
Q Consensus 510 T~eL~~~~L~~g 521 (528)
|++||..++++.
T Consensus 153 ta~l~~~l~~~~ 164 (309)
T PRK06195 153 CSNILLNISKEL 164 (309)
T ss_pred HHHHHHHHHHHh
Confidence 999999887654
No 30
>KOG2248|consensus
Probab=99.88 E-value=9.9e-24 Score=221.51 Aligned_cols=116 Identities=30% Similarity=0.384 Sum_probs=103.0
Q ss_pred ccceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCCcEeecccccCCCCCC-CCCccHH
Q psy17350 3 LSLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHPYVIDTSVIFNTTGIR-THKPKLK 79 (528)
Q Consensus 3 ~~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp~i~DTa~~~~~~~~~-~~~~SLk 79 (528)
+-+++|||+++++ .+++- .+++||.+|..++.. ++|||||||||| |||+.||.|||||.+|+++.++ +++.|||
T Consensus 261 y~T~~SGIT~~~~-e~~t~-tl~dvq~~l~~~~~~-~TILVGHSLenDL~aLKl~H~~ViDTa~lf~~~~g~~~~k~sLk 337 (380)
T KOG2248|consen 261 YNTRYSGITEEDL-ENSTI-TLEDVQKELLELISK-NTILVGHSLENDLKALKLDHPSVIDTAVLFKHPTGPYPFKSSLK 337 (380)
T ss_pred cccccccccHHHH-hcCcc-CHHHHHHHHHhhcCc-CcEEEeechhhHHHHHhhhCCceeeeeEEEecCCCCccchHHHH
Confidence 3578999999965 45543 466799999996654 899999999999 9999999999999999999985 8999999
Q ss_pred HHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCCCCC
Q psy17350 80 MLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLCS 121 (528)
Q Consensus 80 ~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~~~~ 121 (528)
.||+.+||+.||++..||||+|||.|||+|+++++++++.+|
T Consensus 338 ~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~g 379 (380)
T KOG2248|consen 338 NLAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIKNSESQG 379 (380)
T ss_pred HHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHhcccccC
Confidence 999999999999665699999999999999999999988766
No 31
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.88 E-value=2.4e-22 Score=230.11 Aligned_cols=157 Identities=22% Similarity=0.277 Sum_probs=134.1
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
..+|+++|+||||+++. ++|++|++|.. +|+++ |++||+|..+|+++++++||||++||+++ |++++|+++|.++
T Consensus 6 ~~~~vvvD~ETTGl~~~-d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~a-p~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPN-ASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQA-PDFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCC-CeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcC-CCHHHHHHHHHHH
Confidence 35799999999999875 89999999998 56554 88899999999999999999999999995 9999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHccc-----C---CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMM-----H---PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIA 509 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~-----h---p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~A 509 (528)
++ ++++||||+.||+.+|+.. + ...+||..+++...+...+++|..||+. +|++... +|+|++||+|
T Consensus 84 l~-~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~-lgl~~~~---~H~Al~DA~a 158 (820)
T PRK07246 84 IE-DCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRE-LNIDLAD---AHTAIADARA 158 (820)
T ss_pred hC-CCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHH-cCCCCCC---CCCHHHHHHH
Confidence 98 9999999999999999642 1 2479999887653333357899999985 6888653 7999999999
Q ss_pred HHHHHHHHHHcCCcC
Q psy17350 510 ALRLVKLKLSKGDLI 524 (528)
Q Consensus 510 T~eL~~~~L~~g~~f 524 (528)
|++||..++++....
T Consensus 159 ta~L~~~l~~~l~~l 173 (820)
T PRK07246 159 TAELFLKLLQKIESL 173 (820)
T ss_pred HHHHHHHHHHHHhhc
Confidence 999999888765443
No 32
>PRK07883 hypothetical protein; Validated
Probab=99.88 E-value=4.3e-22 Score=219.48 Aligned_cols=161 Identities=22% Similarity=0.308 Sum_probs=138.0
Q ss_pred CCCCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 360 PTSPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
....||+||+||||+++..++|++|++|.. +|+++ |+.||+|..+|+++.+++||||++||+++ |++.+|+.+|.+
T Consensus 13 ~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~a-p~~~evl~~f~~ 91 (557)
T PRK07883 13 RDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGA-PPIEEVLPAFLE 91 (557)
T ss_pred cCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCC-CCHHHHHHHHHH
Confidence 346899999999999988899999999998 66665 89999999999999999999999999995 999999999999
Q ss_pred cCCCCcEEEEcCchhhHHHHccc-------C--CCEeeehhhchhcCC--CCCCCCHHHHHHHhhCCcccCCCCCCChHH
Q psy17350 437 LLPPDAILVGQSLNCDLHALKMM-------H--PYVIDTSVIFNTTGI--RTHKPKLKMLTSHFLGLDIQNQDGGHCSKE 505 (528)
Q Consensus 437 ~i~~d~ILVGHnL~fDL~~L~~~-------h--p~vIDTs~L~~~~~~--~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlE 505 (528)
|++ +.++||||+.||+.+|+.. . ..++||..+++.... ...+++|..||+ ++|++... +|+|++
T Consensus 92 fl~-~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~-~~gi~~~~---~H~Al~ 166 (557)
T PRK07883 92 FAR-GAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLAR-LFGATTTP---THRALD 166 (557)
T ss_pred Hhc-CCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHH-HCCcccCC---CCCHHH
Confidence 998 8999999999999999642 1 258999998764322 345789999998 57888753 799999
Q ss_pred HHHHHHHHHHHHHHcCCcCCC
Q psy17350 506 DAIAALRLVKLKLSKGDLIGL 526 (528)
Q Consensus 506 DA~AT~eL~~~~L~~g~~fg~ 526 (528)
||+||++||...+++-...|.
T Consensus 167 DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 167 DARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred HHHHHHHHHHHHHHHHHhcCC
Confidence 999999999998877655443
No 33
>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=99.88 E-value=3.9e-22 Score=193.34 Aligned_cols=158 Identities=18% Similarity=0.143 Sum_probs=125.8
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEe----CCcEE----EEEEEcCC--CCCCCCceeecCCChh-hhcccCCCHHHH
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDE----QENVV----YESLVKPY--NPITNYLTAYSGITRA-LLAPVATRLEHV 430 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~----~G~vi----~d~LVkP~--~~I~dy~T~isGIT~e-~L~~a~p~l~dV 430 (528)
..+++||+||||+++..++|++|++|.. +|.+. |+++|+|. .+|+...+++||||++ |++++ ++..++
T Consensus 8 ~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~-~~~~~~ 86 (200)
T TIGR01298 8 YLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGA-VSEYEA 86 (200)
T ss_pred CeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcC-cchHHH
Confidence 4679999999999987789999999976 34442 88999984 6899999999999976 68884 888887
Q ss_pred HHHHHhcC--------CCCcEEEEcCchhhHHHHcccC------------CCEeeehhhchhcCCCCCCCCHHHHHHHhh
Q psy17350 431 QKILSELL--------PPDAILVGQSLNCDLHALKMMH------------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFL 490 (528)
Q Consensus 431 ~~~L~~~i--------~~d~ILVGHnL~fDL~~L~~~h------------p~vIDTs~L~~~~~~~~~k~sLk~La~~~L 490 (528)
+.++.+++ ..+.+|||||+.||+++|+... .+++||..+++...+ .++|..||+. +
T Consensus 87 ~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~---~~~L~~l~~~-~ 162 (200)
T TIGR01298 87 LHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG---QTVLAKACQA-A 162 (200)
T ss_pred HHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC---cccHHHHHHH-c
Confidence 77777765 1378999999999999996421 138999999865432 3589999996 6
Q ss_pred CCcccCCCCCCChHHHHHHHHHHHHHHHHcCCcCC
Q psy17350 491 GLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLIG 525 (528)
Q Consensus 491 g~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g~~fg 525 (528)
|+++.. ...|+|+.||+||++||..++++..+.|
T Consensus 163 gi~~~~-~~~H~Al~Da~ata~lf~~l~~~~~~~~ 196 (200)
T TIGR01298 163 GXDFDS-TQAHSALYDTEKTAELFCEIVNRWKRLG 196 (200)
T ss_pred CCCccc-cchhhhHHhHHHHHHHHHHHHHHHHHcc
Confidence 888642 2479999999999999999887755443
No 34
>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=99.87 E-value=1.5e-21 Score=187.45 Aligned_cols=153 Identities=20% Similarity=0.221 Sum_probs=119.1
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEeC----CcE----EEEEEEcC--CCCCCCCceeecCCChhh-hcccCCC----
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDEQ----ENV----VYESLVKP--YNPITNYLTAYSGITRAL-LAPVATR---- 426 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~~----G~v----i~d~LVkP--~~~I~dy~T~isGIT~e~-L~~a~p~---- 426 (528)
...+++|+||||+++..++|++|++|... |.+ .|++||+| ..+|+...+++||||+++ +++ ++.
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~-~~~~~~~ 83 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRF-AVDEKEA 83 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhcc-ccchHHH
Confidence 35699999999999887999999999873 433 49999999 568999999999999987 444 354
Q ss_pred HHHHHHHHHhcCC----CCcEEEEcCchhhHHHHccc-----------CC-CEeeehhhchhcCCCCCCCCHHHHHHHhh
Q psy17350 427 LEHVQKILSELLP----PDAILVGQSLNCDLHALKMM-----------HP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFL 490 (528)
Q Consensus 427 l~dV~~~L~~~i~----~d~ILVGHnL~fDL~~L~~~-----------hp-~vIDTs~L~~~~~~~~~k~sLk~La~~~L 490 (528)
+.++.+.|.+++. .+.+|||||+.||+.+|+.. ++ +++||..|++...+ .++|..||+. +
T Consensus 84 ~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~---~~~L~~l~~~-~ 159 (189)
T cd06134 84 LKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG---QTVLAKACQA-A 159 (189)
T ss_pred HHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC---CCcHHHHHHH-C
Confidence 4455555555553 26899999999999999632 12 48999999865432 4589999996 5
Q ss_pred CCcccCCCCCCChHHHHHHHHHHHHHHHHc
Q psy17350 491 GLDIQNQDGGHCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 491 g~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~ 520 (528)
|+++.. ...|+|+.||+||++||.+++++
T Consensus 160 gi~~~~-~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 160 GIEFDN-KEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCC-CCCcChHHHHHHHHHHHHHHHHh
Confidence 888653 24799999999999999988763
No 35
>PRK05168 ribonuclease T; Provisional
Probab=99.87 E-value=1.5e-21 Score=190.61 Aligned_cols=159 Identities=18% Similarity=0.166 Sum_probs=127.8
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEeC----CcE----EEEEEEcC--CCCCCCCceeecCCChhh-hcccCCCHHHH
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDEQ----ENV----VYESLVKP--YNPITNYLTAYSGITRAL-LAPVATRLEHV 430 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~~----G~v----i~d~LVkP--~~~I~dy~T~isGIT~e~-L~~a~p~l~dV 430 (528)
..+++||+||||.++..++|++|++|... |.+ .|++||+| ..+|+...+++||||+++ +++ +++..++
T Consensus 17 ~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~-~~~~~~~ 95 (211)
T PRK05168 17 FLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRG-AVSEKEA 95 (211)
T ss_pred CceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhc-CCChHHH
Confidence 46799999999999887999999999863 543 48999999 568999999999999986 666 5888777
Q ss_pred HHHHHhcCC--------CCcEEEEcCchhhHHHHccc-----------CC-CEeeehhhchhcCCCCCCCCHHHHHHHhh
Q psy17350 431 QKILSELLP--------PDAILVGQSLNCDLHALKMM-----------HP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFL 490 (528)
Q Consensus 431 ~~~L~~~i~--------~d~ILVGHnL~fDL~~L~~~-----------hp-~vIDTs~L~~~~~~~~~k~sLk~La~~~L 490 (528)
+.++.+++. .+.++||||+.||+.+|+.. ++ +++||..+++...+ ..+|..+|+. +
T Consensus 96 l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~---~~~L~~l~~~-~ 171 (211)
T PRK05168 96 LHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG---QTVLAKACQA-A 171 (211)
T ss_pred HHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC---CCCHHHHHHH-C
Confidence 777777553 27899999999999999642 12 48999999875432 3589999986 6
Q ss_pred CCcccCCCCCCChHHHHHHHHHHHHHHHHcCCcCCC
Q psy17350 491 GLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLIGL 526 (528)
Q Consensus 491 g~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g~~fg~ 526 (528)
|+++.. ..+|+|++||+||++||.+++++....|.
T Consensus 172 gl~~~~-~~~H~Al~DA~ata~l~~~l~~~~~~~~~ 206 (211)
T PRK05168 172 GIEFDN-KEAHSALYDTEKTAELFCEIVNRWKRLGG 206 (211)
T ss_pred CCCCCC-CCCCChHHHHHHHHHHHHHHHHHHHHccC
Confidence 888743 24799999999999999999887665553
No 36
>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=99.87 E-value=1.8e-21 Score=223.85 Aligned_cols=153 Identities=24% Similarity=0.312 Sum_probs=133.9
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP 439 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~ 439 (528)
+|+++|+||||++++.++|++|++|.. +|+++ |+++|+|..+|+++.+++||||++||+++ |.+++|.++|.++++
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~a-p~~~ev~~~l~~~l~ 79 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQA-PYFSQVAQEIYDLLE 79 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCC-CCHHHHHHHHHHHhC
Confidence 489999999999988899999999998 67765 99999999999999999999999999995 999999999999998
Q ss_pred CCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHH
Q psy17350 440 PDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAA 510 (528)
Q Consensus 440 ~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT 510 (528)
++++||||+.||+.+|+.. ...++||..+++...+...+++|..||+. +|++.. ++|+|++||+||
T Consensus 80 -~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~-~gi~~~---~~H~Al~DA~at 154 (850)
T TIGR01407 80 -DGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEA-LGLTHE---NPHRADSDAQAT 154 (850)
T ss_pred -CCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHH-CCCCCC---CCCChHHHHHHH
Confidence 9999999999999999642 12589999987754444457899999986 688764 379999999999
Q ss_pred HHHHHHHHHcC
Q psy17350 511 LRLVKLKLSKG 521 (528)
Q Consensus 511 ~eL~~~~L~~g 521 (528)
++||.+.+++-
T Consensus 155 a~l~~~l~~~~ 165 (850)
T TIGR01407 155 AELLLLLFEKM 165 (850)
T ss_pred HHHHHHHHHHH
Confidence 99999887654
No 37
>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=99.86 E-value=2.8e-21 Score=173.63 Aligned_cols=144 Identities=26% Similarity=0.329 Sum_probs=123.1
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEeCC--cE--EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDEQE--NV--VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~~G--~v--i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
|++||||||..+...+|++|++|..++ ++ .|+.+|+|...+..+.+.++|||++++++ ++++.++..++.+++.
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~-~~~~~~~~~~~~~~l~- 78 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLAD-APPFEEVLPEFLEFLG- 78 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhc-CCCHHHHHHHHHHHHC-
Confidence 579999999998779999999998844 33 49999999999999999999999999998 5999999999999998
Q ss_pred CcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCCCCCCCCHHHH-HHHhhCCcccCCCCCCChHHHHHHH
Q psy17350 441 DAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGIRTHKPKLKML-TSHFLGLDIQNQDGGHCSKEDAIAA 510 (528)
Q Consensus 441 d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~~~~k~sLk~L-a~~~Lg~~Iq~~~~~HdAlEDA~AT 510 (528)
+.++||||..||+.+|+.. +..++||..+++........++|+.+ ++ ++|.+.. .+|+|++||+||
T Consensus 79 ~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~---~~H~Al~Da~~t 154 (159)
T cd06127 79 GRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAE-RYGIPLE---GAHRALADALAT 154 (159)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHH-HcCCCCC---CCCCcHHHHHHH
Confidence 6999999999999999643 23589999998765444456789998 55 5677653 379999999999
Q ss_pred HHHH
Q psy17350 511 LRLV 514 (528)
Q Consensus 511 ~eL~ 514 (528)
++||
T Consensus 155 ~~l~ 158 (159)
T cd06127 155 AELL 158 (159)
T ss_pred HHHh
Confidence 9997
No 38
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=2.5e-21 Score=224.52 Aligned_cols=156 Identities=24% Similarity=0.322 Sum_probs=134.1
Q ss_pred CCeEEEeeceecCCCCc-CcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 362 SPLYGLDCEMCKTSNDQ-NELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~-~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
.+|+++||||||..+.. ++|++|++|.. +|+++ |++||+|..+|+.+++++||||++||+++ |++.+|+++|.+|
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~a-p~f~ev~~~l~~~ 81 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQA-PLFEDVAPEIVEL 81 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcC-CCHHHHHHHHHHH
Confidence 47999999999998653 79999999998 66665 89999999999999999999999999995 9999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI 508 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~ 508 (528)
++ ++++||||+.||+.+|+.. ...+|||..+++...+....++|..||+. +|++.. .+|+|++||+
T Consensus 82 l~-~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~-l~i~~~---~~H~Al~DA~ 156 (928)
T PRK08074 82 LE-GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEE-LGLEHD---QPHRADSDAE 156 (928)
T ss_pred hC-CCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHh-CCCCCC---CCCChHHHHH
Confidence 98 9999999999999999742 12589999887654333457899999986 687754 3899999999
Q ss_pred HHHHHHHHHHHcCCc
Q psy17350 509 AALRLVKLKLSKGDL 523 (528)
Q Consensus 509 AT~eL~~~~L~~g~~ 523 (528)
||++||..++++...
T Consensus 157 ata~l~~~l~~~~~~ 171 (928)
T PRK08074 157 VTAELFLQLLNKLER 171 (928)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999998876543
No 39
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.86 E-value=7e-21 Score=198.68 Aligned_cols=152 Identities=16% Similarity=0.225 Sum_probs=127.6
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEe--CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDE--QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~--~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
..+|++||+||||+++..++|++|++|.. +|+++ |.+||+|..++.. ..+||||++||++ +|.|.+|+++|.+
T Consensus 45 ~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~-AP~f~eVl~el~~ 121 (377)
T PRK05601 45 AAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQ-GKRFSQILKPLDR 121 (377)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhc-CCCHHHHHHHHHH
Confidence 35899999999999998899999999986 56664 9999999986553 4799999999999 5999999999999
Q ss_pred cCCCCcEEEEcCchhhHHHHccc--------------------------------C----CCEeeehhhchhcCCCCCCC
Q psy17350 437 LLPPDAILVGQSLNCDLHALKMM--------------------------------H----PYVIDTSVIFNTTGIRTHKP 480 (528)
Q Consensus 437 ~i~~d~ILVGHnL~fDL~~L~~~--------------------------------h----p~vIDTs~L~~~~~~~~~k~ 480 (528)
||+ +.+|||||+.||++||... | ..++||..+.+.......++
T Consensus 122 fL~-g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~~ 200 (377)
T PRK05601 122 LID-GRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDDI 200 (377)
T ss_pred HhC-CCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCCC
Confidence 998 9999999999999998542 1 14899999987655555689
Q ss_pred CHHHHHHHhhCCcccC-------CCCCCChH--HHHHHHHHHHHHH
Q psy17350 481 KLKMLTSHFLGLDIQN-------QDGGHCSK--EDAIAALRLVKLK 517 (528)
Q Consensus 481 sLk~La~~~Lg~~Iq~-------~~~~HdAl--EDA~AT~eL~~~~ 517 (528)
+|..||++ +|++... ....|+++ +||+..++||...
T Consensus 201 rL~~La~~-lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 201 RIRGVAHT-LGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred CHHHHHHH-hCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 99999996 6888711 12368988 7999999999864
No 40
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.86 E-value=2.1e-22 Score=228.43 Aligned_cols=160 Identities=23% Similarity=0.316 Sum_probs=143.6
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
...||++|+||||+++..++|+++++|.. +|++| |+.|++|..|++...|.+||||.+||+++ +++.+|+.++++|
T Consensus 420 datyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a-~~i~~vL~kf~~~ 498 (1444)
T COG2176 420 DATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENA-PEIEEVLEKFREF 498 (1444)
T ss_pred cccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCC-ccHHHHHHHHHHH
Confidence 45799999999999999999999999998 88887 88999999999999999999999999995 9999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHcccC---------CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMMH---------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI 508 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~h---------p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~ 508 (528)
++ |+|||+||+.||++||+... ..+|||..|.+...+..++++|..||++ ||+.+. .+|+|.-||.
T Consensus 499 ~~-d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk-~~v~le---~hHRA~yDae 573 (1444)
T COG2176 499 IG-DSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKK-LGVELE---RHHRADYDAE 573 (1444)
T ss_pred hc-CcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHH-hCccHH---HhhhhhhhHH
Confidence 99 99999999999999997532 2589999998876667788999999998 588884 3899999999
Q ss_pred HHHHHHHHHHHcCCcCCC
Q psy17350 509 AALRLVKLKLSKGDLIGL 526 (528)
Q Consensus 509 AT~eL~~~~L~~g~~fg~ 526 (528)
||+.||..+++...+-|.
T Consensus 574 at~~vf~~f~~~~ke~Gi 591 (1444)
T COG2176 574 ATAKVFFVFLKDLKEKGI 591 (1444)
T ss_pred HHHHHHHHHHHHHHHhch
Confidence 999999999877655454
No 41
>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=99.86 E-value=3.7e-21 Score=226.07 Aligned_cols=161 Identities=23% Similarity=0.363 Sum_probs=140.5
Q ss_pred CCCCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 360 PTSPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
....||++||||||+++..++|++|++|.. +|+++ |++||+|..+|+++.+++||||++||++ ++++++|+++|.+
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~-ap~~~evl~~f~~ 266 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLEN-APEIEEVLEKFKE 266 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhC-CCCHHHHHHHHHH
Confidence 345899999999999998899999999998 67665 8999999999999999999999999999 5999999999999
Q ss_pred cCCCCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHH
Q psy17350 437 LLPPDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDA 507 (528)
Q Consensus 437 ~i~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA 507 (528)
|++ +++|||||+.||+.+|+.. ...++||..+++...+...+++|..||++ +|++... +|+|++||
T Consensus 267 fl~-~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~-lgi~~~~---~HrAl~DA 341 (1213)
T TIGR01405 267 FFK-DSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKK-LGVDLDD---HHRADYDA 341 (1213)
T ss_pred HhC-CCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHH-cCCCCCC---CcCHHHHH
Confidence 998 8999999999999999743 23589999998765544567999999996 6888754 79999999
Q ss_pred HHHHHHHHHHHHcCCcCCC
Q psy17350 508 IAALRLVKLKLSKGDLIGL 526 (528)
Q Consensus 508 ~AT~eL~~~~L~~g~~fg~ 526 (528)
+||++||..++++..+.|.
T Consensus 342 ~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 342 EATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred HHHHHHHHHHHHHHHHcCC
Confidence 9999999998876554443
No 42
>PRK06722 exonuclease; Provisional
Probab=99.85 E-value=5.1e-21 Score=194.65 Aligned_cols=154 Identities=20% Similarity=0.218 Sum_probs=123.1
Q ss_pred CCCeEEEeeceecCCCC----cCcEEEEEEEEe-CC--cEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 361 TSPLYGLDCEMCKTSND----QNELTRVTLVDE-QE--NVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g----~~eLirIs~Vd~-~G--~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
...|++||+|||+ ++. .++|++|++|.. +| +++ |++||+|..+|+.+++++||||++||+++ |++++|+
T Consensus 4 ~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~A-P~f~eVl 81 (281)
T PRK06722 4 ATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGV-EKFPQII 81 (281)
T ss_pred CCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCC-CCHHHHH
Confidence 4579999999985 332 279999999998 44 455 99999999999999999999999999995 9999999
Q ss_pred HHHHhcCCCCcEEEEcCchhhHHHHccc-------CC-----CEeeehhhchh--cCCCCCCCCHHHHHHHhhCCcccCC
Q psy17350 432 KILSELLPPDAILVGQSLNCDLHALKMM-------HP-----YVIDTSVIFNT--TGIRTHKPKLKMLTSHFLGLDIQNQ 497 (528)
Q Consensus 432 ~~L~~~i~~d~ILVGHnL~fDL~~L~~~-------hp-----~vIDTs~L~~~--~~~~~~k~sLk~La~~~Lg~~Iq~~ 497 (528)
.+|.+|++ +.++|+||..||+++|+.. .| +.+|+..++.. .......++|..|++. +|++...
T Consensus 82 ~ef~~fig-~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~-lgL~~~g- 158 (281)
T PRK06722 82 EKFIQFIG-EDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQ-LGLIWEG- 158 (281)
T ss_pred HHHHHHHC-CCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHH-CCCCCCC-
Confidence 99999998 6677777789999999753 12 13788765432 1222245789999985 6888642
Q ss_pred CCCCChHHHHHHHHHHHHHHHHc
Q psy17350 498 DGGHCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 498 ~~~HdAlEDA~AT~eL~~~~L~~ 520 (528)
.+|+|++||++|+.||..++.+
T Consensus 159 -~~HrAL~DA~~TA~L~l~l~~~ 180 (281)
T PRK06722 159 -KQHRALADAENTANILLKAYSE 180 (281)
T ss_pred -CCcCcHHHHHHHHHHHHHHhcc
Confidence 3799999999999999988753
No 43
>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=99.85 E-value=3.4e-21 Score=179.36 Aligned_cols=149 Identities=21% Similarity=0.203 Sum_probs=121.7
Q ss_pred eEEEeeceecCCCCc-----CcEEEEEEEEe--CCc-E--EEEEEEcCCC--CCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 364 LYGLDCEMCKTSNDQ-----NELTRVTLVDE--QEN-V--VYESLVKPYN--PITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 364 ~vALDcEmtgt~~g~-----~eLirIs~Vd~--~G~-v--i~d~LVkP~~--~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
||++||||+|..+.+ ++|++|++|.. ++. + .|++||+|.. +++++.+++||||+++++++ +++.+|+
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~-~~~~~vl 79 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNA-PSFPEVL 79 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcC-CCHHHHH
Confidence 689999999999764 89999999976 333 3 3999999998 89999999999999999995 9999999
Q ss_pred HHHHhcCCCCc--EEEEcCchhhHHHHccc------------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCC
Q psy17350 432 KILSELLPPDA--ILVGQSLNCDLHALKMM------------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQ 497 (528)
Q Consensus 432 ~~L~~~i~~d~--ILVGHnL~fDL~~L~~~------------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~ 497 (528)
++|.++++ +. .++.|+..||++++... ...++|+..+++...+....++|..||+. +|++...
T Consensus 80 ~~~~~~l~-~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~- 156 (176)
T cd06133 80 KEFLEWLG-KNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEY-LGLEFEG- 156 (176)
T ss_pred HHHHHHHH-hCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHH-CCCCCCC-
Confidence 99999998 54 44444459998776321 12589999998764443457899999985 6888762
Q ss_pred CCCCChHHHHHHHHHHHHHH
Q psy17350 498 DGGHCSKEDAIAALRLVKLK 517 (528)
Q Consensus 498 ~~~HdAlEDA~AT~eL~~~~ 517 (528)
..|+|+.||++|++|++++
T Consensus 157 -~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 157 -RHHRGLDDARNIARILKRL 175 (176)
T ss_pred -CCcCcHHHHHHHHHHHHHh
Confidence 4799999999999999865
No 44
>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=99.84 E-value=7.8e-21 Score=181.24 Aligned_cols=146 Identities=17% Similarity=0.159 Sum_probs=116.2
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEeCC--cEE--EEEEEcCCC--CCCCCceeecCCChhhhcccCCCHHHHHHHHHhcC
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDEQE--NVV--YESLVKPYN--PITNYLTAYSGITRALLAPVATRLEHVQKILSELL 438 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~~G--~vi--~d~LVkP~~--~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i 438 (528)
+.+|+||||+++..++|++|++|..++ .++ |+.+|+|.. ++....+.+||||++||++.++++.+++++|.+|+
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~~ 80 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRLF 80 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHHH
Confidence 469999999999889999999998743 444 889999975 45667889999999999994599999999999999
Q ss_pred C-CCcEEEEcC-chhhHHHHcccC------C---------CEeeehhhchhcC---------C----CCCCCCHHHHHHH
Q psy17350 439 P-PDAILVGQS-LNCDLHALKMMH------P---------YVIDTSVIFNTTG---------I----RTHKPKLKMLTSH 488 (528)
Q Consensus 439 ~-~d~ILVGHn-L~fDL~~L~~~h------p---------~vIDTs~L~~~~~---------~----~~~k~sLk~La~~ 488 (528)
. ++.++|||| +.||+.+|+... + .++||..+.+... + ...+++|..||++
T Consensus 81 ~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~ 160 (183)
T cd06138 81 NTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQA 160 (183)
T ss_pred ccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHHHH
Confidence 5 478999997 899999996431 1 2478876544210 0 1246889999986
Q ss_pred hhCCcccCCCCCCChHHHHHHHHHHH
Q psy17350 489 FLGLDIQNQDGGHCSKEDAIAALRLV 514 (528)
Q Consensus 489 ~Lg~~Iq~~~~~HdAlEDA~AT~eL~ 514 (528)
+|++... +|+|++||+||++|+
T Consensus 161 -~gi~~~~---~H~Al~Da~~ta~l~ 182 (183)
T cd06138 161 -NGIEHSN---AHDALSDVEATIALA 182 (183)
T ss_pred -CCCCccc---cccHHHHHHHHHHHh
Confidence 6887643 799999999999986
No 45
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.84 E-value=5.4e-20 Score=181.38 Aligned_cols=156 Identities=21% Similarity=0.254 Sum_probs=132.9
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE---EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV---YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi---~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
.++++||+||||.++..+++++|++|.. +++++ |+.||+|..+|+++.+++||||.+||.++ |.+.+|.+++.++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~-p~~~~v~~~~~~~ 91 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADA-PKFAEVLPEFLDF 91 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcC-CCHHHHHHHHHHH
Confidence 5789999999999986699999999998 66554 88999998899999999999999999995 9999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHcccC---------CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMMH---------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI 508 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~h---------p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~ 508 (528)
+.+..++||||+.||+.+|+... ..++||..+.+...+...+++|+.||. ++|++.. ....|+|+.||.
T Consensus 92 i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~-~~gi~~~-~~~~H~Al~Da~ 169 (243)
T COG0847 92 IGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAE-RLGIDRN-PFHPHRALFDAL 169 (243)
T ss_pred HCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHH-HcCCCcC-CcCCcchHHHHH
Confidence 99339999999999999996432 247899888765433335789999999 5788854 224699999999
Q ss_pred HHHHHHHHHHHc
Q psy17350 509 AALRLVKLKLSK 520 (528)
Q Consensus 509 AT~eL~~~~L~~ 520 (528)
+|+++|.+.+++
T Consensus 170 ~~a~~~~~~~~~ 181 (243)
T COG0847 170 ALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHhc
Confidence 999999988875
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=99.83 E-value=4.1e-22 Score=179.13 Aligned_cols=146 Identities=26% Similarity=0.339 Sum_probs=118.0
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEe-CCc----EEEEEEEcCCCC--CCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDE-QEN----VVYESLVKPYNP--ITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~-~G~----vi~d~LVkP~~~--I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
|+|||||||+.+..+++++|++|.. .+. ..|++||+|..+ ++++.+++||||.++|+++ +++.+++.++.++
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~-~~~~~~~~~~~~~ 79 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDA-PSFEEALDEFEEF 79 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCH-CEHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccC-CcHHHHHHhhhhh
Confidence 6899999999997799999999987 332 359999999998 9999999999999999996 8999999999999
Q ss_pred CCCCcEEEEcCchhhHHHH--------cccCC---CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHH
Q psy17350 438 LPPDAILVGQSLNCDLHAL--------KMMHP---YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKED 506 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L--------~~~hp---~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlED 506 (528)
++++.++||||..||..++ +..+| .++|+..+.+........++|+.||+.| |.+.... +|+|++|
T Consensus 80 ~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~-~~~~~~~--~H~Al~D 156 (164)
T PF00929_consen 80 LKKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLAEYF-GIPFDGT--AHDALDD 156 (164)
T ss_dssp HHHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHHHHT-TSSSTST--TTSHHHH
T ss_pred hhcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHHHHc-CCCCCCC--CcChHHH
Confidence 9878999999988886443 23233 4788877654321111237999999975 6665432 6999999
Q ss_pred HHHHHHHH
Q psy17350 507 AIAALRLV 514 (528)
Q Consensus 507 A~AT~eL~ 514 (528)
|++|++||
T Consensus 157 a~~t~~l~ 164 (164)
T PF00929_consen 157 ARATAELF 164 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHhCcC
Confidence 99999987
No 47
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.82 E-value=7.2e-20 Score=187.54 Aligned_cols=151 Identities=21% Similarity=0.264 Sum_probs=117.9
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeC----CcE-----EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQ----ENV-----VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~----G~v-----i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
...+++||+||||+++..++|++|++|.++ |.+ .|+.||+|..+|+...+++||||++|++++ +...
T Consensus 36 ~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~-~~~~--- 111 (294)
T PRK09182 36 VRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQ-TIDP--- 111 (294)
T ss_pred CCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcC-CCcH---
Confidence 346899999999999988999999999873 543 288999999999999999999999999996 5433
Q ss_pred HHHHhcCCCCcEEEEcCchhhHHHHcccCC-----CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHH
Q psy17350 432 KILSELLPPDAILVGQSLNCDLHALKMMHP-----YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKED 506 (528)
Q Consensus 432 ~~L~~~i~~d~ILVGHnL~fDL~~L~~~hp-----~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlED 506 (528)
.+|.+|+....+|||||+.||+.+|+...+ .+.+|............+++|..||.. +|.. . .+|+|++|
T Consensus 112 ~~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~-~g~~--~--~aHrAl~D 186 (294)
T PRK09182 112 AAVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQ-AGFF--H--EGHRAVDD 186 (294)
T ss_pred HHHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHH-cCCC--C--CCcChHHH
Confidence 345667775679999999999999975432 345665443322222357899999986 5732 2 37999999
Q ss_pred HHHHHHHHHHHHHc
Q psy17350 507 AIAALRLVKLKLSK 520 (528)
Q Consensus 507 A~AT~eL~~~~L~~ 520 (528)
|+||++|+...+..
T Consensus 187 a~Ata~ll~~~l~~ 200 (294)
T PRK09182 187 CQALLELLARPLPE 200 (294)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999977654
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.76 E-value=3.7e-18 Score=184.77 Aligned_cols=158 Identities=15% Similarity=0.161 Sum_probs=123.1
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeCC--cEE---EEEEEcCCCC--CCCCceeecCCChhhhcccCCCHHHHHHH
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQE--NVV---YESLVKPYNP--ITNYLTAYSGITRALLAPVATRLEHVQKI 433 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G--~vi---~d~LVkP~~~--I~dy~T~isGIT~e~L~~a~p~l~dV~~~ 433 (528)
...|+++|+||||+++..++|++|++|..++ .++ ++.+|+|... +....+.+||||++|+.+.+....++.++
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~ 84 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAAR 84 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHH
Confidence 4579999999999999889999999998743 233 8899999863 34567899999999998766789999999
Q ss_pred HHhcCC-CCcEEEEcC-chhhHHHHcccC------C------------CEeeehhhchhcC------C----CCCCCCHH
Q psy17350 434 LSELLP-PDAILVGQS-LNCDLHALKMMH------P------------YVIDTSVIFNTTG------I----RTHKPKLK 483 (528)
Q Consensus 434 L~~~i~-~d~ILVGHn-L~fDL~~L~~~h------p------------~vIDTs~L~~~~~------~----~~~k~sLk 483 (528)
|.+++. +++++|||| +.||+.+|+... + .++|++.++...+ + ....++|.
T Consensus 85 i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe 164 (476)
T PRK11779 85 IHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLE 164 (476)
T ss_pred HHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHH
Confidence 999994 589999997 799999886532 1 1346656533211 0 12458999
Q ss_pred HHHHHhhCCcccCCCCCCChHHHHHHHHHHHHHHHHcCC
Q psy17350 484 MLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGD 522 (528)
Q Consensus 484 ~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g~ 522 (528)
.||+. +|++.. .+|||+.||+||++|+++..++.+
T Consensus 165 ~L~~~-~gI~~~---~AHdALsDa~aT~~la~~l~~~qP 199 (476)
T PRK11779 165 HLTKA-NGIEHE---NAHDAMSDVYATIAMAKLIKQKQP 199 (476)
T ss_pred HHHHH-cCCCCC---CCCCcHHHHHHHHHHHHHHHHhCh
Confidence 99997 577754 379999999999999987776644
No 49
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.75 E-value=1.2e-17 Score=182.84 Aligned_cols=160 Identities=17% Similarity=0.180 Sum_probs=125.8
Q ss_pred CCeEEEeeceecCCCC---cCcEEEEEEEEe---CCcEE--EEEEEcCCC--CCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 362 SPLYGLDCEMCKTSND---QNELTRVTLVDE---QENVV--YESLVKPYN--PITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g---~~eLirIs~Vd~---~G~vi--~d~LVkP~~--~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
..|++||+|||+.++. .+||++|++|.. +|+++ |.+||||.. +|+.+++++||||++||+++ |+|.+|+
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~A-p~F~eVl 134 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRA-DPFPVVY 134 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcC-CCHHHHH
Confidence 4789999999998753 379999999986 56664 899999987 69999999999999999995 9999999
Q ss_pred HHHHhcCCCC---------cEEEEcCchhhHH-HHcc--------c----CCCEeeehhhchhc-C-----------CCC
Q psy17350 432 KILSELLPPD---------AILVGQSLNCDLH-ALKM--------M----HPYVIDTSVIFNTT-G-----------IRT 477 (528)
Q Consensus 432 ~~L~~~i~~d---------~ILVGHnL~fDL~-~L~~--------~----hp~vIDTs~L~~~~-~-----------~~~ 477 (528)
.+|.+|+... ..+|+|+..||+. +|.. . ..+++|....+... . ...
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~~ 214 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPPL 214 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccccccccc
Confidence 9999999722 3699999999995 6631 1 12356643232211 0 122
Q ss_pred CCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHHHHHHcCCcCC
Q psy17350 478 HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLIG 525 (528)
Q Consensus 478 ~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g~~fg 525 (528)
..++|..+++. +|+++.. .+|+|++||++|+.||.+++++|-.|-
T Consensus 215 ~~~~L~~al~~-lgL~~eG--r~HrAlDDA~ntA~L~~~Ll~~g~~~~ 259 (582)
T PTZ00315 215 GPSDMPDMLQM-LGLPLQG--RHHSGIDDCRNIAAVLCELLRRGLVID 259 (582)
T ss_pred CCcCHHHHHHH-CCCCCCC--CCcCcHHHHHHHHHHHHHHHHcCCEEE
Confidence 45899999985 7888753 479999999999999999999886553
No 50
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.75 E-value=5.3e-18 Score=201.95 Aligned_cols=160 Identities=23% Similarity=0.302 Sum_probs=138.5
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEE--EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVV--YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi--~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
..+++++|+||||..+..++|++|++|.. +|.++ |+.||+|..+++.+.+++||||++|+.+ ++++.+|.++|.+|
T Consensus 418 ~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~-aps~~EaL~~f~~f 496 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKD-APSIEEVLPKFKEF 496 (1437)
T ss_pred cCcEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcC-CCCHHHHHHHHHHH
Confidence 45799999999999998899999999987 77775 8999999999999999999999999998 59999999999999
Q ss_pred CCCCcEEEEcCchhhHHHHccc---------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH
Q psy17350 438 LPPDAILVGQSLNCDLHALKMM---------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI 508 (528)
Q Consensus 438 i~~d~ILVGHnL~fDL~~L~~~---------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~ 508 (528)
++ +.+|||||..||+.+|+.. ...++||..+++...+...+++|..||++ +|+.... +|+|++||+
T Consensus 497 ig-g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~-lGL~~~~---~HrAl~DA~ 571 (1437)
T PRK00448 497 CG-DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKK-FGVELEH---HHRADYDAE 571 (1437)
T ss_pred hC-CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHH-cCCCCCC---CcChHHHHH
Confidence 98 9999999999999988421 12589999987755444568899999996 6888753 799999999
Q ss_pred HHHHHHHHHHHcCCcCCC
Q psy17350 509 AALRLVKLKLSKGDLIGL 526 (528)
Q Consensus 509 AT~eL~~~~L~~g~~fg~ 526 (528)
||++||..+++.....|.
T Consensus 572 aTa~lf~~ll~~l~~~gi 589 (1437)
T PRK00448 572 ATAYLLIKFLKDLKEKGI 589 (1437)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 999999999877655554
No 51
>PRK05359 oligoribonuclease; Provisional
Probab=99.75 E-value=5e-18 Score=162.54 Aligned_cols=147 Identities=17% Similarity=0.219 Sum_probs=112.4
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEeCCc--EE---EEEEEcCCCC----CCCCceeec---CCChhhhcccCCCHHH
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDEQEN--VV---YESLVKPYNP----ITNYLTAYS---GITRALLAPVATRLEH 429 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~--vi---~d~LVkP~~~----I~dy~T~is---GIT~e~L~~a~p~l~d 429 (528)
.+||+|||||||+++..++|++|++|..++. ++ ++.+|+|... ++.+.+++| |||++++++ ++++.+
T Consensus 3 ~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~-~~~~~e 81 (181)
T PRK05359 3 DNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRAS-TVSEAE 81 (181)
T ss_pred CcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhc-CCCHHH
Confidence 4799999999999998899999999987553 33 8889999865 466777877 999999999 599999
Q ss_pred HHHHHHhcCC-----CCcEEEEcCchhhHHHHccc--------CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC
Q psy17350 430 VQKILSELLP-----PDAILVGQSLNCDLHALKMM--------HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN 496 (528)
Q Consensus 430 V~~~L~~~i~-----~d~ILVGHnL~fDL~~L~~~--------hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~ 496 (528)
|+++|.+|++ .+.+|||||+.||+.||+.. |.+++|++.++...+. ..+.+ +++++-.
T Consensus 82 ~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~--~~P~~------~~~~~~~- 152 (181)
T PRK05359 82 AEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARR--WKPEI------LNGFKKQ- 152 (181)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHH--hChhh------hhCCCCc-
Confidence 9999999995 36899999999999999753 2357786544321110 01122 2233322
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHc
Q psy17350 497 QDGGHCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 497 ~~~~HdAlEDA~AT~eL~~~~L~~ 520 (528)
..|+|++||+++.+.++++.+.
T Consensus 153 --~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 153 --GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred --CCcccHHHHHHHHHHHHHHHHH
Confidence 3699999999999999887764
No 52
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.74 E-value=3.1e-18 Score=162.29 Aligned_cols=142 Identities=19% Similarity=0.256 Sum_probs=108.4
Q ss_pred eEEEeeceecCCCCcCcEEEEEEEEeCCc--EE---EEEEEcCCCCCC----CCceee---cCCChhhhcccCCCHHHHH
Q psy17350 364 LYGLDCEMCKTSNDQNELTRVTLVDEQEN--VV---YESLVKPYNPIT----NYLTAY---SGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 364 ~vALDcEmtgt~~g~~eLirIs~Vd~~G~--vi---~d~LVkP~~~I~----dy~T~i---sGIT~e~L~~a~p~l~dV~ 431 (528)
+++||+||||+++..++|++|++|.+++. .+ |+.+|+|..+++ .+..++ ||||++|+++ +|++.+++
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~-~~~~~~vl 79 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRAS-TVTLAQAE 79 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhC-CCCHHHHH
Confidence 47899999999987799999999988653 32 899999998654 344555 5999999999 59999999
Q ss_pred HHHHhcCCC-----CcEEEEcCchhhHHHHccc--------CCCEeeehhh---chhcCCCCCCCCHHHHHHHhhCCccc
Q psy17350 432 KILSELLPP-----DAILVGQSLNCDLHALKMM--------HPYVIDTSVI---FNTTGIRTHKPKLKMLTSHFLGLDIQ 495 (528)
Q Consensus 432 ~~L~~~i~~-----d~ILVGHnL~fDL~~L~~~--------hp~vIDTs~L---~~~~~~~~~k~sLk~La~~~Lg~~Iq 495 (528)
++|.+|+.. ..+|||||+.||+.+|+.. +.+++||..+ .+... +.++. ++..-
T Consensus 80 ~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~-----p~~~~-----~~~~~- 148 (173)
T cd06135 80 AELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWY-----PEIYR-----KAPKK- 148 (173)
T ss_pred HHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhC-----cHhhh-----cCCCC-
Confidence 999999973 3699999999999999643 2356887543 32211 11111 23322
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHH
Q psy17350 496 NQDGGHCSKEDAIAALRLVKLKLS 519 (528)
Q Consensus 496 ~~~~~HdAlEDA~AT~eL~~~~L~ 519 (528)
...|+|++||+||+.+|++++.
T Consensus 149 --~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 149 --KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred --CCCcchHHHHHHHHHHHHHHHH
Confidence 2479999999999999998875
No 53
>KOG1275|consensus
Probab=99.72 E-value=2.9e-18 Score=190.73 Aligned_cols=160 Identities=29% Similarity=0.426 Sum_probs=137.2
Q ss_pred ccCCCCCCeEEEeeceecCCCC----------------cCcEEEEEEEEeCC----cEEEEEEEcCCCCCCCCceeecCC
Q psy17350 356 AEVTPTSPLYGLDCEMCKTSND----------------QNELTRVTLVDEQE----NVVYESLVKPYNPITNYLTAYSGI 415 (528)
Q Consensus 356 ~~~~~~~~~vALDcEmtgt~~g----------------~~eLirIs~Vd~~G----~vi~d~LVkP~~~I~dy~T~isGI 415 (528)
.+++.....||||-|.+.+... +..++||++|+.+| -...|-||--.+.|.||.|+||||
T Consensus 904 dEmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI 983 (1118)
T KOG1275|consen 904 DEMPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGI 983 (1118)
T ss_pred cccCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCC
Confidence 3456677899999999877532 34689999999753 234799999999999999999999
Q ss_pred ChhhhcccC-----CCHHHHHHHHHhcCCCCcEEEEcCchhhHHHHcccCC--CEeeehhhchhcCCCCCCCCHHHHHHH
Q psy17350 416 TRALLAPVA-----TRLEHVQKILSELLPPDAILVGQSLNCDLHALKMMHP--YVIDTSVIFNTTGIRTHKPKLKMLTSH 488 (528)
Q Consensus 416 T~e~L~~a~-----p~l~dV~~~L~~~i~~d~ILVGHnL~fDL~~L~~~hp--~vIDTs~L~~~~~~~~~k~sLk~La~~ 488 (528)
.|.||+.-. ++++-+..+++-+++.+.|.|||+|++|++++++.-| .+|||..+|.. +..+..+|+.||++
T Consensus 984 ~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~--~s~R~LSLrfLa~~ 1061 (1118)
T KOG1275|consen 984 KPGDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRL--GSQRMLSLRFLAWE 1061 (1118)
T ss_pred CccccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEec--ccccEEEHHHHHHH
Confidence 999998631 3588999999999999999999999999999998766 49999999954 33567899999999
Q ss_pred hhCCcccCCCCCCChHHHHHHHHHHHHHHHH
Q psy17350 489 FLGLDIQNQDGGHCSKEDAIAALRLVKLKLS 519 (528)
Q Consensus 489 ~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~~L~ 519 (528)
+||..||.+ .|||+|||+.|++||+++++
T Consensus 1062 lLg~~IQ~~--~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1062 LLGETIQME--AHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred Hhcchhhcc--ccccHHHHHHHHHHHHHHHH
Confidence 999999985 89999999999999998875
No 54
>KOG1275|consensus
Probab=99.72 E-value=4.3e-18 Score=189.45 Aligned_cols=130 Identities=22% Similarity=0.178 Sum_probs=104.1
Q ss_pred ceeeccCCCCCCchhhhhhHH---HHHHHHHHHHhcCCcEEEeccCCcC--cccccCC--cEeecccccCCCCCCCCCcc
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNA---RQIKRLENKKRKMDALVEIKTLNEA--DKQMMHP--YVIDTSVIFNTTGIRTHKPK 77 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~---~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp--~i~DTa~~~~~~~~~~~~~S 77 (528)
+++|||.|+||..+...+-+. .+..+|. ++-+.+.|+|||||+|| ++.+..| +||||+.+|..+. .++.|
T Consensus 978 TqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~-~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s--~R~LS 1054 (1118)
T KOG1275|consen 978 TQYSGIKPGDLDPTTSEKRLTTLKVLYLKLR-LLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS--QRMLS 1054 (1118)
T ss_pred HHhcCCCccccCCccCcceehhHHHHHHHHH-HHHHcCcEEEcccccccceEEEEecChhhheeeeEEEeccc--ccEEE
Confidence 689999999988765544332 2333333 33345899999999999 9999999 6999999997764 57999
Q ss_pred HHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHH--cCCCCCCCCCCcccccchhhhhhhhhcccCCCCcc
Q psy17350 78 LKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLS--KGDLCSTKPAHHTVNLGFSLNDYLMFAHELPGLRD 150 (528)
Q Consensus 78 Lk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~--~g~~~~~~~~~~~~~~~~~l~~ya~lGk~~p~~p~ 150 (528)
||+||+.+||.+||.+ .|||+||||+|+.||+.+++ +... ++..|...+-.|+.+.+++|
T Consensus 1055 LrfLa~~lLg~~IQ~~--~HDSIeDA~taLkLYk~Yl~lkeq~~-----------~~~~l~niye~gr~~q~k~P 1116 (1118)
T KOG1275|consen 1055 LRFLAWELLGETIQME--AHDSIEDARTALKLYKKYLKLKEQGK-----------LESELRNIYECGRPNQFKVP 1116 (1118)
T ss_pred HHHHHHHHhcchhhcc--ccccHHHHHHHHHHHHHHHHHHHhhH-----------HHHHHHHHhhcCccccCCCC
Confidence 9999999999999998 89999999999999998775 4323 33678888889998876654
No 55
>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=99.56 E-value=3.1e-15 Score=139.92 Aligned_cols=104 Identities=27% Similarity=0.255 Sum_probs=86.4
Q ss_pred ccceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCCc--EeecccccCCCC---CC-CC
Q psy17350 3 LSLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHPY--VIDTSVIFNTTG---IR-TH 74 (528)
Q Consensus 3 ~~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp~--i~DTa~~~~~~~---~~-~~ 74 (528)
.++.++||+|+++ .+|.. ++.|..++.+.++ ++|||||.+.+| +|++.||. ++||+.+++.++ .+ ..
T Consensus 46 ~~~~i~GIt~~~l-~~a~~--~~~v~~~l~~~l~--~~vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~ 120 (157)
T cd06149 46 YRTRWSGIRRQHL-VNATP--FAVAQKEILKILK--GKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENC 120 (157)
T ss_pred cceECCCCCHHHH-hcCCC--HHHHHHHHHHHcC--CCEEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccC
Confidence 3578999999965 45533 5669999999987 699999999999 99999995 899998765432 11 24
Q ss_pred CccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 75 KPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 75 ~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
+.+|+.||+++|++.||.+..+|++.|||+|||+|||
T Consensus 121 ~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 121 RVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred ChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 6899999999999999986568999999999999986
No 56
>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=99.52 E-value=1.5e-14 Score=134.20 Aligned_cols=105 Identities=34% Similarity=0.436 Sum_probs=86.8
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCCcEeecccccCCCCCCCCCccHHHH
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHPYVIDTSVIFNTTGIRTHKPKLKML 81 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp~i~DTa~~~~~~~~~~~~~SLk~L 81 (528)
.++++||+++++ .++.. .+++|..++.+.+.+ +.|||||.+++| .|+..|+.++||..+++.......+.+|+.|
T Consensus 44 ~t~itGIt~~~l-~~a~~-~~~~v~~~~~~fl~~-~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L 120 (150)
T cd06145 44 NTRFSGITEEML-ENVTT-TLEDVQKKLLSLISP-DTILVGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNL 120 (150)
T ss_pred ccCcCCCCHHHh-ccCCC-CHHHHHHHHHHHhCC-CCEEEEcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHH
Confidence 578999999955 44421 346699999999863 589999999999 9999999999999998765443456899999
Q ss_pred HHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 82 TSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 82 a~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
|+.+++..||.+...|++.+||++|++||+
T Consensus 121 ~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 121 AKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred HHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 999999999973348999999999999984
No 57
>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=99.48 E-value=3.5e-14 Score=133.04 Aligned_cols=107 Identities=26% Similarity=0.281 Sum_probs=85.9
Q ss_pred ccceeeccCCCCCCchhhh-h----hHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCCcEeecccccCCCCCCC--
Q psy17350 3 LSLEVLGLNPGGVLLNAYF-K----MNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHPYVIDTSVIFNTTGIRT-- 73 (528)
Q Consensus 3 ~~~~vSGI~p~~~~~~a~~-~----~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp~i~DTa~~~~~~~~~~-- 73 (528)
.+++++||+++++ .++.. . .+++++.++.+.+.+ ++|||||.+.+| +|+..|+.++||..+++......
T Consensus 45 ~~~~i~GIt~~~l-~~a~~~~~~~~~~~~~~~~~~~~i~~-~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~~~~~ 122 (161)
T cd06137 45 WRTRFSGVTPADL-EEAAKAGKTIFGWEAARAALWKFIDP-DTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLA 122 (161)
T ss_pred cceeccCCCHHHH-hhhhhcCCccccHHHHHHHHHHhcCC-CcEEEeccHHHHHHHHhCcCCCeeEehhhhhhccCCCcC
Confidence 3678999999965 43321 1 124588888888863 389999999999 89999999999999988643222
Q ss_pred -CCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 74 -HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 74 -~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
...+|+.||+.+||.+||.+..+|++.+||+|||+||.
T Consensus 123 ~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 123 KRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred CCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHHhC
Confidence 47999999999999999984458999999999999983
No 58
>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=99.12 E-value=8.1e-11 Score=109.26 Aligned_cols=101 Identities=30% Similarity=0.349 Sum_probs=82.7
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCC--cEeecccccCCCCCC-CCCccH
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHP--YVIDTSVIFNTTGIR-THKPKL 78 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp--~i~DTa~~~~~~~~~-~~~~SL 78 (528)
+.+++||+++++ .++.. +.++..++.+.+. ++++|||....| .|++.+| .++||..+....... ...+||
T Consensus 47 ~~~ihGIt~~~v-~~a~~--~~~~~~~l~~~l~--~~vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL 121 (152)
T cd06144 47 RTAVSGIRPEHL-KDAPD--FEEVQKKVAELLK--GRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSL 121 (152)
T ss_pred cccCCCCCHHHH-cCCCC--HHHHHHHHHHHhC--CCEEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhH
Confidence 577899999965 44432 4568889999887 589999999999 8998888 489999876654321 357999
Q ss_pred HHHHHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 79 KMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 79 k~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
+.||+.+||.+++.+ .|+..+||+||++||+
T Consensus 122 ~~l~~~~lgi~~~~~--~H~Al~DA~at~~l~~ 152 (152)
T cd06144 122 KKLAKQLLGLDIQEG--EHSSVEDARAAMRLYR 152 (152)
T ss_pred HHHHHHHcCcccCCC--CcCcHHHHHHHHHHhC
Confidence 999999999999865 7999999999999985
No 59
>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=98.88 E-value=2.7e-08 Score=95.49 Aligned_cols=123 Identities=15% Similarity=0.148 Sum_probs=91.1
Q ss_pred eEEEeeceecC----CCCcCcEEEEEEEEe-CCcEE-EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 364 LYGLDCEMCKT----SNDQNELTRVTLVDE-QENVV-YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 364 ~vALDcEmtgt----~~g~~eLirIs~Vd~-~G~vi-~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
++++|+||++. ++..++|+.|+++.. +|... +.....+...... ||+..++..+ ++..+++.++.++
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~~~------~i~~~~v~~~-~~E~~lL~~f~~~ 73 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDDIE------FIDGIEVEYF-ADEKELLKRFFDI 73 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCcCC------CCCCceEEEe-CCHHHHHHHHHHH
Confidence 47899999998 666799999999997 77643 3333333222111 8999999996 9999999999999
Q ss_pred CCCC--cEEEEcCc-hhhHHHHcc-------cC-----------------------C-CEeeehhhchhcCCCCCCCCHH
Q psy17350 438 LPPD--AILVGQSL-NCDLHALKM-------MH-----------------------P-YVIDTSVIFNTTGIRTHKPKLK 483 (528)
Q Consensus 438 i~~d--~ILVGHnL-~fDL~~L~~-------~h-----------------------p-~vIDTs~L~~~~~~~~~k~sLk 483 (528)
+..- .||||||. .||+.+|.. .. . .++|+..+++... +..+|+|+
T Consensus 74 i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~-~l~sy~L~ 152 (199)
T cd05160 74 IREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDF-KLKSYTLD 152 (199)
T ss_pred HHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhc-CcccCCHH
Confidence 9732 69999999 899988832 11 0 1678888776433 25679999
Q ss_pred HHHHHhhCCcc
Q psy17350 484 MLTSHFLGLDI 494 (528)
Q Consensus 484 ~La~~~Lg~~I 494 (528)
.+|+++||..-
T Consensus 153 ~v~~~~l~~~k 163 (199)
T cd05160 153 AVAEELLGEGK 163 (199)
T ss_pred HHHHHHhCCCC
Confidence 99999987653
No 60
>KOG3242|consensus
Probab=98.74 E-value=1e-08 Score=97.41 Aligned_cols=144 Identities=20% Similarity=0.314 Sum_probs=103.6
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEeCCc--EE---EEEEEcCCCCC----CCCce---eecCCChhhhcccCCCHHH
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDEQEN--VV---YESLVKPYNPI----TNYLT---AYSGITRALLAPVATRLEH 429 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~--vi---~d~LVkP~~~I----~dy~T---~isGIT~e~L~~a~p~l~d 429 (528)
.++|.|||||||++-+.+.|++|+++=-+|. ++ +|..|+-...+ .+|.. .-||+|+.-+.. ..+++|
T Consensus 26 q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S-~~tl~~ 104 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLAS-KITLAD 104 (208)
T ss_pred CceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHh-hccHHH
Confidence 4799999999999999999999998755444 33 67777755433 34433 347899998888 589999
Q ss_pred HHHHHHhcCC-----CCcEEEEcCchhhHHHHcccCC--------CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC
Q psy17350 430 VQKILSELLP-----PDAILVGQSLNCDLHALKMMHP--------YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN 496 (528)
Q Consensus 430 V~~~L~~~i~-----~d~ILVGHnL~fDL~~L~~~hp--------~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~ 496 (528)
+-.++++|+. ...+|-|.++.-|..||....| ++||+|.+- .||+++ ..+++.
T Consensus 105 aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIk-------------eL~~Rw-~P~~~~ 170 (208)
T KOG3242|consen 105 AENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIK-------------ELARRW-YPDIKA 170 (208)
T ss_pred HHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHH-------------HHHHHh-Cchhhc
Confidence 9999988864 3678889999999999976543 688987753 223322 111111
Q ss_pred ----CCCCCChHHHHHHHHHHHHHHHHc
Q psy17350 497 ----QDGGHCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 497 ----~~~~HdAlEDA~AT~eL~~~~L~~ 520 (528)
....|+|++|.+-+..=++++.++
T Consensus 171 ~aPkK~~~HrAldDI~ESI~ELq~Yr~n 198 (208)
T KOG3242|consen 171 RAPKKKATHRALDDIRESIKELQYYREN 198 (208)
T ss_pred cCcccccccchHHHHHHHHHHHHHHHHH
Confidence 123699999999988777766543
No 61
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.74 E-value=1.5e-08 Score=95.45 Aligned_cols=148 Identities=17% Similarity=0.193 Sum_probs=104.6
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEe--CCcEE---EEEEEcCCC----CCCCCceee---cCCChhhhcccCCCHH
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDE--QENVV---YESLVKPYN----PITNYLTAY---SGITRALLAPVATRLE 428 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~--~G~vi---~d~LVkP~~----~I~dy~T~i---sGIT~e~L~~a~p~l~ 428 (528)
..+.|-|||||||++++.+.|++|+.+-- +-+++ .+.-|.-.. ...+|+++- ||+++.-.+. ..+..
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S-~~t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKAS-TVTEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHh-hccHH
Confidence 35789999999999999999999997743 44444 333343322 456777755 5677766666 57888
Q ss_pred HHHHHHHhcCC-----CCcEEEEcCchhhHHHHcccCCC--------EeeehhhchhcCCCCCCCCHHHHHHHhhCCccc
Q psy17350 429 HVQKILSELLP-----PDAILVGQSLNCDLHALKMMHPY--------VIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQ 495 (528)
Q Consensus 429 dV~~~L~~~i~-----~d~ILVGHnL~fDL~~L~~~hp~--------vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq 495 (528)
++-.++++||+ ..+++-|.++.-|-+||....|. .+|+|. ||.||+.+ ..+|.
T Consensus 84 ~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVST-------------lKELa~RW-~P~i~ 149 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVST-------------LKELARRW-NPEIL 149 (184)
T ss_pred HHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHH-------------HHHHHHhh-CcHhh
Confidence 88888888764 26789999999999999766553 455544 55555543 33333
Q ss_pred CC---CCCCChHHHHHHHHHHHHHHHHcCCc
Q psy17350 496 NQ---DGGHCSKEDAIAALRLVKLKLSKGDL 523 (528)
Q Consensus 496 ~~---~~~HdAlEDA~AT~eL~~~~L~~g~~ 523 (528)
.+ ++.|.|++|.+-+..=++++.++...
T Consensus 150 ~~~~K~~~H~Al~DI~ESI~EL~~YR~~f~~ 180 (184)
T COG1949 150 AGFKKGGTHRALDDIRESIAELRYYREHFLK 180 (184)
T ss_pred hccccccchhHHHHHHHHHHHHHHHHHHhcc
Confidence 21 25799999999998887877776543
No 62
>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=98.61 E-value=5.2e-07 Score=84.98 Aligned_cols=142 Identities=24% Similarity=0.231 Sum_probs=96.9
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
..+++|+|+|+++..+....++.+++....+..+|- -+++ +.+ .+ ++.+.++..+|.+++..
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~-~~~~--------~~~--------~~-~~~~~~~~~~l~~~l~~ 65 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYI-PLGH--------DYG--------GE-QLPREEVLAALKPLLED 65 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEE-ecCC--------Ccc--------cc-CCCHHHHHHHHHHHHhC
Confidence 457899999999988755788888887555544321 0111 111 12 35688899999998873
Q ss_pred C-cEEEEcCchhhHHHHcccC----CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC-----C---------C---
Q psy17350 441 D-AILVGQSLNCDLHALKMMH----PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN-----Q---------D--- 498 (528)
Q Consensus 441 d-~ILVGHnL~fDL~~L~~~h----p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~-----~---------~--- 498 (528)
. ..+||||+.||+.+|+... ..++||..+.....+...+++|+.|++.|++.++.. + .
T Consensus 66 ~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~ 145 (193)
T cd06139 66 PSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL 145 (193)
T ss_pred CCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH
Confidence 3 3799999999999997432 257999888654433221569999999998765210 0 0
Q ss_pred --CCCChHHHHHHHHHHHHHHHHc
Q psy17350 499 --GGHCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 499 --~~HdAlEDA~AT~eL~~~~L~~ 520 (528)
..|.+..||.++..|+....++
T Consensus 146 ~~~~~ya~~d~~~~~~l~~~l~~~ 169 (193)
T cd06139 146 EKAAEYAAEDADITLRLYELLKPK 169 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1235788899999998877654
No 63
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=98.56 E-value=2.1e-08 Score=94.95 Aligned_cols=159 Identities=20% Similarity=0.211 Sum_probs=117.1
Q ss_pred CeEEEeeceecCCCC----cCcEEEEEE--EEe-CCcEE--EEEEEcCCC--CCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 363 PLYGLDCEMCKTSND----QNELTRVTL--VDE-QENVV--YESLVKPYN--PITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 363 ~~vALDcEmtgt~~g----~~eLirIs~--Vd~-~G~vi--~d~LVkP~~--~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
..++||+|.|-.+.+ ..||++|.+ |+. +.+++ |.+||+|.. ..++|.-.++|||...++.| |-|.+|+
T Consensus 5 ~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~a-pifs~v~ 83 (210)
T COG5018 5 SLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEA-PIFSMVF 83 (210)
T ss_pred eEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhcccc-chHHHHH
Confidence 468999999876543 467877764 443 44554 889999987 46788899999999999995 9999999
Q ss_pred HHHHhcCCCCcE----EEEcCchhhHHHHccc---C---C-----CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC
Q psy17350 432 KILSELLPPDAI----LVGQSLNCDLHALKMM---H---P-----YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN 496 (528)
Q Consensus 432 ~~L~~~i~~d~I----LVGHnL~fDL~~L~~~---h---p-----~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~ 496 (528)
+++..++...+. -.+---+.|++.|... | | ..+|.+.-|......++-.+|....++ .|..++.
T Consensus 84 E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~-~G~sf~G 162 (210)
T COG5018 84 EDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEE-YGDSFTG 162 (210)
T ss_pred HHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHHH-hccccCC
Confidence 999888763221 1222236799998642 2 1 368988888765444555788887776 4888875
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHcCCcCC
Q psy17350 497 QDGGHCSKEDAIAALRLVKLKLSKGDLIG 525 (528)
Q Consensus 497 ~~~~HdAlEDA~AT~eL~~~~L~~g~~fg 525 (528)
.+|+|++|||.+..||++.+.....|.
T Consensus 163 --~~HraldDArn~~rl~klv~~~~~~~e 189 (210)
T COG5018 163 --THHRALDDARNAYRLFKLVEQDKQYLE 189 (210)
T ss_pred --chhhhHHHHHHHHHHHHHHcchhhhcc
Confidence 589999999999999998776655554
No 64
>KOG0542|consensus
Probab=98.49 E-value=1.8e-07 Score=93.52 Aligned_cols=158 Identities=19% Similarity=0.306 Sum_probs=114.5
Q ss_pred eEEEeeceecCCCC----cCcEEEEEEEEe----CCcE--EEEEEEcCCC--CCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 364 LYGLDCEMCKTSND----QNELTRVTLVDE----QENV--VYESLVKPYN--PITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 364 ~vALDcEmtgt~~g----~~eLirIs~Vd~----~G~v--i~d~LVkP~~--~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
+++||+|.|--+.+ ..||++..+|-. .+.+ -|+.||+|.. ...+|.+.+|||..++++.+ ++|.+|.
T Consensus 58 LliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a-~~f~~vl 136 (280)
T KOG0542|consen 58 LLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEA-PTFPQVL 136 (280)
T ss_pred EEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccC-CCHHHHH
Confidence 58999999866544 359999999833 3333 3889999976 56899999999999999995 9999999
Q ss_pred HHHHhcCCCCcE--------EEEcCchhhHH-HHc-------ccCC----CEeeehhhchhcCCCCCCCCHHHHHHHhhC
Q psy17350 432 KILSELLPPDAI--------LVGQSLNCDLH-ALK-------MMHP----YVIDTSVIFNTTGIRTHKPKLKMLTSHFLG 491 (528)
Q Consensus 432 ~~L~~~i~~d~I--------LVGHnL~fDL~-~L~-------~~hp----~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg 491 (528)
.++..++..... +|--+ .-||. +|. +.-| ..||.-..|......+...++..+-++ +|
T Consensus 137 ~~f~~Wlr~~~~~~k~~~~Afvtdg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~-~g 214 (280)
T KOG0542|consen 137 SEFDSWLRKDSLGDKNGKFAFVTDG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEH-YG 214 (280)
T ss_pred HHHHHHHHHhhcccccCceEEEeCc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHHH-hC
Confidence 999988752211 12211 34553 332 2223 478888887643222245678887665 68
Q ss_pred CcccCCCCCCChHHHHHHHHHHHHHHHHcCCcCCC
Q psy17350 492 LDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLIGL 526 (528)
Q Consensus 492 ~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g~~fg~ 526 (528)
.+.+. ..|+.++||+-.+.|++++++.|-.|-.
T Consensus 215 L~f~G--r~HsGiDDa~Nia~I~~kM~~dg~~~~I 247 (280)
T KOG0542|consen 215 LQFEG--RAHSGIDDARNIARIAQKMIRDGAEFRI 247 (280)
T ss_pred CcccC--CcccCchhHHHHHHHHHHHHhCCcEEEe
Confidence 88765 4899999999999999999999877643
No 65
>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=98.42 E-value=1.8e-06 Score=79.74 Aligned_cols=133 Identities=23% Similarity=0.265 Sum_probs=78.9
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEe-CCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC-
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDE-QENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP- 439 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~- 439 (528)
.+++|+|||+++.... ..-.+++++-. .+... .++.|...-.+ . +...|.+++.
T Consensus 20 ~~~~a~D~E~~~~~~~-~~~~~~~~iq~~~~~~~--~i~~~~~~~~~-----------------~----~~~~l~~ll~~ 75 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPY-SYNPKIALIQLATGEGC--YIIDPIDLGDN-----------------W----ILDALKELLED 75 (176)
T ss_dssp TSEEEEEEEEETSTST-TSSEEEEEEEEEESCEE--EEECGTTSTTT-----------------T----HHHHHHHHHTT
T ss_pred CCeEEEEEEECCCCcc-ccCCeEEEEEEecCCCc--eeeeecccccc-----------------c----hHHHHHHHHhC
Confidence 4599999999999872 11233333333 22211 11122111000 0 4555566555
Q ss_pred CCcEEEEcCchhhHHHHccc----CCCEeeehhhchhcCCCCCCCCHHHHHHHhhC-Cccc----CCCCC-CC-------
Q psy17350 440 PDAILVGQSLNCDLHALKMM----HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLG-LDIQ----NQDGG-HC------- 502 (528)
Q Consensus 440 ~d~ILVGHnL~fDL~~L~~~----hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg-~~Iq----~~~~~-Hd------- 502 (528)
++.+.||||+.||+.+|... ...++||....... .+.++++|+.|+..|+| .... .+... -+
T Consensus 76 ~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l-~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~ 154 (176)
T PF01612_consen 76 PNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLL-DPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQI 154 (176)
T ss_dssp TTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHT-TTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHH
T ss_pred CCccEEEEEEechHHHHHHHhccccCCccchhhhhhcc-cccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHH
Confidence 45689999999999999763 24689994443332 23334899999999999 3332 11111 12
Q ss_pred --hHHHHHHHHHHHHHHHH
Q psy17350 503 --SKEDAIAALRLVKLKLS 519 (528)
Q Consensus 503 --AlEDA~AT~eL~~~~L~ 519 (528)
|..||.++.+||..+.+
T Consensus 155 ~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 155 EYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp HHHHHHHHTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 45799999999986554
No 66
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.36 E-value=1.8e-06 Score=90.73 Aligned_cols=159 Identities=16% Similarity=0.204 Sum_probs=112.6
Q ss_pred CCCCeEEEeeceecCCCCcCcEEEEEEEEe--CCcEE---EEEEEcCCCCCCC--CceeecCCChhhhcccCCCHHHHHH
Q psy17350 360 PTSPLYGLDCEMCKTSNDQNELTRVTLVDE--QENVV---YESLVKPYNPITN--YLTAYSGITRALLAPVATRLEHVQK 432 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g~~eLirIs~Vd~--~G~vi---~d~LVkP~~~I~d--y~T~isGIT~e~L~~a~p~l~dV~~ 432 (528)
....|+..|.||.|..+..+...+++.|+- +-++| ..-|+||.+..-. ...-|+||||+.....+..-.+...
T Consensus 7 ~~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~ 86 (475)
T COG2925 7 KQPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAA 86 (475)
T ss_pred CCCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHH
Confidence 345799999999999999999999999964 44444 6679999874322 3678999999988876677666666
Q ss_pred HHHh-cCCCCcEEEEcC-chhhHHHHccc------CCC------------Eeeehhh-chhc--C-------CCCCCCCH
Q psy17350 433 ILSE-LLPPDAILVGQS-LNCDLHALKMM------HPY------------VIDTSVI-FNTT--G-------IRTHKPKL 482 (528)
Q Consensus 433 ~L~~-~i~~d~ILVGHn-L~fDL~~L~~~------hp~------------vIDTs~L-~~~~--~-------~~~~k~sL 482 (528)
.|.. |..|++++||+| +.||=.+-|.. -|+ .+|.... |..+ | ...-..+|
T Consensus 87 ~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkL 166 (475)
T COG2925 87 RIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKL 166 (475)
T ss_pred HHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchhh
Confidence 6655 666899999986 79997666532 121 3454443 2211 1 11235789
Q ss_pred HHHHHHhhCCcccCCCCCCChHHHHHHHHHHHHHHHHcCC
Q psy17350 483 KMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGD 522 (528)
Q Consensus 483 k~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g~ 522 (528)
..|++. -|++ ++ .+|||+.|.+||..+.++.-++.+
T Consensus 167 EhLt~A-Ngie--H~-nAHdAmsDVyATIamAklvk~~QP 202 (475)
T COG2925 167 EHLTKA-NGIE--HS-NAHDAMSDVYATIAMAKLVKTAQP 202 (475)
T ss_pred HHHhhc-cccc--cc-hhhHHHHHHHHHHHHHHHHHhhCc
Confidence 999886 3544 42 489999999999999875544433
No 67
>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=98.35 E-value=3.9e-06 Score=81.24 Aligned_cols=134 Identities=17% Similarity=0.200 Sum_probs=86.0
Q ss_pred CCCCeEEEeeceecCCC----CcCcEEEEEEEEeCCcE-EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHH
Q psy17350 360 PTSPLYGLDCEMCKTSN----DQNELTRVTLVDEQENV-VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKIL 434 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~----g~~eLirIs~Vd~~G~v-i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L 434 (528)
...++++||||.+.... +.-.+++|+. .+.+ ++|-+--+. . .-+.+-+.|
T Consensus 20 ~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat---~~~~~lid~~~~~~-------------------~---~~~~~~~~L 74 (193)
T cd06146 20 EAGRVVGIDSEWKPSFLGDSDPRVAILQLAT---EDEVFLLDLLALEN-------------------L---ESEDWDRLL 74 (193)
T ss_pred ccCCEEEEECccCCCccCCCCCCceEEEEec---CCCEEEEEchhccc-------------------c---chHHHHHHH
Confidence 45689999999986542 3346666663 2333 232211110 0 112233446
Q ss_pred HhcCCCC-cEEEEcCchhhHHHHcccC----------CCEeeehhhchhcCC----------CCCCCCHHHHHHHhhCCc
Q psy17350 435 SELLPPD-AILVGQSLNCDLHALKMMH----------PYVIDTSVIFNTTGI----------RTHKPKLKMLTSHFLGLD 493 (528)
Q Consensus 435 ~~~i~~d-~ILVGHnL~fDL~~L~~~h----------p~vIDTs~L~~~~~~----------~~~k~sLk~La~~~Lg~~ 493 (528)
.+++... -+-|||++.+|++.|+..+ ..++||..++..... ....++|+.||+.+||.+
T Consensus 75 ~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~~lg~~ 154 (193)
T cd06146 75 KRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQEVLGKP 154 (193)
T ss_pred HHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHHHhCCC
Confidence 6666533 4559999999999997432 258999988763211 135689999999999988
Q ss_pred ccCCC-------------CCCChHHHHHHHHHHHHHHH
Q psy17350 494 IQNQD-------------GGHCSKEDAIAALRLVKLKL 518 (528)
Q Consensus 494 Iq~~~-------------~~HdAlEDA~AT~eL~~~~L 518 (528)
+.... +-+-|..||.++++||.++.
T Consensus 155 l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 155 LDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred cCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 76531 23457899999999998654
No 68
>PRK05755 DNA polymerase I; Provisional
Probab=98.11 E-value=1.6e-05 Score=93.18 Aligned_cols=134 Identities=28% Similarity=0.352 Sum_probs=94.0
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
...++|+|+||++.++...+++.|++-..+|.+.| | |. +++.. +++..|.+++..
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~---i-p~----------~~i~~-----------~~l~~l~~~L~d 368 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAY---I-PL----------DQLDR-----------EVLAALKPLLED 368 (880)
T ss_pred ccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEE---E-ec----------ccccH-----------HHHHHHHHHHhC
Confidence 35789999999999887778888887544554332 2 11 11110 466777787774
Q ss_pred Cc-EEEEcCchhhHHHHcccC----CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC-------C---------CC
Q psy17350 441 DA-ILVGQSLNCDLHALKMMH----PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN-------Q---------DG 499 (528)
Q Consensus 441 d~-ILVGHnL~fDL~~L~~~h----p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~-------~---------~~ 499 (528)
.. ++||||+.||+.+|.... .+++||........+.. .++|+.|+++|+|.++-. + ..
T Consensus 369 ~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~-~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~ 447 (880)
T PRK05755 369 PAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGR-RHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEA 447 (880)
T ss_pred CCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCC-CCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHH
Confidence 33 489999999999997422 35899988766544322 389999999998877310 0 02
Q ss_pred CCChHHHHHHHHHHHHHHHHc
Q psy17350 500 GHCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 500 ~HdAlEDA~AT~eL~~~~L~~ 520 (528)
.|.|..|+.+++.||.+..++
T Consensus 448 ~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 448 AEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999877765
No 69
>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=98.03 E-value=4.5e-06 Score=76.37 Aligned_cols=98 Identities=18% Similarity=0.178 Sum_probs=72.4
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cc-------cccCC--cEeecccccCCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DK-------QMMHP--YVIDTSVIFNTTGIR 72 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL-------~l~Hp--~i~DTa~~~~~~~~~ 72 (528)
..+++||+++++. .+.. +.++.+++.+.+. +.++|||....| .| ++..| ..+||..++......
T Consensus 47 ~~~i~GIt~e~l~-~~~~--~~~v~~~l~~~l~--~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~ 121 (156)
T cd06130 47 NIAIHGITPEDVA-DAPT--FPEVWPEIKPFLG--GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL 121 (156)
T ss_pred hccccCcCHHHHh-cCCC--HHHHHHHHHHHhC--CCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhcc
Confidence 3578999999654 3332 4568888888887 489999998888 33 23333 479998776432211
Q ss_pred CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 73 THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
...++|..|++. +|...+ .|++..||+++++|+.
T Consensus 122 ~~~~~L~~l~~~-~g~~~~----~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 122 LPNHKLNTVAEH-LGIELN----HHDALEDARACAEILL 155 (156)
T ss_pred CCCCCHHHHHHH-cCCCcc----CcCchHHHHHHHHHHh
Confidence 246899999997 688777 4999999999999974
No 70
>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=98.02 E-value=2.5e-05 Score=67.55 Aligned_cols=58 Identities=29% Similarity=0.402 Sum_probs=43.3
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEeC-CcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCCC--
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDEQ-ENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPD-- 441 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~~-G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d-- 441 (528)
+++|+||++..+...+|+.|++.+.+ +... +.. +.+++...
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~----~~~--------------------------------f~~~l~~~~~ 44 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTA----VID--------------------------------LKDILRDKPL 44 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEE----Eeh--------------------------------HHHHHhhCCC
Confidence 57999999999888899999999873 3322 111 44445422
Q ss_pred cEEEEcCchhhHHHHcc
Q psy17350 442 AILVGQSLNCDLHALKM 458 (528)
Q Consensus 442 ~ILVGHnL~fDL~~L~~ 458 (528)
.++||||..||+.+|+.
T Consensus 45 ~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 45 AILVGHNGSFDLPFLNN 61 (96)
T ss_pred CEEEEeCcHHhHHHHHH
Confidence 69999999999999864
No 71
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.01 E-value=3.2e-06 Score=77.85 Aligned_cols=105 Identities=24% Similarity=0.146 Sum_probs=73.4
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccc-------cCC---cEeecccccCCCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQM-------MHP---YVIDTSVIFNTTGIR 72 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l-------~Hp---~i~DTa~~~~~~~~~ 72 (528)
+++.||+++++.. +. .++++..++.+.+.+ ..+++||+...| .|+- .-| ..+||..++....+
T Consensus 51 ~~~~Git~~~l~~-~~--~~~~~~~~~~~~l~~-~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~- 125 (169)
T smart00479 51 TEIHGITPEMLDD-AP--TFEEVLEELLEFLKG-KILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNP- 125 (169)
T ss_pred HHHhCCCHHHHhC-CC--CHHHHHHHHHHHhcC-CEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCC-
Confidence 5688999996543 43 345688899998875 345666676888 3332 112 27999877654322
Q ss_pred CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcC
Q psy17350 73 THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g 117 (528)
...++|..|++.+.....+. .|++.+||+++++||+..++.+
T Consensus 126 ~~~~~L~~l~~~~~~~~~~~---~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 126 GRKYSLKKLAERLGLEVIGR---AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CCCCCHHHHHHHCCCCCCCC---CcCcHHHHHHHHHHHHHHHHHh
Confidence 23899999998864444332 5999999999999999877653
No 72
>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=97.97 E-value=4.5e-05 Score=71.34 Aligned_cols=128 Identities=22% Similarity=0.283 Sum_probs=83.5
Q ss_pred CCCeEEEeeceecCCC----CcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 361 TSPLYGLDCEMCKTSN----DQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~----g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
..+++++|||.+.... +.-.+++|+. .+.+. +|.+... ..+.+.|.+
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~~---~~~~~---l~~~~~~-----------------------~~~~~~l~~ 67 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLAT---ESRCL---LFQLAHM-----------------------DKLPPSLKQ 67 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEec---CCcEE---EEEhhhh-----------------------hcccHHHHH
Confidence 5689999999998754 3345666661 22222 1111110 111234555
Q ss_pred cCC-CCcEEEEcCchhhHHHHcccC----CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCccc--CC------------
Q psy17350 437 LLP-PDAILVGQSLNCDLHALKMMH----PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQ--NQ------------ 497 (528)
Q Consensus 437 ~i~-~d~ILVGHnL~fDL~~L~~~h----p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq--~~------------ 497 (528)
++. ++.+.|||++.+|+..|...+ ..++||..++...+......+|+.||+.|||..+. ..
T Consensus 68 ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~rpLt 147 (170)
T cd06141 68 LLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLS 147 (170)
T ss_pred HhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCCCCCC
Confidence 554 345679999999999996433 35799999876554432346999999999999886 21
Q ss_pred -CCCCChHHHHHHHHHHHHHH
Q psy17350 498 -DGGHCSKEDAIAALRLVKLK 517 (528)
Q Consensus 498 -~~~HdAlEDA~AT~eL~~~~ 517 (528)
++-|-|..||..+.+||..+
T Consensus 148 ~~qi~YAa~Da~~~~~l~~~l 168 (170)
T cd06141 148 KEQILYAATDAYASLELYRKL 168 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 02355789999999999754
No 73
>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=97.86 E-value=0.00034 Score=62.66 Aligned_cols=130 Identities=24% Similarity=0.277 Sum_probs=79.6
Q ss_pred eEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC-Cc
Q psy17350 364 LYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP-DA 442 (528)
Q Consensus 364 ~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~-d~ 442 (528)
++++|||+.+.......+..+++-.. ++++| +-.... ...+.+.+.+++.. +.
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~~~~---i~~~~~----------------------~~~~~~~l~~~l~~~~~ 55 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATA-GEAAY---IPDELE----------------------LEEDLEALKELLEDEDI 55 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEEC-CcEEE---EEcCCC----------------------HHHHHHHHHHHHcCCCC
Confidence 58999998766632345555555443 33332 110000 14466667777763 34
Q ss_pred EEEEcCchhhHHHHcccC----CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC-C---CCC----CC--------
Q psy17350 443 ILVGQSLNCDLHALKMMH----PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN-Q---DGG----HC-------- 502 (528)
Q Consensus 443 ILVGHnL~fDL~~L~~~h----p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~-~---~~~----Hd-------- 502 (528)
..||||+.+|+.+|+... ..++||..++....+...+++|+.|+++|++..+.. . ..+ -+
T Consensus 56 ~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 135 (155)
T cd00007 56 TKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELDKDEQIYGKGAKTFARPLSEELLE 135 (155)
T ss_pred cEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCCccHHHHhcCCCCccccCCHHHHHH
Confidence 599999999999996432 357999888665443331469999999998887421 0 001 01
Q ss_pred -hHHHHHHHHHHHHHHHH
Q psy17350 503 -SKEDAIAALRLVKLKLS 519 (528)
Q Consensus 503 -AlEDA~AT~eL~~~~L~ 519 (528)
+..||.++.+|+..+.+
T Consensus 136 y~~~da~~~~~l~~~l~~ 153 (155)
T cd00007 136 YAAEDADALLRLYEKLLE 153 (155)
T ss_pred HHHHhHHHHHHHHHHHHh
Confidence 45667788888775544
No 74
>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=97.82 E-value=0.00012 Score=68.57 Aligned_cols=127 Identities=20% Similarity=0.261 Sum_probs=81.0
Q ss_pred CCCeEEEeeceecCCC--CcCcEEEEEEEEeCCcE-EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 361 TSPLYGLDCEMCKTSN--DQNELTRVTLVDEQENV-VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~--g~~eLirIs~Vd~~G~v-i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
..+++++|||...... +.-.+++|+. .++.+ ++|-+-.+. ..+.|.++
T Consensus 12 ~~~~ig~D~E~~~~~~~~~~~~liQl~~--~~~~~~l~d~~~~~~---------------------------~~~~L~~l 62 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYYGEVALIQLCV--SEEKCYLFDPLSLSV---------------------------DWQGLKML 62 (161)
T ss_pred CCCEEEEECCccCCCCCCCceEEEEEEE--CCCCEEEEecccCcc---------------------------CHHHHHHH
Confidence 4689999999998754 3334455543 11333 344221100 01223344
Q ss_pred CC-CCcEEEEcCchhhHHHHcccC----CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCC-------------CC
Q psy17350 438 LP-PDAILVGQSLNCDLHALKMMH----PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQ-------------DG 499 (528)
Q Consensus 438 i~-~d~ILVGHnL~fDL~~L~~~h----p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~-------------~~ 499 (528)
+. ++.+.|||++..|+..|...+ ..++||...+...+.. .+.+|+.|+++|||..+... ++
T Consensus 63 L~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~-~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~q 141 (161)
T cd06129 63 LENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQ 141 (161)
T ss_pred hCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCC-CCchHHHHHHHHhCCCCCccceeccCCCCCCCHHH
Confidence 44 344569999999999986533 2478998887654433 35699999999999887432 12
Q ss_pred CCChHHHHHHHHHHHHHH
Q psy17350 500 GHCSKEDAIAALRLVKLK 517 (528)
Q Consensus 500 ~HdAlEDA~AT~eL~~~~ 517 (528)
-|-|..||.++.+||.++
T Consensus 142 i~YAa~Da~~l~~l~~~l 159 (161)
T cd06129 142 KLYAAADVYALLIIYTKL 159 (161)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455779999999999753
No 75
>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=97.78 E-value=0.0002 Score=69.34 Aligned_cols=117 Identities=15% Similarity=0.224 Sum_probs=76.7
Q ss_pred CCCeEEEeeceecC----CCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 361 TSPLYGLDCEMCKT----SNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 361 ~~~~vALDcEmtgt----~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
.-+++++|+||++- ++..++|+.|+++...++.++.. ++.. ...+... .+-.++..++.+
T Consensus 2 ~l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~--~~~~-------------~~~v~~~-~~E~~lL~~F~~ 65 (195)
T cd05780 2 DLKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITW--KKFD-------------LPFVEVV-KTEKEMIKRFIE 65 (195)
T ss_pred CceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEe--cCCC-------------CCeEEEe-CCHHHHHHHHHH
Confidence 35789999999832 44568999999998765544311 1111 0123332 455778888888
Q ss_pred cCCC--CcEEEEcCc-hhhHHHHcc-------cCC-----------------------C-EeeehhhchhcCCCCCCCCH
Q psy17350 437 LLPP--DAILVGQSL-NCDLHALKM-------MHP-----------------------Y-VIDTSVIFNTTGIRTHKPKL 482 (528)
Q Consensus 437 ~i~~--d~ILVGHnL-~fDL~~L~~-------~hp-----------------------~-vIDTs~L~~~~~~~~~k~sL 482 (528)
++.. -.+|||||. .||+.+|.- ..+ + ++|+..+++.. .....++|
T Consensus 66 ~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~-~~l~sy~L 144 (195)
T cd05780 66 IVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT-LNLTRYTL 144 (195)
T ss_pred HHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhh-CCCCcCcH
Confidence 7763 479999997 689988731 111 1 56666655432 23457999
Q ss_pred HHHHHHhhCCcc
Q psy17350 483 KMLTSHFLGLDI 494 (528)
Q Consensus 483 k~La~~~Lg~~I 494 (528)
+++|+++||.+-
T Consensus 145 ~~v~~~~Lg~~k 156 (195)
T cd05780 145 ERVYEELFGIEK 156 (195)
T ss_pred HHHHHHHhCCCC
Confidence 999999999874
No 76
>PRK07740 hypothetical protein; Provisional
Probab=97.66 E-value=4.5e-05 Score=76.71 Aligned_cols=104 Identities=18% Similarity=0.151 Sum_probs=74.7
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc------ccC---CcEeecccccCCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ------MMH---PYVIDTSVIFNTTGIR 72 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~------l~H---p~i~DTa~~~~~~~~~ 72 (528)
..++.||+++++ .++. .+.+|..++.+.+. ++++|||....| .|+ ... ..++||..++..-...
T Consensus 111 ~~~ltGIt~e~l-~~ap--~~~evl~~f~~fi~--~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~ 185 (244)
T PRK07740 111 ILELTGITAEDV-AFAP--PLAEVLHRFYAFIG--AGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHE 185 (244)
T ss_pred heeccCCCHHHH-hCCC--CHHHHHHHHHHHhC--CCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCC
Confidence 357899999965 4443 34568888888776 579999998888 221 112 2589998876421111
Q ss_pred CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 73 THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
...+||..|+.. +|..... -|++.+||+||++|+...+.+
T Consensus 186 ~~~~sL~~l~~~-~gi~~~~---~H~Al~Da~ata~l~~~ll~~ 225 (244)
T PRK07740 186 RDFPTLDDALAY-YGIPIPR---RHHALGDALMTAKLWAILLVE 225 (244)
T ss_pred CCCCCHHHHHHH-CCcCCCC---CCCcHHHHHHHHHHHHHHHHH
Confidence 246899999965 6887664 499999999999999887764
No 77
>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=97.49 E-value=0.00014 Score=65.17 Aligned_cols=99 Identities=14% Similarity=0.079 Sum_probs=70.5
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc---------ccCCcEeecccccCCCCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ---------MMHPYVIDTSVIFNTTGIRT 73 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~---------l~Hp~i~DTa~~~~~~~~~~ 73 (528)
.++.||+++.+ .++.. +.++..++.+.+.+ .++|||....| .|+ ..+...+||..++....+.+
T Consensus 50 ~~~~gi~~~~~-~~~~~--~~~~~~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~ 124 (159)
T cd06127 50 TAIHGITDEML-ADAPP--FEEVLPEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGL 124 (159)
T ss_pred eeccCCCHHHH-hcCCC--HHHHHHHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCC
Confidence 45689999854 34432 44588888888875 79999999888 332 23446899998875433334
Q ss_pred CCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 74 HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 74 ~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
...+|+.+...++|.... ..|+..+||+++++||.
T Consensus 125 ~~~~l~~~~~~~~~~~~~---~~H~Al~Da~~t~~l~~ 159 (159)
T cd06127 125 RSHRLGLLLAERYGIPLE---GAHRALADALATAELLL 159 (159)
T ss_pred CcCchHHHHHHHcCCCCC---CCCCcHHHHHHHHHHhC
Confidence 457888885566776543 37999999999999973
No 78
>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=97.44 E-value=5.5e-06 Score=74.30 Aligned_cols=100 Identities=18% Similarity=0.043 Sum_probs=69.0
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC----------cccccCC---cEeecccccCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA----------DKQMMHP---YVIDTSVIFNTTG 70 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D----------aL~l~Hp---~i~DTa~~~~~~~ 70 (528)
++.++||+++++ .++.. +.++...+.+.+++ ..++|||....| .++..+| .++||..+.....
T Consensus 52 ~~~~~gIt~~~l-~~~~~--~~~~~~~~~~~~~~-~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 127 (164)
T PF00929_consen 52 ATKVHGITQEDL-EDAPS--FEEALDEFEEFLKK-NDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALF 127 (164)
T ss_dssp HHHHHHHCHHHH-HCHCE--HHHHHHHHHHHHHH-HTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHH
T ss_pred HeeecCCccccc-ccCCc--HHHHHHhhhhhhhc-ccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHh
Confidence 457899999964 43332 33477778888874 479999984444 2244444 4788887755422
Q ss_pred CCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHH
Q psy17350 71 IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLV 110 (528)
Q Consensus 71 ~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~ 110 (528)
+...+++|+.|++.+.....+. .|++++||+++++||
T Consensus 128 ~~~~~~~l~~l~~~~~~~~~~~---~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 128 PNRKKYSLDDLAEYFGIPFDGT---AHDALDDARATAELF 164 (164)
T ss_dssp HHHHHHSHHHHHHHTTSSSTST---TTSHHHHHHHHHHHH
T ss_pred hccccCCHHHHHHHcCCCCCCC---CcChHHHHHHHhCcC
Confidence 1112379999999987666555 599999999999986
No 79
>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=97.41 E-value=0.0012 Score=66.86 Aligned_cols=150 Identities=15% Similarity=0.149 Sum_probs=86.0
Q ss_pred CCCeEEEeeceecCCCC---------------------cCcEEEEEEEEe---CCcEE--E-----EEEEcCCCCCCCCc
Q psy17350 361 TSPLYGLDCEMCKTSND---------------------QNELTRVTLVDE---QENVV--Y-----ESLVKPYNPITNYL 409 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g---------------------~~eLirIs~Vd~---~G~vi--~-----d~LVkP~~~I~dy~ 409 (528)
+.+|||||+||+|.... ...++++++--+ +++.- | +-++-|... +..
T Consensus 21 ~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~--~~~ 98 (262)
T PF04857_consen 21 KADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDR--DFS 98 (262)
T ss_dssp HSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTT--CEE
T ss_pred hCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeecccccc--cee
Confidence 46799999999998642 134777776655 34432 2 222223222 111
Q ss_pred e-------eecCCChhhhcccCCCHHHHH--------HHHHhcC----CCCcEEEEcCchhhHHHHc-------------
Q psy17350 410 T-------AYSGITRALLAPVATRLEHVQ--------KILSELL----PPDAILVGQSLNCDLHALK------------- 457 (528)
Q Consensus 410 T-------~isGIT~e~L~~a~p~l~dV~--------~~L~~~i----~~d~ILVGHnL~fDL~~L~------------- 457 (528)
. +-+|+.-+.+...+-+..... .-++.++ +...++||||.-.|+-+|-
T Consensus 99 ~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~e 178 (262)
T PF04857_consen 99 QASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEE 178 (262)
T ss_dssp EHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHH
T ss_pred cchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHH
Confidence 1 236666554443233332222 1122233 4458999999999997752
Q ss_pred ------ccCCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcc----------------------cCCCCCCChHHHHHH
Q psy17350 458 ------MMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI----------------------QNQDGGHCSKEDAIA 509 (528)
Q Consensus 458 ------~~hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~I----------------------q~~~~~HdAlEDA~A 509 (528)
...|.++||-.|..... ....+|..|+.. ++..- ..++..|.|--||.+
T Consensus 179 F~~~~~~~FP~i~DtK~la~~~~--~~~~~L~~l~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~m 255 (262)
T PF04857_consen 179 FKELLRELFPRIYDTKYLAEECP--GKSTSLQELAEE-LGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYM 255 (262)
T ss_dssp HHHHHHHHSSSEEEHHHHHTSTT--TS-SSHHHHHHH-TTSTT----EEE-TTS-------------SS-TTSHHHHHHH
T ss_pred HHHHHHHHCcccccHHHHHHhcc--ccccCHHHHHHH-hCCCccccccccccccccccccccccccCCCCCCCcchHHHH
Confidence 12477999999986432 346799999885 56543 123348999999999
Q ss_pred HHHHHH
Q psy17350 510 ALRLVK 515 (528)
Q Consensus 510 T~eL~~ 515 (528)
|+.+|.
T Consensus 256 Tg~~F~ 261 (262)
T PF04857_consen 256 TGCVFI 261 (262)
T ss_dssp HHHHHH
T ss_pred HHHHHc
Confidence 999985
No 80
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=97.31 E-value=0.00026 Score=68.74 Aligned_cols=101 Identities=14% Similarity=0.122 Sum_probs=69.9
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc--------ccCC-cEeecccccCC---CC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ--------MMHP-YVIDTSVIFNT---TG 70 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~--------l~Hp-~i~DTa~~~~~---~~ 70 (528)
..+.||+++++ .++. .+.+|..++.+.+. +.++|||....| .|. ...| ..+||..++.. ..
T Consensus 82 ~~ihGIt~~~l-~~~~--~~~~vl~~~~~~i~--~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~ 156 (202)
T PRK09145 82 IKIHRLRHQDL-EDGL--SEEEALRQLLAFIG--NRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERH 156 (202)
T ss_pred hhhcCcCHHHH-hcCC--CHHHHHHHHHHHHc--CCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhcc
Confidence 56789999965 4442 34568888888887 579999998888 332 1222 47899876531 11
Q ss_pred CC--CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHH
Q psy17350 71 IR--THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKL 114 (528)
Q Consensus 71 ~~--~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~ 114 (528)
.+ ....+|..|++. +|.+.. + .|+..+||+||.+||..-+
T Consensus 157 ~~~~~~~~~L~~l~~~-~gi~~~-~--~H~Al~DA~ata~l~~~l~ 198 (202)
T PRK09145 157 LPDAYIDLRFDAILKH-LDLPVL-G--RHDALNDAIMAALIFLRLR 198 (202)
T ss_pred CCCcccCCCHHHHHHH-cCCCCC-C--CCCcHHHHHHHHHHHHHHH
Confidence 11 235799999977 476653 2 6999999999999998543
No 81
>PRK10829 ribonuclease D; Provisional
Probab=97.27 E-value=0.0027 Score=67.97 Aligned_cols=129 Identities=19% Similarity=0.240 Sum_probs=83.9
Q ss_pred CCCCeEEEeeceecCCCC--cCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 360 PTSPLYGLDCEMCKTSND--QNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g--~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
...+++|||+|+.....- .-.+++|+ + |..+ .+|.|-. +.| ...|.++
T Consensus 20 ~~~~~lalDtEf~~~~ty~~~l~LiQl~--~--~~~~--~LiD~l~-~~d-----------------------~~~L~~l 69 (373)
T PRK10829 20 RAFPAIALDTEFVRTRTYYPQLGLIQLY--D--GEQL--SLIDPLG-ITD-----------------------WSPFKAL 69 (373)
T ss_pred hcCCeEEEecccccCccCCCceeEEEEe--c--CCce--EEEecCC-ccc-----------------------hHHHHHH
Confidence 456889999999877643 24455555 2 2222 2343431 111 1234555
Q ss_pred CCCCcEE-EEcCchhhHHHHccc---C-CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCC-------------
Q psy17350 438 LPPDAIL-VGQSLNCDLHALKMM---H-PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDG------------- 499 (528)
Q Consensus 438 i~~d~IL-VGHnL~fDL~~L~~~---h-p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~------------- 499 (528)
+....|+ |+|+..+|+.+|... . ..++||...+...+.+ ...+|+.|++.|||+.+..+.+
T Consensus 70 l~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~-~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~q 148 (373)
T PRK10829 70 LRDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRP-LSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQ 148 (373)
T ss_pred HcCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCC-ccccHHHHHHHHhCCccCcccccCCCCCCCCCHHH
Confidence 5545555 899999999998432 2 3699998877655432 3579999999999998865421
Q ss_pred CCChHHHHHHHHHHHHHHHH
Q psy17350 500 GHCSKEDAIAALRLVKLKLS 519 (528)
Q Consensus 500 ~HdAlEDA~AT~eL~~~~L~ 519 (528)
-+-|..|+....+||..+.+
T Consensus 149 l~YAa~Dv~~L~~l~~~L~~ 168 (373)
T PRK10829 149 CEYAAADVFYLLPIAAKLMA 168 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 23367899999998887554
No 82
>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=97.24 E-value=0.0029 Score=61.29 Aligned_cols=129 Identities=15% Similarity=0.156 Sum_probs=81.4
Q ss_pred CCeEEEeeceec---C-CCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhc
Q psy17350 362 SPLYGLDCEMCK---T-SNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSEL 437 (528)
Q Consensus 362 ~~~vALDcEmtg---t-~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~ 437 (528)
-+++++|+||++ . +++.+.|+.|++...+|.+.+-. .+ ..+-.++...+.++
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~-----------------------~~-~~~E~~lL~~F~~~ 58 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFIL-----------------------AE-GLDDRKIIREFVKY 58 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEE-----------------------ec-CCCHHHHHHHHHHH
Confidence 478999999983 2 45568999999988766632110 01 24556677777776
Q ss_pred CCCC--cEEEEcCc-hhhHHHHcc-------cCC---------C-------------EeeehhhchhcCCCCCCCCHHHH
Q psy17350 438 LPPD--AILVGQSL-NCDLHALKM-------MHP---------Y-------------VIDTSVIFNTTGIRTHKPKLKML 485 (528)
Q Consensus 438 i~~d--~ILVGHnL-~fDL~~L~~-------~hp---------~-------------vIDTs~L~~~~~~~~~k~sLk~L 485 (528)
+..- .+|+|||. .||+.+|.. ..+ . ++|...+.+... ....++|+++
T Consensus 59 i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~-~l~~y~L~~V 137 (188)
T cd05781 59 VKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP-EVKVKTLENV 137 (188)
T ss_pred HHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC-CCCCCCHHHH
Confidence 6533 68999996 799988731 110 0 566655544322 2457999999
Q ss_pred HHHhhCCc-------cc---------CC----CCCCChHHHHHHHHHHHHH
Q psy17350 486 TSHFLGLD-------IQ---------NQ----DGGHCSKEDAIAALRLVKL 516 (528)
Q Consensus 486 a~~~Lg~~-------Iq---------~~----~~~HdAlEDA~AT~eL~~~ 516 (528)
|+ +||.. +. .+ .-++-.+.||+.|+.|+.+
T Consensus 138 a~-~Lg~~k~~~k~~~~~~~i~~~~~~~~~~~~l~~Y~~~D~~~t~~l~~~ 187 (188)
T cd05781 138 AE-YLGVMKKSERVLIEWYRIYEYWDDEKKRDILLKYNRDDARSTYGLAEK 187 (188)
T ss_pred HH-HHCCCccccccCCCHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHhh
Confidence 97 58863 11 00 0122346888888888763
No 83
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=97.22 E-value=0.00066 Score=66.30 Aligned_cols=104 Identities=15% Similarity=0.106 Sum_probs=71.6
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCC-cC--ccc-----ccCCcEeeccccc-CCCC---C
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLN-EA--DKQ-----MMHPYVIDTSVIF-NTTG---I 71 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~-~D--aL~-----l~Hp~i~DTa~~~-~~~~---~ 71 (528)
...+.||+++++ .++. .+.+|..++.+.+. +.++|||... .| .|+ +..+..+||.... ..+. .
T Consensus 54 ~~~lhGIt~~~v-~~ap--~~~evl~~f~~f~~--~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~ 128 (195)
T PRK07247 54 INGLTGITADKI-ADAP--KVEEVLAAFKEFVG--ELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLN 128 (195)
T ss_pred ceecCCCCHHHH-hCCC--CHHHHHHHHHHHHC--CCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccC
Confidence 457899999965 4443 35668899999887 5789999886 67 443 2233457764322 1110 0
Q ss_pred CCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcC
Q psy17350 72 RTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117 (528)
Q Consensus 72 ~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g 117 (528)
.-...+|..||+. +|... . .|+..+||++|..+|+..+..+
T Consensus 129 ~~~~~~L~~La~~-~gi~~--~--~HrAl~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 129 GIANLKLQTVADF-LGIKG--R--GHNSLEDARMTARVYESFLESD 169 (195)
T ss_pred CCCCCCHHHHHHh-cCCCC--C--CcCCHHHHHHHHHHHHHHHhhc
Confidence 1135789999996 57653 2 6999999999999998877653
No 84
>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=97.20 E-value=0.00079 Score=64.98 Aligned_cols=109 Identities=16% Similarity=0.133 Sum_probs=70.9
Q ss_pred cceeeccCCCCCCchhh--hhhHHHHHHHHHHHHhc---CCcEEEeccCCcC--ccc-------c----cCC-cEeeccc
Q psy17350 4 SLEVLGLNPGGVLLNAY--FKMNARQIKRLENKKRK---MDALVEIKTLNEA--DKQ-------M----MHP-YVIDTSV 64 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~--~~~~~~v~~~l~~l~~~---~~~IlvGH~l~~D--aL~-------l----~Hp-~i~DTa~ 64 (528)
..++.||+++++...+. .+.+.++...+.+.+.. .+.+||||-...| .|+ + .+| .++||..
T Consensus 62 ~~~ihGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~ 141 (189)
T cd06134 62 ALEFNGIDPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTAT 141 (189)
T ss_pred HHhhcCCCchhhhccccchHHHHHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHH
Confidence 35789999985433322 12233344555555532 2579999998888 222 1 233 4899988
Q ss_pred ccCCCCCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcC
Q psy17350 65 IFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117 (528)
Q Consensus 65 ~~~~~~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g 117 (528)
+.....+ ..+|..||.. +|.++... ..|+...||+||.+|+...+++|
T Consensus 142 la~~~~~---~~~L~~l~~~-~gi~~~~~-~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 142 LAGLAYG---QTVLAKACQA-AGIEFDNK-EAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred HHHHHhC---CCcHHHHHHH-CCCCCCCC-CCcChHHHHHHHHHHHHHHHHhC
Confidence 7543211 3479999997 57776532 37999999999999998776653
No 85
>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=97.17 E-value=0.00035 Score=68.82 Aligned_cols=110 Identities=14% Similarity=0.088 Sum_probs=75.0
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-----cc-----CCcEeecccccCC--C
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-----MM-----HPYVIDTSVIFNT--T 69 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-----l~-----Hp~i~DTa~~~~~--~ 69 (528)
+..+.||+++++.. +. .+.+|...+.+.+. +.++|||....| .|+ +. ...++||-.+... +
T Consensus 57 a~~ihGIt~e~l~~-~p--~~~ev~~~~~~~~~--~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~ 131 (217)
T TIGR00573 57 AIKIHGITDDMLKD-KP--DFKEIAEDFADYIR--GAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARP 131 (217)
T ss_pred HHhhcCCCHHHHcC-CC--CHHHHHHHHHHHhC--CCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHH
Confidence 45789999996643 32 34568888888886 479999999888 222 21 1246787554221 1
Q ss_pred CCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCCCC
Q psy17350 70 GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLC 120 (528)
Q Consensus 70 ~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~~~ 120 (528)
..++.+.+|..|++.+ |..... ...|+...||++|++|++..+.+.+..
T Consensus 132 ~~~~~~~~L~~l~~~~-gl~~~~-~~~H~Al~DA~~ta~l~~~l~~~~~~~ 180 (217)
T TIGR00573 132 EFPGKRNTLDALCKRY-EITNSH-RALHGALADAFILAKLYLVMTGKQTKY 180 (217)
T ss_pred hCCCCCCCHHHHHHHc-CCCCCC-cccCCHHHHHHHHHHHHHHHHhcchhh
Confidence 1223568999999885 655431 137999999999999999888765443
No 86
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.15 E-value=0.00046 Score=69.67 Aligned_cols=104 Identities=13% Similarity=0.136 Sum_probs=73.7
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-----------ccCCcEeecccccCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-----------MMHPYVIDTSVIFNTTG 70 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-----------l~Hp~i~DTa~~~~~~~ 70 (528)
+.++.||+++++. ++. .+.+|..++.+.+.+ ..+||||....| .|+ ..+..++||..+...-
T Consensus 57 a~~ihgIt~e~v~-~~p--~~~ev~~~~~~fl~~-~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~- 131 (250)
T PRK06310 57 SQRIHHISDAMLR-DKP--KIAEVFPQIKGFFKE-GDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEY- 131 (250)
T ss_pred hhhccCcCHHHHh-CCC--CHHHHHHHHHHHhCC-CCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhc-
Confidence 3578999999654 332 245578888887763 379999998888 332 1234689998765421
Q ss_pred CCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 71 IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 71 ~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
+.....+|..|++.+ |..... .|+..+||.||.+|++..+++
T Consensus 132 ~~~~~~~L~~l~~~~-g~~~~~---aH~Al~Da~at~~vl~~l~~~ 173 (250)
T PRK06310 132 GDSPNNSLEALAVHF-NVPYDG---NHRAMKDVEINIKVFKHLCKR 173 (250)
T ss_pred ccCCCCCHHHHHHHC-CCCCCC---CcChHHHHHHHHHHHHHHHHh
Confidence 111257999999886 766443 699999999999999987754
No 87
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=97.09 E-value=0.00057 Score=71.38 Aligned_cols=102 Identities=17% Similarity=0.122 Sum_probs=71.9
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--c-------ccccCC--cEeecccccCCCCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--D-------KQMMHP--YVIDTSVIFNTTGIRT 73 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--a-------L~l~Hp--~i~DTa~~~~~~~~~~ 73 (528)
+++.||+++++ .++. .+++|...+.+.+. +.++|||....| . .++..| .++||..+........
T Consensus 59 ~~ihGIT~e~l-~~~~--~~~evl~~f~~fl~--~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~ 133 (313)
T PRK06807 59 TSLTGITNYRV-SDAP--TIEEVLPLFLAFLH--TNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHA 133 (313)
T ss_pred hccCCCCHHHH-hCCC--CHHHHHHHHHHHHc--CCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCC
Confidence 57899999965 4442 35568888888886 578999987777 2 233334 4799877643111111
Q ss_pred CCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 74 HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 74 ~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
...+|..|++. +|... . .|+...||++|.+||+....+
T Consensus 134 ~~~kL~~L~~~-lgi~~--~--~H~Al~DA~~ta~l~~~l~~~ 171 (313)
T PRK06807 134 PNHKLETLKRM-LGIRL--S--SHNAFDDCITCAAVYQKCASI 171 (313)
T ss_pred CCCCHHHHHHH-cCCCC--C--CcChHHHHHHHHHHHHHHHHh
Confidence 24589999854 68777 3 699999999999999877664
No 88
>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=97.08 E-value=0.011 Score=58.15 Aligned_cols=150 Identities=17% Similarity=0.136 Sum_probs=84.7
Q ss_pred CCeEEEeeceecC-----CCCcCcEEEEEEEEe-CCcEEE-EEEEcCCCCCCCCc--eeecCCChhhhcccCCCHHHHHH
Q psy17350 362 SPLYGLDCEMCKT-----SNDQNELTRVTLVDE-QENVVY-ESLVKPYNPITNYL--TAYSGITRALLAPVATRLEHVQK 432 (528)
Q Consensus 362 ~~~vALDcEmtgt-----~~g~~eLirIs~Vd~-~G~vi~-d~LVkP~~~I~dy~--T~isGIT~e~L~~a~p~l~dV~~ 432 (528)
.+++|+|+|+... ++..+.|+.||++.. .|..+. ..++.+...-..+. -.+.|. -.+.. -.+-.++..
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~v~~-~~~E~~lL~ 78 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGP--FKVFN-EPDEKALLQ 78 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCc--eEEec-CCCHHHHHH
Confidence 3689999999753 344689999999865 453321 11111100000000 011121 01112 146677888
Q ss_pred HHHhcCCCC--cEEEEcCc-hhhHHHHccc---C----C--------C----------Eeeehhhchhc-CCCCCCCCHH
Q psy17350 433 ILSELLPPD--AILVGQSL-NCDLHALKMM---H----P--------Y----------VIDTSVIFNTT-GIRTHKPKLK 483 (528)
Q Consensus 433 ~L~~~i~~d--~ILVGHnL-~fDL~~L~~~---h----p--------~----------vIDTs~L~~~~-~~~~~k~sLk 483 (528)
++.+++..- .+|+|+|. .||+.+|... | . . .+|...++... ......++|+
T Consensus 79 ~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd 158 (204)
T cd05779 79 RFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLK 158 (204)
T ss_pred HHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHH
Confidence 888887633 49999996 8999887310 1 0 0 45665554421 1123478999
Q ss_pred HHHHHhhCCcc-cCC-------------CCCCChHHHHHHHHHHH
Q psy17350 484 MLTSHFLGLDI-QNQ-------------DGGHCSKEDAIAALRLV 514 (528)
Q Consensus 484 ~La~~~Lg~~I-q~~-------------~~~HdAlEDA~AT~eL~ 514 (528)
.+|+++||..= ..+ .-++-.+.||.+|+.||
T Consensus 159 ~Va~~~Lg~~K~~~~~~~I~~~~~~~~~~l~~Y~~~D~~~T~~l~ 203 (204)
T cd05779 159 AVTKAKLGYDPVELDPEDMVPLAREDPQTLASYSVSDAVATYYLY 203 (204)
T ss_pred HHHHHHhCCCcCcCCHHHHHHHHhCCcHHHHhccHHHHHHHHHHh
Confidence 99999998642 110 01234478888888886
No 89
>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=97.05 E-value=0.008 Score=58.62 Aligned_cols=116 Identities=19% Similarity=0.154 Sum_probs=69.6
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
.-++++||+|+.+-. +|..|+..+...+.++- +.-..+.. |. .+.-. ++-.++...+.+++..
T Consensus 2 ~l~~~~fDIE~~~~~----~i~~i~~~~~~~~~i~~--~~~~~~~~-------~~---~v~~~-~~E~~lL~~f~~~i~~ 64 (193)
T cd05784 2 KLKVVSLDIETSMDG----ELYSIGLYGEGQERVLM--VGDPEDDA-------PD---NIEWF-ADEKSLLLALIAWFAQ 64 (193)
T ss_pred CccEEEEEeecCCCC----CEEEEEeecCCCCEEEE--ECCCCCCC-------CC---EEEEE-CCHHHHHHHHHHHHHh
Confidence 357899999997532 88888887764333321 11111111 11 12221 4556667777666653
Q ss_pred C--cEEEEcCc-hhhHHHHc-------ccCC-------------------------C-EeeehhhchhcCCCCCCCCHHH
Q psy17350 441 D--AILVGQSL-NCDLHALK-------MMHP-------------------------Y-VIDTSVIFNTTGIRTHKPKLKM 484 (528)
Q Consensus 441 d--~ILVGHnL-~fDL~~L~-------~~hp-------------------------~-vIDTs~L~~~~~~~~~k~sLk~ 484 (528)
- .||+|||. .||+.+|. +.++ + ++|+..+.+.......+|+|++
T Consensus 65 ~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~kl~sy~L~~ 144 (193)
T cd05784 65 YDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLEN 144 (193)
T ss_pred hCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCCCCcCCHHH
Confidence 3 69999998 77998872 2110 0 4676555543222456899999
Q ss_pred HHHHhhCCc
Q psy17350 485 LTSHFLGLD 493 (528)
Q Consensus 485 La~~~Lg~~ 493 (528)
+|+++||..
T Consensus 145 Va~~~Lg~~ 153 (193)
T cd05784 145 VAQELLGEG 153 (193)
T ss_pred HHHHHhCCC
Confidence 999999864
No 90
>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=97.00 E-value=0.0012 Score=61.20 Aligned_cols=106 Identities=20% Similarity=0.202 Sum_probs=51.6
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEe-CCcEE-EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCCCc
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDE-QENVV-YESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPPDA 442 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~-~G~vi-~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d~ 442 (528)
+.+|+||+|+.++...+.-|+++.. +++.. |..+.-.. ++ .-+.+.+.+ .++....
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~--------------~~-------ee~~~~~~~-~~l~~~~ 58 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAED--------------PD-------EEEIILEFF-ELLDEAD 58 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGG--------------HH-------HHHHHHH---HHHHTT-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccC--------------cH-------HHHHHHHHH-HHHhcCC
Confidence 4699999999987677788888764 33322 22222211 00 011222223 4444578
Q ss_pred EEEEcC-chhhHHHHcccC--------CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCccc
Q psy17350 443 ILVGQS-LNCDLHALKMMH--------PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQ 495 (528)
Q Consensus 443 ILVGHn-L~fDL~~L~~~h--------p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq 495 (528)
.+|+|| ..||+.+|+... ...+|.......... .+++|+.+++. ||++.+
T Consensus 59 ~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~--~~~~Lk~ve~~-lg~~~~ 117 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL--ESYSLKNVEKF-LGIERR 117 (164)
T ss_dssp -EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS--CCTT--SHHH--------
T ss_pred eEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccC--CCCCHHHHhhh-cccccc
Confidence 999998 589999997432 147898777653322 56899999885 787764
No 91
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=97.00 E-value=0.019 Score=52.37 Aligned_cols=88 Identities=28% Similarity=0.309 Sum_probs=56.7
Q ss_pred HHHHhcCC-CCcEEEEcCchhhHHHHcc---cCCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC--CC----CC-
Q psy17350 432 KILSELLP-PDAILVGQSLNCDLHALKM---MHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN--QD----GG- 500 (528)
Q Consensus 432 ~~L~~~i~-~d~ILVGHnL~fDL~~L~~---~hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~--~~----~~- 500 (528)
..|.+++. ++...||||+.+|+.+|+. .-+.++||...+....+....++|+.+++.|+|..+.. +. ..
T Consensus 65 ~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~~ 144 (172)
T smart00474 65 EILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGARP 144 (172)
T ss_pred HHHHHHhcCCCceEEEechHHHHHHHHHCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccCC
Confidence 34555554 3456899999999999964 11235899887653332223369999999999887531 10 00
Q ss_pred --C----ChHHHHHHHHHHHHHHHH
Q psy17350 501 --H----CSKEDAIAALRLVKLKLS 519 (528)
Q Consensus 501 --H----dAlEDA~AT~eL~~~~L~ 519 (528)
. -+..||.++.+|+....+
T Consensus 145 l~~~~~~ya~~~a~~~~~L~~~l~~ 169 (172)
T smart00474 145 LSEEQLQYAAEDADALLRLYEKLEK 169 (172)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 156778888888775544
No 92
>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=96.97 E-value=0.00063 Score=63.33 Aligned_cols=102 Identities=21% Similarity=0.095 Sum_probs=71.5
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcC-CcEEEeccCCcC-c-cc-----------ccCCcEeecccccCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKM-DALVEIKTLNEA-D-KQ-----------MMHPYVIDTSVIFNTTG 70 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~-~~IlvGH~l~~D-a-L~-----------l~Hp~i~DTa~~~~~~~ 70 (528)
.++.||+++++ .++ ..+.+|..++.+.+++. ..++|+|+-.++ . ++ ..+...+|+..++....
T Consensus 59 ~~i~gIt~e~l-~~~--~~~~~vl~~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~ 135 (176)
T cd06133 59 TELTGITQEDV-DNA--PSFPEVLKEFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFY 135 (176)
T ss_pred HHhcCcCHHHH-hcC--CCHHHHHHHHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHh
Confidence 56899999965 444 23556888999999852 158888883332 1 11 12225799998877543
Q ss_pred CCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHH
Q psy17350 71 IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKL 112 (528)
Q Consensus 71 ~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~ 112 (528)
+.....+|..|++. +|.+.. +..|+...||++++++++.
T Consensus 136 ~~~~~~~L~~l~~~-~gi~~~--~~~H~Al~DA~~~a~l~~~ 174 (176)
T cd06133 136 GLKKRTGLSKALEY-LGLEFE--GRHHRGLDDARNIARILKR 174 (176)
T ss_pred CCCCCCCHHHHHHH-CCCCCC--CCCcCcHHHHHHHHHHHHH
Confidence 33358999999976 476665 2389999999999999875
No 93
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.93 E-value=0.001 Score=69.49 Aligned_cols=104 Identities=17% Similarity=0.136 Sum_probs=71.8
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------ccCC--cEeecccccCCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------MMHP--YVIDTSVIFNTTGIR 72 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l~Hp--~i~DTa~~~~~~~~~ 72 (528)
.+++.||+++++. .+. .++++..++.+.+. +++||||-...| .|+ +.-| ..+||-.+...-...
T Consensus 64 ~~~IhGIt~e~l~-~ap--~f~ev~~~l~~~l~--~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~ 138 (313)
T PRK06063 64 PTHVHGLTAEMLE-GQP--QFADIAGEVAELLR--GRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLG 138 (313)
T ss_pred CeecCCCCHHHHh-CCC--CHHHHHHHHHHHcC--CCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccC
Confidence 4578999999654 332 24558888888887 589999999888 332 1112 478987654321111
Q ss_pred CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 73 THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
....+|..||+. +|.+... .|+..+||+||.+|+...+++
T Consensus 139 ~~~~kL~~l~~~-~gi~~~~---~H~Al~DA~ata~l~~~ll~~ 178 (313)
T PRK06063 139 LPNLRLETLAAH-WGVPQQR---PHDALDDARVLAGILRPSLER 178 (313)
T ss_pred CCCCCHHHHHHH-cCCCCCC---CCCcHHHHHHHHHHHHHHHHH
Confidence 235679999986 5766432 699999999999999766543
No 94
>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=96.91 E-value=0.015 Score=54.03 Aligned_cols=129 Identities=19% Similarity=0.246 Sum_probs=76.3
Q ss_pred CCeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC-C
Q psy17350 362 SPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP-P 440 (528)
Q Consensus 362 ~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~-~ 440 (528)
.+.+++|+|+....+....+..+++-.. +.+.| +.+. .+ . +.+.|.+++. +
T Consensus 12 ~~~l~~~~e~~~~~~~~~~~~~i~l~~~-~~~~~---i~~~----------------~~-~-------~~~~l~~ll~~~ 63 (178)
T cd06142 12 AGVIAVDTEFMRLNTYYPRLCLIQISTG-GEVYL---IDPL----------------AI-G-------DLSPLKELLADP 63 (178)
T ss_pred CCeEEEECCccCCCcCCCceEEEEEeeC-CCEEE---EeCC----------------Cc-c-------cHHHHHHHHcCC
Confidence 3689999998765532345555555433 33322 2111 00 0 2233445454 3
Q ss_pred CcEEEEcCchhhHHHHccc----CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCC---C-CC---------Ch
Q psy17350 441 DAILVGQSLNCDLHALKMM----HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQD---G-GH---------CS 503 (528)
Q Consensus 441 d~ILVGHnL~fDL~~L~~~----hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~---~-~H---------dA 503 (528)
+...|||++.+|+.+|+.. ...+.||........+ .++.+|+.|++.|||..+-... . +- -+
T Consensus 64 ~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p-~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~ya 142 (178)
T cd06142 64 NIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGL-GDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYA 142 (178)
T ss_pred CceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCC-CccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHH
Confidence 5678999999999999543 2357899876544333 2335999999999988732110 0 11 25
Q ss_pred HHHHHHHHHHHHHHHH
Q psy17350 504 KEDAIAALRLVKLKLS 519 (528)
Q Consensus 504 lEDA~AT~eL~~~~L~ 519 (528)
..||.++.+|+....+
T Consensus 143 a~~a~~l~~L~~~l~~ 158 (178)
T cd06142 143 ALDVRYLLPLYEKLKE 158 (178)
T ss_pred HHhHHHHHHHHHHHHH
Confidence 6677778887765443
No 95
>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=96.82 E-value=0.0012 Score=63.11 Aligned_cols=100 Identities=16% Similarity=0.153 Sum_probs=67.3
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcC--CcEEEeccC-CcC--cc-----c----ccC-CcEeecccccCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKM--DALVEIKTL-NEA--DK-----Q----MMH-PYVIDTSVIFNT 68 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~--~~IlvGH~l-~~D--aL-----~----l~H-p~i~DTa~~~~~ 68 (528)
+.++.||+++++..+.. ..+++.+.+.+.+... +.+||||-. ..| .| + +.. ..++||..++..
T Consensus 63 a~~IhGIt~e~l~~~~~--~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~ 140 (177)
T cd06136 63 ASEITGLSNDLLEHKAP--FDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRE 140 (177)
T ss_pred HHHHhCcCHHHHhcCCC--ccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhh
Confidence 35778999996544332 2223556666666532 359999997 678 22 1 112 246898766543
Q ss_pred CCCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHH
Q psy17350 69 TGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLK 113 (528)
Q Consensus 69 ~~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k 113 (528)
. .++|..|+++++|..... .|+...||.||.++++.|
T Consensus 141 ~-----~~~L~~l~~~~~~~~~~~---~H~A~~Da~at~~v~~~~ 177 (177)
T cd06136 141 L-----DQSLGSLYKRLFGQEPKN---SHTAEGDVLALLKCALHK 177 (177)
T ss_pred h-----HhhHHHHHHHHhCCCccc---ccchHHHHHHHHHHHhhC
Confidence 2 129999999988887654 599999999999998753
No 96
>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=96.78 E-value=0.026 Score=56.12 Aligned_cols=145 Identities=19% Similarity=0.278 Sum_probs=85.0
Q ss_pred CCCeEEEeeceecC-----CCCcCcEEEEEEEEe-CCc--EEEEE-E-EcCCCCCCCCceeecCCChhhhcccCCCHHHH
Q psy17350 361 TSPLYGLDCEMCKT-----SNDQNELTRVTLVDE-QEN--VVYES-L-VKPYNPITNYLTAYSGITRALLAPVATRLEHV 430 (528)
Q Consensus 361 ~~~~vALDcEmtgt-----~~g~~eLirIs~Vd~-~G~--vi~d~-L-VkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV 430 (528)
.-+++|+|+|+... ++..++|+.|+++.. +|. ..... + +++..++. | ..+... .+-.++
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~-------~---~~v~~~-~~E~eL 74 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV-------G---AQVFSF-ETEEEL 74 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC-------C---CEEEEE-CCHHHH
Confidence 45789999999743 345789999999865 453 11111 1 23322222 1 122222 456677
Q ss_pred HHHHHhcCCC--CcEEEEcCc-hhhHHHHc-------ccC-C-----------------------------------CEe
Q psy17350 431 QKILSELLPP--DAILVGQSL-NCDLHALK-------MMH-P-----------------------------------YVI 464 (528)
Q Consensus 431 ~~~L~~~i~~--d~ILVGHnL-~fDL~~L~-------~~h-p-----------------------------------~vI 464 (528)
...+.+++.. -.||+|||. .||+.+|. +.. . -++
T Consensus 75 L~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~i 154 (230)
T cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQF 154 (230)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEee
Confidence 7777776652 369999997 67998762 110 0 023
Q ss_pred eehhhchhcCCCCCCCCHHHHHHHhhCCcccCC----------C-------CCCChHHHHHHHHHHHHHH
Q psy17350 465 DTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQ----------D-------GGHCSKEDAIAALRLVKLK 517 (528)
Q Consensus 465 DTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~----------~-------~~HdAlEDA~AT~eL~~~~ 517 (528)
|+..+++.. .....|+|+++|+++||.....= + -..-.+.||+.|++|+.++
T Consensus 155 D~~~~~~~~-~kl~sy~L~~Va~~~Lg~~k~d~~~~~i~~~~~~~~~~~~~l~~Y~~~Da~l~l~L~~kl 223 (230)
T cd05777 155 DLLQVIQRD-YKLRSYSLNSVSAHFLGEQKEDVHYSIITDLQNGNPETRRRLAVYCLKDAYLPLRLLDKL 223 (230)
T ss_pred eHHHHHHHh-cCcccCcHHHHHHHHhCCCCCCCCHHHHHHHHccCHhHhHHHHHhhHHHHHHHHHHHHHH
Confidence 443333322 23468999999999999764320 0 0122357777788777643
No 97
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.77 E-value=0.0016 Score=64.93 Aligned_cols=105 Identities=13% Similarity=0.073 Sum_probs=71.7
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccC-CcC--ccc-----ccC----CcEeecccccCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTL-NEA--DKQ-----MMH----PYVIDTSVIFNTTGI 71 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l-~~D--aL~-----l~H----p~i~DTa~~~~~~~~ 71 (528)
++++.||+++++.. +. .+.+|..++.+.+.+ +.++|||.. ..| .|+ ... ...+||..++.....
T Consensus 49 a~~IhGIt~e~v~~-~p--~f~ev~~~~~~fi~~-~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~ 124 (232)
T PRK06309 49 ASKIHGITTDEVAD-AP--KFPEAYQKFIEFCGT-DNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRP 124 (232)
T ss_pred HHhhcCCCHHHHhC-CC--CHHHHHHHHHHHHcC-CCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcC
Confidence 46789999996543 32 245677888888864 579999984 567 222 111 257999877643211
Q ss_pred CCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 72 RTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 72 ~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
...+.+|..|++.+ |.+.. ..|+..+||.++.++++..+.+
T Consensus 125 ~~~~~~L~~l~~~~-~~~~~---~aH~Al~Da~~t~~vl~~l~~~ 165 (232)
T PRK06309 125 DLPKHNLQYLRQVY-GFEEN---QAHRALDDVITLHRVFSALVGD 165 (232)
T ss_pred CCCCCCHHHHHHHc-CCCCC---CCCCcHHHHHHHHHHHHHHHHH
Confidence 11256899999886 54432 3799999999999999887653
No 98
>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=96.74 E-value=0.0083 Score=59.03 Aligned_cols=73 Identities=16% Similarity=0.196 Sum_probs=50.3
Q ss_pred CCCCeEEEeeceecCC--------CCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 360 PTSPLYGLDCEMCKTS--------NDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~--------~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
+.-+++++|+|+.... +..++|+.|++.+..|.... +. .. ..+-+++.
T Consensus 7 ~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~---~~--------------------~~-~~~E~~lL 62 (207)
T cd05785 7 DDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEV---LH--------------------AE-DAAEKELL 62 (207)
T ss_pred CCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceee---ec--------------------cC-CCCHHHHH
Confidence 3468999999996532 23478999998876542111 10 01 25677788
Q ss_pred HHHHhcCCCC--cEEEEcCc-hhhHHHH
Q psy17350 432 KILSELLPPD--AILVGQSL-NCDLHAL 456 (528)
Q Consensus 432 ~~L~~~i~~d--~ILVGHnL-~fDL~~L 456 (528)
.++.+++..- .||||||. .||+.+|
T Consensus 63 ~~f~~~i~~~dPdii~g~N~~~FD~pyl 90 (207)
T cd05785 63 EELVAIIRERDPDVIEGHNIFRFDLPYL 90 (207)
T ss_pred HHHHHHHHHhCCCEEeccCCcccCHHHH
Confidence 8888877632 79999999 8999887
No 99
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.70 E-value=0.0017 Score=75.94 Aligned_cols=103 Identities=17% Similarity=0.103 Sum_probs=72.6
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------ccCC-cEeecccccCCCCCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------MMHP-YVIDTSVIFNTTGIRTH 74 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l~Hp-~i~DTa~~~~~~~~~~~ 74 (528)
.++.||+++++ .+|. .+++|..++.+.+. ++++|||....| .|+ +..+ ..+||..+...--....
T Consensus 57 ~~ltGIt~e~l-~~ap--~~~ev~~~~~~~l~--~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~ 131 (820)
T PRK07246 57 KHLTGITDQQL-AQAP--DFSQVARHIYDLIE--DCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLE 131 (820)
T ss_pred hhcCCCCHHHH-hcCC--CHHHHHHHHHHHhC--CCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCC
Confidence 57899999965 4443 35568888888887 689999999888 332 1111 35898765321100113
Q ss_pred CccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 75 KPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 75 ~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
+.+|..||.. +|..... .|+..+||+||.+|+..-+.+
T Consensus 132 ~~~L~~L~~~-lgl~~~~---~H~Al~DA~ata~L~~~l~~~ 169 (820)
T PRK07246 132 KYSLSHLSRE-LNIDLAD---AHTAIADARATAELFLKLLQK 169 (820)
T ss_pred CCCHHHHHHH-cCCCCCC---CCCHHHHHHHHHHHHHHHHHH
Confidence 5799999986 6877543 699999999999999876654
No 100
>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=96.70 E-value=0.0045 Score=60.10 Aligned_cols=88 Identities=22% Similarity=0.094 Sum_probs=56.9
Q ss_pred HHHhcCC-CCcEEEEcCchhhHHHHccc----CCCEeeehhhchhcCC-------CCCCCCHHHHHHHhhCCcccC----
Q psy17350 433 ILSELLP-PDAILVGQSLNCDLHALKMM----HPYVIDTSVIFNTTGI-------RTHKPKLKMLTSHFLGLDIQN---- 496 (528)
Q Consensus 433 ~L~~~i~-~d~ILVGHnL~fDL~~L~~~----hp~vIDTs~L~~~~~~-------~~~k~sLk~La~~~Lg~~Iq~---- 496 (528)
.|.+++. ++.+-|||++.+|+.+|... -..+.||...+...+. +.+..+|..|++.|||.++..
T Consensus 56 ~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~ 135 (197)
T cd06148 56 GLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDV 135 (197)
T ss_pred HHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHH
Confidence 3444454 34456999999999998422 2357999876432110 112359999999999987621
Q ss_pred ----------C-------CCCCChHHHHHHHHHHHHHHHHc
Q psy17350 497 ----------Q-------DGGHCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 497 ----------~-------~~~HdAlEDA~AT~eL~~~~L~~ 520 (528)
. +.-.-|..||.....|+..++..
T Consensus 136 ~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~ 176 (197)
T cd06148 136 KKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDA 176 (197)
T ss_pred HHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 1 01233568999999998877654
No 101
>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=96.66 E-value=0.021 Score=60.88 Aligned_cols=128 Identities=21% Similarity=0.251 Sum_probs=78.9
Q ss_pred CCCeEEEeeceecCCC--CcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcC
Q psy17350 361 TSPLYGLDCEMCKTSN--DQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELL 438 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~--g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i 438 (528)
..+++|||+|+..... ++-.+++|+. |..+ .+|.|-.. .+ ...|.+++
T Consensus 17 ~~~~ia~DtE~~~~~~y~~~l~LiQia~----~~~~--~liD~~~~-~~-----------------------~~~L~~lL 66 (367)
T TIGR01388 17 TFPFVALDTEFVRERTFWPQLGLIQVAD----GEQL--ALIDPLVI-ID-----------------------WSPLKELL 66 (367)
T ss_pred cCCEEEEeccccCCCCCCCcceEEEEee----CCeE--EEEeCCCc-cc-----------------------HHHHHHHH
Confidence 3579999999987653 2245666653 3322 24444211 00 12233444
Q ss_pred C-CCcEEEEcCchhhHHHHccc---CC-CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCC----CCC-------
Q psy17350 439 P-PDAILVGQSLNCDLHALKMM---HP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDG----GHC------- 502 (528)
Q Consensus 439 ~-~d~ILVGHnL~fDL~~L~~~---hp-~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~----~Hd------- 502 (528)
. ++.+.|+|++.+|+.+|+.. .+ .++||.......+. ....+|..|++.|||+.+..+.. ..+
T Consensus 67 ~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~-~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~ 145 (367)
T TIGR01388 67 RDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGF-GMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQL 145 (367)
T ss_pred CCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCC-CCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHH
Confidence 3 34557999999999998643 23 57999887554432 23469999999999998754210 022
Q ss_pred --hHHHHHHHHHHHHHHHH
Q psy17350 503 --SKEDAIAALRLVKLKLS 519 (528)
Q Consensus 503 --AlEDA~AT~eL~~~~L~ 519 (528)
|..||.+...|+..+.+
T Consensus 146 ~YAa~Dv~~L~~L~~~L~~ 164 (367)
T TIGR01388 146 EYAAADVTYLLPLYAKLME 164 (367)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 56778888888775543
No 102
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=96.53 E-value=0.023 Score=60.42 Aligned_cols=120 Identities=20% Similarity=0.287 Sum_probs=79.2
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
+.++||||.|+.+...-...++=|=+-+.++ ..+|.|-.++.+ .+.|..++. ++
T Consensus 16 ~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~----~~lIdpl~~~~d----------------~~~l~~Ll~------d~ 69 (361)
T COG0349 16 GSKAIAIDTEFMRLRTYYPRLCLIQISDGEG----ASLIDPLAGILD----------------LPPLVALLA------DP 69 (361)
T ss_pred CCCceEEecccccccccCCceEEEEEecCCC----ceEecccccccc----------------cchHHHHhc------CC
Confidence 4678999999999988766554444444444 356666654332 133332221 12
Q ss_pred CcEEEEcCchhhHHHHccc---CC-CEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCC----CCChHHHH
Q psy17350 441 DAILVGQSLNCDLHALKMM---HP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDG----GHCSKEDA 507 (528)
Q Consensus 441 d~ILVGHnL~fDL~~L~~~---hp-~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~----~HdAlEDA 507 (528)
+-+=|=|+..||+.+|... +| .++||.+..+..+... +++|+.||++++|++|..+++ +++.+.++
T Consensus 70 ~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~-~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~ 143 (361)
T COG0349 70 NVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGT-SHGLADLVEELLGVELDKSEQRSDWLARPLSEA 143 (361)
T ss_pred ceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCCcc-cccHHHHHHHHhCCcccccccccccccCCCCHH
Confidence 3333789999999998643 33 6899988877655444 789999999999999986422 45555443
No 103
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.53 E-value=0.0034 Score=62.66 Aligned_cols=112 Identities=21% Similarity=0.142 Sum_probs=68.7
Q ss_pred ceeeccCCCCCCchhhh--hhHHHHHHHHHHHHhcCCcEEEeccCCcC--cc----c-cc----CC-cEeecccccCC-C
Q psy17350 5 LEVLGLNPGGVLLNAYF--KMNARQIKRLENKKRKMDALVEIKTLNEA--DK----Q-MM----HP-YVIDTSVIFNT-T 69 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~--~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL----~-l~----Hp-~i~DTa~~~~~-~ 69 (528)
+++.||+++++...+.. +.+.++...+.....+ +++||||-...| .| + .. .+ .++||-.+... .
T Consensus 58 ~~IhGIt~e~l~~~g~~~~~vl~e~~~~l~~~~~~-~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~ 136 (232)
T PRK07942 58 SAVHGITTEYARAHGRPAAEVLAEIADALREAWAR-GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVD 136 (232)
T ss_pred HHHhCCCHHHHHhhCCCHHHHHHHHHHHHHHHhhc-CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhh
Confidence 57899999955432322 2233333333333322 679999998888 22 2 11 12 36898765321 1
Q ss_pred CCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCCCCC
Q psy17350 70 GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLCS 121 (528)
Q Consensus 70 ~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~~~~ 121 (528)
.....+.+|..||+. +|..... .|+...||+||.+|+...+++.+..+
T Consensus 137 ~~~~~~~~L~~l~~~-~gi~~~~---aH~Al~Da~ata~l~~~l~~~~~~l~ 184 (232)
T PRK07942 137 RYRKGKRTLTALCEH-YGVRLDN---AHEATADALAAARVAWALARRFPELA 184 (232)
T ss_pred cccCCCCCHHHHHHH-cCCCCCC---CCChHHHHHHHHHHHHHHHHHHHHhh
Confidence 111225689999987 4766433 69999999999999988776544443
No 104
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=96.51 E-value=0.0039 Score=60.80 Aligned_cols=109 Identities=17% Similarity=0.121 Sum_probs=68.7
Q ss_pred ceeeccCCCCCCchhhh--hhHHHHHHHHHHHHhc---CCcEEEeccCCcC--ccc-------cc----CC-cEeecccc
Q psy17350 5 LEVLGLNPGGVLLNAYF--KMNARQIKRLENKKRK---MDALVEIKTLNEA--DKQ-------MM----HP-YVIDTSVI 65 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~--~~~~~v~~~l~~l~~~---~~~IlvGH~l~~D--aL~-------l~----Hp-~i~DTa~~ 65 (528)
.++.||+++++..++.. +.+.++...+.+.+.. .+.+||||-...| .|+ +. ++ .++||..+
T Consensus 66 ~~ihGIt~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~l 145 (200)
T TIGR01298 66 LEFTGIDLDHPLRGAVSEYEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATL 145 (200)
T ss_pred HHccCCChhhhhhcCcchHHHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHH
Confidence 46789998744443321 2222233344333321 2679999999988 332 11 12 48999887
Q ss_pred cCCCCCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCC
Q psy17350 66 FNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGD 118 (528)
Q Consensus 66 ~~~~~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~ 118 (528)
..... ...+|..||+. +|..+... ..|+...||.+|.+|+...+.+..
T Consensus 146 ar~~~---~~~~L~~l~~~-~gi~~~~~-~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 146 AGLAY---GQTVLAKACQA-AGXDFDST-QAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred HHHHc---CcccHHHHHHH-cCCCcccc-chhhhHHhHHHHHHHHHHHHHHHH
Confidence 54221 13479999996 47765421 279999999999999988776543
No 105
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=96.51 E-value=0.0045 Score=60.44 Aligned_cols=111 Identities=14% Similarity=0.150 Sum_probs=73.0
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--c----cc---ccCC---cEeecccccCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--D----KQ---MMHP---YVIDTSVIFNTTGI 71 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--a----L~---l~Hp---~i~DTa~~~~~~~~ 71 (528)
.+.+.||+++++. ++.. +++|...+.+.+.+...++|+|+ +.| . ++ +.-| ..+|+...+..-.+
T Consensus 62 ~~~ltGIt~~~l~-~ap~--~~evl~~f~~~~~~~~~~iv~~~-~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~ 137 (207)
T PRK07748 62 CKSFLGITQEDVD-KGIS--FEELVEKLAEYDKRCKPTIVTWG-NMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFG 137 (207)
T ss_pred hhhhcCcCHHHHc-cCCC--HHHHHHHHHHHhCcCCeEEEEEC-HHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhC
Confidence 4678999999654 4432 45688888888874234777775 566 2 22 2223 35777765432111
Q ss_pred CCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCCCCC
Q psy17350 72 RTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLCS 121 (528)
Q Consensus 72 ~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~~~~ 121 (528)
.....||..+++. +|...-. ..|+-..||++|.+|++...+++....
T Consensus 138 ~~~~~~L~~~~~~-~gi~~~~--~~H~Al~DA~~ta~l~~~l~~~~~~~~ 184 (207)
T PRK07748 138 ERNQTGLWKAIEE-YGKEGTG--KHHCALDDAMTTYNIFKLVEKDKEYLV 184 (207)
T ss_pred cCCCCCHHHHHHH-cCCCCCC--CCcChHHHHHHHHHHHHHHHhCcceee
Confidence 2235799998887 4665322 269999999999999998887765444
No 106
>PRK07883 hypothetical protein; Validated
Probab=96.51 E-value=0.0029 Score=70.91 Aligned_cols=109 Identities=14% Similarity=0.058 Sum_probs=76.2
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------ccCC--cEeecccccC--CCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------MMHP--YVIDTSVIFN--TTG 70 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l~Hp--~i~DTa~~~~--~~~ 70 (528)
.+.+.||+++++ .++. .+.++..++.+.+. +.++|||....| .|+ +..| ..+||..+.. ++.
T Consensus 65 ~~~itGIt~e~l-~~ap--~~~evl~~f~~fl~--~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~ 139 (557)
T PRK07883 65 ITVLTGITTAMV-AGAP--PIEEVLPAFLEFAR--GAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPR 139 (557)
T ss_pred HHhhcCCCHHHH-hCCC--CHHHHHHHHHHHhc--CCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhccc
Confidence 356899999954 4443 34557788888887 589999998777 332 2233 4689976642 121
Q ss_pred CCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCCCCC
Q psy17350 71 IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLCS 121 (528)
Q Consensus 71 ~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~~~~ 121 (528)
......+|..|++ ++|.++-. .|+...||+||.+|+...+.+....|
T Consensus 140 ~~~~~~~L~~L~~-~~gi~~~~---~H~Al~DA~ata~l~~~l~~~~~~~~ 186 (557)
T PRK07883 140 DEAPNVRLSTLAR-LFGATTTP---THRALDDARATVDVLHGLIERLGNLG 186 (557)
T ss_pred CCCCCCCHHHHHH-HCCcccCC---CCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 1234678999998 56887633 69999999999999988877644444
No 107
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.51 E-value=0.0037 Score=64.98 Aligned_cols=103 Identities=13% Similarity=0.095 Sum_probs=71.3
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------c--cCCcEeecccccCCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------M--MHPYVIDTSVIFNTTGIR 72 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l--~Hp~i~DTa~~~~~~~~~ 72 (528)
.+++.||+++++.. +. .+.+|-.++.+.+. +.+||||-...| .|+ + .....+||..+...-...
T Consensus 50 ~~~IhGIT~e~v~~-ap--~f~ev~~~~~~fl~--~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~ 124 (309)
T PRK06195 50 NIGIHGIRPHMVED-EL--EFDKIWEKIKHYFN--NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSN 124 (309)
T ss_pred heeccCcCHHHHhC-CC--CHHHHHHHHHHHhC--CCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCC
Confidence 46789999996544 32 24557888888886 589999998888 331 1 222579997654311000
Q ss_pred CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 73 THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
....+|..|++.+ |... . .|+..+||+||.+|+...+++
T Consensus 125 ~~~~~L~~L~~~~-gi~~--~--~H~Al~DA~ata~l~~~l~~~ 163 (309)
T PRK06195 125 IDNARLNTVNNFL-GYEF--K--HHDALADAMACSNILLNISKE 163 (309)
T ss_pred CCcCCHHHHHHHc-CCCC--c--ccCCHHHHHHHHHHHHHHHHH
Confidence 1256899999984 6553 2 699999999999999876664
No 108
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=96.50 E-value=0.0025 Score=74.68 Aligned_cols=103 Identities=19% Similarity=0.147 Sum_probs=72.9
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------cc-CC-cEeecccccCCCCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------MM-HP-YVIDTSVIFNTTGIRT 73 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l~-Hp-~i~DTa~~~~~~~~~~ 73 (528)
.+++||+++++. ++. .+++|..++.+.+. ++++|||....| .|+ +. .+ ..+||..+...-....
T Consensus 51 ~~ltGIt~e~l~-~ap--~~~ev~~~l~~~l~--~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~ 125 (850)
T TIGR01407 51 QELTGISDNMLQ-QAP--YFSQVAQEIYDLLE--DGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTE 125 (850)
T ss_pred hhhcCcCHHHHh-CCC--CHHHHHHHHHHHhC--CCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCC
Confidence 578999999654 442 34568888888886 689999998888 332 11 22 4799977643211112
Q ss_pred CCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 74 HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 74 ~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
...+|..|++. +|.+.. ..|+...||+||.+|+...+.+
T Consensus 126 ~~~~L~~l~~~-~gi~~~---~~H~Al~DA~ata~l~~~l~~~ 164 (850)
T TIGR01407 126 ESYQLSELSEA-LGLTHE---NPHRADSDAQATAELLLLLFEK 164 (850)
T ss_pred CCCCHHHHHHH-CCCCCC---CCCChHHHHHHHHHHHHHHHHH
Confidence 36799999998 576643 2799999999999999877654
No 109
>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=96.49 E-value=0.037 Score=54.40 Aligned_cols=127 Identities=17% Similarity=0.114 Sum_probs=72.7
Q ss_pred CCCeEEEeeceecCC----CC----cCcEEEEEEEEeCCcEEEEEEEc-CCCCCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 361 TSPLYGLDCEMCKTS----ND----QNELTRVTLVDEQENVVYESLVK-PYNPITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 361 ~~~~vALDcEmtgt~----~g----~~eLirIs~Vd~~G~vi~d~LVk-P~~~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
.-+++|+|+|+..-. |. .++|+.|++++.+|..-+ .++. +.....+... .-| ..+... .+-+++.
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v-~~~~~~~~~~~~~~~-~~~---~~v~~~-~~E~~lL 77 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRV-LVLKREGVEGLEGLL-PEG---AEVEFF-DSEKELI 77 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEE-EEEecCCcccccccC-CCC---CeEEec-CCHHHHH
Confidence 468999999997522 21 268999999864443211 1111 1110000000 001 112232 4677888
Q ss_pred HHHHhcCCCCcEEEEcCc-hhhHHHHccc---C--C------------------CEeeehhhchhc-------CCCCCCC
Q psy17350 432 KILSELLPPDAILVGQSL-NCDLHALKMM---H--P------------------YVIDTSVIFNTT-------GIRTHKP 480 (528)
Q Consensus 432 ~~L~~~i~~d~ILVGHnL-~fDL~~L~~~---h--p------------------~vIDTs~L~~~~-------~~~~~k~ 480 (528)
.++.+++..-.+|||+|. .||+.+|... | + ..+|....+... +.....+
T Consensus 78 ~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~ 157 (204)
T cd05783 78 REAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREY 157 (204)
T ss_pred HHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccccccC
Confidence 888888887789999996 8999887310 1 1 135654443221 0123578
Q ss_pred CHHHHHHHhhCCc
Q psy17350 481 KLKMLTSHFLGLD 493 (528)
Q Consensus 481 sLk~La~~~Lg~~ 493 (528)
+|+.+|+.+||..
T Consensus 158 ~L~~Va~~~lg~~ 170 (204)
T cd05783 158 TLDAVAKALLGEG 170 (204)
T ss_pred cHHHHHHHhcCCC
Confidence 9999999988864
No 110
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.36 E-value=0.0045 Score=62.98 Aligned_cols=103 Identities=19% Similarity=0.138 Sum_probs=72.5
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc---------ccCCcEeecccccCCCCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ---------MMHPYVIDTSVIFNTTGIRT 73 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~---------l~Hp~i~DTa~~~~~~~~~~ 73 (528)
.++.||+++++ .++. .+.+|..++.+.+. +.++|||..+.| .|+ ..++..+||-.+..... +.
T Consensus 118 ~~itGIt~e~l-~~ap--~~~evl~~f~~fl~--~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~-~~ 191 (257)
T PRK08517 118 TELTGITYEDL-ENAP--SLKEVLEEFRLFLG--DSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTI-ES 191 (257)
T ss_pred hhhcCcCHHHH-cCCC--CHHHHHHHHHHHHC--CCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHc-cC
Confidence 46899999965 4443 35568888888876 579999998777 332 12234577765543111 12
Q ss_pred CCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcC
Q psy17350 74 HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117 (528)
Q Consensus 74 ~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g 117 (528)
.+.+|..|++. +|.+... .|+...||.||.+|+...+.+.
T Consensus 192 ~~~~L~~L~~~-lgi~~~~---~HrAl~DA~ata~ll~~ll~~~ 231 (257)
T PRK08517 192 PRYGLSFLKEL-LGIEIEV---HHRAYADALAAYEIFKICLLNL 231 (257)
T ss_pred CCCCHHHHHHH-cCcCCCC---CCChHHHHHHHHHHHHHHHHHh
Confidence 46789999985 6877543 6999999999999999888764
No 111
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=96.34 E-value=0.0024 Score=77.13 Aligned_cols=104 Identities=17% Similarity=0.216 Sum_probs=75.2
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------c--cCCcEeecccccCCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------M--MHPYVIDTSVIFNTTGIR 72 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l--~Hp~i~DTa~~~~~~~~~ 72 (528)
.++++||+++++ .++. .+++|..++.+.+. +++||||....| .|+ + .+..++||..+...-...
T Consensus 240 ~~~ltGIT~e~L-~~ap--~~~evl~~f~~fl~--~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~ 314 (1213)
T TIGR01405 240 VTELTGITQDML-ENAP--EIEEVLEKFKEFFK--DSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPE 314 (1213)
T ss_pred HHHHhCCCHHHH-hCCC--CHHHHHHHHHHHhC--CCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhcc
Confidence 357899999955 4443 35568888888887 589999998888 332 1 122579998775422111
Q ss_pred CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 73 THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
....+|..||+. +|..... .|+..+||+||.++++..+++
T Consensus 315 ~k~~kL~~Lak~-lgi~~~~---~HrAl~DA~aTa~I~~~ll~~ 354 (1213)
T TIGR01405 315 YKSHRLGNICKK-LGVDLDD---HHRADYDAEATAKVFKVMVEQ 354 (1213)
T ss_pred CCCCCHHHHHHH-cCCCCCC---CcCHHHHHHHHHHHHHHHHHH
Confidence 246899999998 4776654 699999999999999887643
No 112
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.97 E-value=0.0071 Score=71.66 Aligned_cols=102 Identities=19% Similarity=0.102 Sum_probs=72.7
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------ccC--CcEeecccccC--CCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------MMH--PYVIDTSVIFN--TTGI 71 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l~H--p~i~DTa~~~~--~~~~ 71 (528)
.++.||+++++. ++. .+.+|..++.+++. ++++|||..+.| .|+ +.. ...+||..+.. ++..
T Consensus 55 ~~ltGIt~~~l~-~ap--~f~ev~~~l~~~l~--~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~ 129 (928)
T PRK08074 55 TELTGISEEMVK-QAP--LFEDVAPEIVELLE--GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTA 129 (928)
T ss_pred hhcCCCCHHHHh-cCC--CHHHHHHHHHHHhC--CCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCC
Confidence 468999999654 442 25568889999887 689999999988 332 111 25799976532 1221
Q ss_pred CCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcC
Q psy17350 72 RTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117 (528)
Q Consensus 72 ~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g 117 (528)
...+|..|++. ||.... ..|+...||+||.+|+..-+++.
T Consensus 130 --~~~~L~~l~~~-l~i~~~---~~H~Al~DA~ata~l~~~l~~~~ 169 (928)
T PRK08074 130 --ESYKLRDLSEE-LGLEHD---QPHRADSDAEVTAELFLQLLNKL 169 (928)
T ss_pred --CCCCHHHHHHh-CCCCCC---CCCChHHHHHHHHHHHHHHHHHH
Confidence 24689999998 465432 37999999999999998877653
No 113
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=95.80 E-value=0.012 Score=58.62 Aligned_cols=103 Identities=12% Similarity=-0.073 Sum_probs=69.0
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccccCCcEeecccccCCCCCCCCCccHHHH
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQMMHPYVIDTSVIFNTTGIRTHKPKLKML 81 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp~i~DTa~~~~~~~~~~~~~SLk~L 81 (528)
..++.||+++++ .++.. +.+|..+ +.. +.+||||-...| .|.-.....+||-.+...-- +..+.+|..|
T Consensus 47 ~~~ihgIt~e~v-~~ap~--~~ev~~~---~~~--~~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~-p~~~~~l~~L 117 (219)
T PRK07983 47 AMAIHRITEAMV-ADKPW--IEDVIPH---YYG--SEWYVAHNASFDRRVLPEMPGEWICTMKLARRLW-PGIKYSNMAL 117 (219)
T ss_pred HhhcCCCCHHHH-cCCCC--HHHHHHH---HcC--CCEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHc-cCCCCCHHHH
Confidence 357899999965 34332 3334333 332 679999999999 66654456899987642110 1124688999
Q ss_pred HHHHhCcccc--CCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 82 TSHFLGLDIQ--NQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 82 a~~~L~~~IQ--~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
++. +|.... .....|+...||.+|.+|+...+++
T Consensus 118 ~~~-~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 118 YKS-RKLNVQTPPGLHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred HHH-cCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 975 566543 2224899999999999999887754
No 114
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=95.78 E-value=0.0097 Score=60.02 Aligned_cols=103 Identities=17% Similarity=0.027 Sum_probs=69.5
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc---------cc----CCcEeecccccCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ---------MM----HPYVIDTSVIFNTT 69 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~---------l~----Hp~i~DTa~~~~~~ 69 (528)
.+|.||+++++.. +. .+++|...+.+.+. +..||||-...| .|+ +. ...++||-.+....
T Consensus 57 ~~VHGIT~e~l~~-~p--~f~ev~~~f~~fi~--~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~ 131 (240)
T PRK05711 57 LAVHGITDEFLAD-KP--TFAEVADEFLDFIR--GAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRM 131 (240)
T ss_pred hhhcCCCHHHHcC-CC--CHHHHHHHHHHHhC--CCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHH
Confidence 5788999996543 32 24568888888876 578999998877 221 11 12479997654321
Q ss_pred CCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHH
Q psy17350 70 GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLS 115 (528)
Q Consensus 70 ~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~ 115 (528)
- +..+.+|..||++| |.+-.. ..-|+...||+++.++|.....
T Consensus 132 ~-p~~~~~L~aL~~~~-gi~~~~-r~~H~AL~DA~~~A~v~~~l~~ 174 (240)
T PRK05711 132 F-PGKRNSLDALCKRY-GIDNSH-RTLHGALLDAEILAEVYLAMTG 174 (240)
T ss_pred c-CCCCCCHHHHHHHC-CCCCCC-CCCCCHHHHHHHHHHHHHHHHC
Confidence 0 12356999999975 655321 1269999999999999976553
No 115
>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=95.78 E-value=0.0095 Score=55.41 Aligned_cols=100 Identities=18% Similarity=0.054 Sum_probs=67.4
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------cc----CC-cEeecccccCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------MM----HP-YVIDTSVIFNTTG 70 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l~----Hp-~i~DTa~~~~~~~ 70 (528)
.++.||+++++. ++.. +++|...+...+. +.++|||....| .|+ +. .| ..+||..+.....
T Consensus 52 ~~ihGIt~e~l~-~~~~--~~~v~~~l~~~l~--~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~ 126 (167)
T cd06131 52 FKVHGITDEFLA-DKPK--FAEIADEFLDFIR--GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKF 126 (167)
T ss_pred HHHhCCCHHHHh-cCCC--HHHHHHHHHHHHC--CCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHc
Confidence 457899999654 3322 4568888888876 468899998888 221 11 12 4699976643211
Q ss_pred CCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHH
Q psy17350 71 IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKL 112 (528)
Q Consensus 71 ~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~ 112 (528)
+....+|..|++.+ |..... ..-|+...||+++.+|+..
T Consensus 127 -~~~~~~L~~l~~~~-~i~~~~-~~~H~Al~Da~~~a~l~~~ 165 (167)
T cd06131 127 -PGKPNSLDALCKRF-GIDNSH-RTLHGALLDAELLAEVYLE 165 (167)
T ss_pred -CCCCCCHHHHHHHC-CCCCCC-CCCCChHHHHHHHHHHHHH
Confidence 12457999999985 655432 1269999999999999864
No 116
>PRK11779 sbcB exonuclease I; Provisional
Probab=95.68 E-value=0.0092 Score=65.83 Aligned_cols=108 Identities=17% Similarity=0.159 Sum_probs=70.0
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEecc-CCcC--ccc------ccCC------------cEeec
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKT-LNEA--DKQ------MMHP------------YVIDT 62 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~-l~~D--aL~------l~Hp------------~i~DT 62 (528)
+..+.||+|+++...+.. ..++..++.+.+...++++|||. +..| .|+ +.-| .++|+
T Consensus 60 a~~IhGIT~e~l~~~g~~--e~e~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl 137 (476)
T PRK11779 60 AVLITGITPQEALEKGLP--EAEFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDV 137 (476)
T ss_pred HHHHhCCCHHHHHhcCCC--HHHHHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHH
Confidence 457899999965443332 23467788877754478999995 7777 332 1111 23576
Q ss_pred cccc-CCC-CC--C------CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcC
Q psy17350 63 SVIF-NTT-GI--R------THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117 (528)
Q Consensus 63 a~~~-~~~-~~--~------~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g 117 (528)
+.+. ++. .+ . ....+|..|++.+ |.... ..|+...||.||++|+++-.++.
T Consensus 138 ~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~-gI~~~---~AHdALsDa~aT~~la~~l~~~q 198 (476)
T PRK11779 138 VRACYALRPEGINWPENEDGLPSFKLEHLTKAN-GIEHE---NAHDAMSDVYATIAMAKLIKQKQ 198 (476)
T ss_pred HHHHHHhccccccCcccccCCCCCcHHHHHHHc-CCCCC---CCCCcHHHHHHHHHHHHHHHHhC
Confidence 6643 221 11 0 1347899999985 55433 27999999999999999877653
No 117
>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=95.64 E-value=0.014 Score=58.03 Aligned_cols=103 Identities=14% Similarity=0.040 Sum_probs=70.2
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--c----cc-c------cCC--cEeecccccCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--D----KQ-M------MHP--YVIDTSVIFNTT 69 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--a----L~-l------~Hp--~i~DTa~~~~~~ 69 (528)
++|.||+++++. .+. .+++|..++.+.+. +..||||-...| . ++ + .++ .++||-.+....
T Consensus 53 ~~vhGIt~e~l~-~~p--~f~ev~~~f~~fi~--~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~ 127 (225)
T TIGR01406 53 AKVHGITDEFLA-DKP--KFKEIADEFLDFIG--GSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARER 127 (225)
T ss_pred HhccCCCHHHHh-CCC--CHHHHHHHHHHHhC--CCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHH
Confidence 578899999654 332 35568888888887 478999988777 2 21 1 121 479997764321
Q ss_pred CCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHH
Q psy17350 70 GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLS 115 (528)
Q Consensus 70 ~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~ 115 (528)
.+..+.+|..||+.| |.+.+. ...|+..+||+++.++|.....
T Consensus 128 -~p~~~~~L~~L~~~~-gi~~~~-r~~H~Al~DA~~~a~v~~~l~~ 170 (225)
T TIGR01406 128 -FPGQRNSLDALCKRF-KVDNSH-RTLHGALLDAHLLAEVYLALTG 170 (225)
T ss_pred -cCCCCCCHHHHHHhc-CCCCCC-CCCcCHHHHHHHHHHHHHHHHc
Confidence 112467999999995 554332 1369999999999999986544
No 118
>PRK05168 ribonuclease T; Provisional
Probab=95.63 E-value=0.015 Score=57.16 Aligned_cols=107 Identities=16% Similarity=0.157 Sum_probs=68.1
Q ss_pred ceeeccCCCCCCchhhh--hhHHHHHHHHHHHHhc---CCcEEEeccCCcC--ccc-------c----cCC-cEeecccc
Q psy17350 5 LEVLGLNPGGVLLNAYF--KMNARQIKRLENKKRK---MDALVEIKTLNEA--DKQ-------M----MHP-YVIDTSVI 65 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~--~~~~~v~~~l~~l~~~---~~~IlvGH~l~~D--aL~-------l----~Hp-~i~DTa~~ 65 (528)
+++.||++++++..+.. +.+.++...+.+.+.. .+.++|||....| .|+ + .+| .++||..+
T Consensus 75 ~~ihGIt~e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~l 154 (211)
T PRK05168 75 LAFNGIDPDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATL 154 (211)
T ss_pred HhhcCCCchhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHH
Confidence 57899999853333221 2222333344433321 1579999998888 221 1 133 58999877
Q ss_pred cCCCCCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 66 FNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 66 ~~~~~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
.....+ ..+|..++.. +|..++. ...|+...||.||.+|+...+++
T Consensus 155 ar~~~~---~~~L~~l~~~-~gl~~~~-~~~H~Al~DA~ata~l~~~l~~~ 200 (211)
T PRK05168 155 SGLALG---QTVLAKACQA-AGIEFDN-KEAHSALYDTEKTAELFCEIVNR 200 (211)
T ss_pred HHHHcC---CCCHHHHHHH-CCCCCCC-CCCCChHHHHHHHHHHHHHHHHH
Confidence 542211 2479999887 5777653 13799999999999999877765
No 119
>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=95.54 E-value=0.012 Score=56.32 Aligned_cols=101 Identities=18% Similarity=0.114 Sum_probs=62.8
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEecc-CCcC--ccc-----c-cCC---------cEeeccccc
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKT-LNEA--DKQ-----M-MHP---------YVIDTSVIF 66 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~-l~~D--aL~-----l-~Hp---------~i~DTa~~~ 66 (528)
.++.||+++++..++.. +.++...+...+.+.+.++|||. ...| .|+ . ..| ..+||-.+.
T Consensus 52 ~~ihGIt~e~l~~~~~~--~~~~l~~~~~~~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~ 129 (183)
T cd06138 52 LIVTGITPQQLLKEGLS--EYEFIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVV 129 (183)
T ss_pred HHHhCCCHHHHHhcCCC--HHHHHHHHHHHHccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHH
Confidence 46799999965442333 34467777777754467899984 7777 332 1 111 235665321
Q ss_pred -------C----CCCCC--CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHH
Q psy17350 67 -------N----TTGIR--THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVK 111 (528)
Q Consensus 67 -------~----~~~~~--~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~ 111 (528)
| .+... ....+|..|++. +|..... .|+...||+||.+|++
T Consensus 130 r~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~-~gi~~~~---~H~Al~Da~~ta~l~~ 183 (183)
T cd06138 130 RAYYALRPDGIVWPKNDDGKPSFKLEDLAQA-NGIEHSN---AHDALSDVEATIALAK 183 (183)
T ss_pred HHHHhhChhhccCccccCCCcchhHHHHHHH-CCCCccc---cccHHHHHHHHHHHhC
Confidence 2 11100 134679999987 5776643 6999999999999863
No 120
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=95.33 E-value=0.02 Score=57.71 Aligned_cols=104 Identities=19% Similarity=0.122 Sum_probs=70.0
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cc----c----cc-CCcEeecccccC----C
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DK----Q----MM-HPYVIDTSVIFN----T 68 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL----~----l~-Hp~i~DTa~~~~----~ 68 (528)
+.++.||+++++ ..+. .+++|..++...+. +.++|||-...| .| + .. ...++||..+.. .
T Consensus 99 ~~~IhGIt~e~l-~~ap--~~~evl~~l~~~~~--~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~ 173 (239)
T PRK09146 99 SVVIHGITHSEL-QDAP--DLERILDELLEALA--GKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRK 173 (239)
T ss_pred hhhhcCCCHHHH-hCCC--CHHHHHHHHHHHhC--CCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHccc
Confidence 457899999965 3342 24557788888776 579999988778 22 1 11 124799998732 1
Q ss_pred C--------CCC-CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 69 T--------GIR-THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 69 ~--------~~~-~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
. .+. ....+|-.|++. +|.. .. ..|+...||+||.+|+..-+.+
T Consensus 174 ~~~~~~~~~~~~~~~~~~L~~l~~~-~gl~--~~-~~H~Al~DA~ata~l~~~~~~~ 226 (239)
T PRK09146 174 QAGGLWNRLKGKKPESIRLADSRLR-YGLP--AY-SPHHALTDAIATAELLQAQIAH 226 (239)
T ss_pred ccccccchhccCCCCCCCHHHHHHH-cCCC--CC-CCCCcHHHHHHHHHHHHHHHHH
Confidence 1 010 134578899987 4544 22 2699999999999999887765
No 121
>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=95.27 E-value=0.35 Score=45.26 Aligned_cols=105 Identities=17% Similarity=0.139 Sum_probs=68.5
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC-CC
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP-PD 441 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~-~d 441 (528)
+.+++|+|+.+.++...+++.+++-..+ ++.| |.+... + .+.+.+.+++. ++
T Consensus 4 ~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~~---i~~~~~----------~-------------~~~~~l~~~l~~~~ 56 (178)
T cd06140 4 DEVALYVELLGENYHTADIIGLALANGG-GAYY---IPLELA----------L-------------LDLAALKEWLEDEK 56 (178)
T ss_pred CceEEEEEEcCCCcceeeEEEEEEEeCC-cEEE---Eeccch----------H-------------HHHHHHHHHHhCCC
Confidence 5688999999998766777777776532 3322 222211 0 13344555554 34
Q ss_pred cEEEEcCchhhHHHHccc---C-CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcc
Q psy17350 442 AILVGQSLNCDLHALKMM---H-PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI 494 (528)
Q Consensus 442 ~ILVGHnL~fDL~~L~~~---h-p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~I 494 (528)
...|+||+.+|+.+|... - ..+.||........+....++|+.|+++||+.++
T Consensus 57 ~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 57 IPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred CceeccchhHHHHHHHHCCCcCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCC
Confidence 579999999999999632 1 2368998876544332223699999999998874
No 122
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=95.19 E-value=0.029 Score=55.52 Aligned_cols=108 Identities=18% Similarity=0.078 Sum_probs=73.8
Q ss_pred ccceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--ccc-------ccCC--cEeecccccCCCCC
Q psy17350 3 LSLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQ-------MMHP--YVIDTSVIFNTTGI 71 (528)
Q Consensus 3 ~~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~-------l~Hp--~i~DTa~~~~~~~~ 71 (528)
.+.++.||+.+++. ++ ..+..|...+.+...+ ..++|+|-...| .|+ ...+ .++||-.+.-....
T Consensus 63 ~~~~i~git~e~l~-~~--p~~~~v~~~~~~~i~~-~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~ 138 (243)
T COG0847 63 EIFKIHGITDEMLA-DA--PKFAEVLPEFLDFIGG-LRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFP 138 (243)
T ss_pred hhhhhcCCCHHHHh-cC--CCHHHHHHHHHHHHCC-CCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcC
Confidence 45678999999554 33 2345588888888874 289999998888 332 1111 34566555322111
Q ss_pred CCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 72 RTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 72 ~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
...+.+|..||. .+|.+.. ....|+.++||.++.++|...+.+
T Consensus 139 ~~~~~~L~~l~~-~~gi~~~-~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 139 GFDRSSLDALAE-RLGIDRN-PFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CCccchHHHHHH-HcCCCcC-CcCCcchHHHHHHHHHHHHHHHhc
Confidence 125889999999 6677744 234699999999999999887764
No 123
>PRK05762 DNA polymerase II; Reviewed
Probab=95.10 E-value=0.19 Score=58.87 Aligned_cols=138 Identities=17% Similarity=0.218 Sum_probs=81.3
Q ss_pred CCCCeEEEeeceecCCCCcCcEEEEEEEEeCC-cEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcC
Q psy17350 360 PTSPLYGLDCEMCKTSNDQNELTRVTLVDEQE-NVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELL 438 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G-~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i 438 (528)
+..+++++|+|+... .+|..|++.+... .++. +-+..+.. .+.+... ++-.++...+.+++
T Consensus 153 p~lrvlsfDIE~~~~----~~i~sI~~~~~~~~~vi~---ig~~~~~~----------~~~v~~~-~sE~~LL~~F~~~i 214 (786)
T PRK05762 153 PPLKVVSLDIETSNK----GELYSIGLEGCGQRPVIM---LGPPNGEA----------LDFLEYV-ADEKALLEKFNAWF 214 (786)
T ss_pred CCCeEEEEEEEEcCC----CceEEeeecCCCCCeEEE---EECCCCCC----------cceEEEc-CCHHHHHHHHHHHH
Confidence 567899999999753 3677777764322 2222 12221110 0113332 56677777777766
Q ss_pred CC--CcEEEEcCc-hhhHHHHc-------ccC--------------C------------C-EeeehhhchhcCCCCCCCC
Q psy17350 439 PP--DAILVGQSL-NCDLHALK-------MMH--------------P------------Y-VIDTSVIFNTTGIRTHKPK 481 (528)
Q Consensus 439 ~~--d~ILVGHnL-~fDL~~L~-------~~h--------------p------------~-vIDTs~L~~~~~~~~~k~s 481 (528)
.. -+||||||. .||+.+|. +.. + + ++|+-.+.+........++
T Consensus 215 ~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sys 294 (786)
T PRK05762 215 AEHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFS 294 (786)
T ss_pred HhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCC
Confidence 52 369999997 68998772 110 1 0 3555544432211335789
Q ss_pred HHHHHHHhhCCcccCCCCCC-------------------ChHHHHHHHHHHHHH
Q psy17350 482 LKMLTSHFLGLDIQNQDGGH-------------------CSKEDAIAALRLVKL 516 (528)
Q Consensus 482 Lk~La~~~Lg~~Iq~~~~~H-------------------dAlEDA~AT~eL~~~ 516 (528)
|+++|+++||..-... ..| -.+.||..|++|+.+
T Consensus 295 L~~Va~~~Lg~~K~~~-d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~k 347 (786)
T PRK05762 295 LEYVSQRLLGEGKAID-DPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEK 347 (786)
T ss_pred HHHHHHHHhCCCeecc-CccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999998653210 011 146889999999873
No 124
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=94.86 E-value=0.089 Score=59.36 Aligned_cols=133 Identities=25% Similarity=0.282 Sum_probs=86.8
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC-CCcE
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP-PDAI 443 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~-~d~I 443 (528)
+++|+||.+.++-...++.+++.... +..|- |.. ++ ++.+ ++...+..++. ++..
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~-~~~yi----~~~---------~~--~~~~--------~~~~~l~~~l~~~~~~ 80 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE-EAAYI----PLL---------HG--PEQL--------NVLAALKPLLEDEGIK 80 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc-cceeE----eec---------cc--hhhh--------hhHHHHHHHhhCcccc
Confidence 99999999999865778777766544 22211 110 11 1111 16677777776 2446
Q ss_pred EEEcCchhhHHHHcccC---CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCC-----CC--------------CC
Q psy17350 444 LVGQSLNCDLHALKMMH---PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQ-----DG--------------GH 501 (528)
Q Consensus 444 LVGHnL~fDL~~L~~~h---p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~-----~~--------------~H 501 (528)
.||||+.+|+.+|.... ....||+...-...+....+.+..|+++||+...... ++ .-
T Consensus 81 kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~ 160 (593)
T COG0749 81 KVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATE 160 (593)
T ss_pred hhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHH
Confidence 99999999999997654 3467887764333323346899999999988765431 00 12
Q ss_pred ChHHHHHHHHHHHHHHHHcC
Q psy17350 502 CSKEDAIAALRLVKLKLSKG 521 (528)
Q Consensus 502 dAlEDA~AT~eL~~~~L~~g 521 (528)
.+.+||.++..|+.....+.
T Consensus 161 y~a~~a~~~~~L~~~l~~~l 180 (593)
T COG0749 161 YAAEDADATLRLESILEPEL 180 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 35689999999988766543
No 125
>PRK06722 exonuclease; Provisional
Probab=94.59 E-value=0.04 Score=57.01 Aligned_cols=104 Identities=16% Similarity=0.187 Sum_probs=68.3
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC------ccc---ccCCc-----Eeeccccc-C-
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA------DKQ---MMHPY-----VIDTSVIF-N- 67 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D------aL~---l~Hp~-----i~DTa~~~-~- 67 (528)
...+.||+++++. +|.. +++|..++.+.+.+ +.+|++|+ ..| .++ +..|. .+|++.+. +
T Consensus 60 i~~LTGIT~emV~-~AP~--f~eVl~ef~~fig~-~~lvahna-~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~ 134 (281)
T PRK06722 60 TTKLTGITKKDLI-GVEK--FPQIIEKFIQFIGE-DSIFVTWG-KEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQA 134 (281)
T ss_pred HhhhcCCCHHHHc-CCCC--HHHHHHHHHHHHCC-CcEEEEEe-HHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHH
Confidence 3578999999654 4432 55688888888864 46788887 456 222 22332 26777543 2
Q ss_pred CCCCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHH
Q psy17350 68 TTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLS 115 (528)
Q Consensus 68 ~~~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~ 115 (528)
++...+..+||..|++.+ |... .+..|+-..||++|.+|+...+.
T Consensus 135 ~~~l~~~~~sL~~l~~~l-gL~~--~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 135 YEELFEHTPSLQSAVEQL-GLIW--EGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred hhhhccCCCCHHHHHHHC-CCCC--CCCCcCcHHHHHHHHHHHHHHhc
Confidence 222223457899999984 5543 22379999999999999977653
No 126
>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=94.30 E-value=0.066 Score=51.90 Aligned_cols=86 Identities=14% Similarity=0.086 Sum_probs=58.0
Q ss_pred HHHHHHHHHhcCCcEEEeccCCcC--ccccc---------CC-cEeecccccCC-C---------CCCCCCccHHHHHHH
Q psy17350 27 QIKRLENKKRKMDALVEIKTLNEA--DKQMM---------HP-YVIDTSVIFNT-T---------GIRTHKPKLKMLTSH 84 (528)
Q Consensus 27 v~~~l~~l~~~~~~IlvGH~l~~D--aL~l~---------Hp-~i~DTa~~~~~-~---------~~~~~~~SLk~La~~ 84 (528)
....|+.++...+.+-|||+..+| .|+-. .+ .++||+.+... . .....+.||+.|++.
T Consensus 70 ~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~ 149 (193)
T cd06146 70 WDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQE 149 (193)
T ss_pred HHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHH
Confidence 345688888876667799999999 44422 23 58999876432 1 112357899999999
Q ss_pred HhCccccCCCC----C---------CCcHHHHHHHHHHHHH
Q psy17350 85 FLGLDIQNQDG----G---------HCSKEDAIAALRLVKL 112 (528)
Q Consensus 85 ~L~~~IQ~~~~----g---------HdSvEDA~Aam~L~~~ 112 (528)
+||..+..... + +-..-||.++++||..
T Consensus 150 ~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~ 190 (193)
T cd06146 150 VLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDK 190 (193)
T ss_pred HhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99988876421 1 1125677777777764
No 127
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=94.29 E-value=0.06 Score=66.45 Aligned_cols=102 Identities=18% Similarity=0.130 Sum_probs=71.7
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cc-------cccCC--cEeecccccCCCCCCC
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DK-------QMMHP--YVIDTSVIFNTTGIRT 73 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL-------~l~Hp--~i~DTa~~~~~~~~~~ 73 (528)
+++.||+++++. ++. .+++|...+.+... +++||+|-...| .| ++..+ ..+||-.+........
T Consensus 470 ~~LTGIT~e~L~-~ap--s~~EaL~~f~~fig--g~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~ 544 (1437)
T PRK00448 470 TELTGITDDMVK-DAP--SIEEVLPKFKEFCG--DSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPEL 544 (1437)
T ss_pred HHHhCCCHHHHc-CCC--CHHHHHHHHHHHhC--CCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCcc
Confidence 568899999554 443 24457777777665 589999998888 22 23222 4799877653221123
Q ss_pred CCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHH
Q psy17350 74 HKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLS 115 (528)
Q Consensus 74 ~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~ 115 (528)
.+.+|..||+. +|...-. .|+...||.|+.+|+...++
T Consensus 545 k~~kL~~LAk~-lGL~~~~---~HrAl~DA~aTa~lf~~ll~ 582 (1437)
T PRK00448 545 KSHRLNTLAKK-FGVELEH---HHRADYDAEATAYLLIKFLK 582 (1437)
T ss_pred ccccHHHHHHH-cCCCCCC---CcChHHHHHHHHHHHHHHHH
Confidence 57899999997 5766543 59999999999999987664
No 128
>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=93.70 E-value=1.2 Score=44.51 Aligned_cols=154 Identities=11% Similarity=0.114 Sum_probs=82.7
Q ss_pred CCeEEEeeceecCC-----CCcCcEEEEEEEEe-CCcEE-E------EEEEcCCCCCCCCceeecCCChhhhcccCCCHH
Q psy17350 362 SPLYGLDCEMCKTS-----NDQNELTRVTLVDE-QENVV-Y------ESLVKPYNPITNYLTAYSGITRALLAPVATRLE 428 (528)
Q Consensus 362 ~~~vALDcEmtgt~-----~g~~eLirIs~Vd~-~G~vi-~------d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~ 428 (528)
-.++++|+|+...+ |..++|+.|+.+-. +.... . --++.+...-.+......++....+.-. ++-.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~-~~E~ 82 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVV-ESEL 82 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEe-CCHH
Confidence 35789999986533 33678999987743 22211 1 1223332211110011223333334433 4556
Q ss_pred HHHHHHHhc---CCCCcEEEEcCc-hhhHHHHc-------ccC-------------C---------------------C-
Q psy17350 429 HVQKILSEL---LPPDAILVGQSL-NCDLHALK-------MMH-------------P---------------------Y- 462 (528)
Q Consensus 429 dV~~~L~~~---i~~d~ILVGHnL-~fDL~~L~-------~~h-------------p---------------------~- 462 (528)
++..++.++ ++ -.||+|||+ .||+..|- ... . +
T Consensus 83 ~LL~~f~~~i~~~D-PDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi 161 (231)
T cd05778 83 ELFEELIDLVRRFD-PDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRH 161 (231)
T ss_pred HHHHHHHHHHHHhC-CCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEE
Confidence 666666554 44 479999998 77987761 100 0 0
Q ss_pred EeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHH------HHHHHHHHHHHc
Q psy17350 463 VIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAI------AALRLVKLKLSK 520 (528)
Q Consensus 463 vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~------AT~eL~~~~L~~ 520 (528)
++|...+.+.. .....|+|.++|.++||..... ..|..+.+.. .-..+..++++.
T Consensus 162 ~lD~~~~~r~~-~kl~sYsL~~V~~~~L~~~k~~--~~~~~i~~~~~~~~~~~r~~v~~Y~l~d 222 (231)
T cd05778 162 ILNVWRLMRSE-LALTNYTLENVVYHVLHQRIPL--YSNKTLTEWYKSGSASERWRVLEYYLKR 222 (231)
T ss_pred EeEhHHHHHHH-cCcccCCHHHHHHHHhCCCCCC--CCHHHHHHHHHcCCHhHhHHHHHHHHHH
Confidence 23443333321 2446899999999999997653 2355555542 345566666553
No 129
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=93.05 E-value=0.27 Score=52.85 Aligned_cols=103 Identities=17% Similarity=0.235 Sum_probs=69.1
Q ss_pred ceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cc----c-------------------------
Q psy17350 5 LEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DK----Q------------------------- 53 (528)
Q Consensus 5 ~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL----~------------------------- 53 (528)
..+.||+++++ .++. .+.+|...+.+++. +++||+|-...| .| +
T Consensus 96 ~~LHGIT~e~L-a~AP--~f~eVl~el~~fL~--g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~r 170 (377)
T PRK05601 96 FHLHGLSAEEF-AQGK--RFSQILKPLDRLID--GRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRR 170 (377)
T ss_pred ccccCCCHHHH-hcCC--CHHHHHHHHHHHhC--CCEEEEECcHHHHHHHHHHHHHhhhhhhhccccccccccccccccc
Confidence 46899999955 4442 35668899999998 689999998777 11 1
Q ss_pred ---ccC---C-cEeecccccCCCCCCCCCccHHHHHHHHhCccc-------cCCCCCCC--cHHHHHHHHHHHHHH
Q psy17350 54 ---MMH---P-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI-------QNQDGGHC--SKEDAIAALRLVKLK 113 (528)
Q Consensus 54 ---l~H---p-~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~I-------Q~~~~gHd--SvEDA~Aam~L~~~k 113 (528)
..| | .++||-.+--.....-...+|..||+. +|.+. |.....|+ +.|||+...+||...
T Consensus 171 r~~~g~~p~p~~~iDTL~LARrl~p~l~~~rL~~La~~-lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 171 RQRVGHIPKPVVIVDTLATARRQGVALDDIRIRGVAHT-LGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred ccccCCCCCCCCEEEhHHHHHHHcCCCCCCCHHHHHHH-hCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 112 2 479996642211101135899999998 57776 33223566 448999999999764
No 130
>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=93.01 E-value=0.44 Score=47.67 Aligned_cols=130 Identities=18% Similarity=0.281 Sum_probs=73.7
Q ss_pred CeEEEeeceecCCC-CcCcEEEEEEEEeC-----Cc-------EEEEEEEcCCCC--CCCCceeecCCChhhhcccCCCH
Q psy17350 363 PLYGLDCEMCKTSN-DQNELTRVTLVDEQ-----EN-------VVYESLVKPYNP--ITNYLTAYSGITRALLAPVATRL 427 (528)
Q Consensus 363 ~~vALDcEmtgt~~-g~~eLirIs~Vd~~-----G~-------vi~d~LVkP~~~--I~dy~T~isGIT~e~L~~a~p~l 427 (528)
.+++|-+-|+.-.. ...||+.||++-.+ +- .-+-++++|... .+......-......+.-. .+-
T Consensus 4 ~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~-~~E 82 (234)
T cd05776 4 TVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIF-ENE 82 (234)
T ss_pred EEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEe-CCH
Confidence 35566666654443 36789888877431 11 124456677653 2222222211112223332 455
Q ss_pred HHHHHHHHhcCCC--CcEEEEcCc-hhhHHHHc-------ccC------------C----------------C-Eeeehh
Q psy17350 428 EHVQKILSELLPP--DAILVGQSL-NCDLHALK-------MMH------------P----------------Y-VIDTSV 468 (528)
Q Consensus 428 ~dV~~~L~~~i~~--d~ILVGHnL-~fDL~~L~-------~~h------------p----------------~-vIDTs~ 468 (528)
.+....+..++.. -+||||||+ .||+.+|- +.+ | + ++|+..
T Consensus 83 ~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~ 162 (234)
T cd05776 83 RALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYL 162 (234)
T ss_pred HHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHH
Confidence 6666666665542 479999999 88998771 111 0 0 356655
Q ss_pred hchhcCCCCCCCCHHHHHHHhhCCcc
Q psy17350 469 IFNTTGIRTHKPKLKMLTSHFLGLDI 494 (528)
Q Consensus 469 L~~~~~~~~~k~sLk~La~~~Lg~~I 494 (528)
.++.. .....|+|.++|+.+||.+-
T Consensus 163 ~~k~~-~~~~sY~L~~va~~~Lg~~k 187 (234)
T cd05776 163 SAKEL-IRCKSYDLTELSQQVLGIER 187 (234)
T ss_pred HHHHH-hCCCCCChHHHHHHHhCcCc
Confidence 55432 23568999999999999843
No 131
>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=92.92 E-value=0.14 Score=48.79 Aligned_cols=92 Identities=16% Similarity=0.117 Sum_probs=56.0
Q ss_pred eeccCCCCCCchhhhhhHHHHHHHHHHHHhc----CCcEEEeccCCcC--ccc--------ccCCcEeecccccCCCCCC
Q psy17350 7 VLGLNPGGVLLNAYFKMNARQIKRLENKKRK----MDALVEIKTLNEA--DKQ--------MMHPYVIDTSVIFNTTGIR 72 (528)
Q Consensus 7 vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~----~~~IlvGH~l~~D--aL~--------l~Hp~i~DTa~~~~~~~~~ 72 (528)
.+||+++++ .++.. +.++-..+.+.+.+ ...+|+||+...| .|+ ..|..++||..+
T Consensus 61 ~tgIt~~~l-~~~~~--~~~vl~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l------- 130 (173)
T cd06135 61 KSGLTERVR-ASTVT--LAQAEAELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSI------- 130 (173)
T ss_pred ccccHHHHH-hCCCC--HHHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHH-------
Confidence 369998844 43332 34466777777753 2469999999888 221 222345666332
Q ss_pred CCCccHHHHHHHHhC----ccccCCCCCCCcHHHHHHHHHHHHHHHH
Q psy17350 73 THKPKLKMLTSHFLG----LDIQNQDGGHCSKEDAIAALRLVKLKLS 115 (528)
Q Consensus 73 ~~~~SLk~La~~~L~----~~IQ~~~~gHdSvEDA~Aam~L~~~k~~ 115 (528)
..|++.+.- ..+-. +.-|....||+|+..+|+.++.
T Consensus 131 ------~~l~~~l~p~~~~~~~~~-~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 131 ------KELARRWYPEIYRKAPKK-KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred ------HHHHHHhCcHhhhcCCCC-CCCcchHHHHHHHHHHHHHHHH
Confidence 233332211 11111 2369999999999999999875
No 132
>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=92.65 E-value=0.11 Score=47.73 Aligned_cols=87 Identities=18% Similarity=0.070 Sum_probs=56.9
Q ss_pred HHHHHHHHHhcCCcEEEeccCCcC--ccc----ccCCcEeecccccCCCCCCCCCccHHHHHHHHhC-----ccccCCCC
Q psy17350 27 QIKRLENKKRKMDALVEIKTLNEA--DKQ----MMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLG-----LDIQNQDG 95 (528)
Q Consensus 27 v~~~l~~l~~~~~~IlvGH~l~~D--aL~----l~Hp~i~DTa~~~~~~~~~~~~~SLk~La~~~L~-----~~IQ~~~~ 95 (528)
+...++.++...+.+.|||...+| +|. +....+.|| .+-.+-.++....||+.|+..+|| ++.|.+..
T Consensus 65 ~~~~l~~ll~~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~ 143 (176)
T PF01612_consen 65 ILDALKELLEDPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDW 143 (176)
T ss_dssp HHHHHHHHHTTTTSEEEESSHHHHHHHHHHHHTS--SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSST
T ss_pred hHHHHHHHHhCCCccEEEEEEechHHHHHHHhccccCCccch-hhhhhcccccccccHHHHHHHHhhhccCcHHHhhccC
Confidence 456889999988889999999999 333 333468999 544332222233999999999999 33333321
Q ss_pred C-CC---------cHHHHHHHHHHHHHHH
Q psy17350 96 G-HC---------SKEDAIAALRLVKLKL 114 (528)
Q Consensus 96 g-Hd---------SvEDA~Aam~L~~~k~ 114 (528)
+ -. ...||.++++||....
T Consensus 144 ~~~~~l~~~~~~YAa~D~~~~~~l~~~l~ 172 (176)
T PF01612_consen 144 RKARPLSEEQIEYAAQDAVVTFRLYEKLK 172 (176)
T ss_dssp TTSSS-HHHHHHHHHHHHHTHHHHHHHHH
T ss_pred CcCCCChHHHHHHHHHHHHHHHHHHHHHH
Confidence 2 11 2457778888877543
No 133
>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=92.61 E-value=0.28 Score=50.09 Aligned_cols=86 Identities=14% Similarity=0.199 Sum_probs=50.1
Q ss_pred CCCCeEEEeeceecCC-----CCcCcEEEEEEE-EeC-----CcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHH
Q psy17350 360 PTSPLYGLDCEMCKTS-----NDQNELTRVTLV-DEQ-----ENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLE 428 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~-----~g~~eLirIs~V-d~~-----G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~ 428 (528)
+...++++|+||.... +..++|+.|+++ ... .....-.+..+.. +.+ ...+.-+ .+-.
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~-~~~---------~~~v~~~-~~E~ 223 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDS-IED---------NVEVIYF-DSEK 223 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCC-TTC---------TTEEEEE-SSHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCC-CCC---------CcEEEEE-CCHH
Confidence 4568999999998775 346899999964 222 2223334443332 221 2222222 3444
Q ss_pred HHHHHHHhcCC--CCcEEEEcCc-hhhHHHH
Q psy17350 429 HVQKILSELLP--PDAILVGQSL-NCDLHAL 456 (528)
Q Consensus 429 dV~~~L~~~i~--~d~ILVGHnL-~fDL~~L 456 (528)
+++..+.+++. .-.||+|||+ .||+..|
T Consensus 224 ~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl 254 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDPDIITGYNIDGFDLPYL 254 (325)
T ss_dssp HHHHHHHHHHHHHS-SEEEESSTTTTHHHHH
T ss_pred HHHHHHHHHHHhcCCcEEEEecccCCCHHHH
Confidence 44444444432 1469999998 5899887
No 134
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=92.49 E-value=0.94 Score=43.37 Aligned_cols=103 Identities=17% Similarity=0.169 Sum_probs=62.4
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCC-CC
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSELLP-PD 441 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~-~d 441 (528)
..+++|+|+....+...+++.+++-..++ +. +|.+ +.. ......|.+++. .+
T Consensus 25 ~~l~~~~e~~~~~~~~~~~~~l~l~~~~~-~~---~i~~------------------l~~-----~~~~~~L~~~L~~~~ 77 (192)
T cd06147 25 KEIAVDLEHHSYRSYLGFTCLMQISTREE-DY---IVDT------------------LKL-----RDDMHILNEVFTDPN 77 (192)
T ss_pred CeEEEEeEecCCccCCCceEEEEEecCCC-cE---EEEe------------------ccc-----ccchHHHHHHhcCCC
Confidence 58999998765443235677676665443 22 1211 010 111123444444 35
Q ss_pred cEEEEcCchhhHHHHc-ccC---CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcc
Q psy17350 442 AILVGQSLNCDLHALK-MMH---PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI 494 (528)
Q Consensus 442 ~ILVGHnL~fDL~~L~-~~h---p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~I 494 (528)
...|||++..|+..|+ ... ..+.||........+. . .+|+.|++.||+..+
T Consensus 78 i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~-~~l~~l~~~yl~~~~ 132 (192)
T cd06147 78 ILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-R-HSLAYLLQKYCNVDA 132 (192)
T ss_pred ceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-c-ccHHHHHHHHhCCCc
Confidence 6789999999999996 211 1238998876544433 3 499999999998763
No 135
>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=92.19 E-value=1.2 Score=39.96 Aligned_cols=61 Identities=25% Similarity=0.244 Sum_probs=42.1
Q ss_pred HHhcCC-CCcEEEEcCchhhHHHHccc---C-CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcc
Q psy17350 434 LSELLP-PDAILVGQSLNCDLHALKMM---H-PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI 494 (528)
Q Consensus 434 L~~~i~-~d~ILVGHnL~fDL~~L~~~---h-p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~I 494 (528)
|.+++. ++...|||++..|+.+|+.. . ..+.||...+....+...+.+|+.|+++||+.++
T Consensus 45 l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~~ 110 (150)
T cd09018 45 LKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKL 110 (150)
T ss_pred HHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCCc
Confidence 344443 35668999999999999532 2 2468998876543332213599999999998873
No 136
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=92.11 E-value=1.6 Score=53.03 Aligned_cols=147 Identities=16% Similarity=0.195 Sum_probs=81.9
Q ss_pred CCCCeEEEeeceecCC------CCcCcEEEEEEEE-eCCcE---EEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHH
Q psy17350 360 PTSPLYGLDCEMCKTS------NDQNELTRVTLVD-EQENV---VYESLVKPYNPITNYLTAYSGITRALLAPVATRLEH 429 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~------~g~~eLirIs~Vd-~~G~v---i~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~d 429 (528)
+..+++++|+|+.+.. +..++|+.|+.+- ..|.. ....++-+.. ...+.|. .+... .+-.+
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~-----c~~i~g~---~V~~f-~sE~e 332 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE-----CASIAGA---NVLSF-ETEKE 332 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc-----cccCCCc---eEEEe-CCHHH
Confidence 4467999999998642 2358999999874 35532 1111221111 0111221 12221 34455
Q ss_pred HHHHHHhc---CCCCcEEEEcCc-hhhHHHHc-------ccC-C----------------------------------C-
Q psy17350 430 VQKILSEL---LPPDAILVGQSL-NCDLHALK-------MMH-P----------------------------------Y- 462 (528)
Q Consensus 430 V~~~L~~~---i~~d~ILVGHnL-~fDL~~L~-------~~h-p----------------------------------~- 462 (528)
++..+.++ ++ -+||+|||+ .||+..|- +.. + +
T Consensus 333 LL~~f~~~I~~~D-PDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~ 411 (1054)
T PTZ00166 333 LLLAWAEFVIAVD-PDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRI 411 (1054)
T ss_pred HHHHHHHHHHhcC-CCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEE
Confidence 55555544 44 479999998 68997761 110 0 0
Q ss_pred EeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCC----------CCCC-------ChHHHHHHHHHHHHHH
Q psy17350 463 VIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQ----------DGGH-------CSKEDAIAALRLVKLK 517 (528)
Q Consensus 463 vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~----------~~~H-------dAlEDA~AT~eL~~~~ 517 (528)
++|+..+++.. .....|+|.++|.+|||.....= +..+ -.+.||+.+++|+.+.
T Consensus 412 ~iDl~~~~~~~-~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl 482 (1054)
T PTZ00166 412 QFDVMDLIRRD-YKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKL 482 (1054)
T ss_pred EEEHHHHHHHh-cCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 23444443321 23458999999999999754210 0011 2368888888888754
No 137
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=92.09 E-value=0.15 Score=53.03 Aligned_cols=101 Identities=14% Similarity=0.060 Sum_probs=61.2
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cccc-----cCCcEeecccccCCCCCCCCCc
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DKQM-----MHPYVIDTSVIFNTTGIRTHKP 76 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~l-----~Hp~i~DTa~~~~~~~~~~~~~ 76 (528)
.+++.||+++++..+. . .. ..+..+++. ..+||||-...| .|.- ......+|-.............
T Consensus 93 ~t~IhGIt~e~v~~~~-~-~~----~~l~~fl~~-~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~ 165 (294)
T PRK09182 93 ITRLTGITDEMVAGQT-I-DP----AAVDALIAP-ADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGT 165 (294)
T ss_pred HHHhcCCCHHHHhcCC-C-cH----HHHHHHhcC-CCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCC
Confidence 3578899999543322 2 12 245666654 469999998888 3321 1111223322111111112468
Q ss_pred cHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 77 KLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 77 SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
+|..|+..+ | +..+ +|+...||+|+.+|+...+.+
T Consensus 166 kL~~La~~~-g--~~~~--aHrAl~Da~Ata~ll~~~l~~ 200 (294)
T PRK09182 166 KLGYLAGQA-G--FFHE--GHRAVDDCQALLELLARPLPE 200 (294)
T ss_pred CHHHHHHHc-C--CCCC--CcChHHHHHHHHHHHHHHHhh
Confidence 999999874 6 3333 899999999999999976654
No 138
>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=91.84 E-value=0.29 Score=45.62 Aligned_cols=63 Identities=19% Similarity=0.121 Sum_probs=46.5
Q ss_pred HHHHHHHhcCCcEEEeccCCcC--cccccCC----cEeecccccCCCCCCCCCccHHHHHHHHhCcccc
Q psy17350 29 KRLENKKRKMDALVEIKTLNEA--DKQMMHP----YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQ 91 (528)
Q Consensus 29 ~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp----~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ 91 (528)
..+.+++...+.+.|||+...| .|+-.++ .+.||......-.....+.||+.|+..+||.++.
T Consensus 63 ~~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~ 131 (170)
T cd06141 63 PSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLS 131 (170)
T ss_pred HHHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccC
Confidence 4677888776677899999999 5542222 5799998876544322346999999999999887
No 139
>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=90.42 E-value=0.27 Score=46.01 Aligned_cols=83 Identities=17% Similarity=0.145 Sum_probs=54.2
Q ss_pred HHHHHHHhcCCcEEEeccCCcC--cccccCC----cEeecccccCCCCCCCCCccHHHHHHHHhCccccCCC----CCCC
Q psy17350 29 KRLENKKRKMDALVEIKTLNEA--DKQMMHP----YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQD----GGHC 98 (528)
Q Consensus 29 ~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp----~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ~~~----~gHd 98 (528)
..+..++...+.+.|||+...| .|.-.+. .+.||......-. ++.+.||+.|++.+||..+.... =+..
T Consensus 57 ~~L~~lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~-~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~r 135 (161)
T cd06129 57 QGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKG-LPERWSLASLVEHFLGKTLDKSISCADWSYR 135 (161)
T ss_pred HHHHHHhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhC-CCCCchHHHHHHHHhCCCCCccceeccCCCC
Confidence 4577778766667899999999 5432222 4689988765432 22356999999999999874331 1222
Q ss_pred c---------HHHHHHHHHHHHH
Q psy17350 99 S---------KEDAIAALRLVKL 112 (528)
Q Consensus 99 S---------vEDA~Aam~L~~~ 112 (528)
+ ..||.+.++||+.
T Consensus 136 pLt~~qi~YAa~Da~~l~~l~~~ 158 (161)
T cd06129 136 PLTEDQKLYAAADVYALLIIYTK 158 (161)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Confidence 2 5566666666653
No 140
>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=90.34 E-value=0.32 Score=47.95 Aligned_cols=64 Identities=22% Similarity=0.353 Sum_probs=42.8
Q ss_pred HHHHHHHHhcCCC-CcEEEEcCc-hhhHHHHccc---C----C------------------CEeeehhhchhcCCCCCCC
Q psy17350 428 EHVQKILSELLPP-DAILVGQSL-NCDLHALKMM---H----P------------------YVIDTSVIFNTTGIRTHKP 480 (528)
Q Consensus 428 ~dV~~~L~~~i~~-d~ILVGHnL-~fDL~~L~~~---h----p------------------~vIDTs~L~~~~~~~~~k~ 480 (528)
.++..++.+++.. +.+|||||. .||+-+|... | | +.+|+..+....+ ...++
T Consensus 79 ~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~-~~~~~ 157 (208)
T cd05782 79 KELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYG-ARARA 157 (208)
T ss_pred HHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccC-ccCCC
Confidence 5666777777664 568999997 8999888421 1 2 1566666654322 23578
Q ss_pred CHHHHHHHhhCCc
Q psy17350 481 KLKMLTSHFLGLD 493 (528)
Q Consensus 481 sLk~La~~~Lg~~ 493 (528)
+|+.+|+ +||.+
T Consensus 158 ~L~~va~-~lG~~ 169 (208)
T cd05782 158 SLDLLAK-LLGIP 169 (208)
T ss_pred CHHHHHH-HhCCC
Confidence 9999997 57774
No 141
>PRK05359 oligoribonuclease; Provisional
Probab=89.91 E-value=0.65 Score=44.79 Aligned_cols=93 Identities=15% Similarity=0.064 Sum_probs=56.9
Q ss_pred eeccCCCCCCchhhhhhHHHHHHHHHHHHhc----CCcEEEeccCCcC--ccc--------ccCCcEeecccccCCCCCC
Q psy17350 7 VLGLNPGGVLLNAYFKMNARQIKRLENKKRK----MDALVEIKTLNEA--DKQ--------MMHPYVIDTSVIFNTTGIR 72 (528)
Q Consensus 7 vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~----~~~IlvGH~l~~D--aL~--------l~Hp~i~DTa~~~~~~~~~ 72 (528)
.+||+.+. +..+. .++++...+.+.+++ .+.+|+||+...| -|+ ..|..++|++
T Consensus 65 ~tGIt~~~-l~~~~--~~~e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~--------- 132 (181)
T PRK05359 65 RSGLIDRV-RASTV--SEAEAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVS--------- 132 (181)
T ss_pred cccCcHHH-HhcCC--CHHHHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchh---------
Confidence 46999884 34333 234577777777753 2468899999888 221 1223345543
Q ss_pred CCCccHHHHHHHHhCc---cccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 73 THKPKLKMLTSHFLGL---DIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~---~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
+||.|++.++-. .|-.. ..|=..+||+++.+.|+++...
T Consensus 133 ----tl~~l~r~~~P~~~~~~~~~-~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 133 ----TLKELARRWKPEILNGFKKQ-GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred ----HHHHHHHHhChhhhhCCCCc-CCcccHHHHHHHHHHHHHHHHH
Confidence 344444443321 23222 3699999999999999988764
No 142
>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=89.53 E-value=4.9 Score=40.09 Aligned_cols=91 Identities=19% Similarity=0.238 Sum_probs=59.6
Q ss_pred HHHHHHHHHhcCCC-CcEEEEcC-chhhHHHHcc---cC----CC-------------------EeeehhhchhcCCCCC
Q psy17350 427 LEHVQKILSELLPP-DAILVGQS-LNCDLHALKM---MH----PY-------------------VIDTSVIFNTTGIRTH 478 (528)
Q Consensus 427 l~dV~~~L~~~i~~-d~ILVGHn-L~fDL~~L~~---~h----p~-------------------vIDTs~L~~~~~~~~~ 478 (528)
-+++..++.+++++ ...||||| -+||+-+|.. .| |. -+|+..+....+ ...
T Consensus 37 E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g-~~~ 115 (209)
T PF10108_consen 37 EKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYG-AKA 115 (209)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccC-ccc
Confidence 56777888888863 44799999 5999988842 12 21 366666543322 345
Q ss_pred CCCHHHHHHHhhCCcccCC-----------CC-----CCChHHHHHHHHHHHHHHHH
Q psy17350 479 KPKLKMLTSHFLGLDIQNQ-----------DG-----GHCSKEDAIAALRLVKLKLS 519 (528)
Q Consensus 479 k~sLk~La~~~Lg~~Iq~~-----------~~-----~HdAlEDA~AT~eL~~~~L~ 519 (528)
+.+|+.||.. ||++=..+ ++ ..-...|+++|..||.+..-
T Consensus 116 ~~sLd~la~~-lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 116 RTSLDELAAL-LGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred cCCHHHHHHH-cCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7899999985 78874221 00 11235899999999987653
No 143
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.29 E-value=1.1 Score=53.29 Aligned_cols=93 Identities=16% Similarity=0.094 Sum_probs=62.2
Q ss_pred HHHHHHHHHhcCCC-CcEEEEcCchhhHHHHcccC----CCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccC-----
Q psy17350 427 LEHVQKILSELLPP-DAILVGQSLNCDLHALKMMH----PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN----- 496 (528)
Q Consensus 427 l~dV~~~L~~~i~~-d~ILVGHnL~fDL~~L~~~h----p~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~----- 496 (528)
...+...|.+++.. +...||||+.||+.+|.... ..+.||........+ ..+.+|+.|+.+||+...-.
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~~-~~~~~l~~la~~yl~~~~~~~~~~~ 441 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLDP-AQVSTLDTLARRYLVEELILDEKIG 441 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcCC-CCCCCHHHHHHHHcCcccccHHHhc
Confidence 44566667777763 34589999999999996321 246899887554332 23459999999998865211
Q ss_pred CCC-C----------CChHHHHHHHHHHHHHHHHc
Q psy17350 497 QDG-G----------HCSKEDAIAALRLVKLKLSK 520 (528)
Q Consensus 497 ~~~-~----------HdAlEDA~AT~eL~~~~L~~ 520 (528)
+.+ . .-+.+||.+|+.|+....++
T Consensus 442 ~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 442 GKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred cCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 100 0 13667899999998876554
No 144
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.01 E-value=7.3 Score=47.96 Aligned_cols=129 Identities=14% Similarity=0.114 Sum_probs=76.4
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEe-CC-------c----EEEEEEEcCCCCC--CCCceeecCCChhhhcccCCCHH
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDE-QE-------N----VVYESLVKPYNPI--TNYLTAYSGITRALLAPVATRLE 428 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~-~G-------~----vi~d~LVkP~~~I--~dy~T~isGIT~e~L~~a~p~l~ 428 (528)
.++.|++|+...+....+++.|+.+=. ++ . +.+...++|.... .++....-|+.+..|... .+-.
T Consensus 507 ~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~L~~~-~sEr 585 (1172)
T TIGR00592 507 VVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGKKPSLVEDL-ATER 585 (1172)
T ss_pred EEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCCCCCchhhhhhhccCCcEEEEe-cCHH
Confidence 345556565544444567888776532 21 1 1233445553211 122334446666666664 5666
Q ss_pred HHHHHHHhcCC--CCcEEEEcCc-hhhHHHHcc-------cC----------------------CC-EeeehhhchhcCC
Q psy17350 429 HVQKILSELLP--PDAILVGQSL-NCDLHALKM-------MH----------------------PY-VIDTSVIFNTTGI 475 (528)
Q Consensus 429 dV~~~L~~~i~--~d~ILVGHnL-~fDL~~L~~-------~h----------------------p~-vIDTs~L~~~~~~ 475 (528)
+....+.+++. .-.+++|||. +|||.+|-- .+ .+ ++|+...++.. .
T Consensus 586 ~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~-~ 664 (1172)
T TIGR00592 586 ALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKEL-I 664 (1172)
T ss_pred HHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHH-h
Confidence 77777777664 4689999997 889987721 11 11 46776665432 1
Q ss_pred CCCCCCHHHHHHHhhCCc
Q psy17350 476 RTHKPKLKMLTSHFLGLD 493 (528)
Q Consensus 476 ~~~k~sLk~La~~~Lg~~ 493 (528)
....|+|..+|.++||.+
T Consensus 665 ~~~sy~L~~v~~~~L~~~ 682 (1172)
T TIGR00592 665 RCKSYDLSELVQQILKTE 682 (1172)
T ss_pred CcCCCCHHHHHHHHhCCC
Confidence 345799999999999853
No 145
>PHA02528 43 DNA polymerase; Provisional
Probab=86.89 E-value=3.3 Score=49.42 Aligned_cols=153 Identities=12% Similarity=0.122 Sum_probs=83.5
Q ss_pred CCCCeEEEeeceecCC----CC--cCcEEEEEEEEeCCcEEEEEEEc---CCCCCCCCc--eeecCCChhhhcccCCCHH
Q psy17350 360 PTSPLYGLDCEMCKTS----ND--QNELTRVTLVDEQENVVYESLVK---PYNPITNYL--TAYSGITRALLAPVATRLE 428 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~----~g--~~eLirIs~Vd~~G~vi~d~LVk---P~~~I~dy~--T~isGIT~e~L~~a~p~l~ 428 (528)
+.-+++++|+|+.... +. .++|+.|++.+..+..++-..+. |.....+.. ....++ .+... .+-.
T Consensus 104 p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v---~~~~~-~sE~ 179 (881)
T PHA02528 104 SKIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKV---VYMPF-DTER 179 (881)
T ss_pred CCccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCe---eEEEc-CCHH
Confidence 4578999999997522 22 56899999987755542222221 100000000 000011 11111 4566
Q ss_pred HHHHHHHhcCCC--CcEEEEcCc-hhhHHHHc--cc---C-------C-C-------------------------Eeeeh
Q psy17350 429 HVQKILSELLPP--DAILVGQSL-NCDLHALK--MM---H-------P-Y-------------------------VIDTS 467 (528)
Q Consensus 429 dV~~~L~~~i~~--d~ILVGHnL-~fDL~~L~--~~---h-------p-~-------------------------vIDTs 467 (528)
++...+.+++.. -.||+|||+ .|||..|. .. . . . ++|..
T Consensus 180 eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~ 259 (881)
T PHA02528 180 EMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYL 259 (881)
T ss_pred HHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHH
Confidence 777777777631 379999997 78997762 10 0 0 0 22333
Q ss_pred hhchhcC-CCCCCCCHHHHHHHhhCCcccCC--------------CCCCChHHHHHHHHHHHHH
Q psy17350 468 VIFNTTG-IRTHKPKLKMLTSHFLGLDIQNQ--------------DGGHCSKEDAIAALRLVKL 516 (528)
Q Consensus 468 ~L~~~~~-~~~~k~sLk~La~~~Lg~~Iq~~--------------~~~HdAlEDA~AT~eL~~~ 516 (528)
.+++... .....|+|.++|+++||..-..- .-.+-.+.||+-+.+|+.+
T Consensus 260 dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 260 DLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3333211 12347899999999998754320 0012236788888888865
No 146
>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=84.57 E-value=1 Score=40.10 Aligned_cols=66 Identities=14% Similarity=0.134 Sum_probs=45.3
Q ss_pred HHHHHHHHHHhcCCcEEEeccCCcC--ccc---ccCC-cEeecccccCCCCCCCCCccHHHHHHHHhCcccc
Q psy17350 26 RQIKRLENKKRKMDALVEIKTLNEA--DKQ---MMHP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQ 91 (528)
Q Consensus 26 ~v~~~l~~l~~~~~~IlvGH~l~~D--aL~---l~Hp-~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ 91 (528)
.+...+.+++...+..+|||....| +|+ +..+ .+.||......-.....+.+|+.|++++|+..+.
T Consensus 41 ~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~~ 112 (155)
T cd00007 41 EDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELD 112 (155)
T ss_pred HHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCCc
Confidence 3566688888876667999999888 543 2233 4689877654322111135999999999998854
No 147
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=83.87 E-value=1.7 Score=39.35 Aligned_cols=62 Identities=15% Similarity=0.092 Sum_probs=43.3
Q ss_pred HHHHHHHHhcCCcEEEeccCCcC--cccccCC----cEeecccccCC-CCCCCCCccHHHHHHHHhCcccc
Q psy17350 28 IKRLENKKRKMDALVEIKTLNEA--DKQMMHP----YVIDTSVIFNT-TGIRTHKPKLKMLTSHFLGLDIQ 91 (528)
Q Consensus 28 ~~~l~~l~~~~~~IlvGH~l~~D--aL~l~Hp----~i~DTa~~~~~-~~~~~~~~SLk~La~~~L~~~IQ 91 (528)
...+.+++...+...|||.+..| +|+- +. .+.||...... .... ...+|+.|+..+||.++.
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~k~~~~~L~~-~gi~~~~~~D~~laayll~p~~-~~~~l~~l~~~~l~~~~~ 132 (172)
T smart00474 64 LEILKDLLEDETITKVGHNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGP-SKHGLATLLKEYLGVELD 132 (172)
T ss_pred HHHHHHHhcCCCceEEEechHHHHHHHHH-CCCcccchhHHHHHHHHHcCCC-CcCCHHHHHHHHhCCCCC
Confidence 34477777766677999999998 6541 22 35899887653 2222 224999999999998863
No 148
>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=83.41 E-value=2 Score=45.81 Aligned_cols=144 Identities=17% Similarity=0.224 Sum_probs=80.1
Q ss_pred CCeEEEeeceecCCC-----C--cCcEEEEEEEEeCCcE--E---EEEEEcCCCCCCCCceeecCCChhhhcccCCCHHH
Q psy17350 362 SPLYGLDCEMCKTSN-----D--QNELTRVTLVDEQENV--V---YESLVKPYNPITNYLTAYSGITRALLAPVATRLEH 429 (528)
Q Consensus 362 ~~~vALDcEmtgt~~-----g--~~eLirIs~Vd~~G~v--i---~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~d 429 (528)
..++++|+||..... . .++++.|+.+...+.. . ....+.+...+. |+. +... ..-.+
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~---~~~~-~~E~~ 71 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEID-------GVE---VYEF-NNEKE 71 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCCC-------CCe---EEec-CCHHH
Confidence 468999999976431 1 4789999988763321 1 111223333322 222 1111 13344
Q ss_pred HHHHHHhcCCC--CcEEEEcCc-hhhHHHHccc-------C-----------------------------------CCEe
Q psy17350 430 VQKILSELLPP--DAILVGQSL-NCDLHALKMM-------H-----------------------------------PYVI 464 (528)
Q Consensus 430 V~~~L~~~i~~--d~ILVGHnL-~fDL~~L~~~-------h-----------------------------------p~vI 464 (528)
...++.+++.. ..+++|||. .||+.+|... . .-++
T Consensus 72 lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 151 (471)
T smart00486 72 LLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVI 151 (471)
T ss_pred HHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEEE
Confidence 55555554431 369999998 4899776210 0 0135
Q ss_pred eehhhchhcCCCCCCCCHHHHHHHhhCCcccCCC---------C--------CCChHHHHHHHHHHHHHH
Q psy17350 465 DTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQD---------G--------GHCSKEDAIAALRLVKLK 517 (528)
Q Consensus 465 DTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~---------~--------~HdAlEDA~AT~eL~~~~ 517 (528)
|+..+++... ....++|+.+|+++||..-..-. . ..-.+.||..+.+|+.+.
T Consensus 152 Dl~~~~~~~~-kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 152 DLYNLYKNKL-KLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EhHHHHHHHh-CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6655554322 24578999999999984322100 0 011256888888888764
No 149
>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=82.41 E-value=1.8 Score=40.55 Aligned_cols=92 Identities=16% Similarity=0.082 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHhcCCcEEEeccCCcC--ccc---cc-CCcEeecccccCCCCCCCCCccHHHHHHHHhCccccC-----
Q psy17350 24 NARQIKRLENKKRKMDALVEIKTLNEA--DKQ---MM-HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN----- 92 (528)
Q Consensus 24 ~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL~---l~-Hp~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ~----- 92 (528)
.+.+...+..++.+.+..+|||....| +|+ +. ...+.||......-.....+.+|+.|++.+|+.++..
T Consensus 52 ~~~~~~~l~~~l~~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~ 131 (193)
T cd06139 52 REEVLAALKPLLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLV 131 (193)
T ss_pred HHHHHHHHHHHHhCCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHc
Confidence 334667788888765568999999988 553 11 1246899877443211111459999999999877321
Q ss_pred CC--------------CCCCcHHHHHHHHHHHHHHHH
Q psy17350 93 QD--------------GGHCSKEDAIAALRLVKLKLS 115 (528)
Q Consensus 93 ~~--------------~gHdSvEDA~Aam~L~~~k~~ 115 (528)
+. ..|....||.++.+|+.....
T Consensus 132 ~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~ 168 (193)
T cd06139 132 GKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKP 168 (193)
T ss_pred CCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 10 012345567777777766544
No 150
>KOG4793|consensus
Probab=81.95 E-value=0.8 Score=47.23 Aligned_cols=162 Identities=17% Similarity=0.196 Sum_probs=97.4
Q ss_pred CCCCCCeEEEeeceecCCCCcCcEEEEEEEEe-----CCc---------------EE---EEEEEcCCCCCCCCceeecC
Q psy17350 358 VTPTSPLYGLDCEMCKTSNDQNELTRVTLVDE-----QEN---------------VV---YESLVKPYNPITNYLTAYSG 414 (528)
Q Consensus 358 ~~~~~~~vALDcEmtgt~~g~~eLirIs~Vd~-----~G~---------------vi---~d~LVkP~~~I~dy~T~isG 414 (528)
.+.-..++.+|.|++|+-....+++++++.++ +|. .+ ..-++.|.......-.+++|
T Consensus 9 ~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeitg 88 (318)
T KOG4793|consen 9 VPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEITG 88 (318)
T ss_pred CCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhcc
Confidence 33345688999999999776677888876643 232 12 23456676666666788999
Q ss_pred CChhhhccc-CCCH-HHHHHHHHhcCC---CCcEEEEcCc-hhhHHHHcc-------cCCC---Eeeehhhchh------
Q psy17350 415 ITRALLAPV-ATRL-EHVQKILSELLP---PDAILVGQSL-NCDLHALKM-------MHPY---VIDTSVIFNT------ 472 (528)
Q Consensus 415 IT~e~L~~a-~p~l-~dV~~~L~~~i~---~d~ILVGHnL-~fDL~~L~~-------~hp~---vIDTs~L~~~------ 472 (528)
.+.+-+.-. ..-| .++.+-|..|+. .---||.||- ++|+-.|+. .-|+ ++|+...++.
T Consensus 89 ls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~s 168 (318)
T KOG4793|consen 89 LSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRANS 168 (318)
T ss_pred cccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhcC
Confidence 987443311 1122 334444444543 2334899984 778777654 3332 6888776542
Q ss_pred --cC-CCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHHHHHHcC
Q psy17350 473 --TG-IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 521 (528)
Q Consensus 473 --~~-~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~~L~~g 521 (528)
.+ ...+.++|..+-..|.+-.- -+.+|.+..|--+=.-+|++.+.+.
T Consensus 169 ~~tr~~~~~~~~l~~If~ry~~q~e--ppa~~~~e~d~~~l~~~fqf~~~el 218 (318)
T KOG4793|consen 169 MVTRPEVRRMYSLGSIFLRYVEQRE--PPAGHVAEGDVNGLLFIFQFRINEL 218 (318)
T ss_pred cccCCCCCcccccchHHHhhhcccC--CCcceeeecccchhHHHHHHHHHHH
Confidence 11 22457888888666644321 1347888887776666666655543
No 151
>PHA02570 dexA exonuclease; Provisional
Probab=80.96 E-value=1.7 Score=43.54 Aligned_cols=92 Identities=14% Similarity=0.130 Sum_probs=57.9
Q ss_pred EEEeeceecCCCCcCcEEEEEEEEeC--CcE--EEEEEEcCCC------------CCCCCc--eeecCCChhh---hcc-
Q psy17350 365 YGLDCEMCKTSNDQNELTRVTLVDEQ--ENV--VYESLVKPYN------------PITNYL--TAYSGITRAL---LAP- 422 (528)
Q Consensus 365 vALDcEmtgt~~g~~eLirIs~Vd~~--G~v--i~d~LVkP~~------------~I~dy~--T~isGIT~e~---L~~- 422 (528)
+.||.||-|..+. ..|+.|++|-++ ... -|+++|.... .+++-. ..|-.-++|- |.+
T Consensus 4 lMIDlETmG~~p~-AaIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s 82 (220)
T PHA02570 4 FIIDFETFGNTPD-GAVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPS 82 (220)
T ss_pred EEEEeeccCCCCC-ceEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCC
Confidence 6799999999988 899999999652 222 2555554211 111111 1222222221 111
Q ss_pred -cCCCHHHHHHHHHhcCCCCc------EEEEcCchhhHHHHc
Q psy17350 423 -VATRLEHVQKILSELLPPDA------ILVGQSLNCDLHALK 457 (528)
Q Consensus 423 -a~p~l~dV~~~L~~~i~~d~------ILVGHnL~fDL~~L~ 457 (528)
...++.++..+|.+||..+. .+-|-+..||...|+
T Consensus 83 ~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 83 DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred CccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHH
Confidence 12568999999999987544 478899999998884
No 152
>KOG0969|consensus
Probab=79.71 E-value=0.92 Score=52.53 Aligned_cols=148 Identities=18% Similarity=0.214 Sum_probs=83.2
Q ss_pred CCCeEEEeeceecCCCC-----cCcEEEEE-EEEeCCcE-EE--EEE-EcCCCCCCCCceeecCCChhhhcccCCCHHHH
Q psy17350 361 TSPLYGLDCEMCKTSND-----QNELTRVT-LVDEQENV-VY--ESL-VKPYNPITNYLTAYSGITRALLAPVATRLEHV 430 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g-----~~eLirIs-~Vd~~G~v-i~--d~L-VkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV 430 (528)
..++.++|+|++|.... .+.+++|+ +|...|+- .| +-+ ++|-.+|+- ..-++-++++.+ -+.
T Consensus 273 PlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~capI~G-~~V~~~~~e~el-------L~~ 344 (1066)
T KOG0969|consen 273 PLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAPIVG-SNVHSYETEKEL-------LES 344 (1066)
T ss_pred cccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCCCCC-ceeEEeccHHHH-------HHH
Confidence 35789999999998753 45567776 44443432 12 222 344445543 223334444333 345
Q ss_pred HHHHHhcCCCCcEEEEcCc-hhhHHH-------Hccc--------CC---CEeeehhhchhc------------------
Q psy17350 431 QKILSELLPPDAILVGQSL-NCDLHA-------LKMM--------HP---YVIDTSVIFNTT------------------ 473 (528)
Q Consensus 431 ~~~L~~~i~~d~ILVGHnL-~fDL~~-------L~~~--------hp---~vIDTs~L~~~~------------------ 473 (528)
|..+..-++ -+||+|+|+ .||+-. |++. +. .+.||+.-.+..
T Consensus 345 W~~firevD-PDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqfDl 423 (1066)
T KOG0969|consen 345 WRKFIREVD-PDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQFDL 423 (1066)
T ss_pred HHHHHHhcC-CCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeeehH
Confidence 777777788 579999998 789733 3321 11 244553321110
Q ss_pred ------CCCCCCCCHHHHHHHhhCCcccCCCCCCChHHH-----HHHHHHHHHHHHH
Q psy17350 474 ------GIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKED-----AIAALRLVKLKLS 519 (528)
Q Consensus 474 ------~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlED-----A~AT~eL~~~~L~ 519 (528)
.-..+.|+|..++.+|||-.-. .-+|+.+.| +.+-..|..+||+
T Consensus 424 lqvi~Rd~KLrSytLNaVs~hFL~EQKE--DV~~siItdLQng~~~TRRRlA~YCLk 478 (1066)
T KOG0969|consen 424 LQVILRDYKLRSYTLNAVSAHFLGEQKE--DVHHSIITDLQNGNEQTRRRLAVYCLK 478 (1066)
T ss_pred HHHHHHhhhhhhcchhhhHHHhhhhhcc--cccccchhhhhcCcHHHHHHHHHHHhh
Confidence 1134689999999999976532 246666533 3344444445554
No 153
>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=79.32 E-value=3.5 Score=38.17 Aligned_cols=63 Identities=14% Similarity=0.204 Sum_probs=43.2
Q ss_pred HHHHHHHHHhcCCcEEEeccCCcC--cc----cccCCcEeecccccCCCCCCCCCccHHHHHHHHhCccc
Q psy17350 27 QIKRLENKKRKMDALVEIKTLNEA--DK----QMMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI 90 (528)
Q Consensus 27 v~~~l~~l~~~~~~IlvGH~l~~D--aL----~l~Hp~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~I 90 (528)
+...+..++...+.+.|||.+..| +| .+....+.||......-. +..+.+|+.|++.+||.++
T Consensus 52 ~~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~-p~~~~~l~~l~~~~l~~~~ 120 (178)
T cd06142 52 DLSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLG-LGDSVGLAALVEELLGVEL 120 (178)
T ss_pred cHHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhC-CCccccHHHHHHHHhCCCC
Confidence 344577888876778999999999 55 333225689976543321 1123499999999999873
No 154
>PRK05761 DNA polymerase I; Reviewed
Probab=78.02 E-value=8.2 Score=45.58 Aligned_cols=90 Identities=19% Similarity=0.157 Sum_probs=56.3
Q ss_pred CCHHHHHHHHHhcCCCCcEEEEcCc-hhhHHHHcc-------cCC---------C-EeeehhhchhcC-------C--CC
Q psy17350 425 TRLEHVQKILSELLPPDAILVGQSL-NCDLHALKM-------MHP---------Y-VIDTSVIFNTTG-------I--RT 477 (528)
Q Consensus 425 p~l~dV~~~L~~~i~~d~ILVGHnL-~fDL~~L~~-------~hp---------~-vIDTs~L~~~~~-------~--~~ 477 (528)
.+-.++..++.+++....+.|++|. +||+..|.. ... . .+|....+...+ + ..
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~ 287 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRH 287 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeec
Confidence 3566778888888877778888986 689977731 111 0 155544432210 1 11
Q ss_pred CCCCHHHHHHHhhCCcccC-----C-----CCCCChHHHHHHHHHHH
Q psy17350 478 HKPKLKMLTSHFLGLDIQN-----Q-----DGGHCSKEDAIAALRLV 514 (528)
Q Consensus 478 ~k~sLk~La~~~Lg~~Iq~-----~-----~~~HdAlEDA~AT~eL~ 514 (528)
+.++|...++.+||..=-. . .-+.-++.||..|++|.
T Consensus 288 ~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 288 REARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 2689999999999875210 0 01233589999999985
No 155
>PTZ00315 2'-phosphotransferase; Provisional
Probab=77.69 E-value=4 Score=46.38 Aligned_cols=114 Identities=12% Similarity=0.035 Sum_probs=73.9
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcC--------CcEEEeccCCcC-c--c----c----ccCC----cEe
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKM--------DALVEIKTLNEA-D--K----Q----MMHP----YVI 60 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~--------~~IlvGH~l~~D-a--L----~----l~Hp----~i~ 60 (528)
.+.+.||+.+++ .+|.. +.+|..++.+.+.+. +..+|+|--..| . | + ..-| ..+
T Consensus 113 ct~LTGITqe~V-~~Ap~--F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~wi 189 (582)
T PTZ00315 113 CTELTGITQSMV-SRADP--FPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWC 189 (582)
T ss_pred HhhhcCcCHHHH-hcCCC--HHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEE
Confidence 467899999965 44432 455788888877653 246888887777 1 2 2 1122 346
Q ss_pred ecccc-----cCCCC-------CCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCCCCCCC
Q psy17350 61 DTSVI-----FNTTG-------IRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGDLCSTK 123 (528)
Q Consensus 61 DTa~~-----~~~~~-------~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~~~~~~ 123 (528)
|...+ ||... ......+|..+++. +|.+.+. ..|..+.||+++.+|+...++.|-.+...
T Consensus 190 dLk~~lar~l~p~~~~~~~~~~~~~~~~~L~~al~~-lgL~~eG--r~HrAlDDA~ntA~L~~~Ll~~g~~~~~t 261 (582)
T PTZ00315 190 NLKKYMSQLGFGNGSGCGGGATPPLGPSDMPDMLQM-LGLPLQG--RHHSGIDDCRNIAAVLCELLRRGLVIDPT 261 (582)
T ss_pred EhHHHHHHHhCccccccccccccccCCcCHHHHHHH-CCCCCCC--CCcCcHHHHHHHHHHHHHHHHcCCEEEec
Confidence 64222 33110 01245789999996 6766443 37999999999999999998887666544
No 156
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=76.83 E-value=2 Score=51.96 Aligned_cols=104 Identities=17% Similarity=0.147 Sum_probs=74.1
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEeccCCcC--cc-----cccCC----cEeecccccCCCCCC
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKTLNEA--DK-----QMMHP----YVIDTSVIFNTTGIR 72 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~l~~D--aL-----~l~Hp----~i~DTa~~~~~~~~~ 72 (528)
.+..+||+-+ +++++.. .++|..++.+.+. |+|||-|-.+.| -| +..-+ -+|||-.+-..-...
T Consensus 471 ~telTgITde-ml~~a~~--i~~vL~kf~~~~~--d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~ 545 (1444)
T COG2176 471 ITELTGITDE-MLENAPE--IEEVLEKFREFIG--DSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPE 545 (1444)
T ss_pred hhhccccCHH-HHcCCcc--HHHHHHHHHHHhc--CcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChh
Confidence 4678999999 4566643 4567888888887 799999999999 22 22222 279996653221111
Q ss_pred CCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHc
Q psy17350 73 THKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 73 ~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
-++.+|-.||+.+ |...- .-|--.-||.|+-.++..++++
T Consensus 546 ~ksh~Lg~l~kk~-~v~le---~hHRA~yDaeat~~vf~~f~~~ 585 (1444)
T COG2176 546 FKSHRLGTLCKKL-GVELE---RHHRADYDAEATAKVFFVFLKD 585 (1444)
T ss_pred hhhcchHHHHHHh-CccHH---HhhhhhhhHHHHHHHHHHHHHH
Confidence 2467899999985 66652 3699999999999999888864
No 157
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=76.76 E-value=32 Score=40.67 Aligned_cols=123 Identities=15% Similarity=0.217 Sum_probs=69.3
Q ss_pred CCCCCCeEEEeeceecCCCC-----cCcEEEEEEEEe-CCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHH
Q psy17350 358 VTPTSPLYGLDCEMCKTSND-----QNELTRVTLVDE-QENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQ 431 (528)
Q Consensus 358 ~~~~~~~vALDcEmtgt~~g-----~~eLirIs~Vd~-~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~ 431 (528)
..+..+++|+|+|+...... .+.+..|+.... .+... ++. ..+...|.. +..+ ..-.+++
T Consensus 150 ~~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~-----~~~-----~~~~~~~~~---v~~~-~~e~e~l 215 (792)
T COG0417 150 VRPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI-----EVF-----IYTSGEGFS---VEVV-ISEAELL 215 (792)
T ss_pred cCCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc-----ccc-----cccCCCCce---eEEe-cCHHHHH
Confidence 34567899999999987532 456777776665 22222 100 011111111 2221 3444555
Q ss_pred HHHHhcCC--CCcEEEEcCch-hhHHHHccc-------CC---------------------CEeeehhhchhcCCCCCCC
Q psy17350 432 KILSELLP--PDAILVGQSLN-CDLHALKMM-------HP---------------------YVIDTSVIFNTTGIRTHKP 480 (528)
Q Consensus 432 ~~L~~~i~--~d~ILVGHnL~-fDL~~L~~~-------hp---------------------~vIDTs~L~~~~~~~~~k~ 480 (528)
..+..++. .-+|+||||.+ ||+..|... .. ..+|....+.........+
T Consensus 216 ~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~~~~~y 295 (792)
T COG0417 216 ERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPLNLKSY 295 (792)
T ss_pred HHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhcccccc
Confidence 55555432 25799999996 999887321 11 1355555544212234578
Q ss_pred CHHHHHHHhhCCcc
Q psy17350 481 KLKMLTSHFLGLDI 494 (528)
Q Consensus 481 sLk~La~~~Lg~~I 494 (528)
+|...+..+|+..-
T Consensus 296 sl~~v~~~~l~~~k 309 (792)
T COG0417 296 SLEAVSEALLGEGK 309 (792)
T ss_pred cHHHHHHHhccccc
Confidence 99999998877664
No 158
>PRK10829 ribonuclease D; Provisional
Probab=76.09 E-value=5.7 Score=42.87 Aligned_cols=134 Identities=10% Similarity=0.067 Sum_probs=80.0
Q ss_pred HHHHHHHhcCCcEEEeccCCcC--cc----cccCCcEeecccccCCCCCCCCCccHHHHHHHHhCccccCCCC----CCC
Q psy17350 29 KRLENKKRKMDALVEIKTLNEA--DK----QMMHPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDG----GHC 98 (528)
Q Consensus 29 ~~l~~l~~~~~~IlvGH~l~~D--aL----~l~Hp~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ~~~~----gHd 98 (528)
..|..++.+.+.+-|+|+...| .| ++.-..+.||.+...+-+ .+.+.||+.|++.+||.++-.+.. +.-
T Consensus 64 ~~L~~ll~~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg-~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~R 142 (373)
T PRK10829 64 SPFKALLRDPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCG-RPLSCGFASMVEEYTGVTLDKSESRTDWLAR 142 (373)
T ss_pred HHHHHHHcCCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcC-CCccccHHHHHHHHhCCccCcccccCCCCCC
Confidence 4688888886666699999999 44 232236899988665433 234679999999999999876521 111
Q ss_pred c---------HHHHHHHHHHHHHHHHcCCCCCCCCCCcccccchhhhhhhhhcccC--CCCcc-ccccccccCCCcceeE
Q psy17350 99 S---------KEDAIAALRLVKLKLSKGDLCSTKPAHHTVNLGFSLNDYLMFAHEL--PGLRD-RFVKMEVIPPSSYTTS 166 (528)
Q Consensus 99 S---------vEDA~Aam~L~~~k~~~g~~~~~~~~~~~~~~~~~l~~ya~lGk~~--p~~p~-rWc~lek~~~ls~tvv 166 (528)
+ ..|+...++||..-..+-.. ...+.|-..+...+-... +..|. .|-.+.....++.---
T Consensus 143 PLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~--------~g~~~w~~ee~~~l~~~~~~~~~~~~~~~~ik~~~~L~~~~l 214 (373)
T PRK10829 143 PLSERQCEYAAADVFYLLPIAAKLMAETEA--------AGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQL 214 (373)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH--------cCcHHHHHHHHHHHHhccccCCChHHHHHHhccccCCCHHHH
Confidence 1 56777777777654332111 123447777776654432 22233 5777654444443333
Q ss_pred EEecc
Q psy17350 167 LVHEL 171 (528)
Q Consensus 167 lvleg 171 (528)
-|++.
T Consensus 215 avl~~ 219 (373)
T PRK10829 215 ACLQL 219 (373)
T ss_pred HHHHH
Confidence 34443
No 159
>KOG0304|consensus
Probab=69.10 E-value=15 Score=37.03 Aligned_cols=105 Identities=19% Similarity=0.163 Sum_probs=70.9
Q ss_pred eecCCChhhhcccCCCHHHHHHH---HHhcCCCCcEEEEcCchhhHHHHc--------------------ccCCCEeeeh
Q psy17350 411 AYSGITRALLAPVATRLEHVQKI---LSELLPPDAILVGQSLNCDLHALK--------------------MMHPYVIDTS 467 (528)
Q Consensus 411 ~isGIT~e~L~~a~p~l~dV~~~---L~~~i~~d~ILVGHnL~fDL~~L~--------------------~~hp~vIDTs 467 (528)
+-+||.-+..+..+....+-.+. ..-.++.+-..|-..-.+|+..|= ...|.+.|+-
T Consensus 109 r~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK 188 (239)
T KOG0304|consen 109 RRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVK 188 (239)
T ss_pred HHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHH
Confidence 66888877777655554433333 333455566677777788887661 1225677887
Q ss_pred hhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHHHHHHHHHHH
Q psy17350 468 VIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKL 518 (528)
Q Consensus 468 ~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~AT~eL~~~~L 518 (528)
.++..-.+...+.+|..||.. |+++-. | ..|.|-.|+.-|+..|.+..
T Consensus 189 ~l~~~c~~~~l~~GL~~lA~~-L~~~Rv-G-~~HqAGSDSlLT~~~F~kl~ 236 (239)
T KOG0304|consen 189 YLMKFCEGLSLKGGLQRLADL-LGLKRV-G-IAHQAGSDSLLTARVFFKLK 236 (239)
T ss_pred HHHHhhhhhhhhcCHHHHHHH-hCCCee-e-cccccCcHHHHHHHHHHHHH
Confidence 776543333457899999986 677753 2 47999999999999997543
No 160
>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=64.55 E-value=12 Score=40.06 Aligned_cols=63 Identities=16% Similarity=0.143 Sum_probs=44.6
Q ss_pred HHHHHHHhcCCcEEEeccCCcC--ccc---ccCC-cEeecccccCCCCCCCCCccHHHHHHHHhCccccC
Q psy17350 29 KRLENKKRKMDALVEIKTLNEA--DKQ---MMHP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQN 92 (528)
Q Consensus 29 ~~l~~l~~~~~~IlvGH~l~~D--aL~---l~Hp-~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ~ 92 (528)
..+.+++.+.+.+.|||+...| +|+ ...| .+.||.+...+-+ +..+.+|+.|++.+||.++-.
T Consensus 60 ~~L~~lL~d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~-~~~~~~l~~Lv~~~Lg~~l~K 128 (367)
T TIGR01388 60 SPLKELLRDESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCG-FGMSMGYAKLVQEVLGVELDK 128 (367)
T ss_pred HHHHHHHCCCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhC-CCCCccHHHHHHHHcCCCCCc
Confidence 4677788766666899999999 543 3344 5799987543321 223469999999999998764
No 161
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=61.13 E-value=11 Score=40.94 Aligned_cols=109 Identities=14% Similarity=0.088 Sum_probs=66.3
Q ss_pred cceeeccCCCCCCchhhhhhHHHHHHHHHHHHhcCCcEEEecc-CCcC--ccc-ccCCcEeecccc--------------
Q psy17350 4 SLEVLGLNPGGVLLNAYFKMNARQIKRLENKKRKMDALVEIKT-LNEA--DKQ-MMHPYVIDTSVI-------------- 65 (528)
Q Consensus 4 ~~~vSGI~p~~~~~~a~~~~~~~v~~~l~~l~~~~~~IlvGH~-l~~D--aL~-l~Hp~i~DTa~~-------------- 65 (528)
+.=++||+|++-..++..+. +--+++...+..+.++++|=- +..| +-| +.....+|---+
T Consensus 63 a~LITGITPQ~~~~~G~~E~--~F~~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~ 140 (475)
T COG2925 63 AVLITGITPQEAREKGINEA--AFAARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDV 140 (475)
T ss_pred ceeeecCCHHHHHhcCCChH--HHHHHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHH
Confidence 45589999997666666543 245677777777889999965 5555 443 222223332111
Q ss_pred -------cCCCCCC----CCCcc--HHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcCC
Q psy17350 66 -------FNTTGIR----THKPK--LKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKGD 118 (528)
Q Consensus 66 -------~~~~~~~----~~~~S--Lk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g~ 118 (528)
-|-.-.. -..+| |-.|++. --|+.+ ..||-.-|.+|+.++.|+..+..|
T Consensus 141 ~RacyALRPeGI~Wp~n~dG~pSFkLEhLt~A---NgieH~-nAHdAmsDVyATIamAklvk~~QP 202 (475)
T COG2925 141 VRACYALRPEGINWPENDDGLPSFKLEHLTKA---NGIEHS-NAHDAMSDVYATIAMAKLVKTAQP 202 (475)
T ss_pred HHHHHhcCcccCCCCcCCCCCcchhhHHHhhc---cccccc-hhhHHHHHHHHHHHHHHHHHhhCc
Confidence 1110001 13455 4456665 344443 489999999999999999877643
No 162
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=61.06 E-value=14 Score=33.48 Aligned_cols=60 Identities=23% Similarity=0.220 Sum_probs=39.7
Q ss_pred HHhcCC-CCcEEEEcCchhhHHHHccc----CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCc
Q psy17350 434 LSELLP-PDAILVGQSLNCDLHALKMM----HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLD 493 (528)
Q Consensus 434 L~~~i~-~d~ILVGHnL~fDL~~L~~~----hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~ 493 (528)
|.+++. .+...|||++.+++.+|+.. ...+.||....-...+.....+|+.|+++||+..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 344454 23458999999999999532 1235798876443332222149999999998887
No 163
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=53.98 E-value=47 Score=37.43 Aligned_cols=128 Identities=13% Similarity=0.081 Sum_probs=73.2
Q ss_pred CCCeEEEeeceecCCC-----CcCcEEEEEEEEeC-Cc---EEEEEE--EcCCCCCCCCceeecCCChhhhccc----CC
Q psy17350 361 TSPLYGLDCEMCKTSN-----DQNELTRVTLVDEQ-EN---VVYESL--VKPYNPITNYLTAYSGITRALLAPV----AT 425 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~-----g~~eLirIs~Vd~~-G~---vi~d~L--VkP~~~I~dy~T~isGIT~e~L~~a----~p 425 (528)
.-++..||+|.+...- ...+|..|+..|.. +. .+|+.+ +.+ |....+=...+.+.++ =.
T Consensus 105 ~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~v~v~~f~ 178 (498)
T PHA02524 105 DVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLVKDVGH------WDPKKSVLEKYILDNVVYMPFE 178 (498)
T ss_pred hceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEeccccccC------CCcccccccccccCCeEEEEeC
Confidence 3578999999976421 13578889888752 22 345544 221 1111111111112221 14
Q ss_pred CHHHHHHHHHhcCCC--CcEEEEcCc-hhhHHHH--------ccc-----------CC-----------------C-Eee
Q psy17350 426 RLEHVQKILSELLPP--DAILVGQSL-NCDLHAL--------KMM-----------HP-----------------Y-VID 465 (528)
Q Consensus 426 ~l~dV~~~L~~~i~~--d~ILVGHnL-~fDL~~L--------~~~-----------hp-----------------~-vID 465 (528)
+-.+++.++.+++.. -.||+|||+ +||+..| +.. .. + ++|
T Consensus 179 sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iD 258 (498)
T PHA02524 179 DEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMD 258 (498)
T ss_pred CHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeE
Confidence 567788888888762 389999997 7899655 110 00 0 245
Q ss_pred ehhhchhc-CCCCCCCCHHHHHHHhhCCcc
Q psy17350 466 TSVIFNTT-GIRTHKPKLKMLTSHFLGLDI 494 (528)
Q Consensus 466 Ts~L~~~~-~~~~~k~sLk~La~~~Lg~~I 494 (528)
...+++.. ......|+|++++..+||..-
T Consensus 259 l~~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K 288 (498)
T PHA02524 259 YMDVFKKFSFTPMPDYKLGNVGYREVKADK 288 (498)
T ss_pred HHHHHHHhhhccCCCCCHHHHHHHhcCCcc
Confidence 55555432 123457999999998887653
No 164
>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=52.41 E-value=14 Score=35.78 Aligned_cols=63 Identities=19% Similarity=0.098 Sum_probs=43.2
Q ss_pred HHHHHHHHhcCCcEEEeccCCcC--ccc----ccCCcEeecccccCC----CCC---CCCCccHHHHHHHHhCccc
Q psy17350 28 IKRLENKKRKMDALVEIKTLNEA--DKQ----MMHPYVIDTSVIFNT----TGI---RTHKPKLKMLTSHFLGLDI 90 (528)
Q Consensus 28 ~~~l~~l~~~~~~IlvGH~l~~D--aL~----l~Hp~i~DTa~~~~~----~~~---~~~~~SLk~La~~~L~~~I 90 (528)
...+.+++...+.+-|||+...| +|. +.-..+.||...... ..+ ..+..||+.|++.+||..+
T Consensus 54 ~~~L~~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~ 129 (197)
T cd06148 54 INGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISI 129 (197)
T ss_pred HHHHHHHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCCh
Confidence 45677888876666799999999 552 211247899876332 111 1234699999999999887
No 165
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=50.38 E-value=60 Score=33.56 Aligned_cols=113 Identities=16% Similarity=0.079 Sum_probs=62.9
Q ss_pred CCCeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCC-HHHHHHHHHhcCC
Q psy17350 361 TSPLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATR-LEHVQKILSELLP 439 (528)
Q Consensus 361 ~~~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~-l~dV~~~L~~~i~ 439 (528)
..+++-+|+||||++...+-|+-++.-...+.++ +||-. +..+ |. -..|.+.+....+
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~---~Vrq~-----------------~lp~-p~~E~avle~fl~~~~ 155 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVDDTM---HVRQH-----------------FLPA-PEEEVAVLENFLHDPD 155 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccCceE---EEEee-----------------cCCC-cchhhHHHHHHhcCCC
Confidence 3578999999999997434444444434332222 12211 1111 11 2236677777775
Q ss_pred CCcEEEEcC-chhhHHHHc-ccC---CC-----EeeehhhchhcC-CCCCCCCHHHHHHHhhCCcccC
Q psy17350 440 PDAILVGQS-LNCDLHALK-MMH---PY-----VIDTSVIFNTTG-IRTHKPKLKMLTSHFLGLDIQN 496 (528)
Q Consensus 440 ~d~ILVGHn-L~fDL~~L~-~~h---p~-----vIDTs~L~~~~~-~~~~k~sLk~La~~~Lg~~Iq~ 496 (528)
..+||-.| ..||.-+++ +.+ +. -+|.....+... .....-+|+.+=+ +||+.-..
T Consensus 156 -~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr-~LGi~R~e 221 (278)
T COG3359 156 -FNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVER-ILGIRREE 221 (278)
T ss_pred -cceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHH-HhCccccc
Confidence 88999987 589999887 221 11 244333222111 1123458999755 88887543
No 166
>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=49.91 E-value=1.3e+02 Score=33.22 Aligned_cols=54 Identities=19% Similarity=0.293 Sum_probs=35.6
Q ss_pred CCcEEEEcCchhhHHHHccc---CC-----------CEeeehhhch-hcCCCCCCCCHHHHHHHhhCCccc
Q psy17350 440 PDAILVGQSLNCDLHALKMM---HP-----------YVIDTSVIFN-TTGIRTHKPKLKMLTSHFLGLDIQ 495 (528)
Q Consensus 440 ~d~ILVGHnL~fDL~~L~~~---hp-----------~vIDTs~L~~-~~~~~~~k~sLk~La~~~Lg~~Iq 495 (528)
++..|+-+| .+...+|+.. |+ ++||.-.+.+ ....+..+||||.++. ++|.+..
T Consensus 343 ~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~-~lg~~~~ 411 (457)
T TIGR03491 343 PDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIAR-WLGFEWR 411 (457)
T ss_pred CCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHH-HhCcccC
Confidence 377899999 8888777532 21 3577654432 2223446799999987 5788765
No 167
>PRK05755 DNA polymerase I; Provisional
Probab=49.64 E-value=20 Score=42.71 Aligned_cols=89 Identities=17% Similarity=0.112 Sum_probs=60.1
Q ss_pred HHHHHHHHHhcCCcEEEeccCCcC--ccc---ccC-CcEeecccccCCCCCCCCCccHHHHHHHHhCccc---c---CC-
Q psy17350 27 QIKRLENKKRKMDALVEIKTLNEA--DKQ---MMH-PYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI---Q---NQ- 93 (528)
Q Consensus 27 v~~~l~~l~~~~~~IlvGH~l~~D--aL~---l~H-p~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~I---Q---~~- 93 (528)
+...+.+++.....++|+|....| +|. +.- ..+.||-....+-.. ....+|+.|++.++|.++ . ..
T Consensus 358 ~l~~l~~~L~d~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~-~~~~~L~~L~~~ylg~~~~~~~~~~gk~ 436 (880)
T PRK05755 358 VLAALKPLLEDPAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDP-GRRHGLDSLAERYLGHKTISFEEVAGKQ 436 (880)
T ss_pred HHHHHHHHHhCCCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCC-CCCCCHHHHHHHHhCCCccchHHhcCCC
Confidence 556778888876667899999999 544 221 247899776544221 113899999999998773 1 00
Q ss_pred -C--------CCCCcHHHHHHHHHHHHHHHHc
Q psy17350 94 -D--------GGHCSKEDAIAALRLVKLKLSK 116 (528)
Q Consensus 94 -~--------~gHdSvEDA~Aam~L~~~k~~~ 116 (528)
. ..|-..+||.++.+||....++
T Consensus 437 ~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 437 LTFAQVDLEEAAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred CCccccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0 1255678999999999776543
No 168
>KOG0970|consensus
Probab=48.40 E-value=44 Score=40.95 Aligned_cols=91 Identities=13% Similarity=0.168 Sum_probs=53.9
Q ss_pred CCCCCeEEEeeceecCCCC-cCcEEEEEEEEeCCc--------E----EEEEEEcCCCCCCCC------ceeecCCChhh
Q psy17350 359 TPTSPLYGLDCEMCKTSND-QNELTRVTLVDEQEN--------V----VYESLVKPYNPITNY------LTAYSGITRAL 419 (528)
Q Consensus 359 ~~~~~~vALDcEmtgt~~g-~~eLirIs~Vd~~G~--------v----i~d~LVkP~~~I~dy------~T~isGIT~e~ 419 (528)
++.-.+.+|-++|..-... ..||+.|++.-+... . -+..+++|..-+-++ ..+.+++.-.
T Consensus 526 ~Ppl~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~v~~~- 604 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSKVVLH- 604 (1429)
T ss_pred CCCeeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHhccCceEEe-
Confidence 3455678888888765543 479999987643211 1 266788988755444 1122221111
Q ss_pred hcccCCCHHHHHHHHHhc---CCCCcEEEEcC-chhhHHHH
Q psy17350 420 LAPVATRLEHVQKILSEL---LPPDAILVGQS-LNCDLHAL 456 (528)
Q Consensus 420 L~~a~p~l~dV~~~L~~~---i~~d~ILVGHn-L~fDL~~L 456 (528)
-+-...+..|... ++ -+++|||| .+++|.+|
T Consensus 605 -----~sErALLs~fla~~~~~d-pD~iVgHn~~~~~l~VL 639 (1429)
T KOG0970|consen 605 -----NSERALLSHFLAMLNKED-PDVIVGHNIQGFYLDVL 639 (1429)
T ss_pred -----cCHHHHHHHHHHHhhccC-CCEEEEeccccchHHHH
Confidence 1223344444443 34 57999999 68999888
No 169
>KOG1798|consensus
Probab=42.75 E-value=2.5e+02 Score=36.03 Aligned_cols=149 Identities=17% Similarity=0.193 Sum_probs=84.2
Q ss_pred CCCCeEEEeeceecCC-----CCcCcEEEEE-EEEeCCcEEEEE-EEc---------CCCCCCCCceeecCCChhhhccc
Q psy17350 360 PTSPLYGLDCEMCKTS-----NDQNELTRVT-LVDEQENVVYES-LVK---------PYNPITNYLTAYSGITRALLAPV 423 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~-----~g~~eLirIs-~Vd~~G~vi~d~-LVk---------P~~~I~dy~T~isGIT~e~L~~a 423 (528)
+...++|+|+|||.+- ...++|.-|+ .||..|..|.+. .|- |.....-+-+-+ |
T Consensus 244 adp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs~DIedfEYTPKpE~eG~F~v~---------N- 313 (2173)
T KOG1798|consen 244 ADPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVSEDIEDFEYTPKPEYEGPFCVF---------N- 313 (2173)
T ss_pred CCceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhccchhhcccCCccccccceEEe---------c-
Confidence 3457899999999874 2346787787 556677666543 221 211111111111 1
Q ss_pred CCCHHHHHHHHHhcCC--CCcEEEEcCch-hhHHHHcc---cCC--------CEeeeh-----------hhchhc----C
Q psy17350 424 ATRLEHVQKILSELLP--PDAILVGQSLN-CDLHALKM---MHP--------YVIDTS-----------VIFNTT----G 474 (528)
Q Consensus 424 ~p~l~dV~~~L~~~i~--~d~ILVGHnL~-fDL~~L~~---~hp--------~vIDTs-----------~L~~~~----~ 474 (528)
.+.-..+.+++.+.+. +-+|+|-+|-+ ||+-|+.. .|. ...|.. ..|+.. .
T Consensus 314 e~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSY 393 (2173)
T KOG1798|consen 314 EPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSY 393 (2173)
T ss_pred CCcHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhccc
Confidence 1223334444433221 25899999865 59988842 221 123321 123321 1
Q ss_pred CCCCCCCHHHHHHHhhCCccc-CC-------------CCCCChHHHHHHHHHHHHHHH
Q psy17350 475 IRTHKPKLKMLTSHFLGLDIQ-NQ-------------DGGHCSKEDAIAALRLVKLKL 518 (528)
Q Consensus 475 ~~~~k~sLk~La~~~Lg~~Iq-~~-------------~~~HdAlEDA~AT~eL~~~~L 518 (528)
.|....+||.+++.-||.+-- .+ .-+--|+.||.||..||.++.
T Consensus 394 LPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYV 451 (2173)
T KOG1798|consen 394 LPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYV 451 (2173)
T ss_pred CCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHh
Confidence 344567899999988987621 11 124567899999999998654
No 170
>KOG2613|consensus
Probab=41.18 E-value=94 Score=34.32 Aligned_cols=126 Identities=17% Similarity=0.251 Sum_probs=74.3
Q ss_pred CCCCeEEEeeceecCCCC---cCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhhhcccCCCHHHHHHHHHh
Q psy17350 360 PTSPLYGLDCEMCKTSND---QNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRALLAPVATRLEHVQKILSE 436 (528)
Q Consensus 360 ~~~~~vALDcEmtgt~~g---~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~ 436 (528)
+-..|+++|+|-+|-..| ...+.-|.+++.. =-|+.. .+..++..|..
T Consensus 311 qL~ef~V~dv~~v~~~~~~g~kh~l~dv~v~r~s---------------------d~g~nd--------~~~~~RtHLGh 361 (502)
T KOG2613|consen 311 QLTEFIVLDVDPVGEAGGKGQKHALADVWVARSS---------------------DLGMND--------KFHYARTHLGH 361 (502)
T ss_pred hheEEEEEEEecccccCCccceeeeeeEEEEEcC---------------------ccCccc--------ceeeehhhccc
Confidence 345799999998877665 2245555554421 013332 23345667777
Q ss_pred cCCCCcEEEEcCchh----h--HHHHccc-CCCEeeehhhchhcCCCCCCCCHHHHHHHhhCCcccCCCCCCChHHHHHH
Q psy17350 437 LLPPDAILVGQSLNC----D--LHALKMM-HPYVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIA 509 (528)
Q Consensus 437 ~i~~d~ILVGHnL~f----D--L~~L~~~-hp~vIDTs~L~~~~~~~~~k~sLk~La~~~Lg~~Iq~~~~~HdAlEDA~A 509 (528)
++.++.-+.|+++.+ | +..|+.. -|.+|=.-.+|.+.....+.|+||.|+.+. +++ -+..+++.-
T Consensus 362 il~~gD~vlgydl~~~N~N~~~~d~~~~d~vPdvvlVkK~y~r~~r~~r~WKlK~l~~e~---~~~-----~~~~~~~~~ 433 (502)
T KOG2613|consen 362 ILKPGDLVLGYDLANANLNDEEFDKLNIDGVPDVVLVKKMYDRTKRKSRNWKLKRLAMEM---SRG-----KNESERTEK 433 (502)
T ss_pred cCCCCCeeeeeeeccCccchhhhhhhcccCCCcEEEEEccccccchhccceehhhhhhhh---ccc-----cccchhhHH
Confidence 888888888886532 2 2333332 255666666676544445789999998764 332 233444445
Q ss_pred HHHHHHHHHHcCC
Q psy17350 510 ALRLVKLKLSKGD 522 (528)
Q Consensus 510 T~eL~~~~L~~g~ 522 (528)
-.++|..-+++.+
T Consensus 434 eY~~FledlEEd~ 446 (502)
T KOG2613|consen 434 EYELFLEDLEEDP 446 (502)
T ss_pred HHHHHHHhhhcCH
Confidence 5666666666654
No 171
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=38.87 E-value=32 Score=33.72 Aligned_cols=55 Identities=22% Similarity=0.213 Sum_probs=38.0
Q ss_pred eecccccCCCCCCCCCccHHHHHHHHhCccccCCCCCCCcHHHHHHHHHHHHHHHHcC
Q psy17350 60 IDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDGGHCSKEDAIAALRLVKLKLSKG 117 (528)
Q Consensus 60 ~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ~~~~gHdSvEDA~Aam~L~~~k~~~g 117 (528)
+|-+..|..-.+.|+-.+|..-.+.+ |.+-|.. .|--+||||.+-+|+++..+..
T Consensus 131 vdl~~~yk~v~~~pr~tgln~ale~~-G~sf~G~--~HraldDArn~~rl~klv~~~~ 185 (210)
T COG5018 131 VDLSLEYKNVFGDPRLTGLNKALEEY-GDSFTGT--HHRALDDARNAYRLFKLVEQDK 185 (210)
T ss_pred chHHHHHHHHhcCCccccHHHHHHHh-ccccCCc--hhhhHHHHHHHHHHHHHHcchh
Confidence 66655554433445556776655543 6666654 8999999999999999988643
No 172
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=38.26 E-value=30 Score=38.26 Aligned_cols=138 Identities=17% Similarity=0.216 Sum_probs=73.7
Q ss_pred CeEEEeeceecCCCCcCcEEEEEEEEeCCcEEEEEEEcCCC--CCCCCceeecCCChhhhcccCCCHHHHHHHHHhcCCC
Q psy17350 363 PLYGLDCEMCKTSNDQNELTRVTLVDEQENVVYESLVKPYN--PITNYLTAYSGITRALLAPVATRLEHVQKILSELLPP 440 (528)
Q Consensus 363 ~~vALDcEmtgt~~g~~eLirIs~Vd~~G~vi~d~LVkP~~--~I~dy~T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~ 440 (528)
.-..||+|-.-. ..+++++.-.+...-++-|=+|.. .+.+-.-.-|||--.||.+|.|. +...+...+++
T Consensus 373 ~ttWiDIEG~p~-----DPVElAiyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aqPG---L~S~vi~~LP~ 444 (533)
T PF00843_consen 373 ATTWIDIEGPPN-----DPVELAIYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQPG---LTSAVIELLPK 444 (533)
T ss_dssp S-EEEEEESETT-----SESEEEEEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB-TT---HHHHHHHHS-T
T ss_pred CCeeEecCCCCC-----CCeEEEEeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhccc---hHHHHHHhCCc
Confidence 447899996643 456788887644445566767765 22333345599999999998775 45667788888
Q ss_pred CcEEEEcCchhhHHHHcccCC----CEeeehhhchhcCC--CCCCCCHHHHHHHhhCCcccCC--------CCCCChHHH
Q psy17350 441 DAILVGQSLNCDLHALKMMHP----YVIDTSVIFNTTGI--RTHKPKLKMLTSHFLGLDIQNQ--------DGGHCSKED 506 (528)
Q Consensus 441 d~ILVGHnL~fDL~~L~~~hp----~vIDTs~L~~~~~~--~~~k~sLk~La~~~Lg~~Iq~~--------~~~HdAlED 506 (528)
+-||-.++.+ |++-|=-.|. .+||...-....+. ..-.-+.+.||+.+-|+-+... ...|+|+-|
T Consensus 445 ~MVlT~QGsD-DIrkLld~hGRrDiKlvDV~lt~eqaR~FEd~VWd~f~~LC~~H~GvVv~KKKkg~~~~~t~PHCALlD 523 (533)
T PF00843_consen 445 NMVLTCQGSD-DIRKLLDMHGRRDIKLVDVKLTSEQARKFEDQVWDRFGHLCKKHTGVVVKKKKKGKKPESTNPHCALLD 523 (533)
T ss_dssp T-EEEESSHH-HHHHHHHCTT-TTSEEEE----HHHHTTTHHHHHHHHGGG---B-S-EEE--SSSS-EEE-----HHHH
T ss_pred CcEEEeeChH-HHHHHHHhcCCCcceEEEeecCHHHHHHHHHHHHHHHHHHHHhcCceEEecccCCCCCCCCCchHHHHH
Confidence 8888889866 7766645565 38997553222110 0012256788998888877642 138999999
Q ss_pred HHH
Q psy17350 507 AIA 509 (528)
Q Consensus 507 A~A 509 (528)
|++
T Consensus 524 CiM 526 (533)
T PF00843_consen 524 CIM 526 (533)
T ss_dssp HHH
T ss_pred HHH
Confidence 986
No 173
>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=35.71 E-value=21 Score=31.77 Aligned_cols=61 Identities=15% Similarity=0.033 Sum_probs=40.5
Q ss_pred HHHHHHhcCCcEEEeccCCcC--ccc---ccCC-cEeecccccCCCCCCCCCccHHHHHHHHhCccc
Q psy17350 30 RLENKKRKMDALVEIKTLNEA--DKQ---MMHP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI 90 (528)
Q Consensus 30 ~l~~l~~~~~~IlvGH~l~~D--aL~---l~Hp-~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~I 90 (528)
.+.+++...+...|||.+..| .|+ +.-+ .+.||......-.....+.+|+.|++++|+.++
T Consensus 44 ~l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~~ 110 (150)
T cd09018 44 LLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKL 110 (150)
T ss_pred HHHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCCc
Confidence 467777765677899999888 442 2223 358888775432211103499999999999883
No 174
>KOG3657|consensus
Probab=29.76 E-value=33 Score=40.75 Aligned_cols=31 Identities=16% Similarity=0.285 Sum_probs=23.9
Q ss_pred CCCcEEEEcCchhhHHHHcccC------CCEeeehhh
Q psy17350 439 PPDAILVGQSLNCDLHALKMMH------PYVIDTSVI 469 (528)
Q Consensus 439 ~~d~ILVGHnL~fDL~~L~~~h------p~vIDTs~L 469 (528)
..+.++||||+.||-.-++-.. .+.+||+.|
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSl 275 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSL 275 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeechhh
Confidence 4589999999999998776321 257899776
No 175
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=25.42 E-value=86 Score=31.11 Aligned_cols=65 Identities=12% Similarity=0.157 Sum_probs=45.9
Q ss_pred CcCcEEEEEEEEe---CCcE-EEEEEEcCCCCCCCCc-------eeecCCChhhhcccCCCHHHHHHHHHhcCCCC
Q psy17350 377 DQNELTRVTLVDE---QENV-VYESLVKPYNPITNYL-------TAYSGITRALLAPVATRLEHVQKILSELLPPD 441 (528)
Q Consensus 377 g~~eLirIs~Vd~---~G~v-i~d~LVkP~~~I~dy~-------T~isGIT~e~L~~a~p~l~dV~~~L~~~i~~d 441 (528)
+..-.++|+++.+ +|.+ .|+++|+|.....-|. ..-|+|..+-.......+..++.+|.+||.+.
T Consensus 6 ~~y~PaEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~ 81 (213)
T PF13017_consen 6 DEYVPAEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPN 81 (213)
T ss_pred CcEEeEEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhc
Confidence 3456789999987 4532 4999999996543332 35577776644543457999999999999853
No 176
>PF11906 DUF3426: Protein of unknown function (DUF3426); InterPro: IPR021834 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Probab=23.89 E-value=2.8e+02 Score=25.31 Aligned_cols=61 Identities=11% Similarity=0.118 Sum_probs=45.2
Q ss_pred CCCCCeEEEeeceecCCCC--cCcEEEEEEEEeCCcEEEEEEEcCCCCCCCCceeecCCChhh
Q psy17350 359 TPTSPLYGLDCEMCKTSND--QNELTRVTLVDEQENVVYESLVKPYNPITNYLTAYSGITRAL 419 (528)
Q Consensus 359 ~~~~~~vALDcEmtgt~~g--~~eLirIs~Vd~~G~vi~d~LVkP~~~I~dy~T~isGIT~e~ 419 (528)
.+....+.++.+..+.... ..--+++++.|.+|++++...+.|.+.+..-...-.||-+..
T Consensus 64 ~~~~~~l~v~g~i~N~~~~~~~~P~l~l~L~D~~g~~l~~r~~~P~~yl~~~~~~~~~l~pg~ 126 (149)
T PF11906_consen 64 PDGPGVLVVSGTIRNRADFPQALPALELSLLDAQGQPLARRVFTPADYLPPGLAAQAGLPPGE 126 (149)
T ss_pred cCCCCEEEEEEEEEeCCCCcccCceEEEEEECCCCCEEEEEEEChHHhcccccccccccCCCC
Confidence 3567889999999888765 235689999999999999999999766655434455555443
No 177
>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=22.48 E-value=70 Score=29.65 Aligned_cols=63 Identities=13% Similarity=0.062 Sum_probs=41.3
Q ss_pred HHHHHHHHhcCCcEEEeccCCcC--ccc---ccCC-cEeecccccCCCCCCCCCccHHHHHHHHhCccc
Q psy17350 28 IKRLENKKRKMDALVEIKTLNEA--DKQ---MMHP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDI 90 (528)
Q Consensus 28 ~~~l~~l~~~~~~IlvGH~l~~D--aL~---l~Hp-~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~I 90 (528)
...+.+++...+...|||.+..| +|+ +.-+ .+-||.+.-..-.......+|+.|++++|+.++
T Consensus 45 ~~~l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 45 LAALKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred HHHHHHHHhCCCCceeccchhHHHHHHHHCCCcCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCC
Confidence 44577778766677899999888 442 2222 247887664432111112499999999999885
No 178
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=22.04 E-value=1.3e+02 Score=32.74 Aligned_cols=78 Identities=15% Similarity=0.129 Sum_probs=52.6
Q ss_pred HHHHHhcCCcEEEeccCCcC--ccc---ccCC-cEeecccccCCCCCCCCCccHHHHHHHHhCccccCCCC----CCCcH
Q psy17350 31 LENKKRKMDALVEIKTLNEA--DKQ---MMHP-YVIDTSVIFNTTGIRTHKPKLKMLTSHFLGLDIQNQDG----GHCSK 100 (528)
Q Consensus 31 l~~l~~~~~~IlvGH~l~~D--aL~---l~Hp-~i~DTa~~~~~~~~~~~~~SLk~La~~~L~~~IQ~~~~----gHdSv 100 (528)
+..++.....+=|=|+-..| ++. =.+| -+.||.+--.+-+. +.+.||+.|+++++|.+|-.+.. ++-+.
T Consensus 62 l~~Ll~d~~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~-~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPL 140 (361)
T COG0349 62 LVALLADPNVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGF-GTSHGLADLVEELLGVELDKSEQRSDWLARPL 140 (361)
T ss_pred HHHHhcCCceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCC-cccccHHHHHHHHhCCcccccccccccccCCC
Confidence 34445443334478998888 221 2344 58999887766544 33899999999999999987631 66666
Q ss_pred HHHH---HHHHH
Q psy17350 101 EDAI---AALRL 109 (528)
Q Consensus 101 EDA~---Aam~L 109 (528)
.+++ ||.+.
T Consensus 141 s~~Ql~YAa~DV 152 (361)
T COG0349 141 SEAQLEYAAADV 152 (361)
T ss_pred CHHHHHHHHHHH
Confidence 6665 66665
Done!