Query 017210
Match_columns 375
No_of_seqs 338 out of 1296
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 06:34:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017210hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2176 PolC DNA polymerase II 100.0 7.9E-49 1.7E-53 420.4 13.2 231 41-289 346-597 (1444)
2 TIGR01405 polC_Gram_pos DNA po 100.0 1.4E-38 3.1E-43 354.6 24.2 225 44-285 117-362 (1213)
3 KOG0542 Predicted exonuclease 100.0 5.8E-39 1.3E-43 299.3 14.3 195 92-286 51-250 (280)
4 PRK07748 sporulation inhibitor 100.0 8.7E-38 1.9E-42 289.7 19.1 174 97-279 4-181 (207)
5 PTZ00315 2'-phosphotransferase 100.0 1.1E-36 2.4E-41 315.7 25.0 196 91-288 50-265 (582)
6 PRK00448 polC DNA polymerase I 100.0 7.2E-36 1.6E-40 336.7 21.6 224 44-285 347-591 (1437)
7 PRK06722 exonuclease; Provisio 100.0 2.5E-35 5.5E-40 284.7 20.5 171 97-276 5-179 (281)
8 cd06133 ERI-1_3'hExo_like DEDD 100.0 1.1E-33 2.4E-38 252.4 20.2 172 99-275 1-176 (176)
9 TIGR01406 dnaQ_proteo DNA poly 100.0 2.4E-33 5.3E-38 263.6 21.4 168 98-279 1-173 (225)
10 PRK05711 DNA polymerase III su 100.0 2.7E-33 5.9E-38 265.6 20.8 173 97-283 4-181 (240)
11 cd06131 DNA_pol_III_epsilon_Ec 100.0 1.4E-32 2.9E-37 244.8 20.8 162 99-274 1-166 (167)
12 smart00479 EXOIII exonuclease 100.0 3.4E-32 7.3E-37 240.3 22.1 166 98-278 1-167 (169)
13 PRK06807 DNA polymerase III su 100.0 3.4E-32 7.5E-37 267.2 22.0 167 94-278 5-172 (313)
14 PRK06195 DNA polymerase III su 100.0 3.1E-32 6.8E-37 267.1 20.9 166 98-282 2-168 (309)
15 cd06130 DNA_pol_III_epsilon_li 100.0 8.8E-32 1.9E-36 235.9 19.6 154 99-272 1-155 (156)
16 PRK08517 DNA polymerase III su 100.0 8.1E-32 1.8E-36 257.9 20.9 165 97-279 68-232 (257)
17 PRK06063 DNA polymerase III su 100.0 1E-31 2.2E-36 263.9 20.2 169 97-283 15-184 (313)
18 PRK05168 ribonuclease T; Provi 100.0 2.2E-31 4.8E-36 247.9 20.4 189 86-281 7-204 (211)
19 PRK07942 DNA polymerase III su 100.0 2.6E-31 5.5E-36 250.9 20.2 173 97-279 6-181 (232)
20 PRK09146 DNA polymerase III su 100.0 4.7E-31 1E-35 250.2 21.3 165 97-279 47-228 (239)
21 PRK07740 hypothetical protein; 100.0 4.7E-31 1E-35 250.9 20.3 170 97-283 59-231 (244)
22 PRK06310 DNA polymerase III su 100.0 8.3E-31 1.8E-35 250.1 22.0 168 97-278 7-174 (250)
23 TIGR00573 dnaq exonuclease, DN 100.0 1.2E-30 2.7E-35 243.6 21.5 171 97-282 7-181 (217)
24 PRK07247 DNA polymerase III su 100.0 9.3E-31 2E-35 241.2 20.2 162 96-280 4-171 (195)
25 cd06134 RNaseT DEDDh 3'-5' exo 100.0 1.3E-30 2.9E-35 238.7 20.3 174 98-277 6-188 (189)
26 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 7.5E-31 1.6E-35 237.9 18.4 162 99-273 1-176 (177)
27 PRK09145 DNA polymerase III su 100.0 1.7E-30 3.6E-35 239.9 19.6 163 97-277 29-200 (202)
28 PRK06309 DNA polymerase III su 100.0 2.5E-30 5.5E-35 244.0 20.2 163 97-278 2-166 (232)
29 TIGR01298 RNaseT ribonuclease 100.0 3E-30 6.6E-35 238.4 19.6 178 97-280 8-194 (200)
30 COG5018 KapD Inhibitor of the 100.0 9.3E-32 2E-36 237.9 8.8 197 97-298 4-202 (210)
31 PRK07883 hypothetical protein; 100.0 5.9E-30 1.3E-34 268.6 21.8 170 97-283 15-187 (557)
32 PRK07246 bifunctional ATP-depe 100.0 3E-29 6.6E-34 273.4 21.0 165 97-280 7-172 (820)
33 cd06138 ExoI_N N-terminal DEDD 100.0 6.5E-29 1.4E-33 226.0 17.0 162 100-271 1-182 (183)
34 PRK05601 DNA polymerase III su 100.0 3.3E-28 7.1E-33 241.0 22.8 164 97-275 46-246 (377)
35 PRK08074 bifunctional ATP-depe 100.0 1.4E-28 3E-33 271.7 21.5 167 97-280 3-171 (928)
36 TIGR01407 dinG_rel DnaQ family 100.0 5.5E-28 1.2E-32 265.1 21.5 165 98-279 1-166 (850)
37 PRK07983 exodeoxyribonuclease 100.0 8.5E-28 1.8E-32 225.3 18.4 149 99-278 2-154 (219)
38 cd06127 DEDDh DEDDh 3'-5' exon 100.0 1.5E-27 3.2E-32 205.9 16.8 156 100-271 1-158 (159)
39 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 3.9E-28 8.4E-33 216.8 11.2 147 100-272 1-161 (161)
40 COG0847 DnaQ DNA polymerase II 99.9 1.2E-26 2.7E-31 218.6 19.5 166 97-277 13-181 (243)
41 cd06144 REX4_like DEDDh 3'-5' 99.9 7.9E-27 1.7E-31 206.4 13.3 149 100-272 1-152 (152)
42 cd06135 Orn DEDDh 3'-5' exonuc 99.9 3.6E-26 7.9E-31 206.5 15.4 162 99-276 1-170 (173)
43 cd06145 REX1_like DEDDh 3'-5' 99.9 2.4E-26 5.2E-31 203.2 13.5 143 100-271 1-149 (150)
44 cd06149 ISG20 DEDDh 3'-5' exon 99.9 3.1E-26 6.7E-31 204.1 12.7 149 100-272 1-157 (157)
45 PRK09182 DNA polymerase III su 99.9 2.5E-25 5.5E-30 216.9 18.2 172 96-289 36-212 (294)
46 PF00929 RNase_T: Exonuclease; 99.9 1.1E-26 2.4E-31 200.7 7.4 162 100-271 1-164 (164)
47 PRK05359 oligoribonuclease; Pr 99.9 8.2E-24 1.8E-28 192.9 16.8 163 97-278 3-175 (181)
48 PRK11779 sbcB exonuclease I; P 99.9 3.4E-23 7.4E-28 213.2 20.0 171 97-277 6-197 (476)
49 KOG2249 3'-5' exonuclease [Rep 99.4 7.9E-12 1.7E-16 118.6 12.7 158 97-278 105-266 (280)
50 cd05160 DEDDy_DNA_polB_exo DED 99.3 5.9E-11 1.3E-15 108.7 17.8 138 100-252 2-161 (199)
51 PF06839 zf-GRF: GRF zinc fing 99.3 4.1E-13 8.8E-18 95.7 2.4 44 327-373 1-44 (45)
52 cd06143 PAN2_exo DEDDh 3'-5' e 99.2 2.6E-10 5.7E-15 103.4 12.6 154 97-271 5-173 (174)
53 cd06125 DnaQ_like_exo DnaQ-lik 99.0 3.3E-09 7.1E-14 87.1 11.3 94 100-270 1-94 (96)
54 PHA02570 dexA exonuclease; Pro 99.0 3.9E-09 8.4E-14 98.6 11.3 157 99-272 3-193 (220)
55 COG2925 SbcB Exonuclease I [DN 98.9 1.9E-08 4.2E-13 100.0 12.5 165 97-274 9-197 (475)
56 COG1949 Orn Oligoribonuclease 98.7 9.8E-08 2.1E-12 85.1 9.5 153 96-269 5-169 (184)
57 cd05781 DNA_polB_B3_exo DEDDy 98.7 6.5E-07 1.4E-11 82.3 14.7 120 98-252 4-144 (188)
58 cd05780 DNA_polB_Kod1_like_exo 98.7 8.7E-07 1.9E-11 81.6 15.6 130 98-253 4-156 (195)
59 KOG2248 3'-5' exonuclease [Rep 98.6 1.3E-07 2.9E-12 95.3 9.7 157 97-282 216-379 (380)
60 KOG3242 Oligoribonuclease (3'- 98.6 2.9E-07 6.3E-12 82.9 9.9 160 97-273 26-194 (208)
61 cd05782 DNA_polB_like1_exo Unc 98.5 2.6E-06 5.7E-11 79.5 14.1 114 107-252 41-169 (208)
62 PF13482 RNase_H_2: RNase_H su 98.5 4.8E-07 1E-11 80.1 7.9 116 100-254 1-117 (164)
63 cd06139 DNA_polA_I_Ecoli_like_ 98.4 1E-05 2.2E-10 72.8 13.8 145 97-280 5-172 (193)
64 PF04857 CAF1: CAF1 family rib 98.3 2E-05 4.4E-10 75.9 14.6 172 97-273 22-262 (262)
65 KOG0304 mRNA deadenylase subun 98.3 8.1E-06 1.8E-10 76.1 10.7 172 98-276 25-237 (239)
66 cd05779 DNA_polB_epsilon_exo D 98.2 0.00014 3.1E-09 67.8 16.9 145 98-253 3-169 (204)
67 PRK05755 DNA polymerase I; Pro 98.1 2.3E-05 4.9E-10 87.5 13.5 136 97-278 315-469 (880)
68 cd05785 DNA_polB_like2_exo Unc 98.0 0.00025 5.4E-09 66.2 15.8 122 98-253 10-169 (207)
69 PF10108 DNA_pol_B_exo2: Predi 98.0 0.00025 5.5E-09 66.4 15.2 131 115-276 7-171 (209)
70 KOG1956 DNA topoisomerase III 97.9 4E-06 8.6E-11 88.1 2.6 42 325-371 717-758 (758)
71 cd05777 DNA_polB_delta_exo DED 97.9 0.0015 3.2E-08 61.7 18.2 136 98-251 8-181 (230)
72 KOG4793 Three prime repair exo 97.6 0.00023 5E-09 68.5 8.2 172 95-275 11-215 (318)
73 cd05783 DNA_polB_B1_exo DEDDy 97.6 0.0035 7.7E-08 58.4 15.9 136 98-251 6-169 (204)
74 COG3359 Predicted exonuclease 97.2 0.0045 9.8E-08 59.1 11.8 117 97-253 98-219 (278)
75 smart00486 POLBc DNA polymeras 97.1 0.038 8.2E-07 56.2 18.4 161 98-274 4-220 (471)
76 cd05784 DNA_polB_II_exo DEDDy 96.9 0.013 2.7E-07 54.3 11.5 121 98-249 4-149 (193)
77 PTZ00166 DNA polymerase delta 96.9 0.027 5.9E-07 64.3 16.4 162 98-275 265-483 (1054)
78 TIGR03491 RecB family nuclease 96.8 0.0095 2.1E-07 62.0 11.2 123 97-254 284-411 (457)
79 cd05778 DNA_polB_zeta_exo inac 96.8 0.1 2.2E-06 49.5 17.0 173 98-278 5-223 (231)
80 smart00481 POLIIIAc DNA polyme 96.8 0.00075 1.6E-08 51.2 2.0 37 45-81 13-64 (67)
81 PF01612 DNA_pol_A_exo1: 3'-5' 96.7 0.055 1.2E-06 47.4 14.0 91 174-277 65-174 (176)
82 PRK06920 dnaE DNA polymerase I 96.6 0.0011 2.4E-08 75.4 2.3 40 44-83 16-70 (1107)
83 PF03104 DNA_pol_B_exo1: DNA p 96.4 0.036 7.8E-07 53.9 11.6 131 97-245 157-325 (325)
84 PRK07279 dnaE DNA polymerase I 96.4 0.0017 3.6E-08 73.4 2.2 40 44-83 15-69 (1034)
85 PRK05762 DNA polymerase II; Re 96.3 0.16 3.6E-06 56.4 17.2 147 98-274 156-348 (786)
86 PHA02528 43 DNA polymerase; Pr 96.0 0.57 1.2E-05 52.8 19.7 219 37-273 54-323 (881)
87 PRK05898 dnaE DNA polymerase I 95.6 0.006 1.3E-07 68.5 2.2 40 44-83 15-69 (971)
88 KOG1798 DNA polymerase epsilon 95.1 0.37 8E-06 56.0 14.0 161 97-276 246-452 (2173)
89 COG0587 DnaE DNA polymerase II 95.0 0.012 2.6E-07 67.2 2.2 43 44-86 17-74 (1139)
90 PRK07135 dnaE DNA polymerase I 95.0 0.011 2.4E-07 66.6 2.0 39 44-82 16-69 (973)
91 PF13017 Maelstrom: piRNA path 94.8 0.19 4.2E-06 47.2 9.4 157 116-277 7-196 (213)
92 COG5228 POP2 mRNA deadenylase 94.8 0.03 6.6E-07 52.8 3.9 180 98-288 43-263 (299)
93 PRK09532 DNA polymerase III su 94.8 0.015 3.2E-07 65.2 2.0 40 45-84 17-71 (874)
94 COG0349 Rnd Ribonuclease D [Tr 94.7 0.55 1.2E-05 47.5 12.7 132 97-279 17-167 (361)
95 PHA02524 43A DNA polymerase su 94.4 0.9 2E-05 48.0 14.0 189 39-247 56-281 (498)
96 PRK05672 dnaE2 error-prone DNA 94.1 0.023 5.1E-07 64.8 1.8 40 44-83 18-72 (1046)
97 PRK07374 dnaE DNA polymerase I 94.1 0.025 5.4E-07 65.1 2.0 40 44-83 16-70 (1170)
98 cd05776 DNA_polB_alpha_exo ina 94.1 1 2.2E-05 42.6 12.7 148 98-251 4-185 (234)
99 cd06146 mut-7_like_exo DEDDy 3 93.6 1.3 2.8E-05 40.7 12.1 142 97-275 22-192 (193)
100 cd00007 35EXOc 3'-5' exonuclea 93.6 0.7 1.5E-05 39.1 9.7 66 172-249 40-106 (155)
101 PF02811 PHP: PHP domain; Int 93.6 0.029 6.2E-07 49.2 1.0 26 45-70 14-39 (175)
102 PRK05673 dnaE DNA polymerase I 93.3 0.039 8.5E-07 63.4 1.9 41 44-84 15-70 (1135)
103 cd06141 WRN_exo DEDDy 3'-5' ex 93.3 2.4 5.1E-05 37.5 12.9 132 97-275 18-169 (170)
104 TIGR00592 pol2 DNA polymerase 93.1 3.8 8.3E-05 47.8 17.4 143 99-249 506-678 (1172)
105 PHA03036 DNA polymerase; Provi 92.9 2.3 5.1E-05 48.4 14.8 181 96-285 159-399 (1004)
106 COG0417 PolB DNA polymerase el 92.8 2.2 4.7E-05 47.7 14.5 131 97-250 154-305 (792)
107 TIGR00594 polc DNA-directed DN 92.7 0.057 1.2E-06 61.6 2.0 39 45-83 15-68 (1022)
108 PRK05761 DNA polymerase I; Rev 92.3 1.3 2.8E-05 49.5 11.7 97 169-271 208-334 (787)
109 PRK06826 dnaE DNA polymerase I 91.6 0.09 2E-06 60.6 1.9 40 45-84 19-73 (1151)
110 KOG1275 PAB-dependent poly(A) 91.5 0.068 1.5E-06 59.1 0.6 117 140-276 965-1090(1118)
111 KOG4793 Three prime repair exo 90.4 0.24 5.2E-06 48.2 3.2 165 101-277 114-290 (318)
112 PRK06361 hypothetical protein; 89.8 0.21 4.6E-06 46.1 2.3 29 45-73 8-36 (212)
113 smart00474 35EXOc 3'-5' exonuc 88.4 5.6 0.00012 34.2 10.2 90 175-277 64-170 (172)
114 PRK09248 putative hydrolase; V 88.2 0.34 7.3E-06 46.0 2.5 27 45-71 17-43 (246)
115 cd06148 Egl_like_exo DEDDy 3'- 86.1 13 0.00028 34.1 11.7 93 177-281 56-180 (197)
116 cd06129 RNaseD_like DEDDy 3'-5 82.9 8.7 0.00019 33.9 8.7 87 177-275 58-160 (161)
117 PRK10829 ribonuclease D; Provi 82.5 9.1 0.0002 39.1 9.8 134 97-280 22-172 (373)
118 TIGR00593 pola DNA polymerase 81.9 3.3 7.1E-05 46.9 6.9 97 170-278 362-477 (887)
119 TIGR01388 rnd ribonuclease D. 78.0 18 0.00039 36.7 10.2 90 177-279 61-167 (367)
120 cd06142 RNaseD_exo DEDDy 3'-5' 77.6 18 0.0004 31.5 9.1 95 174-281 52-163 (178)
121 cd06140 DNA_polA_I_Bacillus_li 66.3 46 0.001 29.2 9.0 93 174-279 44-157 (178)
122 COG0749 PolA DNA polymerase I 64.1 57 0.0012 35.5 10.5 90 174-277 66-179 (593)
123 KOG0969 DNA polymerase delta, 63.0 5 0.00011 44.4 2.3 146 98-261 275-458 (1066)
124 cd09018 DEDDy_polA_RNaseD_like 53.6 1.3E+02 0.0029 25.1 9.3 63 178-252 45-109 (150)
125 PF01396 zf-C4_Topoisom: Topoi 49.2 14 0.0003 25.3 2.0 28 339-373 11-38 (39)
126 PF06373 CART: Cocaine and amp 48.7 5.5 0.00012 31.1 -0.1 37 323-369 33-69 (73)
127 COG0613 Predicted metal-depend 45.2 18 0.00039 34.9 2.8 29 46-74 16-44 (258)
128 PRK00912 ribonuclease P protei 44.9 15 0.00032 34.7 2.1 28 45-72 14-41 (237)
129 COG1387 HIS2 Histidinol phosph 38.5 21 0.00046 33.9 2.1 29 45-73 14-42 (237)
130 PRK08392 hypothetical protein; 36.6 25 0.00055 32.6 2.3 28 45-72 12-39 (215)
131 PRK07945 hypothetical protein; 36.5 25 0.00054 35.3 2.3 28 45-72 109-136 (335)
132 TIGR01856 hisJ_fam histidinol 36.3 32 0.0007 32.7 3.0 27 46-72 14-40 (253)
133 PRK07328 histidinol-phosphatas 35.6 26 0.00056 33.6 2.3 28 45-72 16-43 (269)
134 PF11074 DUF2779: Domain of un 34.0 1.6E+02 0.0036 25.4 6.8 57 168-233 54-117 (130)
135 cd06147 Rrp6p_like_exo DEDDy 3 29.6 2E+02 0.0044 25.7 7.0 88 177-277 68-171 (192)
136 PF05325 DUF730: Protein of un 29.1 38 0.00082 28.2 1.8 44 327-371 21-65 (122)
137 TIGR01685 MDP-1 magnesium-depe 27.8 2.1E+02 0.0045 26.0 6.6 12 98-109 3-14 (174)
138 PF12860 PAS_7: PAS fold 24.0 1.5E+02 0.0031 23.9 4.5 46 120-179 4-49 (115)
139 PF11079 YqhG: Bacterial prote 22.8 45 0.00098 32.5 1.4 71 100-185 124-195 (260)
140 PRK06319 DNA topoisomerase I/S 22.6 54 0.0012 37.2 2.2 36 327-372 697-732 (860)
141 PRK08123 histidinol-phosphatas 22.4 56 0.0012 31.4 2.0 25 48-72 20-44 (270)
142 TIGR01056 topB DNA topoisomera 22.2 54 0.0012 36.1 2.0 39 328-372 613-653 (660)
No 1
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.9e-49 Score=420.45 Aligned_cols=231 Identities=19% Similarity=0.180 Sum_probs=206.9
Q ss_pred cCCccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccccccccC-----CCCCCCCCcccEE
Q 017210 41 KDDTIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSWSTFY-----PDSQKPQEFQYFV 100 (375)
Q Consensus 41 ~~~~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~~~~~-----~~~~~~~~~~~fV 100 (375)
+.--++.++++||++|++|||+|||||||+ ++|+|||+|++++++-. +.+..+. ..+||
T Consensus 346 S~mDai~sv~~~vk~A~kwghkaIAITDh~~VqafP~~y~~akK~giK~IyG~EanlvdD~vpiv~N~~d~~l~-datyV 424 (1444)
T COG2176 346 SQMDAITSVEELVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKYGIKAIYGLEANLVDDGVPIVYNPDDQKLD-DATYV 424 (1444)
T ss_pred hhhcccCCHHHHHHHHHHcCCceEEEecCcchhhchHHHHhhhhcCceEEEeeeeeeccCCCceecCccccccc-cccEE
Confidence 344577999999999999999999999994 48899999999997763 3344444 36799
Q ss_pred EEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHHH
Q 017210 101 VIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDK 180 (375)
Q Consensus 101 VfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~~ 180 (375)
|||+||||+ ++..++|||||||++ ++|+++|+|+.||+|.. +||.++++|||||++||.+|+++++||++|.+
T Consensus 425 VfDiETTGL---s~~~d~iIE~aAvKi--kng~iId~f~~Fi~P~~--pl~~~~telTgITdeml~~a~~i~~vL~kf~~ 497 (1444)
T COG2176 425 VFDIETTGL---SPVYDEIIEIAAVKI--KNGRIIDKFQFFIKPGR--PLSATITELTGITDEMLENAPEIEEVLEKFRE 497 (1444)
T ss_pred EEEeecCCc---Ccccchhhhheeeee--eCCcchHHHHHhcCCCC--cCchhhhhccccCHHHHcCCccHHHHHHHHHH
Confidence 999999996 689999999999999 79999999999999996 59999999999999999999999999999999
Q ss_pred HHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc-CCCCCCHHHHHHHcCCCCCCCCCc
Q 017210 181 WLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVF-GGVRCNLKEAVEMAGLAWQGRAHC 259 (375)
Q Consensus 181 fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~-~~~~~~L~~l~~~lgI~~~g~~Hr 259 (375)
|+++++ .|+||++||+ +||+..++++|+.. +.+++|||+.++|.++ ..++|+|+.+|++|++.++ +|||
T Consensus 498 ~~~d~I------lVAHNasFD~-gFl~~~~~k~~~~~--~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v~le-~hHR 567 (1444)
T COG2176 498 FIGDSI------LVAHNASFDM-GFLNTNYEKYGLEP--LTNPVIDTLELARALNPEFKSHRLGTLCKKLGVELE-RHHR 567 (1444)
T ss_pred HhcCcE------EEeccCccch-hHHHHHHHHhCCcc--ccCchhhHHHHHHHhChhhhhcchHHHHHHhCccHH-Hhhh
Confidence 999975 5788899998 99999999998763 6789999999999998 4689999999999999996 8999
Q ss_pred HHHHHHHHHHHHHHHHHhcccccccccccc
Q 017210 260 GLDDAKNTARLLALLMHRGFKFSITNSLMW 289 (375)
Q Consensus 260 ALdDA~atA~L~~~ll~~~~~~~i~~~l~~ 289 (375)
|.+||++|++||..|+++..+.+|+++..-
T Consensus 568 A~yDaeat~~vf~~f~~~~ke~Gi~~l~el 597 (1444)
T COG2176 568 ADYDAEATAKVFFVFLKDLKEKGITNLSEL 597 (1444)
T ss_pred hhhhHHHHHHHHHHHHHHHHHhchhhHHHH
Confidence 999999999999999999988888876544
No 2
>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=100.00 E-value=1.4e-38 Score=354.61 Aligned_cols=225 Identities=21% Similarity=0.228 Sum_probs=195.5
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCcccccccccccc-----CCCCCCCCCcccEEEEE
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSWSTF-----YPDSQKPQEFQYFVVID 103 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~~~~-----~~~~~~~~~~~~fVVfD 103 (375)
-++.+++++|++|++|||++||||||+ ++|+|||+|++.+++. ++.+..+-...+|||||
T Consensus 117 Dg~~~~~elv~~A~~~Gl~aiAITDH~~~~~~~~~~~~~~~~~ikvI~GvE~~~~~d~~~~v~n~~~~~l~~~~~~VVfD 196 (1213)
T TIGR01405 117 DAITSVQEYVKQAKKWGHKAIAITDHGVVQAFPEAYKAAKKDGIKIIYGMEANLVDDRVPIVYNPDDQKLLDDATYVVFD 196 (1213)
T ss_pred ccCCCHHHHHHHHHHCCCCEEEEecCCCccCHHHHHHHHHhcCCEEEEEEEEEeecccchhhcCccccccccCCcEEEEE
Confidence 456778999999999999999999994 4889999999998664 22233331235799999
Q ss_pred EeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHHHHHh
Q 017210 104 FEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLE 183 (375)
Q Consensus 104 lETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~~fl~ 183 (375)
+||||+ ++..++|||||||+++ +|+++++|++||+|.. .|+++++++||||++||++++++++|+++|.+|++
T Consensus 197 iETTGL---~~~~d~IIEIGAVkv~--~g~iid~f~~~V~P~~--~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~fl~ 269 (1213)
T TIGR01405 197 IETTGL---SPQYDEIIEFGAVKVK--NGRIIDKFQFFIKPHE--PLSAFVTELTGITQDMLENAPEIEEVLEKFKEFFK 269 (1213)
T ss_pred eEecCC---CCCCCeEEEEEEEEEE--CCeEEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhC
Confidence 999997 5678999999999995 7899999999999985 59999999999999999999999999999999998
Q ss_pred hCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc-CCCCCCHHHHHHHcCCCCCCCCCcHHH
Q 017210 184 NKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVF-GGVRCNLKEAVEMAGLAWQGRAHCGLD 262 (375)
Q Consensus 184 ~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~-~~~~~~L~~l~~~lgI~~~g~~HrALd 262 (375)
+. ++|+||+.||+ .||+++++++|++. +.++++||+.+++.++ +.++++|+++++++|++.+ ++|||++
T Consensus 270 ~~------iLVaHNa~FD~-~fL~~~~~r~g~~~--~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~-~~HrAl~ 339 (1213)
T TIGR01405 270 DS------ILVAHNASFDI-GFLNTNFEKVGLEP--LENPVIDTLELARALNPEYKSHRLGNICKKLGVDLD-DHHRADY 339 (1213)
T ss_pred CC------eEEEEChHHHH-HHHHHHHHHcCCCc--cCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCC-CCcCHHH
Confidence 75 46788899996 99999999999853 4568999999999887 4578999999999999987 5899999
Q ss_pred HHHHHHHHHHHHHHhcccccccc
Q 017210 263 DAKNTARLLALLMHRGFKFSITN 285 (375)
Q Consensus 263 DA~atA~L~~~ll~~~~~~~i~~ 285 (375)
||.+|++||.+|+++..+.++..
T Consensus 340 DA~aTa~I~~~ll~~l~~~~i~~ 362 (1213)
T TIGR01405 340 DAEATAKVFKVMVEQLKEKGITN 362 (1213)
T ss_pred HHHHHHHHHHHHHHHHHHcCCcc
Confidence 99999999999998887666654
No 3
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=5.8e-39 Score=299.30 Aligned_cols=195 Identities=41% Similarity=0.779 Sum_probs=178.9
Q ss_pred CCCCcccEEEEEEeeCCCCCCC-CCCCcEEEEceEEEE-cCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCC
Q 017210 92 KPQEFQYFVVIDFEATCDKDKN-PYPQEIIEFPSVIVS-SVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV 169 (375)
Q Consensus 92 ~~~~~~~fVVfDlETTGl~g~~-~~~~eIIEIGAV~vd-~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap 169 (375)
..+.+++++++|||+||.++.. ...+||||+.||.++ ..++.|.++|+.||+|..+|.||++|++||||.|++|+.||
T Consensus 51 ~~q~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~ 130 (280)
T KOG0542|consen 51 LSQPFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAP 130 (280)
T ss_pred ccCccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCC
Confidence 3467899999999999998755 367999999999766 34566666999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHhhCCCC--CccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHH
Q 017210 170 TLSEALLRHDKWLENKGIK--NTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAV 246 (375)
Q Consensus 170 ~~~evl~~f~~fl~~~~lv--~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~ 246 (375)
+|.+|+.+|..||....+. +.++++|+||+|||..||..+|++.+|..|.++++|||+++.|+..+.. ...++..++
T Consensus 131 ~f~~vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mL 210 (280)
T KOG0542|consen 131 TFPQVLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGML 210 (280)
T ss_pred CHHHHHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHH
Confidence 9999999999999987654 3799999999999999999999999999999999999999999999876 688999999
Q ss_pred HHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhccccccccc
Q 017210 247 EMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNS 286 (375)
Q Consensus 247 ~~lgI~~~g~~HrALdDA~atA~L~~~ll~~~~~~~i~~~ 286 (375)
+++||+++|++|+++|||+++|+|..+|+++|.++.||++
T Consensus 211 e~~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~ 250 (280)
T KOG0542|consen 211 EHYGLQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINEL 250 (280)
T ss_pred HHhCCcccCCcccCchhHHHHHHHHHHHHhCCcEEEechh
Confidence 9999999999999999999999999999999999999954
No 4
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=100.00 E-value=8.7e-38 Score=289.69 Aligned_cols=174 Identities=30% Similarity=0.496 Sum_probs=152.5
Q ss_pred ccEEEEEEeeCCCCC-CCCC--CCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHH
Q 017210 97 QYFVVIDFEATCDKD-KNPY--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 173 (375)
Q Consensus 97 ~~fVVfDlETTGl~g-~~~~--~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~e 173 (375)
.+|||||+||||+++ .+|. .+||||||||+++ +|+++++|++||||...+.|+++++++||||++||++||+|++
T Consensus 4 ~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~--~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~e 81 (207)
T PRK07748 4 QQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVV--GCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEE 81 (207)
T ss_pred ceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEe--cCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHHH
Confidence 469999999999864 2332 5899999999996 6788999999999986556999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCC
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLA 252 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~~lgI~ 252 (375)
|+++|.+|+++. +.+++||++||+ .||+++|+++|++.| +.+.|+|+..+++.+++. ..++|++++++|||+
T Consensus 82 vl~~f~~~~~~~-----~~~iv~~~~fD~-~fL~~~~~~~~~~~~-~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~ 154 (207)
T PRK07748 82 LVEKLAEYDKRC-----KPTIVTWGNMDM-KVLKHNCEKAGVPFP-FKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKE 154 (207)
T ss_pred HHHHHHHHhCcC-----CeEEEEECHHHH-HHHHHHHHHcCCCCc-ccccceeHHHHHHHHhCcCCCCCHHHHHHHcCCC
Confidence 999999999873 246889999997 899999999999876 346899999888877754 468999999999999
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHhcc
Q 017210 253 WQGRAHCGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 253 ~~g~~HrALdDA~atA~L~~~ll~~~~ 279 (375)
..+++|||++||++||+||.+|++++.
T Consensus 155 ~~~~~H~Al~DA~~ta~l~~~l~~~~~ 181 (207)
T PRK07748 155 GTGKHHCALDDAMTTYNIFKLVEKDKE 181 (207)
T ss_pred CCCCCcChHHHHHHHHHHHHHHHhCcc
Confidence 877899999999999999999998864
No 5
>PTZ00315 2'-phosphotransferase; Provisional
Probab=100.00 E-value=1.1e-36 Score=315.72 Aligned_cols=196 Identities=38% Similarity=0.610 Sum_probs=166.7
Q ss_pred CCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCC
Q 017210 91 QKPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVT 170 (375)
Q Consensus 91 ~~~~~~~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~ 170 (375)
...|.+++||||||||||++......+||||||||+|+.++|+++++|++||||..+|.|+++|++|||||++||++||+
T Consensus 50 ~~~q~~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~ 129 (582)
T PTZ00315 50 IAPQPFDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADP 129 (582)
T ss_pred cccCCCCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCC
Confidence 34566789999999999985432346899999999998779999999999999987667999999999999999999999
Q ss_pred HHHHHHHHHHHHhhCCCC----CccEEEEEcCcchHHHHHHHHHHH---cCCCCCCCCCceeehHHHHH-HhcC------
Q 017210 171 LSEALLRHDKWLENKGIK----NTNFAVVTWSNWDCRVMLESECRF---KKIWKPPYFNRWINLKVPFH-EVFG------ 236 (375)
Q Consensus 171 ~~evl~~f~~fl~~~~lv----~~n~~vv~~a~FD~~~fL~~~~~~---~gi~~P~~~~~~iDt~~l~~-~~~~------ 236 (375)
|.+|+++|.+|+++..+. .++++|+|||+||+..||.++|+. .|++ ..+..|+|++..+. .+++
T Consensus 130 F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p--~~f~~widLk~~lar~l~p~~~~~~ 207 (582)
T PTZ00315 130 FPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTP--LSFQRWCNLKKYMSQLGFGNGSGCG 207 (582)
T ss_pred HHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCC--cccceEEEhHHHHHHHhCccccccc
Confidence 999999999999986432 246889999999986799999984 4554 34578999865444 3343
Q ss_pred ------CCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhccccccccccc
Q 017210 237 ------GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLM 288 (375)
Q Consensus 237 ------~~~~~L~~l~~~lgI~~~g~~HrALdDA~atA~L~~~ll~~~~~~~i~~~l~ 288 (375)
.++++|.+|++.+||+++|++|||++||++||+||.+|+++|..+.+|..+.
T Consensus 208 ~~~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~~~t~~~~ 265 (582)
T PTZ00315 208 GGATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTA 265 (582)
T ss_pred cccccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEEEecCCCC
Confidence 2468999999999999999999999999999999999999999999988665
No 6
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=100.00 E-value=7.2e-36 Score=336.65 Aligned_cols=224 Identities=18% Similarity=0.180 Sum_probs=194.0
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCcccccccccccc-----CCCCCCCCCcccEEEEE
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSWSTF-----YPDSQKPQEFQYFVVID 103 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~~~~-----~~~~~~~~~~~~fVVfD 103 (375)
-++.+++++|++|++|||+|||||||+ ++|+|||+|++.+++. +.+...+.. ..|||||
T Consensus 347 Dg~~~~~elv~~A~~~G~~aIAITDH~~v~~~p~a~~~~k~~gikvI~GvE~~~~~~~~~iv~~~~~~~L~~-~~~VVfD 425 (1437)
T PRK00448 347 DAIPSVSELVKRAAKWGHKAIAITDHGVVQAFPEAYNAAKKAGIKVIYGVEANLVDDGVPIVYNEVDRDLKD-ATYVVFD 425 (1437)
T ss_pred ccCCCHHHHHHHHHHCCCCEEEEecCCCCcCHHHHHHHHHhcCCceEeeeeEEEeccceeEEecCCchhhcc-CcEEEEE
Confidence 467889999999999999999999993 5889999999987543 222223332 4799999
Q ss_pred EeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHHHHHh
Q 017210 104 FEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLE 183 (375)
Q Consensus 104 lETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~~fl~ 183 (375)
+||||+ ++..++|||||||+++ +|.++++|++||+|.. .++++++++||||++||.++++++||+++|.+|++
T Consensus 426 LETTGL---~~~~deIIEIgAV~V~--~G~iie~F~~~V~P~~--~I~~~~~~LTGIT~e~L~~aps~~EaL~~f~~fig 498 (1437)
T PRK00448 426 VETTGL---SAVYDEIIEIGAVKIK--NGEIIDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCG 498 (1437)
T ss_pred hhhcCC---CCchhhhheeeeEEEe--CCeEeeeEEEEECCCC--CCCHHHHHHhCCCHHHHcCCCCHHHHHHHHHHHhC
Confidence 999997 4678999999999995 8899999999999986 59999999999999999999999999999999998
Q ss_pred hCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCCCCcHHH
Q 017210 184 NKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGRAHCGLD 262 (375)
Q Consensus 184 ~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~g~~HrALd 262 (375)
+. ++|+||+.||+ .||+..++++|++. +...++|+..+++.+++ .++++|++++++||++.+ .+|||++
T Consensus 499 g~------vLVAHNa~FD~-~fL~~~l~rlgl~~--l~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~-~~HrAl~ 568 (1437)
T PRK00448 499 DS------ILVAHNASFDV-GFINTNYEKLGLEK--IKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELE-HHHRADY 568 (1437)
T ss_pred CC------EEEEeCccccH-HHHHHHHHHcCCcc--ccccceeHHHHHHHHcCccccccHHHHHHHcCCCCC-CCcChHH
Confidence 75 46889999996 99999999998864 35679999999888774 568999999999999987 5799999
Q ss_pred HHHHHHHHHHHHHHhcccccccc
Q 017210 263 DAKNTARLLALLMHRGFKFSITN 285 (375)
Q Consensus 263 DA~atA~L~~~ll~~~~~~~i~~ 285 (375)
||.+||+||.+|+++..+.++..
T Consensus 569 DA~aTa~lf~~ll~~l~~~gi~~ 591 (1437)
T PRK00448 569 DAEATAYLLIKFLKDLKEKGITN 591 (1437)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCC
Confidence 99999999999998877666543
No 7
>PRK06722 exonuclease; Provisional
Probab=100.00 E-value=2.5e-35 Score=284.68 Aligned_cols=171 Identities=26% Similarity=0.400 Sum_probs=145.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..|||||+||||.+..+...++|||||||+|+..+++++++|++||||.. +|++++++|||||++||++||+|++|+.
T Consensus 5 ~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--~I~~~i~~LTGIT~emV~~AP~f~eVl~ 82 (281)
T PRK06722 5 THFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--RLTRHTTKLTGITKKDLIGVEKFPQIIE 82 (281)
T ss_pred CEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--cCCHhHhhhcCCCHHHHcCCCCHHHHHH
Confidence 57999999999754323456899999999997323488999999999986 6999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCC-CceeehHHHHHHhcCC---CCCCHHHHHHHcCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYF-NRWINLKVPFHEVFGG---VRCNLKEAVEMAGLA 252 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~-~~~iDt~~l~~~~~~~---~~~~L~~l~~~lgI~ 252 (375)
+|.+|+++. .+|+||+.||+ .||.++|+++|++.|.+. ..|+|+..+++..++. ..++|++++++|||+
T Consensus 83 ef~~fig~~------~lvahna~FD~-~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~ 155 (281)
T PRK06722 83 KFIQFIGED------SIFVTWGKEDY-RFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLI 155 (281)
T ss_pred HHHHHHCCC------cEEEEEeHHHH-HHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCC
Confidence 999999874 36889999996 999999999998876432 3578988776554421 357899999999999
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHH
Q 017210 253 WQGRAHCGLDDAKNTARLLALLMH 276 (375)
Q Consensus 253 ~~g~~HrALdDA~atA~L~~~ll~ 276 (375)
++|++|||++||++||+||.+|+.
T Consensus 156 ~~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 156 WEGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCCCcCcHHHHHHHHHHHHHHhc
Confidence 888899999999999999999984
No 8
>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=100.00 E-value=1.1e-33 Score=252.40 Aligned_cols=172 Identities=44% Similarity=0.785 Sum_probs=147.3
Q ss_pred EEEEEEeeCCCCCCC--CCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 99 FVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 99 fVVfDlETTGl~g~~--~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
|||||+||||++... ...++|||||||+++..+++++++|++||||...+.++++++++||||++||+++|++++|++
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 799999999985321 235899999999998555558999999999986446999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQ 254 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~-~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~~lgI~~~ 254 (375)
+|.+|+++.. +..++||+.||. .+|..++.+.+.. .+++...|+|++.+++..++. ++++|++++++||++..
T Consensus 81 ~~~~~l~~~~----~~~~v~~~~~d~-~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~ 155 (176)
T cd06133 81 EFLEWLGKNG----KYAFVTWGDWDL-KDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFE 155 (176)
T ss_pred HHHHHHHhCC----CeEEEeecHhhH-HHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCC
Confidence 9999999852 257899999996 7777787776654 345667899999999988876 48999999999999998
Q ss_pred CCCCcHHHHHHHHHHHHHHHH
Q 017210 255 GRAHCGLDDAKNTARLLALLM 275 (375)
Q Consensus 255 g~~HrALdDA~atA~L~~~ll 275 (375)
+++|+||+||++||+||.+|+
T Consensus 156 ~~~H~Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 156 GRHHRGLDDARNIARILKRLL 176 (176)
T ss_pred CCCcCcHHHHHHHHHHHHHhC
Confidence 789999999999999999874
No 9
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=100.00 E-value=2.4e-33 Score=263.63 Aligned_cols=168 Identities=20% Similarity=0.145 Sum_probs=144.6
Q ss_pred cEEEEEEeeCCCCCCCCC-CCcEEEEceEEEEcCCCe-EeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 98 YFVVIDFEATCDKDKNPY-PQEIIEFPSVIVSSVTGQ-LEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~-~~eIIEIGAV~vd~~~g~-i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
++||||+||||++ +. .++|||||||+++ ++. ..++|++||+|.. .|+++++++||||++||+++|+|++|+
T Consensus 1 r~vvlD~ETTGl~---p~~~d~IIEIgav~~~--~~~~~~~~f~~~i~P~~--~i~~~a~~vhGIt~e~l~~~p~f~ev~ 73 (225)
T TIGR01406 1 RQIILDTETTGLD---PKGGHRIVEIGAVELV--NRMLTGDNFHVYVNPER--DMPAEAAKVHGITDEFLADKPKFKEIA 73 (225)
T ss_pred CEEEEEeeCCCcC---CCCCCeEEEEEEEEEE--CCcEecceEEEEECcCC--CCCHHHHhccCCCHHHHhCCCCHHHHH
Confidence 4899999999974 44 3899999999985 443 4589999999986 599999999999999999999999999
Q ss_pred HHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCC--CCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKP--PYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAW 253 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P--~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~ 253 (375)
.+|.+|+++.. +|+||+.||+ .||+.+++++|...+ ...++|+||..+++..++..+++|++++++|||+.
T Consensus 74 ~~f~~fi~~~~------lVaHNa~FD~-~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~ 146 (225)
T TIGR01406 74 DEFLDFIGGSE------LVIHNAAFDV-GFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDN 146 (225)
T ss_pred HHHHHHhCCCE------EEEEecHHHH-HHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCC
Confidence 99999998863 5788999996 999999999984332 12368999999999888777899999999999997
Q ss_pred CCC-CCcHHHHHHHHHHHHHHHHHhcc
Q 017210 254 QGR-AHCGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 254 ~g~-~HrALdDA~atA~L~~~ll~~~~ 279 (375)
.++ +|+|++||++||+||.+|.....
T Consensus 147 ~~r~~H~Al~DA~~~a~v~~~l~~~~~ 173 (225)
T TIGR01406 147 SHRTLHGALLDAHLLAEVYLALTGGQE 173 (225)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHHcCCc
Confidence 643 69999999999999999976544
No 10
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=2.7e-33 Score=265.61 Aligned_cols=173 Identities=18% Similarity=0.199 Sum_probs=148.9
Q ss_pred ccEEEEEEeeCCCCCCCCC-CCcEEEEceEEEEcCCCeE-eeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPY-PQEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~-~~eIIEIGAV~vd~~~g~i-~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ev 174 (375)
.+|||||+||||++ +. .++|||||||+++ ++.+ .++|++||+|.. .|+++++++||||++||.++|+|+||
T Consensus 4 ~r~vvlDtETTGld---p~~~drIIEIGaV~v~--~~~~~~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev 76 (240)
T PRK05711 4 MRQIVLDTETTGLN---QREGHRIIEIGAVELI--NRRLTGRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEV 76 (240)
T ss_pred CeEEEEEeeCCCcC---CCCCCeEEEEEEEEEE--CCEEeccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHH
Confidence 36999999999974 44 7899999999995 5555 468999999986 59999999999999999999999999
Q ss_pred HHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCC--CCceeehHHHHHHhcCCCCCCHHHHHHHcCCC
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPY--FNRWINLKVPFHEVFGGVRCNLKEAVEMAGLA 252 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~--~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~ 252 (375)
+++|.+|++++. +|+||+.||+ .||+.+++++|...|.+ ...++||..+++.+++..+++|+++|++|||+
T Consensus 77 ~~~f~~fi~~~~------lVaHNa~FD~-~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~gi~ 149 (240)
T PRK05711 77 ADEFLDFIRGAE------LIIHNAPFDI-GFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGID 149 (240)
T ss_pred HHHHHHHhCCCE------EEEEccHHhH-HHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHCCCC
Confidence 999999998863 5789999997 99999999998665533 35799999999988877788999999999998
Q ss_pred CCCC-CCcHHHHHHHHHHHHHHHHHhcccccc
Q 017210 253 WQGR-AHCGLDDAKNTARLLALLMHRGFKFSI 283 (375)
Q Consensus 253 ~~g~-~HrALdDA~atA~L~~~ll~~~~~~~i 283 (375)
...+ .|+||.||++||+||.+|+.....+.+
T Consensus 150 ~~~r~~H~AL~DA~~~A~v~~~l~~~~~~l~~ 181 (240)
T PRK05711 150 NSHRTLHGALLDAEILAEVYLAMTGGQTSLGF 181 (240)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCccccccc
Confidence 7543 599999999999999999866444443
No 11
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=100.00 E-value=1.4e-32 Score=244.82 Aligned_cols=162 Identities=21% Similarity=0.209 Sum_probs=140.8
Q ss_pred EEEEEEeeCCCCCCCC-CCCcEEEEceEEEEcCCCeE-eeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 99 FVVIDFEATCDKDKNP-YPQEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 99 fVVfDlETTGl~g~~~-~~~eIIEIGAV~vd~~~g~i-~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
||+||+||||++ + ..++|||||||+++ ++.+ .++|+++|+|.. .++++++++||||++||++++++++|+.
T Consensus 1 ~v~~D~ETTGl~---~~~~~~iieig~v~v~--~~~~~~~~~~~~v~P~~--~i~~~~~~ihGIt~e~l~~~~~~~~v~~ 73 (167)
T cd06131 1 QIVLDTETTGLD---PREGHRIIEIGCVELI--NRRLTGNTFHVYINPER--DIPEEAFKVHGITDEFLADKPKFAEIAD 73 (167)
T ss_pred CEEEEeeCCCCC---CCCCCeEEEEEEEEEE--CCcEeccEEEEEECCCC--CCCHHHHHHhCCCHHHHhcCCCHHHHHH
Confidence 699999999974 4 56899999999996 4554 469999999986 4999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCC-CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP-YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQG 255 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~-~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~g 255 (375)
+|.+|+++. .+|+||+.||+ .||+++++++|+..+. ....|+|+..+++..++..+++|++++++||++.++
T Consensus 74 ~l~~~l~~~------~lv~hn~~fD~-~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~ 146 (167)
T cd06131 74 EFLDFIRGA------ELVIHNASFDV-GFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSH 146 (167)
T ss_pred HHHHHHCCC------eEEEeChHHhH-HHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCC
Confidence 999999875 36789999996 8999999998875432 235799999988888766678999999999999864
Q ss_pred -CCCcHHHHHHHHHHHHHHH
Q 017210 256 -RAHCGLDDAKNTARLLALL 274 (375)
Q Consensus 256 -~~HrALdDA~atA~L~~~l 274 (375)
++|+|++||++||+||.+|
T Consensus 147 ~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCChHHHHHHHHHHHHHh
Confidence 4799999999999999876
No 12
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=100.00 E-value=3.4e-32 Score=240.32 Aligned_cols=166 Identities=34% Similarity=0.434 Sum_probs=147.4
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHH
Q 017210 98 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 177 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~ 177 (375)
+||+||+||||++ +..++|||||||+++ ++++.++|++||+|.. .++++++++||||+++|.+++++.+|+.+
T Consensus 1 ~~v~~D~Ettg~~---~~~~~Iieig~v~~~--~~~~~~~f~~~v~p~~--~i~~~~~~~~Git~~~l~~~~~~~~~~~~ 73 (169)
T smart00479 1 TLVVIDCETTGLD---PGKDEIIEIAAVDVD--GGRIIVVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLEE 73 (169)
T ss_pred CEEEEEeeCCCCC---CCCCeEEEEEEEEEE--CCEeEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence 4899999999974 457899999999997 4568899999999964 69999999999999999999999999999
Q ss_pred HHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCC
Q 017210 178 HDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGR 256 (375)
Q Consensus 178 f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~g~ 256 (375)
|.+|+++. .+|+||+ +||+ .||++++.++|++.|. ...|+|+..+++..++..+++|++++++||++..++
T Consensus 74 ~~~~l~~~------~~v~~n~~~fD~-~~L~~~~~~~~~~~~~-~~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~ 145 (169)
T smart00479 74 LLEFLKGK------ILVAGNALNFDL-RFLKLEHPRLGIKDPP-KNPVIDTLKLARALNPGRKYSLKKLAERLGLEVIGR 145 (169)
T ss_pred HHHHhcCC------EEEEeCCHHHhH-HHHHHHHHHhCCCCCc-CCCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC
Confidence 99999875 4678888 9996 8999999999988763 356999999988877656899999999999998766
Q ss_pred CCcHHHHHHHHHHHHHHHHHhc
Q 017210 257 AHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 257 ~HrALdDA~atA~L~~~ll~~~ 278 (375)
+|+|++||++|++||.+|++++
T Consensus 146 ~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 146 AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CcCcHHHHHHHHHHHHHHHHHh
Confidence 6999999999999999998765
No 13
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=3.4e-32 Score=267.18 Aligned_cols=167 Identities=25% Similarity=0.309 Sum_probs=150.1
Q ss_pred CCcccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHH
Q 017210 94 QEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 173 (375)
Q Consensus 94 ~~~~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~e 173 (375)
+....|||||+||||+ ++..++|||||||+++ +|+++++|+++|+|.. .|+++++++||||++||+++|+|.+
T Consensus 5 ~~~~~~Vv~DlETTGl---~p~~~eIIEIgaV~v~--~g~i~~~f~~lVkP~~--~I~~~a~~ihGIT~e~l~~~~~~~e 77 (313)
T PRK06807 5 SLPLDYVVIDFETTGF---NPYNDKIIQVAAVKYR--NHELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPTIEE 77 (313)
T ss_pred CCCCCEEEEEEECCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHhhhccCCCCHHHHhCCCCHHH
Confidence 3456899999999997 4678999999999996 7899999999999996 5999999999999999999999999
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCC
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLA 252 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~ 252 (375)
|+++|.+|+++. .+|+||+.||+ .||.++|.++|++.| .+++||+..+++.+++ ..+++|++|+++||++
T Consensus 78 vl~~f~~fl~~~------~lVaHNa~FD~-~fL~~~~~~~gl~~~--~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~ 148 (313)
T PRK06807 78 VLPLFLAFLHTN------VIVAHNASFDM-RFLKSNVNMLGLPEP--KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIR 148 (313)
T ss_pred HHHHHHHHHcCC------eEEEEcHHHHH-HHHHHHHHHcCCCCC--CCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCC
Confidence 999999999875 46889999996 899999999998765 4579999999888875 4678999999999999
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHhc
Q 017210 253 WQGRAHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 253 ~~g~~HrALdDA~atA~L~~~ll~~~ 278 (375)
. ++|||++||++|++||.+++...
T Consensus 149 ~--~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 149 L--SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred C--CCcChHHHHHHHHHHHHHHHHhh
Confidence 7 68999999999999999998765
No 14
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=3.1e-32 Score=267.11 Aligned_cols=166 Identities=16% Similarity=0.223 Sum_probs=147.4
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHH
Q 017210 98 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 177 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~ 177 (375)
.|||||+||||. ..++|||||||+++ +|+++++|++||||.. ..+++++++|||||++||+++|+|.+|+++
T Consensus 2 ~~vviD~ETTg~-----~~d~IieIgav~v~--~g~i~~~f~~lv~P~~-~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~ 73 (309)
T PRK06195 2 NFVAIDFETANE-----KRNSPCSIGIVVVK--DGEIVEKVHYLIKPKE-MRFMPINIGIHGIRPHMVEDELEFDKIWEK 73 (309)
T ss_pred cEEEEEEeCCCC-----CCCceEEEEEEEEE--CCEEEEEEEEEECCCC-CCCChhheeccCcCHHHHhCCCCHHHHHHH
Confidence 599999999974 46899999999995 7899999999999984 347889999999999999999999999999
Q ss_pred HHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 017210 178 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 256 (375)
Q Consensus 178 f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~g~ 256 (375)
|.+|+++. .+|+||++||+ .||+++|+++++..| .+.|+||..+++.+++ ..+++|.+++++||+++ +
T Consensus 74 ~~~fl~~~------~lVaHNa~FD~-~fL~~~~~r~~~~~~--~~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~~--~ 142 (309)
T PRK06195 74 IKHYFNNN------LVIAHNASFDI-SVLRKTLELYNIPMP--SFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEF--K 142 (309)
T ss_pred HHHHhCCC------EEEEECcHHHH-HHHHHHHHHhCCCCC--CCCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCC--c
Confidence 99999874 57889999996 999999999998876 3589999999998885 46899999999999985 5
Q ss_pred CCcHHHHHHHHHHHHHHHHHhccccc
Q 017210 257 AHCGLDDAKNTARLLALLMHRGFKFS 282 (375)
Q Consensus 257 ~HrALdDA~atA~L~~~ll~~~~~~~ 282 (375)
+|||++||++||+||.+|+++....+
T Consensus 143 ~H~Al~DA~ata~l~~~l~~~~~~~~ 168 (309)
T PRK06195 143 HHDALADAMACSNILLNISKELNSKD 168 (309)
T ss_pred ccCCHHHHHHHHHHHHHHHHHhccCC
Confidence 89999999999999999988765433
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=100.00 E-value=8.8e-32 Score=235.95 Aligned_cols=154 Identities=23% Similarity=0.311 Sum_probs=138.9
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHH
Q 017210 99 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 178 (375)
Q Consensus 99 fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f 178 (375)
||+||+||||. ..++|||||||+++ +|+++++|+.+|+|.. +++++++++||||+++|++++++.+|+.+|
T Consensus 1 ~v~~D~Ettg~-----~~~~ii~ig~v~~~--~~~~~~~~~~~i~p~~--~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l 71 (156)
T cd06130 1 FVAIDFETANA-----DRASACSIGLVKVR--DGQIVDTFYTLIRPPT--RFDPFNIAIHGITPEDVADAPTFPEVWPEI 71 (156)
T ss_pred CEEEEEeCCCC-----CCCceEEEEEEEEE--CCEEEEEEEEEeCcCC--CCChhhccccCcCHHHHhcCCCHHHHHHHH
Confidence 69999999984 36899999999996 7889999999999996 599999999999999999999999999999
Q ss_pred HHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCCC
Q 017210 179 DKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGRA 257 (375)
Q Consensus 179 ~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~g~~ 257 (375)
.+|+++. .+|+||++||+ .||+++++++|+..|+ .+++|+..+++..++ ..+++|.+++++||++.. +
T Consensus 72 ~~~l~~~------~lv~hn~~fD~-~~l~~~~~~~g~~~~~--~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~ 140 (156)
T cd06130 72 KPFLGGS------LVVAHNASFDR-SVLRAALEAYGLPPPP--YQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--H 140 (156)
T ss_pred HHHhCCC------EEEEeChHHhH-HHHHHHHHHcCCCCCC--CCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--C
Confidence 9999874 46778899996 9999999999988763 579999999988875 468999999999999986 8
Q ss_pred CcHHHHHHHHHHHHH
Q 017210 258 HCGLDDAKNTARLLA 272 (375)
Q Consensus 258 HrALdDA~atA~L~~ 272 (375)
|||++||++||+||.
T Consensus 141 H~Al~Da~~ta~l~~ 155 (156)
T cd06130 141 HDALEDARACAEILL 155 (156)
T ss_pred cCchHHHHHHHHHHh
Confidence 999999999999985
No 16
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=8.1e-32 Score=257.94 Aligned_cols=165 Identities=20% Similarity=0.274 Sum_probs=148.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..|||||+||||+ .+..++|||||||+++ +|+++++|+++|+|. .++++++++||||++||++||++.+|+.
T Consensus 68 ~~~vv~DiETTG~---~~~~~~IIEIGAv~v~--~g~i~~~f~~~v~p~---~ip~~~~~itGIt~e~l~~ap~~~evl~ 139 (257)
T PRK08517 68 QVFCFVDIETNGS---KPKKHQIIEIGAVKVK--NGEIIDRFESFVKAK---EVPEYITELTGITYEDLENAPSLKEVLE 139 (257)
T ss_pred CCEEEEEEeCCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECCC---CCChhhhhhcCcCHHHHcCCCCHHHHHH
Confidence 4799999999996 4567899999999995 789999999999996 4899999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGR 256 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~g~ 256 (375)
+|.+|++++ +.|+||++||. .||++++++.|+.. +.++++|+..+++..+...+++|+++++++|++.+ +
T Consensus 140 ~f~~fl~~~------v~VaHNa~FD~-~fL~~~l~r~g~~~--~~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~-~ 209 (257)
T PRK08517 140 EFRLFLGDS------VFVAHNVNFDY-NFISRSLEEIGLGP--LLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIE-V 209 (257)
T ss_pred HHHHHHCCC------eEEEECHHHHH-HHHHHHHHHcCCCC--CCCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCC-C
Confidence 999999875 46788999996 99999999998764 45689999999988877778999999999999986 7
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcc
Q 017210 257 AHCGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 257 ~HrALdDA~atA~L~~~ll~~~~ 279 (375)
+|||++||.+||+||..++.+..
T Consensus 210 ~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 210 HHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred CCChHHHHHHHHHHHHHHHHHhH
Confidence 89999999999999999987653
No 17
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=1e-31 Score=263.93 Aligned_cols=169 Identities=18% Similarity=0.182 Sum_probs=148.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..|||||+||||+ ++..++|||||||+++ .+|+++++|++||+|.. ++..+.+||||++||.++|+|+++++
T Consensus 15 ~~fvvlD~ETTGl---~p~~d~IIeIgav~v~-~~g~i~~~~~~lv~P~~----~~~~~~IhGIt~e~l~~ap~f~ev~~ 86 (313)
T PRK06063 15 RGWAVVDVETSGF---RPGQARIISLAVLGLD-ADGNVEQSVVTLLNPGV----DPGPTHVHGLTAEMLEGQPQFADIAG 86 (313)
T ss_pred CCEEEEEEECCCC---CCCCCEEEEEEEEEEE-CCceeeeEEEEEECcCC----CCCCeecCCCCHHHHhCCCCHHHHHH
Confidence 5799999999997 4677999999999997 47899999999999974 34568999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc-CCCCCCHHHHHHHcCCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVF-GGVRCNLKEAVEMAGLAWQG 255 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~-~~~~~~L~~l~~~lgI~~~g 255 (375)
+|.+|+++. .+|+||+.||+ .||+++++++|+..| .+.++||..+++.++ +..+++|++++++|||+..
T Consensus 87 ~l~~~l~~~------~lVaHNa~FD~-~fL~~~~~r~g~~~~--~~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~- 156 (313)
T PRK06063 87 EVAELLRGR------TLVAHNVAFDY-SFLAAEAERAGAELP--VDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQ- 156 (313)
T ss_pred HHHHHcCCC------EEEEeCHHHHH-HHHHHHHHHcCCCCC--CCCEEehHHHHHHhccCCCCCCHHHHHHHcCCCCC-
Confidence 999999875 46788999996 999999999998876 357999999998775 4578999999999999975
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcccccc
Q 017210 256 RAHCGLDDAKNTARLLALLMHRGFKFSI 283 (375)
Q Consensus 256 ~~HrALdDA~atA~L~~~ll~~~~~~~i 283 (375)
++|||++||++||+||.+++++....++
T Consensus 157 ~~H~Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 157 RPHDALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 7899999999999999999887655444
No 18
>PRK05168 ribonuclease T; Provisional
Probab=99.98 E-value=2.2e-31 Score=247.89 Aligned_cols=189 Identities=21% Similarity=0.212 Sum_probs=149.5
Q ss_pred cCCCCCCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcC-CCeE--eeEEEEeecCCCCCCCCcchHhhhCCCh
Q 017210 86 FYPDSQKPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSV-TGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQ 162 (375)
Q Consensus 86 ~~~~~~~~~~~~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~-~g~i--~d~F~~lVkP~~~p~Is~~~~~LTGIt~ 162 (375)
+++-+.++.+ .+|||||+||||+ ++..++|||||||++... +|.+ .++|+++|+|.....|+++++++||||+
T Consensus 7 ~~~~~~~~~~-~~~vv~D~ETTGl---~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~ 82 (211)
T PRK05168 7 LNPLKDRFRG-FLPVVIDVETAGF---NAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDP 82 (211)
T ss_pred cchHHHHhcC-CceEEEEeeCCCC---CCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCc
Confidence 3333334444 4699999999997 467899999999999522 4654 5899999999422359999999999999
Q ss_pred HH-HhCCCCHHHHHHHHHHHHhhCCC---CCccEEEEEcCcchHHHHHHHHHHHcCCCCCCC-CCceeehHHHHHHhcCC
Q 017210 163 IQ-VDRGVTLSEALLRHDKWLENKGI---KNTNFAVVTWSNWDCRVMLESECRFKKIWKPPY-FNRWINLKVPFHEVFGG 237 (375)
Q Consensus 163 e~-l~~ap~~~evl~~f~~fl~~~~l---v~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~-~~~~iDt~~l~~~~~~~ 237 (375)
++ +++++++.+++.+|.+|+.+... .+..+.|+||++||+ .||+++++++|+..+++ ..+++||..+++.+++.
T Consensus 83 e~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~-~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~ 161 (211)
T PRK05168 83 DNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDL-SFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ 161 (211)
T ss_pred hhhhhcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhH-HHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC
Confidence 86 88999999999999999874210 112457889999997 89999999998753222 23689999999887763
Q ss_pred CCCCHHHHHHHcCCCCCC-CCCcHHHHHHHHHHHHHHHHHhcccc
Q 017210 238 VRCNLKEAVEMAGLAWQG-RAHCGLDDAKNTARLLALLMHRGFKF 281 (375)
Q Consensus 238 ~~~~L~~l~~~lgI~~~g-~~HrALdDA~atA~L~~~ll~~~~~~ 281 (375)
++|+++++++|++.++ ++|||++||.+||+||.+|+++..+.
T Consensus 162 --~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~~~ 204 (211)
T PRK05168 162 --TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWKRL 204 (211)
T ss_pred --CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHc
Confidence 5899999999998753 58999999999999999999876443
No 19
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=2.6e-31 Score=250.89 Aligned_cols=173 Identities=20% Similarity=0.133 Sum_probs=146.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhC-CCCHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~-ap~~~evl 175 (375)
..|||||+||||+ ++..++|||||+|+++ .+|+++++|++||+|.. .|+++++++||||++||.+ ++++++|+
T Consensus 6 ~~~vv~D~ETTGl---~p~~d~Iieig~v~v~-~~g~~~~~~~~lv~P~~--~i~~~a~~IhGIt~e~l~~~g~~~~~vl 79 (232)
T PRK07942 6 GPLAAFDLETTGV---DPETARIVTAALVVVD-ADGEVVESREWLADPGV--EIPEEASAVHGITTEYARAHGRPAAEVL 79 (232)
T ss_pred CcEEEEEeccCCC---CCCCCeeEEEEEEEEe-CCCccccceEEEECCCC--CCCHHHHHHhCCCHHHHHhhCCCHHHHH
Confidence 4799999999997 4677999999999997 45888899999999986 5999999999999999975 89999999
Q ss_pred HHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHHcCCCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEMAGLAW 253 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~--~~~~~L~~l~~~lgI~~ 253 (375)
.+|.+++.... .+...+|+||+.||+ .||+++++++|+..+ ...+++|+..+.+.+.. ..+++|++++++||++.
T Consensus 80 ~e~~~~l~~~~-~~~~~lVahNa~FD~-~fL~~~~~r~~~~~~-~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~ 156 (232)
T PRK07942 80 AEIADALREAW-ARGVPVVVFNAPYDL-TVLDRELRRHGLPSL-VPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRL 156 (232)
T ss_pred HHHHHHHHHHh-hcCCEEEEeCcHhhH-HHHHHHHHHcCCCCc-cCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCC
Confidence 99999986421 122457899999996 999999999997642 23468999887776543 24689999999999998
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcc
Q 017210 254 QGRAHCGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 254 ~g~~HrALdDA~atA~L~~~ll~~~~ 279 (375)
. ++|||++||.+||+||.+|+++..
T Consensus 157 ~-~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 157 D-NAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred C-CCCChHHHHHHHHHHHHHHHHHHH
Confidence 6 589999999999999999987654
No 20
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=4.7e-31 Score=250.24 Aligned_cols=165 Identities=21% Similarity=0.152 Sum_probs=142.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeE--eeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i--~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ev 174 (375)
..|||||+||||+ ++..++|||||+|+++ ++++ .++|+++|+|.. +|+++++++||||++||.++|++++|
T Consensus 47 ~~~vviD~ETTGl---~p~~d~IieIg~v~v~--~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt~e~l~~ap~~~ev 119 (239)
T PRK09146 47 VPFVALDFETTGL---DAEQDAIVSIGLVPFT--LQRIRCRQARHWVVKPRR--PLEEESVVIHGITHSELQDAPDLERI 119 (239)
T ss_pred CCEEEEEeECCCC---CCCCCcEEEEEEEEEE--CCeEeecceEEEEECCCC--CCChhhhhhcCCCHHHHhCCCCHHHH
Confidence 5799999999997 4678999999999996 5665 589999999986 59999999999999999999999999
Q ss_pred HHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcC-CCCCCCCCceeehHHHHHHhcCC--------------CC
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKK-IWKPPYFNRWINLKVPFHEVFGG--------------VR 239 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~g-i~~P~~~~~~iDt~~l~~~~~~~--------------~~ 239 (375)
+.+|.+|+++. .+|+||+.||. .||++++++.+ ... ..+++||..+++.+++. .+
T Consensus 120 l~~l~~~~~~~------~lVaHna~FD~-~fL~~~l~~~~~~~~---~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~ 189 (239)
T PRK09146 120 LDELLEALAGK------VVVVHYRRIER-DFLDQALRNRIGEGI---EFPVIDTMEIEARIQRKQAGGLWNRLKGKKPES 189 (239)
T ss_pred HHHHHHHhCCC------EEEEECHHHHH-HHHHHHHHHhcCCCC---CCceechHHHHHHHcccccccccchhccCCCCC
Confidence 99999999875 46788999995 99999998753 332 34799999998876421 45
Q ss_pred CCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcc
Q 017210 240 CNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 240 ~~L~~l~~~lgI~~~g~~HrALdDA~atA~L~~~ll~~~~ 279 (375)
++|++++++|||+.. ++|||++||.+||+||..++.+..
T Consensus 190 ~~L~~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 190 IRLADSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred CCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHc
Confidence 799999999999975 689999999999999999987764
No 21
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=4.7e-31 Score=250.94 Aligned_cols=170 Identities=25% Similarity=0.290 Sum_probs=145.9
Q ss_pred ccEEEEEEeeCCCCCCCCCC-CcEEEEceEEEEcCCCeE-eeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYP-QEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~-~eIIEIGAV~vd~~~g~i-~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ev 174 (375)
..|||||+||||++ |.. ++|||||||+++ ++.+ .++|+++|+|.. .++++++++||||+++|+++|++.||
T Consensus 59 ~~~vv~D~ETTGl~---p~~~deIIeIgaV~~~--~~~i~~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev 131 (244)
T PRK07740 59 LPFVVFDLETTGFS---PQQGDEILSIGAVKTK--GGEVETDTFYSLVKPKR--PIPEHILELTGITAEDVAFAPPLAEV 131 (244)
T ss_pred CCEEEEEEeCCCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEEeCcCC--CCChhheeccCCCHHHHhCCCCHHHH
Confidence 36999999999973 444 899999999996 6776 899999999986 59999999999999999999999999
Q ss_pred HHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCC
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAW 253 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~~lgI~~ 253 (375)
+.+|.+|+++. .+|+||+.||. .||+.++.+... . ++...++|+..+++.+++. ++++|++++++||++.
T Consensus 132 l~~f~~fi~~~------~lVahna~fD~-~fL~~~~~~~~~-~-~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~ 202 (244)
T PRK07740 132 LHRFYAFIGAG------VLVAHHAGHDK-AFLRHALWRTYR-Q-PFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPI 202 (244)
T ss_pred HHHHHHHhCCC------EEEEeCHHHHH-HHHHHHHHHhcC-C-CcCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCC
Confidence 99999999875 46788999995 899998876532 2 2456899999998877754 5789999999999998
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcccccc
Q 017210 254 QGRAHCGLDDAKNTARLLALLMHRGFKFSI 283 (375)
Q Consensus 254 ~g~~HrALdDA~atA~L~~~ll~~~~~~~i 283 (375)
.+ +|+|++||++||+||.+++.+..+.++
T Consensus 203 ~~-~H~Al~Da~ata~l~~~ll~~~~~~~~ 231 (244)
T PRK07740 203 PR-RHHALGDALMTAKLWAILLVEAQQRGI 231 (244)
T ss_pred CC-CCCcHHHHHHHHHHHHHHHHHHHHcCC
Confidence 74 699999999999999999987655444
No 22
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=8.3e-31 Score=250.06 Aligned_cols=168 Identities=14% Similarity=0.139 Sum_probs=147.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..||+||+||||+ ++..++|||||+|+++ .++++++|+++|+|.. .|+++++.+||||++||+++|++.+|++
T Consensus 7 ~~~v~~D~ETTGl---~~~~d~IIEIa~v~v~--~~~~~~~~~~li~P~~--~I~~~a~~ihgIt~e~v~~~p~~~ev~~ 79 (250)
T PRK06310 7 TEFVCLDCETTGL---DVKKDRIIEFAAIRFT--FDEVIDSVEFLINPER--VVSAESQRIHHISDAMLRDKPKIAEVFP 79 (250)
T ss_pred CcEEEEEEeCCCC---CCCCCeEEEEEEEEEE--CCeEEEEEEEEECcCC--CCCHhhhhccCcCHHHHhCCCCHHHHHH
Confidence 5799999999997 4677999999999996 4678899999999996 4999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGR 256 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~g~ 256 (375)
+|.+|+++. .++|+||++||+ .||.+++.+.|++.+.....+|||+.+++.+.+..+++|..++++||++.. .
T Consensus 80 ~~~~fl~~~-----~~lvghn~~FD~-~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~-~ 152 (250)
T PRK06310 80 QIKGFFKEG-----DYIVGHSVGFDL-QVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYD-G 152 (250)
T ss_pred HHHHHhCCC-----CEEEEECHHHHH-HHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCC-C
Confidence 999999763 246788899996 999999999998875433689999998886544457899999999999986 5
Q ss_pred CCcHHHHHHHHHHHHHHHHHhc
Q 017210 257 AHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 257 ~HrALdDA~atA~L~~~ll~~~ 278 (375)
+|||++||.+|++||.+++++.
T Consensus 153 aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 153 NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CcChHHHHHHHHHHHHHHHHhc
Confidence 8999999999999999998764
No 23
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.97 E-value=1.2e-30 Score=243.57 Aligned_cols=171 Identities=18% Similarity=0.131 Sum_probs=144.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
.+|||||+||||+ ++..+ |||||||++. .++.++++|+++|+|.. .++++++++||||++||.++|+++||++
T Consensus 7 ~~fvv~D~ETTGl---~~~~~-IIeIgav~v~-~~~~~~~~f~~li~P~~--~i~~~a~~ihGIt~e~l~~~p~~~ev~~ 79 (217)
T TIGR00573 7 DTETTGDNETTGL---YAGHD-IIEIGAVEII-NRRITGNKFHTYIKPDR--PIDPDAIKIHGITDDMLKDKPDFKEIAE 79 (217)
T ss_pred cCEEEEEecCCCC---CCCCC-EEEEEEEEEE-CCCEeeeEEEEEECcCC--CCCHHHHhhcCCCHHHHcCCCCHHHHHH
Confidence 4799999999997 45566 9999999975 34567799999999986 5999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC---CCCCCHHHHHHHcCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG---GVRCNLKEAVEMAGLAW 253 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~---~~~~~L~~l~~~lgI~~ 253 (375)
+|.+|+++. .+|+||+.||+ .||++++++.+...+ ....++|+..+++.+++ ..+++|.+++++||++.
T Consensus 80 ~~~~~~~~~------~lVaHNa~FD~-~fL~~~~~r~~~~~~-~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~ 151 (217)
T TIGR00573 80 DFADYIRGA------ELVIHNASFDV-GFLNYEFSKLYKVEP-KTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITN 151 (217)
T ss_pred HHHHHhCCC------EEEEeccHHHH-HHHHHHHHHhcCCCC-CccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCC
Confidence 999999874 46788999996 999999998765432 24578999887766543 34689999999999986
Q ss_pred CC-CCCcHHHHHHHHHHHHHHHHHhccccc
Q 017210 254 QG-RAHCGLDDAKNTARLLALLMHRGFKFS 282 (375)
Q Consensus 254 ~g-~~HrALdDA~atA~L~~~ll~~~~~~~ 282 (375)
.. .+|+|++||++||+||.+|+.+..+..
T Consensus 152 ~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 152 SHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 42 479999999999999999998876555
No 24
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=9.3e-31 Score=241.24 Aligned_cols=162 Identities=19% Similarity=0.242 Sum_probs=133.7
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 96 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 96 ~~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
..+|||||+||||++ ..++|||||||+++ +|+++++|++||+|.. +++++++++||||++||++||++.+|+
T Consensus 4 ~~~~vvlD~EtTGl~----~~~eIIeIgaV~v~--~g~~~~~f~~lv~P~~--~i~~~~~~lhGIt~~~v~~ap~~~evl 75 (195)
T PRK07247 4 LETYIAFDLEFNTVN----GVSHIIQVSAVKYD--DHKEVDSFDSYVYTDV--PLQSFINGLTGITADKIADAPKVEEVL 75 (195)
T ss_pred CCeEEEEEeeCCCCC----CCCeEEEEEEEEEE--CCEEEEEEEEEECCCC--CCCccceecCCCCHHHHhCCCCHHHHH
Confidence 457999999999974 35899999999996 7888899999999985 599999999999999999999999999
Q ss_pred HHHHHHHhhCCCCCccEEEEEcCc-chHHHHHHHHHHHcCCCCCCCCCceeehHHHH--HHh--c-CCCCCCHHHHHHHc
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWSN-WDCRVMLESECRFKKIWKPPYFNRWINLKVPF--HEV--F-GGVRCNLKEAVEMA 249 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a~-FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~--~~~--~-~~~~~~L~~l~~~l 249 (375)
++|.+|+++.. +|+||+. ||+ .||++ .|+..+ ...++|+.... +.. + +.++++|.+++++|
T Consensus 76 ~~f~~f~~~~~------lVaHNa~~fD~-~fL~~----~g~~~~--~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~ 142 (195)
T PRK07247 76 AAFKEFVGELP------LIGYNAQKSDL-PILAE----NGLDLS--DQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL 142 (195)
T ss_pred HHHHHHHCCCe------EEEEeCcHhHH-HHHHH----cCCCcC--CCceeehHHHHHHhhccccCCCCCCCHHHHHHhc
Confidence 99999998863 5677876 897 88864 465543 22467775332 221 2 34689999999999
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHhccc
Q 017210 250 GLAWQGRAHCGLDDAKNTARLLALLMHRGFK 280 (375)
Q Consensus 250 gI~~~g~~HrALdDA~atA~L~~~ll~~~~~ 280 (375)
||+. .+|||++||++||+||.+|++.+..
T Consensus 143 gi~~--~~HrAl~DA~~ta~v~~~ll~~~~~ 171 (195)
T PRK07247 143 GIKG--RGHNSLEDARMTARVYESFLESDQN 171 (195)
T ss_pred CCCC--CCcCCHHHHHHHHHHHHHHHhhccc
Confidence 9985 5799999999999999999987654
No 25
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.97 E-value=1.3e-30 Score=238.68 Aligned_cols=174 Identities=22% Similarity=0.225 Sum_probs=140.2
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEceEEEEc-CCCe--EeeEEEEeecCCCCCCCCcchHhhhCCChHH-HhCCCCHHH
Q 017210 98 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS-VTGQ--LEACFQTYVRPTCNQLLSDFCKDLTGIQQIQ-VDRGVTLSE 173 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~-~~g~--i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~-l~~ap~~~e 173 (375)
.+||||+||||+ ++..++|||||||+|+. .+|. ++++|+++|+|....+|+++++++||||++| +++++...+
T Consensus 6 ~~vv~D~ETTGl---~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~ 82 (189)
T cd06134 6 LPVVVDVETGGF---NPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKE 82 (189)
T ss_pred eeEEEEecCCCC---CCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHH
Confidence 389999999997 46789999999999952 2454 3689999999942125999999999999986 678888888
Q ss_pred HHHHHHHHHhhCCC---CCccEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc
Q 017210 174 ALLRHDKWLENKGI---KNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA 249 (375)
Q Consensus 174 vl~~f~~fl~~~~l---v~~n~~vv~~a~FD~~~fL~~~~~~~gi~-~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~l 249 (375)
++.+|.+|+.+..- .+..++|+||++||+ .||+++++++|+. .|....+++||..+++.+++ .++|++++++|
T Consensus 83 ~~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~-~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~--~~~L~~l~~~~ 159 (189)
T cd06134 83 ALKEIFKPIRKALKAQGCTRAILVGHNAHFDL-GFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG--QTVLAKACQAA 159 (189)
T ss_pred HHHHHHHHHHHHHhhcccCCCeEEEecchhhH-HHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC--CCcHHHHHHHC
Confidence 88888888764210 113467889999996 9999999999983 22112368999999988776 46899999999
Q ss_pred CCCCC-CCCCcHHHHHHHHHHHHHHHHHh
Q 017210 250 GLAWQ-GRAHCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 250 gI~~~-g~~HrALdDA~atA~L~~~ll~~ 277 (375)
||+++ .++|+|++||.+||+||.+|+++
T Consensus 160 gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 160 GIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 99864 36899999999999999999875
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=99.97 E-value=7.5e-31 Score=237.86 Aligned_cols=162 Identities=17% Similarity=0.104 Sum_probs=132.2
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCC---C--------eEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhC
Q 017210 99 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVT---G--------QLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR 167 (375)
Q Consensus 99 fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~---g--------~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ 167 (375)
|||||+||||++. +..++|||||||+|+... + +++++|+++|||.. .|++.++++||||++||.+
T Consensus 1 ~vv~D~ETTGl~~--~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~--~I~~~a~~IhGIt~e~l~~ 76 (177)
T cd06136 1 FVFLDLETTGLPK--HNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR--AISPGASEITGLSNDLLEH 76 (177)
T ss_pred CeEEeeecCCCCC--CCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC--cCChhHHHHhCcCHHHHhc
Confidence 7999999999731 467999999999996311 1 36789999999986 5999999999999999999
Q ss_pred CCCHHH-HHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHH
Q 017210 168 GVTLSE-ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEA 245 (375)
Q Consensus 168 ap~~~e-vl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l 245 (375)
+|++++ +++.+.+|++... +..++|+||+ .||+ +||+++++++|+.+| ....++|+..+++.+.+ +|+++
T Consensus 77 ~~~~~~~~~~~l~~f~~~~~--~~~~lVaHNa~~FD~-~fL~~~~~r~~~~~~-~~~~~iDtl~l~r~~~~----~L~~l 148 (177)
T cd06136 77 KAPFDSDTANLIKLFLRRQP--KPICLVAHNGNRFDF-PILRSELERLGTKLP-DDILCVDSLPAFRELDQ----SLGSL 148 (177)
T ss_pred CCCccHHHHHHHHHHHHhcC--CCCEEEEcCCcccCH-HHHHHHHHHcCCCCC-CCCEEEEeHHHHhhhHh----hHHHH
Confidence 998874 5666667765421 1125788898 8997 999999999998875 34568999999887664 89999
Q ss_pred HHH-cCCCCCCCCCcHHHHHHHHHHHHHH
Q 017210 246 VEM-AGLAWQGRAHCGLDDAKNTARLLAL 273 (375)
Q Consensus 246 ~~~-lgI~~~g~~HrALdDA~atA~L~~~ 273 (375)
+++ ||++.. ++|||++||.+|+++|.+
T Consensus 149 ~~~~~~~~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 149 YKRLFGQEPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHhCCCcc-cccchHHHHHHHHHHHhh
Confidence 985 899975 689999999999999874
No 27
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.7e-30 Score=239.86 Aligned_cols=163 Identities=21% Similarity=0.253 Sum_probs=137.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEe--eEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLE--ACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~--d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ev 174 (375)
..|||||+||||+ ++..++|||||||+++ ++.+. ++|+.+|+|.. .++++++++||||++||++++++++|
T Consensus 29 ~~~vviD~ETTGl---~~~~d~IieIgaV~~~--~~~~~~~~~f~~~i~p~~--~i~~~~~~ihGIt~~~l~~~~~~~~v 101 (202)
T PRK09145 29 DEWVALDCETTGL---DPRRAEIVSIAAVKIR--GNRILTSERLELLVRPPQ--SLSAESIKIHRLRHQDLEDGLSEEEA 101 (202)
T ss_pred CCEEEEEeECCCC---CCCCCceEEEEEEEEE--CCEEeecCceEEEECCCC--CCCHhHhhhcCcCHHHHhcCCCHHHH
Confidence 4799999999997 4667999999999997 45543 68999999985 59999999999999999999999999
Q ss_pred HHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHH-cCCCCCCCCCceeehHHHHHHh----c-C-CCCCCHHHHHH
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRF-KKIWKPPYFNRWINLKVPFHEV----F-G-GVRCNLKEAVE 247 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~-~gi~~P~~~~~~iDt~~l~~~~----~-~-~~~~~L~~l~~ 247 (375)
+++|.+|+++. .+|+||+.||+ .||++++++ .+.++| ..++|+..++... + + ..+++|+++++
T Consensus 102 l~~~~~~i~~~------~lv~hn~~fD~-~fL~~~~~~~~~~~~~---~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~ 171 (202)
T PRK09145 102 LRQLLAFIGNR------PLVGYYLEFDV-AMLNRYVRPLLGIPLP---NPLIEVSALYYDKKERHLPDAYIDLRFDAILK 171 (202)
T ss_pred HHHHHHHHcCC------eEEEeCHHHHH-HHHHHHHHHhcCCCCC---CCeeeHHHHHHHHhhccCCCcccCCCHHHHHH
Confidence 99999999875 35677889996 999999987 455543 4689998766432 1 1 23689999999
Q ss_pred HcCCCCCCCCCcHHHHHHHHHHHHHHHHHh
Q 017210 248 MAGLAWQGRAHCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 248 ~lgI~~~g~~HrALdDA~atA~L~~~ll~~ 277 (375)
+||++.. .+|+|++||++||+||.+|++.
T Consensus 172 ~~gi~~~-~~H~Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 172 HLDLPVL-GRHDALNDAIMAALIFLRLRKG 200 (202)
T ss_pred HcCCCCC-CCCCcHHHHHHHHHHHHHHHhc
Confidence 9999986 5799999999999999998753
No 28
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.5e-30 Score=243.99 Aligned_cols=163 Identities=23% Similarity=0.250 Sum_probs=141.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
.++||||+||||+ ++..++|||||++ + +...++|+++|+|.. +|+++++++||||++||+++|+|.+|++
T Consensus 2 ~~~vv~D~ETTGl---~~~~d~IIeig~v--~---~~~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~ 71 (232)
T PRK06309 2 PALIFYDTETTGT---QIDKDRIIEIAAY--N---GVTSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQ 71 (232)
T ss_pred CcEEEEEeeCCCC---CCCCCEEEEEEEE--c---CccccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHH
Confidence 3699999999997 4577999999995 2 234578999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQ 254 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~-a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~ 254 (375)
+|.+|+++. .++|+|| ++||+ .||.++++++|++.|. +.++|+..+++.+.+ ..+++|.+++++||++..
T Consensus 72 ~~~~fi~~~-----~~lVaHN~~~FD~-~~L~~e~~r~g~~~~~--~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~~ 143 (232)
T PRK06309 72 KFIEFCGTD-----NILVAHNNDAFDF-PLLRKECRRHGLEPPT--LRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEEN 143 (232)
T ss_pred HHHHHHcCC-----CEEEEeCCHHHHH-HHHHHHHHHcCCCCCC--CcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCCC
Confidence 999999864 2467788 48996 9999999999998753 689999999987764 357899999999999875
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhc
Q 017210 255 GRAHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 255 g~~HrALdDA~atA~L~~~ll~~~ 278 (375)
++|||++||.+|++||.+|+++.
T Consensus 144 -~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 144 -QAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred -CCCCcHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999998765
No 29
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.97 E-value=3e-30 Score=238.44 Aligned_cols=178 Identities=20% Similarity=0.188 Sum_probs=143.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEc-CCCeE--eeEEEEeecCCCCCCCCcchHhhhCCChH-HHhCCCCHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS-VTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQI-QVDRGVTLS 172 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~-~~g~i--~d~F~~lVkP~~~p~Is~~~~~LTGIt~e-~l~~ap~~~ 172 (375)
..+||||+||||+ ++..++|||||||+|.. .+|++ .++|+++|+|....+|++++.++||||++ |+.+++++.
T Consensus 8 ~~~vv~D~ETTGl---~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~~ 84 (200)
T TIGR01298 8 YLPVVVDVETGGF---NAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSEY 84 (200)
T ss_pred CeeEEEEeeCCCC---CCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcchH
Confidence 4699999999997 46779999999999952 24666 36899999984212599999999999976 799999999
Q ss_pred HHHHHHHHHHhhCC---CCCccEEEEEcCcchHHHHHHHHHHHcCCCC-CCCCCceeehHHHHHHhcCCCCCCHHHHHHH
Q 017210 173 EALLRHDKWLENKG---IKNTNFAVVTWSNWDCRVMLESECRFKKIWK-PPYFNRWINLKVPFHEVFGGVRCNLKEAVEM 248 (375)
Q Consensus 173 evl~~f~~fl~~~~---lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~-P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~ 248 (375)
++++++.+|+.+.. ..+..++|+||++||+ .||++++++.|+.. |.....++||..+++..++ .++|++++++
T Consensus 85 ~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~-~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~--~~~L~~l~~~ 161 (200)
T TIGR01298 85 EALHEIFKVVRKAMKASGCQRAILVGHNANFDL-GFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG--QTVLAKACQA 161 (200)
T ss_pred HHHHHHHHHHHHHHHhcccCCCEEEEECchhhH-HHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC--cccHHHHHHH
Confidence 99999999885321 1123467899999997 99999999988743 2112369999999987765 4689999999
Q ss_pred cCCCCC-CCCCcHHHHHHHHHHHHHHHHHhccc
Q 017210 249 AGLAWQ-GRAHCGLDDAKNTARLLALLMHRGFK 280 (375)
Q Consensus 249 lgI~~~-g~~HrALdDA~atA~L~~~ll~~~~~ 280 (375)
|||+.. .++|||++||.+||+||.+|+++..+
T Consensus 162 ~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~ 194 (200)
T TIGR01298 162 AGXDFDSTQAHSALYDTEKTAELFCEIVNRWKR 194 (200)
T ss_pred cCCCccccchhhhHHhHHHHHHHHHHHHHHHHH
Confidence 999864 36899999999999999999987643
No 30
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.97 E-value=9.3e-32 Score=237.89 Aligned_cols=197 Identities=31% Similarity=0.450 Sum_probs=169.9
Q ss_pred ccEEEEEEeeCCCCCC-CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 97 QYFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~-~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
...+|||+|+|+.+|. ++...|||||+|.+|+..+.+++|+|++||||..+|.++.+|..+|||+|..|+.||-|..|+
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v~ 83 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMVF 83 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHHH
Confidence 4689999999999875 467899999999999877889999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCC-CCHHHHHHHcCCCCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVR-CNLKEAVEMAGLAWQ 254 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~-~~L~~l~~~lgI~~~ 254 (375)
++|..||....-. .+-.+++||++|+ ..|.++|..+++..-++..+++|++..|...++..+ .+|..+++++|..+.
T Consensus 84 E~f~r~L~~h~Pr-~~~~wa~wG~~Dm-~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~~G~sf~ 161 (210)
T COG5018 84 EDFIRKLNEHDPR-KNSTWATWGNMDM-KVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEEYGDSFT 161 (210)
T ss_pred HHHHHHHHhcCcc-cCCccccccchhH-HHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHHHhccccC
Confidence 9999999985321 2336899999998 668889999998732355689999999999998765 899999999999999
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcccccccccccccccCCCCcc
Q 017210 255 GRAHCGLDDAKNTARLLALLMHRGFKFSITNSLMWQTNDGSLTW 298 (375)
Q Consensus 255 g~~HrALdDA~atA~L~~~ll~~~~~~~i~~~l~~~~~~~~~~~ 298 (375)
|.+||||+||+++++||..+......+.-.. +| ..++...|
T Consensus 162 G~~HraldDArn~~rl~klv~~~~~~~e~~~--~~-~~~e~~~~ 202 (210)
T COG5018 162 GTHHRALDDARNAYRLFKLVEQDKQYLEKPK--PP-TIGERIDL 202 (210)
T ss_pred CchhhhHHHHHHHHHHHHHHcchhhhccCCC--CC-cccccccc
Confidence 9999999999999999999988877766554 33 44566666
No 31
>PRK07883 hypothetical protein; Validated
Probab=99.97 E-value=5.9e-30 Score=268.61 Aligned_cols=170 Identities=24% Similarity=0.232 Sum_probs=151.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..|||||+||||+ ++..++|||||||+++ +|+++++|+++|+|.. .|+++++++||||++||+++|++++|+.
T Consensus 15 ~~~Vv~D~ETTGl---~p~~~~IIEIgaV~v~--~g~iv~~f~~lV~P~~--~i~~~~~~itGIt~e~l~~ap~~~evl~ 87 (557)
T PRK07883 15 VTFVVVDLETTGG---SPAGDAITEIGAVKVR--GGEVLGEFATLVNPGR--PIPPFITVLTGITTAMVAGAPPIEEVLP 87 (557)
T ss_pred CCEEEEEEecCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHH
Confidence 5799999999997 4677999999999996 7899999999999985 5999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC---CCCCCHHHHHHHcCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG---GVRCNLKEAVEMAGLAW 253 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~---~~~~~L~~l~~~lgI~~ 253 (375)
+|.+|+++. ++|+||++||+ .||+.+|+++|+++| .+.++||..+++.+++ ..+++|+++++++|++.
T Consensus 88 ~f~~fl~~~------~lVaHNa~FD~-~fL~~~~~r~g~~~~--~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~ 158 (557)
T PRK07883 88 AFLEFARGA------VLVAHNAPFDI-GFLRAAAARCGYPWP--GPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATT 158 (557)
T ss_pred HHHHHhcCC------EEEEeCcHHHH-HHHHHHHHHcCCCCC--CCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCccc
Confidence 999999874 46788899996 999999999999875 3579999999988774 35799999999999998
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcccccc
Q 017210 254 QGRAHCGLDDAKNTARLLALLMHRGFKFSI 283 (375)
Q Consensus 254 ~g~~HrALdDA~atA~L~~~ll~~~~~~~i 283 (375)
+ .+|+|++||++||+||.+++.+....++
T Consensus 159 ~-~~H~Al~DA~ata~l~~~l~~~~~~~~~ 187 (557)
T PRK07883 159 T-PTHRALDDARATVDVLHGLIERLGNLGV 187 (557)
T ss_pred C-CCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 6 5799999999999999999988765544
No 32
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=3e-29 Score=273.43 Aligned_cols=165 Identities=22% Similarity=0.258 Sum_probs=147.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..|||||+||||++ + .++|||||||+++ +|+++++|+++|+|.. +|+++++++||||++||++||+|+||++
T Consensus 7 ~~~vvvD~ETTGl~---~-~d~IIeIgaV~v~--~g~i~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~ 78 (820)
T PRK07246 7 RKYAVVDLEATGAG---P-NASIIQVGIVIIE--GGEIIDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFSQVAR 78 (820)
T ss_pred CCEEEEEEecCCcC---C-CCeEEEEEEEEEE--CCEEEEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHHHHHH
Confidence 57999999999973 3 4899999999995 7899999999999985 5999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQG 255 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~g 255 (375)
+|.+|+++. ++|+||+.||+ .||++++.+.|++.+ ++++||..+++.+++ ..+++|++++++||++..
T Consensus 79 ~~~~~l~~~------~lVaHN~~FD~-~fL~~~~~~~g~~~~---~~~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~- 147 (820)
T PRK07246 79 HIYDLIEDC------IFVAHNVKFDA-NLLAEALFLEGYELR---TPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLA- 147 (820)
T ss_pred HHHHHhCCC------EEEEECcHHHH-HHHHHHHHHcCCCCC---CCceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-
Confidence 999999875 46788899996 999999988887653 578999999988885 468999999999999986
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhccc
Q 017210 256 RAHCGLDDAKNTARLLALLMHRGFK 280 (375)
Q Consensus 256 ~~HrALdDA~atA~L~~~ll~~~~~ 280 (375)
++|||++||++||+||.+|+++...
T Consensus 148 ~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 148 DAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 6899999999999999999877543
No 33
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.96 E-value=6.5e-29 Score=226.05 Aligned_cols=162 Identities=19% Similarity=0.164 Sum_probs=131.1
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhC-CCCHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEALLRH 178 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~-ap~~~evl~~f 178 (375)
++||+||||+ ++..++|||||||+++ .++.++++|+++|+|.....+++.+..+||||++||.+ ++++.+++++|
T Consensus 1 ~~~D~ETTGl---~~~~d~Iieig~v~v~-~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~ 76 (183)
T cd06138 1 LFYDYETFGL---NPSFDQILQFAAIRTD-ENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKI 76 (183)
T ss_pred CEEEeecCCC---CCCCCceEEEEEEEEC-CCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 5899999997 4678999999999996 34466699999999974224788999999999999999 99999999999
Q ss_pred HHHHhhCCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCCCC----CCceeehHHHHHHhc--------------CCCC
Q 017210 179 DKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPY----FNRWINLKVPFHEVF--------------GGVR 239 (375)
Q Consensus 179 ~~fl~~~~lv~~n~~vv~~-a~FD~~~fL~~~~~~~gi~~P~~----~~~~iDt~~l~~~~~--------------~~~~ 239 (375)
.+|+++. ..++|+|| +.||+ .||++++.++++..+.. .+.++|+..+++..+ +.++
T Consensus 77 ~~~~~~~----~~~lVahn~~~FD~-~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~ 151 (183)
T cd06138 77 HRLFNTP----GTCIVGYNNIRFDD-EFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPS 151 (183)
T ss_pred HHHHccC----CCcEEeeCchhhHH-HHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcc
Confidence 9999742 12456776 68996 99999999998754311 235688887766532 2346
Q ss_pred CCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHH
Q 017210 240 CNLKEAVEMAGLAWQGRAHCGLDDAKNTARLL 271 (375)
Q Consensus 240 ~~L~~l~~~lgI~~~g~~HrALdDA~atA~L~ 271 (375)
++|++++++|||+.. ++|||++||++||+|+
T Consensus 152 ~~L~~l~~~~gi~~~-~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 152 FKLEDLAQANGIEHS-NAHDALSDVEATIALA 182 (183)
T ss_pred hhHHHHHHHCCCCcc-ccccHHHHHHHHHHHh
Confidence 899999999999974 6899999999999885
No 34
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=3.3e-28 Score=241.03 Aligned_cols=164 Identities=15% Similarity=0.158 Sum_probs=137.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..||||||||||+ ++..++|||||||+++ .+|+++++|++||||.. + +.+ ..|||||++||++||+|++|++
T Consensus 46 ~~fVvlDiETTGL---dp~~drIIeIgAV~i~-~~g~ive~f~tLVnP~~-~-~~p--~~LHGIT~e~La~AP~f~eVl~ 117 (377)
T PRK05601 46 APFVAVSIQTSGI---HPSTSRLITIDAVTLT-ADGEEVEHFHAVLNPGE-D-PGP--FHLHGLSAEEFAQGKRFSQILK 117 (377)
T ss_pred CCEEEEEEECCCC---CCCCCeEEEEEEEEEE-cCCEEEEEEEEEECcCC-C-CCC--ccccCCCHHHHhcCCCHHHHHH
Confidence 4699999999997 5788999999999996 47899999999999986 3 333 3799999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCC-------------------------CCCCCCCceeehHHHH
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKI-------------------------WKPPYFNRWINLKVPF 231 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi-------------------------~~P~~~~~~iDt~~l~ 231 (375)
+|.+||++. .+|+||+.||+ .||..++++.+. ...+..+.++||..+.
T Consensus 118 el~~fL~g~------vLVaHNA~FD~-~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LA 190 (377)
T PRK05601 118 PLDRLIDGR------TLILHNAPRTW-GFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATA 190 (377)
T ss_pred HHHHHhCCC------EEEEECcHHHH-HHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHH
Confidence 999999986 46889999996 999999876421 1112346899999999
Q ss_pred HHhc-CCCCCCHHHHHHHcCCCCC---------CCCCcHH--HHHHHHHHHHHHHH
Q 017210 232 HEVF-GGVRCNLKEAVEMAGLAWQ---------GRAHCGL--DDAKNTARLLALLM 275 (375)
Q Consensus 232 ~~~~-~~~~~~L~~l~~~lgI~~~---------g~~HrAL--dDA~atA~L~~~ll 275 (375)
+.++ ..++|+|.+++++|||+.. ...|+|| +||+.+++||.++.
T Consensus 191 Rrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~ 246 (377)
T PRK05601 191 RRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALR 246 (377)
T ss_pred HHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhh
Confidence 9887 4578999999999999871 1458888 69999999999873
No 35
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.4e-28 Score=271.71 Aligned_cols=167 Identities=23% Similarity=0.309 Sum_probs=148.7
Q ss_pred ccEEEEEEeeCCCCCCCCC-CCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPY-PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~-~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
+.|||||+||||.+ +. .++|||||||+++ +|+++++|+++|||.. .|+++++++||||++||++||+|+||+
T Consensus 3 ~~~vvvD~ETTG~~---p~~~d~IIeigav~v~--~~~i~~~f~~~v~P~~--~i~~~~~~ltGIt~~~l~~ap~f~ev~ 75 (928)
T PRK08074 3 KRFVVVDLETTGNS---PKKGDKIIQIAAVVVE--DGEILERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVA 75 (928)
T ss_pred CCEEEEEEeCCCCC---CCCCCcEEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHhcCCCHHHHH
Confidence 46999999999963 33 4899999999994 8999999999999985 599999999999999999999999999
Q ss_pred HHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQ 254 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~ 254 (375)
++|.+|+++. .+|+||+.||+ .||+++|.+.|++.+ .+++|||..+++.+++ ..+++|.+++++|||+..
T Consensus 76 ~~l~~~l~~~------~~VaHN~~FD~-~fL~~~~~~~g~~~~--~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~~ 146 (928)
T PRK08074 76 PEIVELLEGA------YFVAHNVHFDL-NFLNEELERAGYTEI--HCPKLDTVELARILLPTAESYKLRDLSEELGLEHD 146 (928)
T ss_pred HHHHHHhCCC------eEEEEChHHHH-HHHHHHHHHcCCCCC--CCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCCC
Confidence 9999999875 46788899996 999999999998653 4689999999988875 468999999999999975
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhccc
Q 017210 255 GRAHCGLDDAKNTARLLALLMHRGFK 280 (375)
Q Consensus 255 g~~HrALdDA~atA~L~~~ll~~~~~ 280 (375)
++|||++||++||+||.+|+++...
T Consensus 147 -~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 147 -QPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHHh
Confidence 7899999999999999999877543
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=99.96 E-value=5.5e-28 Score=265.05 Aligned_cols=165 Identities=24% Similarity=0.257 Sum_probs=147.5
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHH
Q 017210 98 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 177 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~ 177 (375)
+|||||+||||+ ++..++|||||||+++ +|+++++|+++|+|.. +|+++++++||||++||+++|+|+||+++
T Consensus 1 ~~vvvD~ETTG~---~~~~~~IIeig~v~v~--~~~i~~~f~~~v~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~~ 73 (850)
T TIGR01407 1 RYAVVDLETTGT---QLSFDKIIQIGIVVVE--DGEIVDTFHTDVNPNE--PIPPFIQELTGISDNMLQQAPYFSQVAQE 73 (850)
T ss_pred CEEEEEEECCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEeCCCC--CCChhhhhhcCcCHHHHhCCCCHHHHHHH
Confidence 499999999997 4567999999999995 7899999999999985 59999999999999999999999999999
Q ss_pred HHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 017210 178 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 256 (375)
Q Consensus 178 f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~g~ 256 (375)
|.+|+++. ++|+||+.||+ .||++++++.|++. +.++++||..+++.+++ ..+++|.+++++||++.+ +
T Consensus 74 l~~~l~~~------~~VahN~~fD~-~fL~~~~~~~g~~~--~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~ 143 (850)
T TIGR01407 74 IYDLLEDG------IFVAHNVHFDL-NFLAKALKDCGYEP--LPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHE-N 143 (850)
T ss_pred HHHHhCCC------EEEEeCcHHHH-HHHHHHHHHcCCCC--CCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-C
Confidence 99999874 46788899996 99999999999864 34679999999988875 468999999999999986 6
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcc
Q 017210 257 AHCGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 257 ~HrALdDA~atA~L~~~ll~~~~ 279 (375)
+|||++||++||+||.+++.+..
T Consensus 144 ~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 144 PHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred CCChHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999977643
No 37
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.96 E-value=8.5e-28 Score=225.27 Aligned_cols=149 Identities=21% Similarity=0.216 Sum_probs=127.8
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHH
Q 017210 99 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 178 (375)
Q Consensus 99 fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f 178 (375)
++|||+||||++ .+|||||+|+|. +|+++++|++||+|.. +|+++++++||||++||.++|++++|+++|
T Consensus 2 ~~vlD~ETTGl~------~~IieIg~v~v~--~~~i~~~~~~lv~P~~--~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~ 71 (219)
T PRK07983 2 LRVIDTETCGLQ------GGIVEIASVDVI--DGKIVNPMSHLVRPDR--PISPQAMAIHRITEAMVADKPWIEDVIPHY 71 (219)
T ss_pred eEEEEEECCCCC------CCCEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHcCCCCHHHHHHHH
Confidence 799999999974 249999999994 8899999999999996 599999999999999999999999999985
Q ss_pred HHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC----
Q 017210 179 DKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ---- 254 (375)
Q Consensus 179 ~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~---- 254 (375)
+++ .++|+||+.||. +||.. ...+|+||..+++.+++..+++|..+++++|++..
T Consensus 72 ---~~~------~~lVaHNa~FD~-~~L~~-----------~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~ 130 (219)
T PRK07983 72 ---YGS------EWYVAHNASFDR-RVLPE-----------MPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPG 130 (219)
T ss_pred ---cCC------CEEEEeCcHhhH-HHHhC-----------cCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCC
Confidence 443 357889999995 88842 12479999999999886556999999999998642
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhc
Q 017210 255 GRAHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 255 g~~HrALdDA~atA~L~~~ll~~~ 278 (375)
.++|||++||.+||+||.+|++..
T Consensus 131 ~~aHrAl~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 131 LHHHRALYDCYITAALLIDIMNTS 154 (219)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHc
Confidence 368999999999999999998653
No 38
>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=99.95 E-value=1.5e-27 Score=205.92 Aligned_cols=156 Identities=27% Similarity=0.292 Sum_probs=136.9
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 179 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~ 179 (375)
|+||+||||+ .+..++|||||+|+++. +++++++|+.+|+|.. .++++++++||||++++.+++++++++.+|.
T Consensus 1 v~~D~Ettg~---~~~~~~iiei~~v~~~~-~~~~~~~~~~~i~p~~--~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~ 74 (159)
T cd06127 1 VVFDTETTGL---DPKKDRIIEIGAVKVDG-GIEIVERFETLVNPGR--PIPPEATAIHGITDEMLADAPPFEEVLPEFL 74 (159)
T ss_pred CeEEeeCCCc---CCCCCeEEEEEEEEEEC-CcChhhhhheeeCcCC--cCCHhheeccCCCHHHHhcCCCHHHHHHHHH
Confidence 6899999997 45789999999999983 4688999999999996 5899999999999999999999999999999
Q ss_pred HHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHH-HHHcCCCCCCCC
Q 017210 180 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEA-VEMAGLAWQGRA 257 (375)
Q Consensus 180 ~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l-~~~lgI~~~g~~ 257 (375)
+|+++. ++|+||+.||. .||++.+.++|.. .....|+|+..+++.+++. +.++|..+ ++.++++.. ++
T Consensus 75 ~~l~~~------~~v~~n~~fD~-~~l~~~~~~~~~~--~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~ 144 (159)
T cd06127 75 EFLGGR------VLVAHNASFDL-RFLNRELRRLGGP--PLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE-GA 144 (159)
T ss_pred HHHCCC------EEEEeCcHhhH-HHHHHHHHHhCCC--CCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC-CC
Confidence 999873 56788899996 8999999998833 3456899999999988864 46889988 899999764 78
Q ss_pred CcHHHHHHHHHHHH
Q 017210 258 HCGLDDAKNTARLL 271 (375)
Q Consensus 258 HrALdDA~atA~L~ 271 (375)
|+|++||.+|++||
T Consensus 145 H~Al~Da~~t~~l~ 158 (159)
T cd06127 145 HRALADALATAELL 158 (159)
T ss_pred CCcHHHHHHHHHHh
Confidence 99999999999987
No 39
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=99.95 E-value=3.9e-28 Score=216.81 Aligned_cols=147 Identities=20% Similarity=0.275 Sum_probs=123.0
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCH-------H
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL-------S 172 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~-------~ 172 (375)
||||+||||+ ++..++|||||||++ ++|+++ |++||||.. +|+++++++||||++||+++|++ +
T Consensus 1 v~lD~EttGl---~~~~d~ii~Ig~V~v--~~g~i~--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~ 71 (161)
T cd06137 1 VALDCEMVGL---ADGDSEVVRISAVDV--LTGEVL--IDSLVRPSV--RVTDWRTRFSGVTPADLEEAAKAGKTIFGWE 71 (161)
T ss_pred CEEEeeeeeE---cCCCCEEEEEEEEEc--CCCeEE--EeccccCCC--CCCccceeccCCCHHHHhhhhhcCCccccHH
Confidence 6899999997 456899999999999 578875 999999985 59999999999999999998864 5
Q ss_pred HHHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC----CCCCHHHHHHH
Q 017210 173 EALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG----VRCNLKEAVEM 248 (375)
Q Consensus 173 evl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~----~~~~L~~l~~~ 248 (375)
+|+++|.+|+++. .++|+||+.||+ .||+.. .++++||..+++.+++. .+++|++++++
T Consensus 72 ~~~~~~~~~i~~~-----~vlVgHn~~fD~-~fL~~~-----------~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~ 134 (161)
T cd06137 72 AARAALWKFIDPD-----TILVGHSLQNDL-DALRMI-----------HTRVVDTAILTREAVKGPLAKRQWSLRTLCRD 134 (161)
T ss_pred HHHHHHHHhcCCC-----cEEEeccHHHHH-HHHhCc-----------CCCeeEehhhhhhccCCCcCCCCccHHHHHHH
Confidence 8999999999872 235677889997 898631 23689999999887753 57999999986
Q ss_pred -cCCCCC--CCCCcHHHHHHHHHHHHH
Q 017210 249 -AGLAWQ--GRAHCGLDDAKNTARLLA 272 (375)
Q Consensus 249 -lgI~~~--g~~HrALdDA~atA~L~~ 272 (375)
+|++.. ..+|+|++||++||+||+
T Consensus 135 ~~~~~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 135 FLGLKIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred HCCchhcCCCCCCCcHHHHHHHHHHhC
Confidence 688763 257999999999999874
No 40
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.95 E-value=1.2e-26 Score=218.64 Aligned_cols=166 Identities=25% Similarity=0.270 Sum_probs=146.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeE-EEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEAC-FQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~-F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
..+||||+||||+ ++..++|||||||.+ .++++++. |+.+|+|.. .|++++.++||||.+||.++|.|.+++
T Consensus 13 ~~~vv~D~ETtg~---~~~~~~iieIgav~~--~~~~i~~~~~~~~v~P~~--~i~~~~~~i~git~e~l~~~p~~~~v~ 85 (243)
T COG0847 13 TRFVVIDLETTGL---NPKKDRIIEIGAVTL--EDGRIVERSFHTLVNPER--PIPPEIFKIHGITDEMLADAPKFAEVL 85 (243)
T ss_pred CcEEEEecccCCC---CCCCCceEEEEeEEE--ECCeeecceeEEEECCCC--CCChhhhhhcCCCHHHHhcCCCHHHHH
Confidence 4799999999997 457899999999999 47888755 999999964 499999999999999999999999999
Q ss_pred HHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQ 254 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~~lgI~~~ 254 (375)
++|.+|+++. ...|+||+.||+ .||..++.+.+.+.+ ...++|+..+.+..++. .+++|+.+++++||+..
T Consensus 86 ~~~~~~i~~~-----~~~Vahna~fD~-~fl~~~~~~~~~~~~--~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~ 157 (243)
T COG0847 86 PEFLDFIGGL-----RLLVAHNAAFDV-GFLRVESERLGIEIP--GDPVLDTLALARRHFPGFDRSSLDALAERLGIDRN 157 (243)
T ss_pred HHHHHHHCCC-----CeEEEEchhhcH-HHHHHHHHHcCCCcc--cCceehHHHHHHHHcCCCccchHHHHHHHcCCCcC
Confidence 9999999983 246788999996 999999999998865 56799999999988866 78999999999999943
Q ss_pred -CCCCcHHHHHHHHHHHHHHHHHh
Q 017210 255 -GRAHCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 255 -g~~HrALdDA~atA~L~~~ll~~ 277 (375)
.++|+|+.||.+||.+|.++...
T Consensus 158 ~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 158 PFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CcCCcchHHHHHHHHHHHHHHHhc
Confidence 25699999999999999999885
No 41
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.94 E-value=7.9e-27 Score=206.42 Aligned_cols=149 Identities=20% Similarity=0.238 Sum_probs=116.6
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 179 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~ 179 (375)
||||+||||++ +. ++++||++|.+...+|+++ |++||+|.. .++++++++||||++||++||++.+++++|.
T Consensus 1 v~lD~EttGl~---~~-~~~~~i~~v~~v~~~~~~~--~~~~v~P~~--~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~ 72 (152)
T cd06144 1 VALDCEMVGVG---PD-GSESALARVSIVNEDGNVV--YDTYVKPQE--PVTDYRTAVSGIRPEHLKDAPDFEEVQKKVA 72 (152)
T ss_pred CEEEEEeeccc---CC-CCEEEEEEEEEEeCCCCEE--EEEEECCCC--CCCcccccCCCCCHHHHcCCCCHHHHHHHHH
Confidence 68999999974 33 3677777664432356554 999999985 5999999999999999999999999999999
Q ss_pred HHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHH-cCCCCCCC
Q 017210 180 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEM-AGLAWQGR 256 (375)
Q Consensus 180 ~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~--~~~~~L~~l~~~-lgI~~~g~ 256 (375)
+|+++. .+|+||+.||+ .||+ +..| .+.++|+..+...... .++++|++++++ +|++....
T Consensus 73 ~~l~~~------vlVgHn~~fD~-~~L~-------~~~~--~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~ 136 (152)
T cd06144 73 ELLKGR------ILVGHALKNDL-KVLK-------LDHP--KKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG 136 (152)
T ss_pred HHhCCC------EEEEcCcHHHH-HHhc-------CcCC--CccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCC
Confidence 999875 46788899997 8886 2333 2467887654332221 467999999997 69987546
Q ss_pred CCcHHHHHHHHHHHHH
Q 017210 257 AHCGLDDAKNTARLLA 272 (375)
Q Consensus 257 ~HrALdDA~atA~L~~ 272 (375)
+|||++||++|++||+
T Consensus 137 ~H~Al~DA~at~~l~~ 152 (152)
T cd06144 137 EHSSVEDARAAMRLYR 152 (152)
T ss_pred CcCcHHHHHHHHHHhC
Confidence 8999999999999984
No 42
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.94 E-value=3.6e-26 Score=206.48 Aligned_cols=162 Identities=15% Similarity=0.159 Sum_probs=122.2
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCC--CCCCcchHhh---hCCChHHHhCCCCHHH
Q 017210 99 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCN--QLLSDFCKDL---TGIQQIQVDRGVTLSE 173 (375)
Q Consensus 99 fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~--p~Is~~~~~L---TGIt~e~l~~ap~~~e 173 (375)
+|+||+||||+ +|..++|||||||+++...+++.++|+++|+|... +.+++++.++ ||||++|++++|++++
T Consensus 1 lv~iD~ETTGl---~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~ 77 (173)
T cd06135 1 LVWIDLEMTGL---DPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQ 77 (173)
T ss_pred CEEEEEecCCC---CCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHH
Confidence 58999999997 56789999999999985556888999999999851 1234555666 5999999999999999
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehH---HHHHHhcCCCCCCHHHHHHHcC
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLK---VPFHEVFGGVRCNLKEAVEMAG 250 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~---~l~~~~~~~~~~~L~~l~~~lg 250 (375)
|+.+|.+|+++..-.+..+++.|+++||+ .||++++++.|.. +.++.+|+. .+++.+++. +.. ++
T Consensus 78 vl~~~~~f~~~~~~~~~~~lvgh~~~FD~-~fL~~~~~~~~~~---~~~~~~D~~~l~~l~~~l~p~----~~~----~~ 145 (173)
T cd06135 78 AEAELLEFIKKYVPKGKSPLAGNSVHQDR-RFLDKYMPELEEY---LHYRILDVSSIKELARRWYPE----IYR----KA 145 (173)
T ss_pred HHHHHHHHHHHhcCCCCCceeecchhhCH-HHHHHHHHHHhcc---CCcchhhHHHHHHHHHHhCcH----hhh----cC
Confidence 99999999986310011123344569996 9999999988732 345678974 455555432 111 56
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHHHHH
Q 017210 251 LAWQGRAHCGLDDAKNTARLLALLMH 276 (375)
Q Consensus 251 I~~~g~~HrALdDA~atA~L~~~ll~ 276 (375)
++. +.+|||++||.+|+.++..+++
T Consensus 146 ~~~-~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 146 PKK-KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred CCC-CCCcchHHHHHHHHHHHHHHHH
Confidence 665 4679999999999999998775
No 43
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.94 E-value=2.4e-26 Score=203.22 Aligned_cols=143 Identities=20% Similarity=0.236 Sum_probs=118.0
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCC-CHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV-TLSEALLRH 178 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap-~~~evl~~f 178 (375)
|++|+||||... . +||+||++|.+ +|++ .|++||||.. .++++++++||||++||+++| ++++|+++|
T Consensus 1 ~~iD~E~~g~~~---g-~ei~~i~~v~~---~~~~--~f~~lv~P~~--~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~ 69 (150)
T cd06145 1 FALDCEMCYTTD---G-LELTRVTVVDE---NGKV--VLDELVKPDG--EIVDYNTRFSGITEEMLENVTTTLEDVQKKL 69 (150)
T ss_pred CEEeeeeeeecC---C-CEEEEEEEEeC---CCCE--EEEEeECCCC--ccchhccCcCCCCHHHhccCCCCHHHHHHHH
Confidence 589999999742 2 99999999977 4554 4999999986 599999999999999999985 999999999
Q ss_pred HHHHh-hCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHc-CCCCC-
Q 017210 179 DKWLE-NKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMA-GLAWQ- 254 (375)
Q Consensus 179 ~~fl~-~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~l-gI~~~- 254 (375)
.+|++ +. ++|+||++||+ .||+. . .++++||..+++..++ .++++|++|+++| ++...
T Consensus 70 ~~fl~~~~------vlVgHn~~fD~-~fL~~-------~----~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~ 131 (150)
T cd06145 70 LSLISPDT------ILVGHSLENDL-KALKL-------I----HPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQ 131 (150)
T ss_pred HHHhCCCC------EEEEcChHHHH-HHhhc-------c----CCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeC
Confidence 99997 43 46778899997 89863 1 2368999998887664 3578999999887 54332
Q ss_pred -CCCCcHHHHHHHHHHHH
Q 017210 255 -GRAHCGLDDAKNTARLL 271 (375)
Q Consensus 255 -g~~HrALdDA~atA~L~ 271 (375)
+.+|||++||++|++||
T Consensus 132 ~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 132 GEGGHDSVEDARAALELV 149 (150)
T ss_pred CCCCCCcHHHHHHHHHHh
Confidence 35799999999999987
No 44
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.94 E-value=3.1e-26 Score=204.08 Aligned_cols=149 Identities=20% Similarity=0.231 Sum_probs=119.4
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 179 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~ 179 (375)
||||+||||++. ....++|++|++|.+ +|+++ |++||||.. +++++++++||||++||++||++++|+++|.
T Consensus 1 v~~D~EttGl~~-~~~~~~i~~i~~v~~---~g~~~--~~~lv~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~ 72 (157)
T cd06149 1 VAIDCEMVGTGP-GGRESELARCSIVNY---HGDVL--YDKYIRPEG--PVTDYRTRWSGIRRQHLVNATPFAVAQKEIL 72 (157)
T ss_pred CEEEeEeccccC-CCCeEEEEEEEEEeC---CCCEE--EEEeECCCC--ccCccceECCCCCHHHHhcCCCHHHHHHHHH
Confidence 689999999842 112588999988876 56665 999999985 5999999999999999999999999999999
Q ss_pred HHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHH--HHHh--cC-CCCCCHHHHHHHc---CC
Q 017210 180 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVP--FHEV--FG-GVRCNLKEAVEMA---GL 251 (375)
Q Consensus 180 ~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l--~~~~--~~-~~~~~L~~l~~~l---gI 251 (375)
+|+++. ++|+||..||+ .||+.. .| ...++||..+ ++.. ++ .++++|+.++++| ++
T Consensus 73 ~~l~~~------vlV~Hn~~~D~-~~l~~~-------~~--~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i 136 (157)
T cd06149 73 KILKGK------VVVGHAIHNDF-KALKYF-------HP--KHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDI 136 (157)
T ss_pred HHcCCC------EEEEeCcHHHH-HHhccc-------CC--CcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhh
Confidence 999885 46778889998 888632 22 2357888654 4433 43 3579999999999 67
Q ss_pred CCCCCCCcHHHHHHHHHHHHH
Q 017210 252 AWQGRAHCGLDDAKNTARLLA 272 (375)
Q Consensus 252 ~~~g~~HrALdDA~atA~L~~ 272 (375)
+..++.|||++||++|++||.
T Consensus 137 ~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 137 QVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred cCCCCCcCcHHHHHHHHHHhC
Confidence 654467999999999999983
No 45
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=2.5e-25 Score=216.91 Aligned_cols=172 Identities=20% Similarity=0.191 Sum_probs=130.5
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcC-CC---eEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCH
Q 017210 96 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSV-TG---QLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL 171 (375)
Q Consensus 96 ~~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~-~g---~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~ 171 (375)
...+||||+||||+ ++..++|||||+|+++.. +| +++++|++||+|.. .|+++++++||||++||.+++..
T Consensus 36 ~~~~vvlD~ETTGL---d~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~--~I~~~~t~IhGIt~e~v~~~~~~ 110 (294)
T PRK09182 36 VRLGVILDTETTGL---DPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR--PIPPEITRLTGITDEMVAGQTID 110 (294)
T ss_pred CCeEEEEEeeCCCC---CCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC--CCCHHHHHhcCCCHHHHhcCCCc
Confidence 35799999999997 567899999999999632 45 45789999999985 59999999999999999998876
Q ss_pred HHHHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHh-cCCCCCCHHHHHHHcC
Q 017210 172 SEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEV-FGGVRCNLKEAVEMAG 250 (375)
Q Consensus 172 ~evl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~-~~~~~~~L~~l~~~lg 250 (375)
.+++ .+|++.. .++|+||+.||. .||++.+....- ..|.++....... .+..+++|++|+++||
T Consensus 111 ~~~l---~~fl~~~-----~vlVAHNA~FD~-~fL~~~~~~~~~------~~~~ct~~~i~~~~~~~~~~kL~~La~~~g 175 (294)
T PRK09182 111 PAAV---DALIAPA-----DLIIAHNAGFDR-PFLERFSPVFAT------KPWACSVSEIDWSARGFEGTKLGYLAGQAG 175 (294)
T ss_pred HHHH---HHHhcCC-----CEEEEeCHHHHH-HHHHHHHHhccC------CcccccHHHHhhccccCCCCCHHHHHHHcC
Confidence 5554 5555543 357899999995 999987654321 2355554333322 2346899999999999
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHHHHHhcccccccccccc
Q 017210 251 LAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLMW 289 (375)
Q Consensus 251 I~~~g~~HrALdDA~atA~L~~~ll~~~~~~~i~~~l~~ 289 (375)
. .. .+|||++||.+|++||.+++.......+.+.+..
T Consensus 176 ~-~~-~aHrAl~Da~Ata~ll~~~l~~~~~~~l~~Ll~~ 212 (294)
T PRK09182 176 F-FH-EGHRAVDDCQALLELLARPLPETGQPPLAELLEA 212 (294)
T ss_pred C-CC-CCcChHHHHHHHHHHHHHHHhhcCCcCHHHHHHH
Confidence 4 33 6899999999999999988766554555555444
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=99.93 E-value=1.1e-26 Score=200.71 Aligned_cols=162 Identities=27% Similarity=0.358 Sum_probs=127.2
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 179 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~ 179 (375)
||||+||||++ +..++|||||+|+++.....+.++|++||+|...+.+++.++++||||+++|++++++.+++.+|.
T Consensus 1 v~~D~Ettg~~---~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~ 77 (164)
T PF00929_consen 1 VVFDTETTGLD---PRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFE 77 (164)
T ss_dssp EEEEEEESSST---TTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHH
T ss_pred cEEEeEcCCCC---CCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhh
Confidence 79999999974 467999999999998544447889999999997445999999999999999999999999999999
Q ss_pred HHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHc-CCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCCC
Q 017210 180 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFK-KIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGRA 257 (375)
Q Consensus 180 ~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~-gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~lgI~~~g~~ 257 (375)
+|+.+. ..++.||+.||+ .++...+.+. +...| ....++|+..+.+..++ ...++|+.++++|+++..+.+
T Consensus 78 ~~~~~~-----~~~v~~n~~fd~-~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~ 150 (164)
T PF00929_consen 78 EFLKKN-----DILVGHNASFDI-GFLRREDKRFLGKPIP-KPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGTA 150 (164)
T ss_dssp HHHHHH-----TEEEETTCCHEE-ESSHHHHHHHHHHHHH-HHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTSTT
T ss_pred hhhhcc-----cccccccccchh-hHHHHhhhhccccccc-ccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCCC
Confidence 999953 234555678997 7888888776 33322 01235554433333321 123799999999999998668
Q ss_pred CcHHHHHHHHHHHH
Q 017210 258 HCGLDDAKNTARLL 271 (375)
Q Consensus 258 HrALdDA~atA~L~ 271 (375)
|+|++||++|++||
T Consensus 151 H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 151 HDALDDARATAELF 164 (164)
T ss_dssp TSHHHHHHHHHHHH
T ss_pred cChHHHHHHHhCcC
Confidence 99999999999987
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=99.91 E-value=8.2e-24 Score=192.87 Aligned_cols=163 Identities=13% Similarity=0.083 Sum_probs=125.1
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEe-eEEEEeecCCCC--CCCCcchHhhh---CCChHHHhCCCC
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLE-ACFQTYVRPTCN--QLLSDFCKDLT---GIQQIQVDRGVT 170 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~-d~F~~lVkP~~~--p~Is~~~~~LT---GIt~e~l~~ap~ 170 (375)
+.|||||+||||+ +|..++|||||||+++. +..++ +.|+.+|+|... ..++++++.+| |||+++++++++
T Consensus 3 ~~~vvlD~ETTGL---dp~~d~IieIgaV~~~~-~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~ 78 (181)
T PRK05359 3 DNLIWIDLEMTGL---DPERDRIIEIATIVTDA-DLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVS 78 (181)
T ss_pred CcEEEEEeecCCC---CCCCCeEEEEEEEEEcC-CceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCC
Confidence 4799999999997 57889999999999962 33444 679999999751 12577888887 899999999999
Q ss_pred HHHHHHHHHHHHhhCCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCCCCCCceeeh--H-HHHHHhcCCCCCCHHHHH
Q 017210 171 LSEALLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPYFNRWINL--K-VPFHEVFGGVRCNLKEAV 246 (375)
Q Consensus 171 ~~evl~~f~~fl~~~~lv~~n~~vv~~-a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt--~-~l~~~~~~~~~~~L~~l~ 246 (375)
+.||+++|++|+++.... ++..+|+| ..||+ .||++.+.+.+..+ .++++|+ . .+++.+++. +
T Consensus 79 ~~e~~~~~l~fl~~~~~~-~~~~l~g~~v~FD~-~FL~~~~~~~~~~l---~~~~~Dv~tl~~l~r~~~P~----~---- 145 (181)
T PRK05359 79 EAEAEAQTLEFLKQWVPA-GKSPLCGNSIGQDR-RFLARYMPELEAYF---HYRNLDVSTLKELARRWKPE----I---- 145 (181)
T ss_pred HHHHHHHHHHHHHHhcCC-CCCceeecchhhCH-HHHHHHHHHhcccC---CCcccchhHHHHHHHHhChh----h----
Confidence 999999999999876542 23334554 59996 99999998877543 4578884 3 456665542 2
Q ss_pred HHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhc
Q 017210 247 EMAGLAWQGRAHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 247 ~~lgI~~~g~~HrALdDA~atA~L~~~ll~~~ 278 (375)
+++++.. ..|||++|++.+.+.+..+.+..
T Consensus 146 -~~~~~~~-~~HRal~D~~~s~~~~~~~~~~~ 175 (181)
T PRK05359 146 -LNGFKKQ-GTHRALADIRESIAELKYYREHF 175 (181)
T ss_pred -hhCCCCc-CCcccHHHHHHHHHHHHHHHHHh
Confidence 3577765 56999999999999888776543
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.91 E-value=3.4e-23 Score=213.22 Aligned_cols=171 Identities=16% Similarity=0.109 Sum_probs=130.8
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCC-eEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhC-CCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTG-QLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g-~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~-ap~~~ev 174 (375)
.+|||||+||||+ +|..|+|||||||+++. ++ .+.+.|+.+|+|.....+++.+..+||||++||.+ +.+..|+
T Consensus 6 ~~fvv~D~ETTGL---dP~~DrIIeiAaVrvd~-~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~ 81 (476)
T PRK11779 6 PTFLWHDYETFGA---NPALDRPAQFAGIRTDA-DLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEF 81 (476)
T ss_pred CcEEEEEEECCCC---CCCCCeeEEEEEEEEeC-CCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHH
Confidence 4699999999997 57889999999999973 33 44578999999985223567899999999999964 6689999
Q ss_pred HHHHHHHHhhCCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCC----CCCCceeehHHHHHHhc--------------
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKP----PYFNRWINLKVPFHEVF-------------- 235 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~-a~FD~~~fL~~~~~~~gi~~P----~~~~~~iDt~~l~~~~~-------------- 235 (375)
+.+|.+|+... ..++|+|| .+||+ .||+..+.+..++.- ...+..+|+..+.+..+
T Consensus 82 ~~~i~~~l~~~----~~~lVGhNni~FD~-eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~ 156 (476)
T PRK11779 82 AARIHAEFSQP----GTCILGYNNIRFDD-EVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENED 156 (476)
T ss_pred HHHHHHHHhcC----CCEEEEeCchhhcH-HHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCccccc
Confidence 99999999621 13456666 58996 899999876554310 00122345554444222
Q ss_pred CCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHh
Q 017210 236 GGVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 236 ~~~~~~L~~l~~~lgI~~~g~~HrALdDA~atA~L~~~ll~~ 277 (375)
|..+++|+++++++||+.. ++|+|++||++|++|+..|.++
T Consensus 157 g~~s~rLe~L~~~~gI~~~-~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 157 GLPSFKLEHLTKANGIEHE-NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCCCcHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHh
Confidence 2356999999999999975 7899999999999999988866
No 49
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.35 E-value=7.9e-12 Score=118.63 Aligned_cols=158 Identities=20% Similarity=0.256 Sum_probs=113.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..+|++|+|+.|.. .....+..--+. +|+ ..|.++ |+.||+|.. +++++-+.++||+.+.+.+|.+|+.|-.
T Consensus 105 ~r~vAmDCEMVG~G-p~G~~s~lARvS--IVN-~~G~Vv--yDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~aQ~ 176 (280)
T KOG2249|consen 105 TRVVAMDCEMVGVG-PDGRESLLARVS--IVN-YHGHVV--YDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVAQK 176 (280)
T ss_pred ceEEEEeeeEeccC-CCccceeeeEEE--Eee-ccCcEe--eeeecCCCc--ccccceeeecccCHHHhccCccHHHHHH
Confidence 36999999999862 112334444443 334 467775 999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHH--HHHHhc-CCCCCCHHHHHH-HcCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKV--PFHEVF-GGVRCNLKEAVE-MAGLA 252 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~--l~~~~~-~~~~~~L~~l~~-~lgI~ 252 (375)
+++++|.+.++|||-. .-|+ .-| ++..|. ....||.. .+..++ ...+.+|..|.+ .||++
T Consensus 177 ev~klL~gRIlVGHaL------hnDl-~~L-------~l~hp~--s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~ 240 (280)
T KOG2249|consen 177 EVLKLLKGRILVGHAL------HNDL-QAL-------KLEHPR--SMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKD 240 (280)
T ss_pred HHHHHHhCCEEecccc------ccHH-HHH-------hhhCch--hhhcccccCchHHHHhhccCCccHHHHHHHHhchh
Confidence 9999999986665531 3354 223 345552 23456642 333333 335789999995 66877
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHhc
Q 017210 253 WQGRAHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 253 ~~g~~HrALdDA~atA~L~~~ll~~~ 278 (375)
...-.|+.+.||.+|.+||.++-.+.
T Consensus 241 IQ~GeHsSvEDA~AtM~LY~~vk~qw 266 (280)
T KOG2249|consen 241 IQVGEHSSVEDARATMELYKRVKVQW 266 (280)
T ss_pred hhccccCcHHHHHHHHHHHHHHHHHH
Confidence 65335999999999999999876543
No 50
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=99.35 E-value=5.9e-11 Score=108.68 Aligned_cols=138 Identities=15% Similarity=0.011 Sum_probs=102.1
Q ss_pred EEEEEeeCCCCCC-CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHH
Q 017210 100 VVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 178 (375)
Q Consensus 100 VVfDlETTGl~g~-~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f 178 (375)
++||+||||+.+. ++..++||+||++.. .+|... .+.....+.. +.++ ||+..+|...++..+.+.+|
T Consensus 2 ~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~--~~g~~~-~~~~~~~~~~-~~~~-------~i~~~~v~~~~~E~~lL~~f 70 (199)
T cd05160 2 LSFDIETTPPVGGPEPDRDPIICITYADS--FDGVKV-VFLLKTSTVG-DDIE-------FIDGIEVEYFADEKELLKRF 70 (199)
T ss_pred ccEEEeecCCCCCcCCCCCCEEEEEEEEe--eCCcee-eEEEeecccC-CcCC-------CCCCceEEEeCCHHHHHHHH
Confidence 6899999997431 467899999999887 345543 2333333321 1111 89999999999999999999
Q ss_pred HHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCC-CC-------------------CCceeehHHHHHHhcCC
Q 017210 179 DKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKP-PY-------------------FNRWINLKVPFHEVFGG 237 (375)
Q Consensus 179 ~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P-~~-------------------~~~~iDt~~l~~~~~~~ 237 (375)
.++++.... .+++.||+ +||+ .||...++.+|++.. .. ...++|+..+++..+..
T Consensus 71 ~~~i~~~dp---diivg~N~~~FD~-~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l 146 (199)
T cd05160 71 FDIIREYDP---DILTGYNIDDFDL-PYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKL 146 (199)
T ss_pred HHHHHhcCC---CEEEEeccCCCcH-HHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCc
Confidence 999997421 34666777 8997 899999999888751 00 12468999889888778
Q ss_pred CCCCHHHHHHHcCCC
Q 017210 238 VRCNLKEAVEMAGLA 252 (375)
Q Consensus 238 ~~~~L~~l~~~lgI~ 252 (375)
.+|+|++++++++..
T Consensus 147 ~sy~L~~v~~~~l~~ 161 (199)
T cd05160 147 KSYTLDAVAEELLGE 161 (199)
T ss_pred ccCCHHHHHHHHhCC
Confidence 899999999877654
No 51
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=99.34 E-value=4.1e-13 Score=95.72 Aligned_cols=44 Identities=34% Similarity=0.924 Sum_probs=40.1
Q ss_pred ccccCCCCCCccccccCCCCCCCCcccCCCCcccCCCCcCcccccCC
Q 017210 327 PSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 373 (375)
Q Consensus 327 ~~c~cg~~a~~~~v~k~Gpn~Gr~fy~C~~~~~~~~~~c~ff~W~~~ 373 (375)
|.|.||..+.++|++|.|+|+||.||+|+++. .+.|+||+|.|+
T Consensus 1 p~C~Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~---~~~C~fF~W~De 44 (45)
T PF06839_consen 1 PKCPCGEPAVRRTSKKTGPNPGRRFYKCPNYK---DKGCNFFQWEDE 44 (45)
T ss_pred CCCCCCCEeEEEEEeCCCCCCCCcceECCCCC---CCCcCCEEeccC
Confidence 57999999999999999999999999998853 378999999997
No 52
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.19 E-value=2.6e-10 Score=103.39 Aligned_cols=154 Identities=21% Similarity=0.230 Sum_probs=106.3
Q ss_pred ccEEEEEEeeCCCCCC-C-----CCCCcEEEEceEEEEc-CCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCC
Q 017210 97 QYFVVIDFEATCDKDK-N-----PYPQEIIEFPSVIVSS-VTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV 169 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~-~-----~~~~eIIEIGAV~vd~-~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap 169 (375)
..||-+|.|++++... . +...++.-|.+|-.++ .+|+++ +..||+|.. ++.++.|+++|||.++++++.
T Consensus 5 ~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vl--lD~~VkP~~--~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 5 AEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPF--IDDYISTTE--PVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred eeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEE--EeeeECCCC--CccCcCccccccCHHHcCccc
Confidence 3577777777765310 0 0123555564443111 356664 889999985 599999999999999998775
Q ss_pred ------CHHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCH
Q 017210 170 ------TLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNL 242 (375)
Q Consensus 170 ------~~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L 242 (375)
++++|..++.+++... .++|.|+ ..|+ . ..++..|. ...+||..+|+. ...++.+|
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~------tILVGHsL~nDL-~-------aL~l~hp~--~~viDTa~l~~~-~~~r~~sL 143 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLG------CIFVGHGLAKDF-R-------VINIQVPK--EQVIDTVELFHL-PGQRKLSL 143 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCC------CEEEeccchhHH-H-------HhcCcCCC--cceEEcHHhccC-CCCCChhH
Confidence 6899999999998632 2344443 5676 2 23465552 368999876643 22246899
Q ss_pred HHHHH-HcCCCCCCCCCcHHHHHHHHHHHH
Q 017210 243 KEAVE-MAGLAWQGRAHCGLDDAKNTARLL 271 (375)
Q Consensus 243 ~~l~~-~lgI~~~g~~HrALdDA~atA~L~ 271 (375)
..|++ ++|.......|+.++||+++.+||
T Consensus 144 k~La~~~L~~~IQ~~~HdSvEDArAam~Ly 173 (174)
T cd06143 144 RFLAWYLLGEKIQSETHDSIEDARTALKLY 173 (174)
T ss_pred HHHHHHHcCCcccCCCcCcHHHHHHHHHHh
Confidence 99995 668777645799999999999987
No 53
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=99.02 E-value=3.3e-09 Score=87.10 Aligned_cols=94 Identities=24% Similarity=0.259 Sum_probs=70.4
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 179 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~ 179 (375)
++||+||||++ +..++|++|+....+ ++. .|.. . |.
T Consensus 1 ~~~DiEt~~~~---~~~~~i~~i~~~~~~--~~~---~~~~---~---------------------------------f~ 36 (96)
T cd06125 1 IAIDTEATGLD---GAVHEIIEIALADVN--PED---TAVI---D---------------------------------LK 36 (96)
T ss_pred CEEEEECCCCC---CCCCcEEEEEEEEcc--CCC---EEEe---h---------------------------------HH
Confidence 57999999974 578999999887542 121 1110 0 88
Q ss_pred HHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCCCCc
Q 017210 180 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGRAHC 259 (375)
Q Consensus 180 ~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~g~~Hr 259 (375)
+|+++... ...|.||++||+ .||+++|++++++.|....+++||+.+
T Consensus 37 ~~l~~~~~---~v~V~hn~~fD~-~fL~~~~~~~~~~~p~~~~~~lDT~~l----------------------------- 83 (96)
T cd06125 37 DILRDKPL---AILVGHNGSFDL-PFLNNRCAELGLKYPLLAGSWIDTIKL----------------------------- 83 (96)
T ss_pred HHHhhCCC---CEEEEeCcHHhH-HHHHHHHHHcCCCCCCcCCcEEEehHH-----------------------------
Confidence 88887531 245677889997 999999999999887666789999865
Q ss_pred HHHHHHHHHHH
Q 017210 260 GLDDAKNTARL 270 (375)
Q Consensus 260 ALdDA~atA~L 270 (375)
|+.||+.++.|
T Consensus 84 ~~~~~~~~~~~ 94 (96)
T cd06125 84 AADDVENTLQI 94 (96)
T ss_pred hhhhHHHHHHh
Confidence 88888888765
No 54
>PHA02570 dexA exonuclease; Provisional
Probab=98.98 E-value=3.9e-09 Score=98.55 Aligned_cols=157 Identities=17% Similarity=0.138 Sum_probs=102.0
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCC----------CCcchHhhhCCChHH----
Q 017210 99 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQL----------LSDFCKDLTGIQQIQ---- 164 (375)
Q Consensus 99 fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~----------Is~~~~~LTGIt~e~---- 164 (375)
=++||+||.|. ....-||+||||.+|...| +..+|+.+|.....-+ ..+..|-.....|..
T Consensus 3 dlMIDlETmG~----~p~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~ 77 (220)
T PHA02570 3 DFIIDFETFGN----TPDGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARK 77 (220)
T ss_pred eEEEEeeccCC----CCCceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHH
Confidence 37899999984 4678999999999997666 6789998886422111 111222222222221
Q ss_pred -Hh---CCCCHHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHc----C--CCCCCCCCceeehHHHHHH
Q 017210 165 -VD---RGVTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFK----K--IWKPPYFNRWINLKVPFHE 233 (375)
Q Consensus 165 -l~---~ap~~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~----g--i~~P~~~~~~iDt~~l~~~ 233 (375)
|. +..++.+++.+|.+||.....-.....+..+| +||+ .+|+..+++. + ++.|..++.-.|++.+...
T Consensus 78 ~L~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~-~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~ 156 (220)
T PHA02570 78 NLKPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDF-PILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEA 156 (220)
T ss_pred hccCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCH-HHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhh
Confidence 21 35789999999999999754211223455665 8997 9999999887 7 5666555566788887665
Q ss_pred hc-CC-------CCCCHHHHHHHcCCCCCC-CCCcHHHHHHHHHHHHH
Q 017210 234 VF-GG-------VRCNLKEAVEMAGLAWQG-RAHCGLDDAKNTARLLA 272 (375)
Q Consensus 234 ~~-~~-------~~~~L~~l~~~lgI~~~g-~~HrALdDA~atA~L~~ 272 (375)
.+ .. .+..| +| .+|+|+.|+-.-|..+.
T Consensus 157 ~~l~r~~~~cp~~~g~l-----------~gfv~H~sihDcakd~lml~ 193 (220)
T PHA02570 157 TLLTRGMTTCPLPKGTL-----------DGFVAHDSIHDCAKDILMLI 193 (220)
T ss_pred hhccCCcccCCCcCccc-----------cchhhcccHHHHHHHHHHHH
Confidence 32 21 11222 23 57999999877665444
No 55
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.88 E-value=1.9e-08 Score=99.95 Aligned_cols=165 Identities=17% Similarity=0.186 Sum_probs=125.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCC-cchHhhhCCChHHHh-CCCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLS-DFCKDLTGIQQIQVD-RGVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is-~~~~~LTGIt~e~l~-~ap~~~ev 174 (375)
.+|.+.|.||.|. .|..|++-+|++|+-|..-+.|.+-...|++|.. .-+| +.+.-+||||+.... .|.+-.+.
T Consensus 9 ~tF~~yDYETfG~---~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsd-DyLP~P~a~LITGITPQ~~~~~G~~E~~F 84 (475)
T COG2925 9 PTFLFYDYETFGV---HPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPAD-DYLPQPGAVLITGITPQEAREKGINEAAF 84 (475)
T ss_pred CcEEEEehhhcCC---CcccccchhhheeeccccccccCCCeEEEecCcc-ccCCCCCceeeecCCHHHHHhcCCChHHH
Confidence 4799999999986 5889999999999998654566788899999986 3354 677889999999885 69999999
Q ss_pred HHHHHHHHhhCCCCCccEEEEEc--CcchHHHHHHHHHHHcCCCCCCCC------CceeehHHHHHHhcC----------
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPPYF------NRWINLKVPFHEVFG---------- 236 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~--a~FD~~~fL~~~~~~~gi~~P~~~------~~~iDt~~l~~~~~~---------- 236 (375)
..++..-+... +.+++.+ .+|| ..+-+..|-|+-++ | +. |.-.|++.+.|..+-
T Consensus 85 ~~~I~~~ls~P-----~Tcv~GYNniRFD-DEvtRy~fyRNF~D-P-Ya~sWqngNSRWDLLD~~RacyALRPeGI~Wp~ 156 (475)
T COG2925 85 AARIHAELTQP-----NTCVLGYNNIRFD-DEVTRYIFYRNFYD-P-YAWSWQNGNSRWDLLDVVRACYALRPEGINWPE 156 (475)
T ss_pred HHHHHHHhCCC-----Ceeeecccccccc-hHHHHHHHHHhcCc-h-hhhhhcCCCchhHHHHHHHHHHhcCcccCCCCc
Confidence 99987766653 3455553 5898 47777777666555 2 22 334577777765432
Q ss_pred ----CCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHH
Q 017210 237 ----GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALL 274 (375)
Q Consensus 237 ----~~~~~L~~l~~~lgI~~~g~~HrALdDA~atA~L~~~l 274 (375)
..+.+|+.|.+.-||+. +++|+|+.|+++|..+...+
T Consensus 157 n~dG~pSFkLEhLt~ANgieH-~nAHdAmsDVyATIamAklv 197 (475)
T COG2925 157 NDDGLPSFKLEHLTKANGIEH-SNAHDAMSDVYATIAMAKLV 197 (475)
T ss_pred CCCCCcchhhHHHhhcccccc-chhhHHHHHHHHHHHHHHHH
Confidence 12678999999999987 48999999999997655433
No 56
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.69 E-value=9.8e-08 Score=85.15 Aligned_cols=153 Identities=18% Similarity=0.172 Sum_probs=98.3
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEe-eEEEEeecCCC--CCCCCcchHhhh---CCChHHHhCCC
Q 017210 96 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLE-ACFQTYVRPTC--NQLLSDFCKDLT---GIQQIQVDRGV 169 (375)
Q Consensus 96 ~~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~-d~F~~lVkP~~--~p~Is~~~~~LT---GIt~e~l~~ap 169 (375)
.+++|=||+|+||+ ++..++||||++++-| .+.+++ +-+..-|.-.. .....+.+++.| |+++.-.....
T Consensus 5 ~~nLiWIDlEMTGL---d~~~drIIEiA~iVTD-~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~ 80 (184)
T COG1949 5 KNNLIWIDLEMTGL---DPERDRIIEIATIVTD-ANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTV 80 (184)
T ss_pred CCceEEEeeeeccC---CcCcceEEEEEEEEec-CcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhc
Confidence 35799999999997 5789999999999998 455553 34444443322 112345666665 57776667899
Q ss_pred CHHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHH
Q 017210 170 TLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEM 248 (375)
Q Consensus 170 ~~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~ 248 (375)
+..+|-.+.++||+..+-.+ ..-++.|+ .-| |+||.+.+-+.-- .+..+++|+. +|.+|+++
T Consensus 81 t~~~aE~~~l~flkkwvp~~-~spicGNSI~qD-RrFl~r~MP~Le~---yfHYR~lDVS------------TlKELa~R 143 (184)
T COG1949 81 TEAEAEAQTLDFLKKWVPKG-VSPICGNSIAQD-RRFLFRYMPKLEA---YFHYRYLDVS------------TLKELARR 143 (184)
T ss_pred cHHHHHHHHHHHHHHhCCCC-CCCCccchhhHH-HHHHHHHhhhHHH---HhhhHhhhHH------------HHHHHHHh
Confidence 99999999999999865432 22345553 458 7999877543211 1223566653 34444444
Q ss_pred cCCC-----CCCCCCcHHHHHHHHHH
Q 017210 249 AGLA-----WQGRAHCGLDDAKNTAR 269 (375)
Q Consensus 249 lgI~-----~~g~~HrALdDA~atA~ 269 (375)
..-+ ..+..|+||+|.+-...
T Consensus 144 W~P~i~~~~~K~~~H~Al~DI~ESI~ 169 (184)
T COG1949 144 WNPEILAGFKKGGTHRALDDIRESIA 169 (184)
T ss_pred hCcHhhhccccccchhHHHHHHHHHH
Confidence 3321 12467999999876543
No 57
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=98.67 E-value=6.5e-07 Score=82.27 Aligned_cols=120 Identities=17% Similarity=0.121 Sum_probs=85.6
Q ss_pred cEEEEEEeeCCCCCC-CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 98 YFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 98 ~fVVfDlETTGl~g~-~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..+.||+||++..+. ++..+.||.||++..+ |.+. .+. ....+-.+.|.
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~---g~~~----~~~-----------------------~~~~~E~~lL~ 53 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSN---GDVE----FIL-----------------------AEGLDDRKIIR 53 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCC---CCEE----EEE-----------------------ecCCCHHHHHH
Confidence 488999999965443 5677999999987653 3210 010 12357889999
Q ss_pred HHHHHHhhCCCCCccEEEEE-cC-cchHHHHHHHHHHHcCCCCCCC--C----------------CceeehHHHHHHhcC
Q 017210 177 RHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIWKPPY--F----------------NRWINLKVPFHEVFG 236 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~-~a-~FD~~~fL~~~~~~~gi~~P~~--~----------------~~~iDt~~l~~~~~~ 236 (375)
+|.+++....- . ++++ |+ .||+ .||..-++++|++.+.- . ...+|+....+....
T Consensus 54 ~F~~~i~~~dP---d-~i~gyN~~~FDl-pyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~ 128 (188)
T cd05781 54 EFVKYVKEYDP---D-IIVGYNSNAFDW-PYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE 128 (188)
T ss_pred HHHHHHHHcCC---C-EEEecCCCcCcH-HHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC
Confidence 99999998521 2 3445 43 7998 89999999999865310 0 016788888887777
Q ss_pred CCCCCHHHHHHHcCCC
Q 017210 237 GVRCNLKEAVEMAGLA 252 (375)
Q Consensus 237 ~~~~~L~~l~~~lgI~ 252 (375)
.++++|+++++++|+.
T Consensus 129 l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 129 VKVKTLENVAEYLGVM 144 (188)
T ss_pred CCCCCHHHHHHHHCCC
Confidence 7899999999999874
No 58
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.67 E-value=8.7e-07 Score=81.56 Aligned_cols=130 Identities=16% Similarity=0.076 Sum_probs=87.6
Q ss_pred cEEEEEEeeCCCCCC-CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 98 YFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 98 ~fVVfDlETTGl~g~-~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..+.||+|||+..+. ++..++||.||.+.. ..+.++ .+ ++.. . + .+..-.+-.+.+.
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~--~~~~~~-~~----~~~~---~-~-----------~v~~~~~E~~lL~ 61 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADE--GGNKVI-TW----KKFD---L-P-----------FVEVVKTEKEMIK 61 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecC--CCceEE-Ee----cCCC---C-C-----------eEEEeCCHHHHHH
Confidence 478999999965543 567899999998653 222222 11 2211 1 0 2223345688999
Q ss_pred HHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCC--------------------CCceeehHHHHHHhc
Q 017210 177 RHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPY--------------------FNRWINLKVPFHEVF 235 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~--------------------~~~~iDt~~l~~~~~ 235 (375)
+|.+++..... .+++.+|+ +||+ .||..-+.++|++.+.- ....+|+..+++..+
T Consensus 62 ~F~~~i~~~dp---diivgyN~~~FD~-pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~ 137 (195)
T cd05780 62 RFIEIVKEKDP---DVIYTYNGDNFDF-PYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTL 137 (195)
T ss_pred HHHHHHHHcCC---CEEEecCCCCCcH-HHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhC
Confidence 99999997321 23444555 6997 89999999999875410 123689988888877
Q ss_pred CCCCCCHHHHHH-HcCCCC
Q 017210 236 GGVRCNLKEAVE-MAGLAW 253 (375)
Q Consensus 236 ~~~~~~L~~l~~-~lgI~~ 253 (375)
...+++|+++++ .+|.+.
T Consensus 138 ~l~sy~L~~v~~~~Lg~~k 156 (195)
T cd05780 138 NLTRYTLERVYEELFGIEK 156 (195)
T ss_pred CCCcCcHHHHHHHHhCCCC
Confidence 888999999986 667654
No 59
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.63 E-value=1.3e-07 Score=95.33 Aligned_cols=157 Identities=20% Similarity=0.288 Sum_probs=114.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHh-CCCCHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVD-RGVTLSEAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~-~ap~~~evl 175 (375)
...+++|+|....+ ..-|+..+++|-+ ++++ -+..||+|.. +|.++.+..+|||.+|++ ...+++++-
T Consensus 216 ~~i~AlDCEm~~te----~g~el~RVt~VD~---~~~v--i~D~fVkP~~--~VvDy~T~~SGIT~~~~e~~t~tl~dvq 284 (380)
T KOG2248|consen 216 PNIFALDCEMVVTE----NGLELTRVTAVDR---DGKV--ILDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLEDVQ 284 (380)
T ss_pred CCeEEEEeeeeeec----cceeeEEeeeeec---cCcE--EeEEeecCCC--cccccccccccccHHHHhcCccCHHHHH
Confidence 57999999998653 2278999988865 5565 4889999985 499999999999999997 588999999
Q ss_pred HHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC--CCCCHHHHHH-HcCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG--VRCNLKEAVE-MAGL 251 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~--~~~~L~~l~~-~lgI 251 (375)
.++.+|+... .++|.|+ +-|+ .-|+ +..| .+|||..+|..-.+. .+.+|..|++ ++|.
T Consensus 285 ~~l~~~~~~~------TILVGHSLenDL-~aLK-------l~H~----~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~ 346 (380)
T KOG2248|consen 285 KELLELISKN------TILVGHSLENDL-KALK-------LDHP----SVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGK 346 (380)
T ss_pred HHHHhhcCcC------cEEEeechhhHH-HHHh-------hhCC----ceeeeeEEEecCCCCccchHHHHHHHHHHHHH
Confidence 9999999875 3555554 5586 3332 3333 589998555433332 2456888885 4454
Q ss_pred CCC-C-CCCcHHHHHHHHHHHHHHHHHhccccc
Q 017210 252 AWQ-G-RAHCGLDDAKNTARLLALLMHRGFKFS 282 (375)
Q Consensus 252 ~~~-g-~~HrALdDA~atA~L~~~ll~~~~~~~ 282 (375)
... + ..|+...||.++.+|+...++.+..++
T Consensus 347 ~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~g 379 (380)
T KOG2248|consen 347 LIQEGVGGHDSVEDALACMKLVKLKIKNSESQG 379 (380)
T ss_pred HHhccCCCCccHHHHHHHHHHHHHHHhcccccC
Confidence 332 2 249999999999999988777665543
No 60
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.60 E-value=2.9e-07 Score=82.91 Aligned_cols=160 Identities=16% Similarity=0.180 Sum_probs=104.0
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCC--CCCCCcchHhhhC---CChHHHhCCCCH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTC--NQLLSDFCKDLTG---IQQIQVDRGVTL 171 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~--~p~Is~~~~~LTG---It~e~l~~ap~~ 171 (375)
..+|=+|+|+||++ -..+.||||++++-|+.=..+.+-+...|+-.. ....++.|.+-|| +|..-+....++
T Consensus 26 q~lVWiD~EMTGLd---vekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl 102 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLD---VEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITL 102 (208)
T ss_pred CceEEEeeeccccc---cccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccH
Confidence 56899999999985 478999999999887433334566777776543 1235577777664 777777899999
Q ss_pred HHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehH---HHHHHhcCCCCCCHHHHHH
Q 017210 172 SEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLK---VPFHEVFGGVRCNLKEAVE 247 (375)
Q Consensus 172 ~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~---~l~~~~~~~~~~~L~~l~~ 247 (375)
+||-.++++|++.....+ +..++.|. --| +.||.+++-..--- +..+.+|+. .+.++.++.-.
T Consensus 103 ~~aEnevl~yikk~ip~~-~~~laGNSV~~D-rlFl~k~mPk~~~~---lhyrivDVStIkeL~~Rw~P~~~-------- 169 (208)
T KOG3242|consen 103 ADAENEVLEYIKKHIPKG-KCPLAGNSVYMD-RLFLKKYMPKLIKH---LHYRIVDVSTIKELARRWYPDIK-------- 169 (208)
T ss_pred HHHHHHHHHHHHHhCCCC-CCCccCcchhhH-HHHHHHHhHHHHHh---cceeeeeHHHHHHHHHHhCchhh--------
Confidence 999999999999876533 33455554 458 68998876543111 124678864 34444433100
Q ss_pred HcCCCCCCCCCcHHHHHHHHHHHHHH
Q 017210 248 MAGLAWQGRAHCGLDDAKNTARLLAL 273 (375)
Q Consensus 248 ~lgI~~~g~~HrALdDA~atA~L~~~ 273 (375)
.+. |-....|||++|.+-...=++.
T Consensus 170 ~~a-PkK~~~HrAldDI~ESI~ELq~ 194 (208)
T KOG3242|consen 170 ARA-PKKKATHRALDDIRESIKELQY 194 (208)
T ss_pred ccC-cccccccchHHHHHHHHHHHHH
Confidence 011 1112359999998765443443
No 61
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.50 E-value=2.6e-06 Score=79.49 Aligned_cols=114 Identities=17% Similarity=0.157 Sum_probs=75.8
Q ss_pred CCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHHHHHhhCC
Q 017210 107 TCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKG 186 (375)
Q Consensus 107 TGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~~fl~~~~ 186 (375)
+|..++.+..+.||-||++..+..++.+ .+. .. . ..+-.+.+.+|.+++....
T Consensus 41 ~~~~~l~~~~~~Iv~Is~~~~~~~~~~~-----~~~--~~-~-------------------~~~E~elL~~F~~~i~~~~ 93 (208)
T cd05782 41 SGSDFLPLPFHKVVSISALYRDDDGGFL-----KVR--TL-D-------------------GADEKELLEDFFQLIEKKN 93 (208)
T ss_pred cCCCCCccccCceEEEEEEEEecCCCeE-----EEe--ec-C-------------------CCCHHHHHHHHHHHHHHhC
Confidence 4433344567899999999875323321 111 10 0 1123788999999999841
Q ss_pred CCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCC--------------ceeehHHHHHHhcCCCCCCHHHHHHHcCC
Q 017210 187 IKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFN--------------RWINLKVPFHEVFGGVRCNLKEAVEMAGL 251 (375)
Q Consensus 187 lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~--------------~~iDt~~l~~~~~~~~~~~L~~l~~~lgI 251 (375)
..+|.+|| .||+ .||..-+..+|++.|..+. +.+|+..+++......+++|+++++.+|+
T Consensus 94 ----p~lv~yNg~~FDl-P~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~~lG~ 168 (208)
T cd05782 94 ----PRLVSFNGRGFDL-PVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAKLLGI 168 (208)
T ss_pred ----CEEEecCCCcCCH-HHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHHHhCC
Confidence 22344465 7998 9999999999997663321 26788877765333468999999999999
Q ss_pred C
Q 017210 252 A 252 (375)
Q Consensus 252 ~ 252 (375)
+
T Consensus 169 ~ 169 (208)
T cd05782 169 P 169 (208)
T ss_pred C
Confidence 5
No 62
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.47 E-value=4.8e-07 Score=80.05 Aligned_cols=116 Identities=16% Similarity=0.118 Sum_probs=60.9
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 179 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~ 179 (375)
++||+||||+ ++..+.|.=||++.++..... .|..+.-.. +.-++.+.++.
T Consensus 1 l~~DIET~Gl---~~~~~~i~liG~~~~~~~~~~---~~~~~~~~~-----------------------~~ee~~~~~~~ 51 (164)
T PF13482_consen 1 LFFDIETTGL---SPDNDTIYLIGVADFDDDEII---TFIQWFAED-----------------------PDEEEIILEFF 51 (164)
T ss_dssp --EEEEESS----GG-G---EEEEEEE-ETTTTE----EEEE-GGG-----------------------HHHHHHHHH--
T ss_pred CcEEecCCCC---CCCCCCEEEEEEEEeCCCceE---EeeHhhccC-----------------------cHHHHHHHHHH
Confidence 6899999997 456678999999988732222 133333221 11233444444
Q ss_pred HHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC
Q 017210 180 KWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ 254 (375)
Q Consensus 180 ~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~ 254 (375)
+++.+. +.++.+|+ +||+ .||++.+.+++++. ...++|+...++.... .+++|+.+++.+|+...
T Consensus 52 ~~l~~~-----~~iv~yng~~FD~-p~L~~~~~~~~~~~---~~~~iDl~~~~~~~~~-~~~~Lk~ve~~lg~~~~ 117 (164)
T PF13482_consen 52 ELLDEA-----DNIVTYNGKNFDI-PFLKRRAKRYGLPP---PFNHIDLLKIIKKHFL-ESYSLKNVEKFLGIERR 117 (164)
T ss_dssp HHHHTT-------EEESSTTTTHH-HHHHHHH-HHHH-----GGGEEEHHHHHT-TTS-CCTT--SHHH-------
T ss_pred HHHhcC-----CeEEEEeCcccCH-HHHHHHHHHcCCCc---ccchhhHHHHHHhccC-CCCCHHHHhhhcccccc
Confidence 667664 23555564 8997 99999998887764 3579999888765443 67899999999998763
No 63
>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=98.36 E-value=1e-05 Score=72.80 Aligned_cols=145 Identities=19% Similarity=0.141 Sum_probs=96.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..+++||+||||+ .+..++|+.++... .+++ .|..-+++. .. .+++++++++.
T Consensus 5 ~~~~a~d~e~~~~---~~~~~~i~~l~~~~---~~~~---~~~~~~~~~---~~---------------~~~~~~~~~~~ 57 (193)
T cd06139 5 AKVFAFDTETTSL---DPMQAELVGISFAV---EPGE---AYYIPLGHD---YG---------------GEQLPREEVLA 57 (193)
T ss_pred CCeEEEEeecCCC---CcCCCeEEEEEEEc---CCCC---EEEEecCCC---cc---------------ccCCCHHHHHH
Confidence 3589999999986 34567888876542 2221 222112221 01 14667889999
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc-CCC--
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA-GLA-- 252 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~-~~~L~~l~~~l-gI~-- 252 (375)
+|.+|+++.. ...|+||+.||+ .+|. ++|+..+ ..++||..++..+.+.. +++|+++++.| +..
T Consensus 58 ~l~~~l~~~~----~~~v~hn~k~d~-~~l~----~~gi~~~---~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~ 125 (193)
T cd06139 58 ALKPLLEDPS----IKKVGQNLKFDL-HVLA----NHGIELR---GPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTI 125 (193)
T ss_pred HHHHHHhCCC----CcEEeeccHHHH-HHHH----HCCCCCC---CCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCc
Confidence 9999998752 135788999996 6774 4677653 46799987766655544 67999999876 332
Q ss_pred --------------CCC-----CCCcHHHHHHHHHHHHHHHHHhccc
Q 017210 253 --------------WQG-----RAHCGLDDAKNTARLLALLMHRGFK 280 (375)
Q Consensus 253 --------------~~g-----~~HrALdDA~atA~L~~~ll~~~~~ 280 (375)
++. ..|.|..||.++.+|+..|.++..+
T Consensus 126 ~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 126 SFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred cHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 000 1246899999999999998876654
No 64
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=98.28 E-value=2e-05 Score=75.89 Aligned_cols=172 Identities=22% Similarity=0.171 Sum_probs=101.0
Q ss_pred ccEEEEEEeeCCCCCCCC------------------CCCcEEEEceEEEEcCCCeEe-----eEEEEeecCCCCCCCCcc
Q 017210 97 QYFVVIDFEATCDKDKNP------------------YPQEIIEFPSVIVSSVTGQLE-----ACFQTYVRPTCNQLLSDF 153 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~------------------~~~eIIEIGAV~vd~~~g~i~-----d~F~~lVkP~~~p~Is~~ 153 (375)
..||.||+|.||+....+ ..-.|||||...+...+++.. ..|..++-|....-.+..
T Consensus 22 ~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~~nf~~f~~~~~~~~~~ 101 (262)
T PF04857_consen 22 ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWPFNFYLFPLDRDFSQAS 101 (262)
T ss_dssp SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEEEEBSTTSTTTCEEEHH
T ss_pred CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEEeeeeccccccceecch
Confidence 359999999999953222 346899999999922566653 344444344321111111
Q ss_pred h---HhhhCCChHHH-hCCCCHHHHHHH--HHHHHhhCCCC-----CccEEEEEcCcchHHHHHHHHHHHcCCCCCC---
Q 017210 154 C---KDLTGIQQIQV-DRGVTLSEALLR--HDKWLENKGIK-----NTNFAVVTWSNWDCRVMLESECRFKKIWKPP--- 219 (375)
Q Consensus 154 ~---~~LTGIt~e~l-~~ap~~~evl~~--f~~fl~~~~lv-----~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~--- 219 (375)
+ ..-+|++-+.+ .+|.++...-++ ..+.++-+.+. .+..+|.||+-+|+ .||-+.+- | ++|.
T Consensus 102 sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl-~~l~~~f~--~-~LP~t~~ 177 (262)
T PF04857_consen 102 SLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDL-MYLYKKFI--G-PLPETLE 177 (262)
T ss_dssp HHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHH-HHHHHHHT--T-S--SSHH
T ss_pred hHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHH-HHHHHHhc--C-CCCCCHH
Confidence 1 22377776665 356666544432 12444444332 24677888999998 67665543 3 4442
Q ss_pred --------CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCC-----------------------CCC-CCcHHHHHHHH
Q 017210 220 --------YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAW-----------------------QGR-AHCGLDDAKNT 267 (375)
Q Consensus 220 --------~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~-----------------------~g~-~HrALdDA~at 267 (375)
++..++||+.++.... ....+|+.+.+.+++.. .+. .|.|-+||..|
T Consensus 178 eF~~~~~~~FP~i~DtK~la~~~~-~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mT 256 (262)
T PF04857_consen 178 EFKELLRELFPRIYDTKYLAEECP-GKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMT 256 (262)
T ss_dssp HHHHHHHHHSSSEEEHHHHHTSTT-TS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHH
T ss_pred HHHHHHHHHCcccccHHHHHHhcc-ccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHH
Confidence 1335789987665322 34578999999999865 344 89999999999
Q ss_pred HHHHHH
Q 017210 268 ARLLAL 273 (375)
Q Consensus 268 A~L~~~ 273 (375)
+.+|.+
T Consensus 257 g~~F~~ 262 (262)
T PF04857_consen 257 GCVFIK 262 (262)
T ss_dssp HHHHHH
T ss_pred HHHHcC
Confidence 999864
No 65
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=98.25 E-value=8.1e-06 Score=76.08 Aligned_cols=172 Identities=19% Similarity=0.186 Sum_probs=113.9
Q ss_pred cEEEEEEeeCCCCC----C--CC------------CCCcEEEEceEEEEcCCCeEee----EEEEeec---CCCCCCCCc
Q 017210 98 YFVVIDFEATCDKD----K--NP------------YPQEIIEFPSVIVSSVTGQLEA----CFQTYVR---PTCNQLLSD 152 (375)
Q Consensus 98 ~fVVfDlETTGl~g----~--~~------------~~~eIIEIGAV~vd~~~g~i~d----~F~~lVk---P~~~p~Is~ 152 (375)
.||++|+|.-|.=. - +. ..-.+|++|....| .+|++.+ +++.-.+ +.. .--++
T Consensus 25 ~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd-~~Gn~p~~g~~tWqfNF~dF~~~~-D~~a~ 102 (239)
T KOG0304|consen 25 PYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSD-EKGNLPDCGTDTWQFNFSDFNLEK-DMYAQ 102 (239)
T ss_pred CeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeec-cCCCCCCCCCceeEEecccCCchh-hccch
Confidence 48999999877510 0 00 23479999999998 5677654 5555444 222 12334
Q ss_pred chHh---hhCCChHHHh-CCCCHHHHHHHHHHHHhhCCCC-CccEEEEE-cCcchHHHHHHHHHHHcCCCCC--------
Q 017210 153 FCKD---LTGIQQIQVD-RGVTLSEALLRHDKWLENKGIK-NTNFAVVT-WSNWDCRVMLESECRFKKIWKP-------- 218 (375)
Q Consensus 153 ~~~~---LTGIt~e~l~-~ap~~~evl~~f~~fl~~~~lv-~~n~~vv~-~a~FD~~~fL~~~~~~~gi~~P-------- 218 (375)
.+.+ -+||.-+..+ .|...+ +|.+.+-.++++ ..++.+|+ ++.+|+ .+|-+-+-...++..
T Consensus 103 ~SIElLr~~Gidf~K~~e~GI~~~----~F~ellm~sg~v~~~~V~WvTFhs~YDf-gYLlK~Lt~~~LP~~~~eF~~~v 177 (239)
T KOG0304|consen 103 DSIELLRRSGIDFEKHREEGIDIE----EFAELLMTSGLVLDENVTWVTFHSGYDF-GYLLKILTGKPLPETEEEFFEIV 177 (239)
T ss_pred hhHHHHHHcCcCHHHHHHcCCCHH----HHHHHHHHhhhhccCceEEEEeeccchH-HHHHHHHcCCCCcchHHHHHHHH
Confidence 4444 4899988886 577766 444445555443 34667777 578997 777665544333211
Q ss_pred -CCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 017210 219 -PYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMH 276 (375)
Q Consensus 219 -~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~~lgI~~~g~~HrALdDA~atA~L~~~ll~ 276 (375)
.++..+.|++.+++..-+. .+.+|+.+++.++++..|..|.|-.|+..||.+|.+|.+
T Consensus 178 ~~~fp~vYDiK~l~~~c~~~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 178 RQLFPFVYDVKYLMKFCEGLSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HHHcchhhhHHHHHHhhhhhhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 1123456777666544332 257899999999999999999999999999999999865
No 66
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=98.15 E-value=0.00014 Score=67.79 Aligned_cols=145 Identities=14% Similarity=0.035 Sum_probs=84.9
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCc-chHhhhCCChHHHhCCCCHHHH
Q 017210 98 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSD-FCKDLTGIQQIQVDRGVTLSEA 174 (375)
Q Consensus 98 ~fVVfDlETTGl~g~--~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~-~~~~LTGIt~e~l~~ap~~~ev 174 (375)
..+.||+||++.++. +|..|.||.|+.+.- .+|..+- ....+.+..+. +.. .+-.+-| .-.+..-.+-.+.
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~--~~g~~~~-~~~~~~~~~~~-~~~~~~~~~~~--~~~v~~~~~E~~l 76 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMID--GQGYLIV-NREIVSEDIED-FEYTPKPEYEG--PFKVFNEPDEKAL 76 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEEe--cCCEEEe-ccccccccccc-ccccCCCCCCC--ceEEecCCCHHHH
Confidence 478999999875443 467899999997753 3453220 00111110000 000 0000001 0112234678899
Q ss_pred HHHHHHHHhhCCCCCccEEEEE-cC-cchHHHHHHHHHHHcCCCCCC-C---CC----------ceeehHHHHHHhc--C
Q 017210 175 LLRHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIWKPP-Y---FN----------RWINLKVPFHEVF--G 236 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~-~a-~FD~~~fL~~~~~~~gi~~P~-~---~~----------~~iDt~~l~~~~~--~ 236 (375)
|.+|.+|+..... . ++++ |+ +||+ .||.+-++.+|+.... + .. -.+|+..+++... .
T Consensus 77 L~~f~~~i~~~~P---d-~i~gyN~~~FD~-pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~ 151 (204)
T cd05779 77 LQRFFEHIREVKP---H-IIVTYNGDFFDW-PFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLP 151 (204)
T ss_pred HHHHHHHHHHhCC---C-EEEecCccccCH-HHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCC
Confidence 9999999998531 2 3344 44 7998 8999999999886431 0 00 1478887776532 3
Q ss_pred CCCCCHHHHHHH-cCCCC
Q 017210 237 GVRCNLKEAVEM-AGLAW 253 (375)
Q Consensus 237 ~~~~~L~~l~~~-lgI~~ 253 (375)
.++++|++++++ +|..-
T Consensus 152 ~~sysLd~Va~~~Lg~~K 169 (204)
T cd05779 152 QGSQGLKAVTKAKLGYDP 169 (204)
T ss_pred CCCccHHHHHHHHhCCCc
Confidence 468999999984 78643
No 67
>PRK05755 DNA polymerase I; Provisional
Probab=98.14 E-value=2.3e-05 Score=87.49 Aligned_cols=136 Identities=21% Similarity=0.176 Sum_probs=94.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
..+++||+||||+ ++..++|+.|+.. . .+|.. .+|.+. +|. .++++
T Consensus 315 ~~~~a~DtEt~~l---~~~~~~i~~i~ls-~--~~g~~-----~~ip~~-------------~i~----------~~~l~ 360 (880)
T PRK05755 315 AGLFAFDTETTSL---DPMQAELVGLSFA-V--EPGEA-----AYIPLD-------------QLD----------REVLA 360 (880)
T ss_pred cCeEEEEeccCCC---CcccccEEEEEEE-e--CCCcE-----EEEecc-------------ccc----------HHHHH
Confidence 4689999999987 4678889998753 3 23421 233221 111 16888
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CCCC--
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GLAW-- 253 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~l-gI~~-- 253 (375)
.|.+|+++..+ ..|.||+.||+ .||.+ +|+..+ ..++||+..+..+.+...++|++++++| |+..
T Consensus 361 ~l~~~L~d~~v----~kV~HNakfDl-~~L~~----~gi~~~---~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~ 428 (880)
T PRK05755 361 ALKPLLEDPAI----KKVGQNLKYDL-HVLAR----YGIELR---GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTIS 428 (880)
T ss_pred HHHHHHhCCCC----cEEEeccHhHH-HHHHh----CCCCcC---CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccc
Confidence 89999998642 25788999997 78863 577653 4689998655544433348999999877 5542
Q ss_pred ----------------CCCCCcHHHHHHHHHHHHHHHHHhc
Q 017210 254 ----------------QGRAHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 254 ----------------~g~~HrALdDA~atA~L~~~ll~~~ 278 (375)
+...|.|..|+..|.+|+.+|.+..
T Consensus 429 ~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L 469 (880)
T PRK05755 429 FEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKL 469 (880)
T ss_pred hHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0124789999999999999887664
No 68
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.02 E-value=0.00025 Score=66.20 Aligned_cols=122 Identities=15% Similarity=0.022 Sum_probs=82.1
Q ss_pred cEEEEEEeeCCCCCC-----CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHH
Q 017210 98 YFVVIDFEATCDKDK-----NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 172 (375)
Q Consensus 98 ~fVVfDlETTGl~g~-----~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ 172 (375)
..+.||+||+...+. ++..+.||.||...- ++. ... +. ....+-.
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~---~~~-----~~~--------~~--------------~~~~~E~ 59 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDN---RGW-----EEV--------LH--------------AEDAAEK 59 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecccC---CCc-----eee--------ec--------------cCCCCHH
Confidence 589999999886542 235689999987421 221 000 00 0157888
Q ss_pred HHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCC-------------C---------------CCc
Q 017210 173 EALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPP-------------Y---------------FNR 223 (375)
Q Consensus 173 evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~-------------~---------------~~~ 223 (375)
+.|.+|.+++....- .+++.+|+ .||+ .+|.+-++++|++.+. + ...
T Consensus 60 ~lL~~f~~~i~~~dP---dii~g~N~~~FD~-pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~ 135 (207)
T cd05785 60 ELLEELVAIIRERDP---DVIEGHNIFRFDL-PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRH 135 (207)
T ss_pred HHHHHHHHHHHHhCC---CEEeccCCcccCH-HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEE
Confidence 999999999998421 23334455 7998 8999999999987630 0 012
Q ss_pred eeehHHHHHH----hcCCCCCCHHHHHHHcCCCC
Q 017210 224 WINLKVPFHE----VFGGVRCNLKEAVEMAGLAW 253 (375)
Q Consensus 224 ~iDt~~l~~~----~~~~~~~~L~~l~~~lgI~~ 253 (375)
.+|+..+++. .+...+++|+++++++|+..
T Consensus 136 ~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~ 169 (207)
T cd05785 136 VIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLAS 169 (207)
T ss_pred EEEcHHHHHhhcccccCCCCCCHHHHHHHhcccC
Confidence 3788777764 23456899999999998743
No 69
>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=97.99 E-value=0.00025 Score=66.41 Aligned_cols=131 Identities=19% Similarity=0.142 Sum_probs=88.3
Q ss_pred CCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHHHHHhhCCCCCccEEE
Q 017210 115 YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNFAV 194 (375)
Q Consensus 115 ~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~~fl~~~~lv~~n~~v 194 (375)
.-.+||-|+++.++ .++.+ +..++-.+. -+-++.+.+|.++++... ...|
T Consensus 7 ~f~kIV~Is~~~~~-~~~~~--~v~s~~~~~-----------------------~~E~~lL~~F~~~~~~~~----p~LV 56 (209)
T PF10108_consen 7 PFHKIVCISVVYAD-DDGQF--KVKSLGGPD-----------------------DDEKELLQDFFDLVEKYN----PQLV 56 (209)
T ss_pred cCCCeEEEEEEEEe-cCCcE--EEEeccCCC-----------------------CCHHHHHHHHHHHHHhCC----CeEE
Confidence 45799999999886 33433 222221111 136789999999998742 2244
Q ss_pred EEcC-cchHHHHHHHHHHHcCCCCCCCCC---------------ceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC----
Q 017210 195 VTWS-NWDCRVMLESECRFKKIWKPPYFN---------------RWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ---- 254 (375)
Q Consensus 195 v~~a-~FD~~~fL~~~~~~~gi~~P~~~~---------------~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~---- 254 (375)
.+|| .||+ .+|..-.-.+|++.|.+++ .-+||..++...-+..+.+|+.+|..+|||-.
T Consensus 57 s~NG~~FDl-P~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~~~sLd~la~~lgiPgK~~id 135 (209)
T PF10108_consen 57 SFNGRGFDL-PVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKARTSLDELAALLGIPGKDDID 135 (209)
T ss_pred ecCCccCCH-HHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccccCCHHHHHHHcCCCCCCCCC
Confidence 4565 7998 9999888889999875432 23677766543222347899999999999842
Q ss_pred C----------C----CCcHHHHHHHHHHHHHHHHH
Q 017210 255 G----------R----AHCGLDDAKNTARLLALLMH 276 (375)
Q Consensus 255 g----------~----~HrALdDA~atA~L~~~ll~ 276 (375)
| + +.--..|+.+|+.||+++..
T Consensus 136 Gs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 136 GSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 0 11226899999999999864
No 70
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=97.95 E-value=4e-06 Score=88.08 Aligned_cols=42 Identities=33% Similarity=0.837 Sum_probs=37.6
Q ss_pred ccccccCCCCCCccccccCCCCCCCCcccCCCCcccCCCCcCccccc
Q 017210 325 YHPSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWA 371 (375)
Q Consensus 325 ~~~~c~cg~~a~~~~v~k~Gpn~Gr~fy~C~~~~~~~~~~c~ff~W~ 371 (375)
..+.|+||..+..++|+|.|||.||.||.|.. . ++|.||.|+
T Consensus 717 ~~~~c~c~~ra~~l~v~k~~~nrGR~f~sc~~----~-k~c~ff~w~ 758 (758)
T KOG1956|consen 717 EEVTCGCGTRAVKLLVAKTEPNRGRKFYSCLP----E-KSCNFFAWE 758 (758)
T ss_pred cccccCCcchhhhhhhhccCccCCCCCcccCC----C-CCcceEeeC
Confidence 46799999999999999999999999999944 2 569999996
No 71
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=97.86 E-value=0.0015 Score=61.74 Aligned_cols=136 Identities=15% Similarity=0.073 Sum_probs=86.0
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEceEEEEcCCCe--EeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHH
Q 017210 98 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQ--LEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 173 (375)
Q Consensus 98 ~fVVfDlETTGl~g~--~~~~~eIIEIGAV~vd~~~g~--i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~e 173 (375)
..+.||+||+...+. +|..|+||.|+.+.-. +|. ...+.-..+++.. + ++ ...|..-.+-.+
T Consensus 8 ~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~--~~~~~~~~~~~~~l~~~~-~-~~----------~~~v~~~~~E~e 73 (230)
T cd05777 8 RILSFDIECAGRKGVFPEPEKDPVIQIANVVTR--QGEGEPFIRNIFTLKTCA-P-IV----------GAQVFSFETEEE 73 (230)
T ss_pred eEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEe--CCCCCCceeEEEEeCCCC-C-CC----------CCEEEEECCHHH
Confidence 589999999976542 4577999999988652 332 1112111123321 1 21 223333467889
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCC-CC-------------------------------
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKP-PY------------------------------- 220 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P-~~------------------------------- 220 (375)
.+.+|.+++....- .+++.+|+ +||+ .+|.+-++.+|++.- .+
T Consensus 74 LL~~f~~~i~~~DP---Dii~GyN~~~FDl-~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~ 149 (230)
T cd05777 74 LLLAWRDFVQEVDP---DIITGYNICNFDL-PYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIE 149 (230)
T ss_pred HHHHHHHHHHhcCC---CEEEEecCCCCCH-HHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEc
Confidence 99999999987421 34455564 7997 888888888877521 00
Q ss_pred CCceeehHHHHHHhcCCCCCCHHHHHH-HcCC
Q 017210 221 FNRWINLKVPFHEVFGGVRCNLKEAVE-MAGL 251 (375)
Q Consensus 221 ~~~~iDt~~l~~~~~~~~~~~L~~l~~-~lgI 251 (375)
..-.+|+...++..+...+|+|+++++ .+|.
T Consensus 150 GR~~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~ 181 (230)
T cd05777 150 GRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGE 181 (230)
T ss_pred CEEeeeHHHHHHHhcCcccCcHHHHHHHHhCC
Confidence 012357777777767778999999997 4453
No 72
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=97.60 E-value=0.00023 Score=68.50 Aligned_cols=172 Identities=12% Similarity=0.090 Sum_probs=111.8
Q ss_pred CcccEEEEEEeeCCCCCCCCCCCcEEEEceEE-----EEcC------C-------CeEeeEEEEeecCCCCCCCCcchHh
Q 017210 95 EFQYFVVIDFEATCDKDKNPYPQEIIEFPSVI-----VSSV------T-------GQLEACFQTYVRPTCNQLLSDFCKD 156 (375)
Q Consensus 95 ~~~~fVVfDlETTGl~g~~~~~~eIIEIGAV~-----vd~~------~-------g~i~d~F~~lVkP~~~p~Is~~~~~ 156 (375)
..++|+++|+|+||+++ ...+|.|+-..- ++.+ + -++.+..+-++-|.. ..++...+
T Consensus 11 r~~tf~fldleat~lp~---~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~aee 85 (318)
T KOG4793|consen 11 RLRTFSFLDLEATGLPG---WIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAEE 85 (318)
T ss_pred ceeEEEeeeeccccCCc---ccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhhh
Confidence 35789999999999864 334566553221 2211 1 145677778888875 57888999
Q ss_pred hhCCChHHH--hCCCCHH-HHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHH
Q 017210 157 LTGIQQIQV--DRGVTLS-EALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFH 232 (375)
Q Consensus 157 LTGIt~e~l--~~ap~~~-evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~ 232 (375)
+||.++.-+ ....-|+ ++.+-+..|+..-. .--+.|+||| .||+ .+|.++++..|+..|. .-..+|+...++
T Consensus 86 itgls~~~~~l~rr~~~D~dla~LL~afls~lp--~p~CLVaHng~~~df-pil~qela~lg~~lpq-~lvcvdslpa~~ 161 (318)
T KOG4793|consen 86 ITGLSQPFLALQRRLAFDKDLAKLLTAFLSRLP--TPGCLVAHNGNEYDF-PILAQELAGLGYSLPQ-DLVCVDSLPALN 161 (318)
T ss_pred hcccccHHHHHHHHhhhhHHHHHHHHHHHhcCC--CCceEEeecCCcccc-HHHHHHHHhcCccchh-hhcCcchhHHHH
Confidence 999999665 3333444 44555677887632 2235678887 6898 8999999999998762 224567766655
Q ss_pred HhcC----------CCCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHH
Q 017210 233 EVFG----------GVRCNLKEAVEMAGLAWQ-GRAHCGLDDAKNTARLLALLM 275 (375)
Q Consensus 233 ~~~~----------~~~~~L~~l~~~lgI~~~-g~~HrALdDA~atA~L~~~ll 275 (375)
.+-. .+.++|..+..+|=-..+ ...|.|+.|.-.+.-+|+...
T Consensus 162 ald~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~ 215 (318)
T KOG4793|consen 162 ALDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRI 215 (318)
T ss_pred HHhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHH
Confidence 4421 125778877765532212 235899988877776666443
No 73
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=97.58 E-value=0.0035 Score=58.40 Aligned_cols=136 Identities=18% Similarity=0.105 Sum_probs=78.9
Q ss_pred cEEEEEEeeCCCC-CCCCC----CCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHH
Q 017210 98 YFVVIDFEATCDK-DKNPY----PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 172 (375)
Q Consensus 98 ~fVVfDlETTGl~-g~~~~----~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ 172 (375)
+.+.||+||+... +..|. .++||+|+.+ + .+|. .++ .+++............ ....+..-.+-.
T Consensus 6 rilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~--~-~~~~--~~v-~~~~~~~~~~~~~~~~-----~~~~v~~~~~E~ 74 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA--G-SDGL--KRV-LVLKREGVEGLEGLLP-----EGAEVEFFDSEK 74 (204)
T ss_pred eEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc--C-CCCC--cEE-EEEecCCcccccccCC-----CCCeEEecCCHH
Confidence 5899999999643 32232 2789999874 2 1231 112 1122110000000000 011233335788
Q ss_pred HHHHHHHHHHhhCCCCCccEEEEE-cC-cchHHHHHHHHHHHcCCC---CCCC---------CCceeehHHHHHH-h---
Q 017210 173 EALLRHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIW---KPPY---------FNRWINLKVPFHE-V--- 234 (375)
Q Consensus 173 evl~~f~~fl~~~~lv~~n~~vv~-~a-~FD~~~fL~~~~~~~gi~---~P~~---------~~~~iDt~~l~~~-~--- 234 (375)
+.|.+|.+|+.+. . ++++ |+ +||+ .+|..-++++|+. .|.. ....+|+...++. .
T Consensus 75 ~lL~~F~~~i~~~-----~-~iig~N~~~FDl-pyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~ 147 (204)
T cd05783 75 ELIREAFKIISEY-----P-IVLTFNGDNFDL-PYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQV 147 (204)
T ss_pred HHHHHHHHHHhcC-----C-EEEEeCCCCcCH-HHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhh
Confidence 9999999999864 2 3455 44 7998 8999999999987 2211 1235788665542 1
Q ss_pred --c--CCCCCCHHHHHHHc-CC
Q 017210 235 --F--GGVRCNLKEAVEMA-GL 251 (375)
Q Consensus 235 --~--~~~~~~L~~l~~~l-gI 251 (375)
+ ...+++|+++++++ |.
T Consensus 148 ~~~~~~~~~~~L~~Va~~~lg~ 169 (204)
T cd05783 148 YAFGNKYREYTLDAVAKALLGE 169 (204)
T ss_pred hhhccccccCcHHHHHHHhcCC
Confidence 2 33689999999866 54
No 74
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.21 E-value=0.0045 Score=59.12 Aligned_cols=117 Identities=16% Similarity=0.103 Sum_probs=70.0
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHH-HHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS-EAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~-evl 175 (375)
+++++||+||||++ +..+.|+=.|...+ .++. .+||-.. ++ +|.-+ .++
T Consensus 98 e~~~FFDiETTGL~---~ag~~I~~~g~a~~--~~~~------~~Vrq~~---lp----------------~p~~E~avl 147 (278)
T COG3359 98 EDVAFFDIETTGLD---RAGNTITLVGGARG--VDDT------MHVRQHF---LP----------------APEEEVAVL 147 (278)
T ss_pred cceEEEeeeccccC---CCCCeEEEEEEEEc--cCce------EEEEeec---CC----------------CcchhhHHH
Confidence 57999999999984 35566776666665 2333 2344432 11 11111 244
Q ss_pred HHHHHHHhhCCCCCccEEEEE-cC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHHcCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEMAGL 251 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~-~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~--~~~~~L~~l~~~lgI 251 (375)
+.|+.-. + -+ .+|+ || .||. .|+++ +.+..++.. +.+.-+|+....|.+.+ +.+.+|+++-+.+||
T Consensus 148 e~fl~~~-~-----~~-~lvsfNGkaFD~-PfikR-~v~~~~el~-l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi 217 (278)
T COG3359 148 ENFLHDP-D-----FN-MLVSFNGKAFDI-PFIKR-MVRDRLELS-LEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGI 217 (278)
T ss_pred HHHhcCC-C-----cc-eEEEecCcccCc-HHHHH-HHhcccccC-ccccchhhhhhhhhhhhccCCCCChhhHHHHhCc
Confidence 4444333 1 12 3555 65 7996 99995 555555542 23456788766666553 347899999999998
Q ss_pred CC
Q 017210 252 AW 253 (375)
Q Consensus 252 ~~ 253 (375)
..
T Consensus 218 ~R 219 (278)
T COG3359 218 RR 219 (278)
T ss_pred cc
Confidence 64
No 75
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=97.11 E-value=0.038 Score=56.18 Aligned_cols=161 Identities=17% Similarity=0.058 Sum_probs=99.3
Q ss_pred cEEEEEEeeCCCCCCCC--C--CCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHH
Q 017210 98 YFVVIDFEATCDKDKNP--Y--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 173 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~--~--~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~e 173 (375)
..++||+||+...+..| . .++||.|+.+.-+...............+.. .+. ++ .+..-.+-.+
T Consensus 4 ~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~-------~~---~~~~~~~E~~ 71 (471)
T smart00486 4 KILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK--EID-------GV---EVYEFNNEKE 71 (471)
T ss_pred eEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC--CCC-------CC---eEEecCCHHH
Confidence 58999999997643112 2 6899999988775322222223333334432 122 22 2222237788
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCC----------C---------------------C
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPP----------Y---------------------F 221 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~----------~---------------------~ 221 (375)
.+.+|.+++..... .+++.||+ .||+ .+|..-+...++.... . .
T Consensus 72 lL~~f~~~i~~~dp---dii~g~N~~~FD~-~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g 147 (471)
T smart00486 72 LLKAFLEFIKKYDP---DIIYGHNISNFDL-PYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKG 147 (471)
T ss_pred HHHHHHHHHHHhCC---CEEEeecCCCCCH-HHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEecc
Confidence 99999999987531 34566675 6997 8888887776653310 0 0
Q ss_pred CceeehHHHHHHhcCCCCCCHHHHHHHcCC-CCCCC---------------C----CcHHHHHHHHHHHHHHH
Q 017210 222 NRWINLKVPFHEVFGGVRCNLKEAVEMAGL-AWQGR---------------A----HCGLDDAKNTARLLALL 274 (375)
Q Consensus 222 ~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI-~~~g~---------------~----HrALdDA~atA~L~~~l 274 (375)
.-.+|+...++..++..+++|+++++++.- ....- . ..-+.||..+.+|+.++
T Consensus 148 ~~~~Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 148 RLVIDLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EEEEEhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 134688888888777778999999976533 11100 0 11266888998888875
No 76
>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=96.90 E-value=0.013 Score=54.27 Aligned_cols=121 Identities=11% Similarity=0.034 Sum_probs=76.8
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHH
Q 017210 98 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 177 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~ 177 (375)
..+.||+||++. .+|+.||-. +.....++ .+=.+.. .. | ..+.--++-.+.|.+
T Consensus 4 ~~~~fDIE~~~~-------~~i~~i~~~--~~~~~~i~----~~~~~~~---~~-------~---~~v~~~~~E~~lL~~ 57 (193)
T cd05784 4 KVVSLDIETSMD-------GELYSIGLY--GEGQERVL----MVGDPED---DA-------P---DNIEWFADEKSLLLA 57 (193)
T ss_pred cEEEEEeecCCC-------CCEEEEEee--cCCCCEEE----EECCCCC---CC-------C---CEEEEECCHHHHHHH
Confidence 478999999963 288888763 22333322 1111211 11 1 112233577889999
Q ss_pred HHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCC-----------------------CceeehHHHHHH
Q 017210 178 HDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYF-----------------------NRWINLKVPFHE 233 (375)
Q Consensus 178 f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~-----------------------~~~iDt~~l~~~ 233 (375)
|.+++..... ++++.+|+ .||+ .+|..-++++|++.+ +. .-.+|+..+.+.
T Consensus 58 f~~~i~~~dP---Dvi~g~N~~~FD~-~yl~~R~~~~~i~~~-~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~ 132 (193)
T cd05784 58 LIAWFAQYDP---DIIIGWNVINFDL-RLLQRRAEAHGLPLR-LGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKT 132 (193)
T ss_pred HHHHHHhhCC---CEEEECCCcCcCH-HHHHHHHHHhCCCcc-cccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHH
Confidence 9999988521 23444554 7998 899988998888742 10 115688777765
Q ss_pred -hcCCCCCCHHHHHHHc
Q 017210 234 -VFGGVRCNLKEAVEMA 249 (375)
Q Consensus 234 -~~~~~~~~L~~l~~~l 249 (375)
.+...+|+|+++++++
T Consensus 133 ~~~kl~sy~L~~Va~~~ 149 (193)
T cd05784 133 ATYHFESFSLENVAQEL 149 (193)
T ss_pred ccCCCCcCCHHHHHHHH
Confidence 4677899999999855
No 77
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=96.89 E-value=0.027 Score=64.32 Aligned_cols=162 Identities=17% Similarity=0.096 Sum_probs=99.0
Q ss_pred cEEEEEEeeCCCCC---CCCCCCcEEEEceEEEEcCCCeEeeEEEE-eecCCCCCCCCcchHhhhCCChHHHhCCCCHHH
Q 017210 98 YFVVIDFEATCDKD---KNPYPQEIIEFPSVIVSSVTGQLEACFQT-YVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 173 (375)
Q Consensus 98 ~fVVfDlETTGl~g---~~~~~~eIIEIGAV~vd~~~g~i~d~F~~-lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~e 173 (375)
..+.|||||++.++ .++..|+||+|+.+... .|.-.+.+.. ++-+.. +..+.| ..|..-.+-.+
T Consensus 265 rilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~--~g~~~~~~~r~vftl~~-------c~~i~g---~~V~~f~sE~e 332 (1054)
T PTZ00166 265 RILSFDIECIKLKGLGFPEAENDPVIQISSVVTN--QGDEEEPLTKFIFTLKE-------CASIAG---ANVLSFETEKE 332 (1054)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEee--CCCccCCcceEEEecCc-------cccCCC---ceEEEeCCHHH
Confidence 58999999998654 13467999999998653 3332111211 111110 111122 23434467888
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCC-C--------C------------CC----------
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWK-P--------P------------YF---------- 221 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~-P--------~------------~~---------- 221 (375)
.|.+|.+|+.... -++++.+|. +||+ .+|..-++.+|+.. + + +.
T Consensus 333 LL~~f~~~I~~~D---PDII~GYNi~~FDl-pYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~ 408 (1054)
T PTZ00166 333 LLLAWAEFVIAVD---PDFLTGYNIINFDL-PYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIE 408 (1054)
T ss_pred HHHHHHHHHHhcC---CCEEEecCCcCCcH-HHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEee
Confidence 9999999998742 134444453 7997 88888777766651 1 0 00
Q ss_pred -CceeehHHHHHHhcCCCCCCHHHHHHHc-CCCCCCCCC-------------------cHHHHHHHHHHHHHHHH
Q 017210 222 -NRWINLKVPFHEVFGGVRCNLKEAVEMA-GLAWQGRAH-------------------CGLDDAKNTARLLALLM 275 (375)
Q Consensus 222 -~~~iDt~~l~~~~~~~~~~~L~~l~~~l-gI~~~g~~H-------------------rALdDA~atA~L~~~ll 275 (375)
.-.+|+..+++..+.+.+|+|++++.++ |...+.-+| -.+.||..+.+|+.+|.
T Consensus 409 GR~~iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 409 GRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred eEEEEEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1236888888777778899999999844 533211111 13688888888888764
No 78
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=96.83 E-value=0.0095 Score=61.98 Aligned_cols=123 Identities=11% Similarity=0.117 Sum_probs=85.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
...++|||||+. ...-.--+|++..+ +|...++|..|+.... ..-.+++.
T Consensus 284 ~~~~ffDiEt~P------~~~~~yL~G~~~~~--~~~~~~~~~~fla~~~----------------------~~E~~~~~ 333 (457)
T TIGR03491 284 PGELIFDIESDP------DENLDYLHGFLVVD--KGQENEKYRPFLAEDP----------------------NTEELAWQ 333 (457)
T ss_pred CccEEEEecCCC------CCCCceEEEEEEec--CCCCCcceeeeecCCc----------------------hHHHHHHH
Confidence 457899999992 34556778887664 3433334655544321 23566899
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCC---CCCCceeehHHHHHHhc--CCCCCCHHHHHHHcCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKP---PYFNRWINLKVPFHEVF--GGVRCNLKEAVEMAGL 251 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P---~~~~~~iDt~~l~~~~~--~~~~~~L~~l~~~lgI 251 (375)
+|.+|+.... +..|+|++.|.. ..|++-++++|.... .+...++|+....+..+ +..+++|+.++..+|.
T Consensus 334 ~f~~~l~~~~----~~~i~hY~~~e~-~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~ 408 (457)
T TIGR03491 334 QFLQLLQSYP----DAPIYHYGETEK-DSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGF 408 (457)
T ss_pred HHHHHHHHCC----CCeEEeeCHHHH-HHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCc
Confidence 9999998742 335788888884 889999999887521 12237899987776543 5678999999999999
Q ss_pred CCC
Q 017210 252 AWQ 254 (375)
Q Consensus 252 ~~~ 254 (375)
++.
T Consensus 409 ~~~ 411 (457)
T TIGR03491 409 EWR 411 (457)
T ss_pred ccC
Confidence 875
No 79
>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=96.79 E-value=0.1 Score=49.51 Aligned_cols=173 Identities=11% Similarity=-0.049 Sum_probs=102.7
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEceEEEEcCCCeEee-----EEEEeecCCCCCCCCcchHhhhCCChHHHhCCCC
Q 017210 98 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEA-----CFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVT 170 (375)
Q Consensus 98 ~fVVfDlETTGl~g~--~~~~~eIIEIGAV~vd~~~g~i~d-----~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~ 170 (375)
+...||+|+.+-.++ +|..|.|+.|..+.-+ +..... ..--++.+.... .... .....+....|.--.+
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~--~~~~~~~~~~~~~~l~~~~~~~~-~~~~-~~~~~~~~~~v~~~~~ 80 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYCIDD--DVSPFILDANKVGVIIVDELKSN-ASNG-RIRSGLSGIPVEVVES 80 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEEEec--CCCcccccccceeEEEEcCccch-hhhh-ccccCCCCCeEEEeCC
Confidence 578999999865443 4678999999988543 222111 112333333210 1100 1112344445566678
Q ss_pred HHHHHHHHHHHHhhCCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCC-----C---------------CC--------
Q 017210 171 LSEALLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKP-----P---------------YF-------- 221 (375)
Q Consensus 171 ~~evl~~f~~fl~~~~lv~~n~~vv~~-a~FD~~~fL~~~~~~~gi~~P-----~---------------~~-------- 221 (375)
-.+.+.+|.+++....- .+++.+| .+||+ .+|.+-++..++..- . +.
T Consensus 81 E~~LL~~f~~~i~~~DP---Dii~GyNi~~fd~-~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~ 156 (231)
T cd05778 81 ELELFEELIDLVRRFDP---DILSGYEIQRSSW-GYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIK 156 (231)
T ss_pred HHHHHHHHHHHHHHhCC---CEEEEeccccCcH-HHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceE
Confidence 88999999999987531 2334444 37997 788877776655320 0 00
Q ss_pred ---CceeehHHHHHHhcCCCCCCHHHHHH-HcCCCCCCCCCcHHHHH------HHHHHHHHHHHHhc
Q 017210 222 ---NRWINLKVPFHEVFGGVRCNLKEAVE-MAGLAWQGRAHCGLDDA------KNTARLLALLMHRG 278 (375)
Q Consensus 222 ---~~~iDt~~l~~~~~~~~~~~L~~l~~-~lgI~~~g~~HrALdDA------~atA~L~~~ll~~~ 278 (375)
.-.+|+..+++..+.+.+|+|++++. .+|-..+.-+|..+.+. ....+++...+++.
T Consensus 157 i~GRi~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~ 223 (231)
T cd05778 157 IVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRV 223 (231)
T ss_pred EeeEEEeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHH
Confidence 01357777777777888999999997 56765443346666665 24566666666553
No 80
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=96.77 E-value=0.00075 Score=51.23 Aligned_cols=37 Identities=5% Similarity=-0.059 Sum_probs=30.0
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccc
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFG 81 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~ 81 (375)
+..++++++++|++.|+++++||||. ++++++|.|.+
T Consensus 13 ~~~~~~~~~~~a~~~g~~~v~iTDh~~~~~~~~~~~~~~~~gi~~i~G~E~~ 64 (67)
T smart00481 13 GALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPIIGLEAN 64 (67)
T ss_pred ccCCHHHHHHHHHHcCCCEEEEeeCCcccCHHHHHHHHHHcCCeEEEEEEEE
Confidence 44578999999999999999999995 35666666654
No 81
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=96.74 E-value=0.055 Score=47.40 Aligned_cols=91 Identities=20% Similarity=0.117 Sum_probs=59.6
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc-C-
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA-G- 250 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~-~~~L~~l~~~l-g- 250 (375)
+++.+.+++.+..+ ..|.||+.||+ .+|.+. +|+.. ..++|+ .+...+.+.. +++|++++..+ |
T Consensus 65 ~~~~l~~ll~~~~i----~kv~~n~~~D~-~~L~~~---~~i~~----~~~~D~-~l~~~~l~~~~~~~L~~L~~~~l~~ 131 (176)
T PF01612_consen 65 ILDALKELLEDPNI----IKVGHNAKFDL-KWLYRS---FGIDL----KNVFDT-MLAAYLLDPTRSYSLKDLAEEYLGN 131 (176)
T ss_dssp HHHHHHHHHTTTTS----EEEESSHHHHH-HHHHHH---HTS------SSEEEH-HHHHHHTTTSTTSSHHHHHHHHHSE
T ss_pred hHHHHHHHHhCCCc----cEEEEEEechH-HHHHHH---hcccc----CCccch-hhhhhcccccccccHHHHHHHHhhh
Confidence 66777788887532 24667789997 667654 67764 367899 5665555543 49999998544 6
Q ss_pred CCCC-----CCC-----------CcHHHHHHHHHHHHHHHHHh
Q 017210 251 LAWQ-----GRA-----------HCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 251 I~~~-----g~~-----------HrALdDA~atA~L~~~ll~~ 277 (375)
+... ++. .-|-.||..|.+|+..|..+
T Consensus 132 ~~~~~~~~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~ 174 (176)
T PF01612_consen 132 IDLDKKEQMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQ 174 (176)
T ss_dssp EE-GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred ccCcHHHhhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3221 111 23677999999999988765
No 82
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=96.56 E-value=0.0011 Score=75.42 Aligned_cols=40 Identities=8% Similarity=-0.059 Sum_probs=36.0
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSW 83 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~ 83 (375)
.++..++++|++|+++|++|||||||+ +||||+|+|+|+.
T Consensus 16 dg~~~i~~lv~~A~~~g~~alAlTDh~~m~Ga~~F~~~a~~~gIkPIiG~e~~v~ 70 (1107)
T PRK06920 16 KSACKIDELVVRAKELGYSSLAITDENVMYGVIPFYKACKKHGIHPIIGLTASIF 70 (1107)
T ss_pred ccCCCHHHHHHHHHHCCCCEEEEEeCChHhHHHHHHHHHHHcCCCEeeeeEEEEe
Confidence 466788999999999999999999993 5999999999875
No 83
>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=96.42 E-value=0.036 Score=53.90 Aligned_cols=131 Identities=15% Similarity=0.054 Sum_probs=82.7
Q ss_pred ccEEEEEEeeCCCCCC--CCCCCcEEEEceEEEEcCCCe---EeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCH
Q 017210 97 QYFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQ---LEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL 171 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~--~~~~~eIIEIGAV~vd~~~g~---i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~ 171 (375)
-+.+.||+||....+. ++..++|+.|+.+.-+ .+. ..+.+.++..+.. ... ...|.--.+-
T Consensus 157 l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~--~~~~~~~~~~~~~~~~~~~---~~~---------~~~v~~~~~E 222 (325)
T PF03104_consen 157 LRILSFDIETYSNDGKFPDPEKDEIIMISYVVYR--NGSSEPYRRKVFTLGSCDS---IED---------NVEVIYFDSE 222 (325)
T ss_dssp SEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEE--TTEEETTEEEEEECSCSCC---TTC---------TTEEEEESSH
T ss_pred cceeEEEEEEccccCCCCCCCCCeEEEEEEEEEe--ccccCCCceEEEEecCCCC---CCC---------CcEEEEECCH
Confidence 4699999999987532 4577999999988764 221 1223334433331 211 3344445788
Q ss_pred HHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCC-----CCC-------------------------
Q 017210 172 SEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWK-----PPY------------------------- 220 (375)
Q Consensus 172 ~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~-----P~~------------------------- 220 (375)
.+.|..|.+++..... .+++.+|. .||+ .+|..-++..|++. +..
T Consensus 223 ~~lL~~f~~~i~~~dP---Dii~GyN~~~fD~-~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 298 (325)
T PF03104_consen 223 KELLEAFLDIIQEYDP---DIITGYNIDGFDL-PYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSRKFSRID 298 (325)
T ss_dssp HHHHHHHHHHHHHHS----SEEEESSTTTTHH-HHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCTTEEEEE
T ss_pred HHHHHHHHHHHHhcCC---cEEEEecccCCCH-HHHHHHHHHhCccccccccccccceeEEeecccccccCCCcceeEEE
Confidence 8999999999987531 34444554 6997 88888888886542 000
Q ss_pred --CCceeehHHHHHHhcCCCCCCHHHH
Q 017210 221 --FNRWINLKVPFHEVFGGVRCNLKEA 245 (375)
Q Consensus 221 --~~~~iDt~~l~~~~~~~~~~~L~~l 245 (375)
..-.+|+..+++..+.+.+|+|+++
T Consensus 299 ~~Gr~~~D~~~~~~~~~~l~sY~L~~V 325 (325)
T PF03104_consen 299 IPGRLVLDLYRLARKDYKLDSYSLDNV 325 (325)
T ss_dssp ETTSEEEEHHHHHHHHS--SS-SHHHH
T ss_pred ECCChHhHHHHHHHhhCCCCCCCCCCC
Confidence 0124688888888887788999864
No 84
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=96.37 E-value=0.0017 Score=73.44 Aligned_cols=40 Identities=8% Similarity=-0.017 Sum_probs=35.7
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSW 83 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~ 83 (375)
.++..++++|++|+++|++|||||||+ +||||+|+|+++.
T Consensus 15 dg~~~i~~lv~~A~~~g~~alAlTD~~~m~Ga~~F~~~a~~~gIkPIiG~e~~v~ 69 (1034)
T PRK07279 15 DSLIDLEKYVERAKELGYQTIGIMDKDNLYGAYHFIEGAQKNGLQPILGLELNIF 69 (1034)
T ss_pred cccCCHHHHHHHHHHCCCCEEEEEcCCccccHHHHHHHHHHcCCcEEEEEEEEEe
Confidence 467788999999999999999999993 5999999999864
No 85
>PRK05762 DNA polymerase II; Reviewed
Probab=96.30 E-value=0.16 Score=56.38 Aligned_cols=147 Identities=10% Similarity=0.027 Sum_probs=92.0
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHH
Q 017210 98 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 177 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~ 177 (375)
..+.||+||++. .+|+.||..-. .+..+ ..|-+.. + .. .+.+..-++-.+.|.+
T Consensus 156 rvlsfDIE~~~~-------~~i~sI~~~~~--~~~~v-----i~ig~~~-~-~~----------~~~v~~~~sE~~LL~~ 209 (786)
T PRK05762 156 KVVSLDIETSNK-------GELYSIGLEGC--GQRPV-----IMLGPPN-G-EA----------LDFLEYVADEKALLEK 209 (786)
T ss_pred eEEEEEEEEcCC-------CceEEeeecCC--CCCeE-----EEEECCC-C-CC----------cceEEEcCCHHHHHHH
Confidence 689999999952 36888876411 12222 1122221 1 10 1114445688899999
Q ss_pred HHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCC-------------CCC----------CceeehHHHHHH
Q 017210 178 HDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKP-------------PYF----------NRWINLKVPFHE 233 (375)
Q Consensus 178 f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P-------------~~~----------~~~iDt~~l~~~ 233 (375)
|.+++..... ++++.+|+ +||+ .+|.+-++.+|++.. +.. .-.+|+..+.+.
T Consensus 210 F~~~i~~~DP---DIIvGyNi~~FDl-pyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~ 285 (786)
T PRK05762 210 FNAWFAEHDP---DVIIGWNVVQFDL-RLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKS 285 (786)
T ss_pred HHHHHHhcCC---CEEEEeCCCCCcH-HHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHH
Confidence 9999998531 33444554 7998 899988898888641 000 025788877776
Q ss_pred hc-CCCCCCHHHHHHHcCCCCCC--CC-C------------------cHHHHHHHHHHHHHHH
Q 017210 234 VF-GGVRCNLKEAVEMAGLAWQG--RA-H------------------CGLDDAKNTARLLALL 274 (375)
Q Consensus 234 ~~-~~~~~~L~~l~~~lgI~~~g--~~-H------------------rALdDA~atA~L~~~l 274 (375)
.. ...+++|+++++++..+... .. + -.+.||..|.+|+.++
T Consensus 286 ~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 286 ATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred hhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 55 66799999999876543210 00 0 1378999999998843
No 86
>PHA02528 43 DNA polymerase; Provisional
Probab=96.02 E-value=0.57 Score=52.83 Aligned_cols=219 Identities=11% Similarity=0.017 Sum_probs=116.8
Q ss_pred ceeccCCccccCchhHhHHHhhcCCcceeeCcCCCCCCccccccccccccCCCCCCCCCcccEEEEEEeeCCCCC-CCCC
Q 017210 37 SVELKDDTIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKPQEFQYFVVIDFEATCDKD-KNPY 115 (375)
Q Consensus 37 ~~~~~~~~~~~~~~~~v~~a~~~g~~aiaitd~~~~kpiyg~e~~~~~~~~~~~~~~~~~~~fVVfDlETTGl~g-~~~~ 115 (375)
++.-..-.+.....+++++.++-|.++. ..+.+-.+++.|. + . .++. ..... -..+.||+||+...+ .+|.
T Consensus 54 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~merfi~~~~~~~-~-~-~~~~---~~~p~-lrv~s~DIE~~~~~gfP~p~ 125 (881)
T PHA02528 54 NCRPKKFDSMRDARKWMKRMKDVGFEAL-GMDDFKLQYISDT-Y-P-GEIK---YDRSK-IRIANLDIEVTAEDGFPDPE 125 (881)
T ss_pred EEeEEECCCHHHHHHHHHHHHhcCCcee-ehhHHhhhhhhhh-c-C-CCCC---CCCCC-ccEEEEEEEECCCCCCCCcc
Confidence 3333333445566788888888887766 3444444444432 1 1 1221 12122 359999999986433 1233
Q ss_pred --CCcEEEEceEEEEcCCCeEeeEEEEeecCCCCC-CCCcchHhhhCCChHHHhCCCCHHHHHHHHHHHHhhCCCCCccE
Q 017210 116 --PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQ-LLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNF 192 (375)
Q Consensus 116 --~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p-~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~~fl~~~~lv~~n~ 192 (375)
.++||.||. .+. .+. ++..+.-+...+ ..........-.....+..-.+-.+.|.+|.+|+....- .+
T Consensus 126 ~~~d~IisIsl--~~~-~~~---~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL~~F~~~i~~~DP---DI 196 (881)
T PHA02528 126 EAKYEIDAITH--YDS-IDD---RFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREMLLEYINFWEENTP---VI 196 (881)
T ss_pred cCCCcEEEEEE--ecC-CCC---EEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHHHHHHHHHHHhCC---cE
Confidence 569999986 232 222 222332211000 000000000001111122245788999999999987421 22
Q ss_pred EEEEc-CcchHHHHHHHHHHH-cCCCC----CCC------------C----------CceeehHHHHHHh-c-CCCCCCH
Q 017210 193 AVVTW-SNWDCRVMLESECRF-KKIWK----PPY------------F----------NRWINLKVPFHEV-F-GGVRCNL 242 (375)
Q Consensus 193 ~vv~~-a~FD~~~fL~~~~~~-~gi~~----P~~------------~----------~~~iDt~~l~~~~-~-~~~~~~L 242 (375)
++-+| -+||+ .+|.+-+++ .|... +++ . ...+|+..+++.+ + ...+++|
T Consensus 197 I~GyNi~~FDl-pYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~dl~k~~~~~~l~SYsL 275 (881)
T PHA02528 197 FTGWNVELFDV-PYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLYKKFTFTNQPSYRL 275 (881)
T ss_pred EEecCCccCCH-HHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHHHHHHhhhcccccCCH
Confidence 33334 37998 788777764 45431 100 0 0135676777763 2 4678999
Q ss_pred HHHHHH-cCCCCCCC----------------CCcHHHHHHHHHHHHHH
Q 017210 243 KEAVEM-AGLAWQGR----------------AHCGLDDAKNTARLLAL 273 (375)
Q Consensus 243 ~~l~~~-lgI~~~g~----------------~HrALdDA~atA~L~~~ 273 (375)
++++++ ||..-... .+-.+.||+.+.+|+.+
T Consensus 276 e~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 276 DYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 999984 77643210 02237899999999887
No 87
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=95.62 E-value=0.006 Score=68.53 Aligned_cols=40 Identities=8% Similarity=-0.120 Sum_probs=35.5
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSW 83 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~ 83 (375)
.++..++++|++|++.|++|||+|||+ +||||.|+|+++-
T Consensus 15 dg~~~~~~lv~~A~e~g~~alALTD~~nl~GaveF~~~ak~~gIkPIiG~e~~v~ 69 (971)
T PRK05898 15 SSTLSIDDIIKFALDNNQPYVCLTDLNNLYGCIEFYDKAKAHNLIPIIGLEIEYQ 69 (971)
T ss_pred cccCCHHHHHHHHHHCCCCEEEEEeCCccccHHHHHHHHHHcCCCEEEEEEEEEc
Confidence 456788999999999999999999993 5999999999863
No 88
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=95.13 E-value=0.37 Score=55.99 Aligned_cols=161 Identities=16% Similarity=0.094 Sum_probs=97.0
Q ss_pred ccEEEEEEeeCCCCCCC--CCCCcEEEEceEEEEcCCCeE---------eeEEEEeecCCCCCCCCcchHhhhCCChHHH
Q 017210 97 QYFVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQL---------EACFQTYVRPTCNQLLSDFCKDLTGIQQIQV 165 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~--~~~~eIIEIGAV~vd~~~g~i---------~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l 165 (375)
-..++||+|||-++=.. ...|+|.=|. ..||+++--| ++-|+.-=||+. .-+| -|
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMIS-YMiDGqGfLItNREiVs~DIedfEYTPKpE~---eG~F----------~v 311 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMIS-YMIDGQGFLITNREIVSEDIEDFEYTPKPEY---EGPF----------CV 311 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEE-EEecCceEEEechhhhccchhhcccCCcccc---ccce----------EE
Confidence 36889999999875322 3568888874 4566543222 234444444442 1112 13
Q ss_pred hCCCCHHHHHHHHHHHHhhCCCCCccEEEEE-cCc-chHHHHHHHHHHHcCCCCCC-----------CCCceeehHHHHH
Q 017210 166 DRGVTLSEALLRHDKWLENKGIKNTNFAVVT-WSN-WDCRVMLESECRFKKIWKPP-----------YFNRWINLKVPFH 232 (375)
Q Consensus 166 ~~ap~~~evl~~f~~fl~~~~lv~~n~~vv~-~a~-FD~~~fL~~~~~~~gi~~P~-----------~~~~~iDt~~l~~ 232 (375)
-+.++-...+.+|.+-+... +..++++ ||+ || +.|+.+-...+|++.-. +..+++--..-|+
T Consensus 312 ~Ne~dEv~Ll~RfFeHiq~~----kP~iivTyNGDFFD-WPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfr 386 (2173)
T KOG1798|consen 312 FNEPDEVGLLQRFFEHIQEV----KPTIIVTYNGDFFD-WPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFR 386 (2173)
T ss_pred ecCCcHHHHHHHHHHHHHhc----CCcEEEEecCcccc-chhhHHHHHhcCCCcchhcCceecccccccccceeehhhhh
Confidence 35667788899998888763 2335666 676 59 69999999999987521 1112221122232
Q ss_pred H-----hcCCCCCCHHHHHH-HcCCCC-------------CCCCC---cHHHHHHHHHHHHHHHHH
Q 017210 233 E-----VFGGVRCNLKEAVE-MAGLAW-------------QGRAH---CGLDDAKNTARLLALLMH 276 (375)
Q Consensus 233 ~-----~~~~~~~~L~~l~~-~lgI~~-------------~g~~H---rALdDA~atA~L~~~ll~ 276 (375)
. .++..+.+|.++.+ ++|... +...| -...||.+|..||++...
T Consensus 387 WVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 387 WVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred hhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhh
Confidence 1 23556788988774 566432 11123 348999999999987654
No 89
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=95.04 E-value=0.012 Score=67.24 Aligned_cols=43 Identities=5% Similarity=-0.163 Sum_probs=37.8
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCcccccccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSWSTF 86 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~~~~ 86 (375)
.++.+++++|++|++.|++|||||||+ +||||.|+|+|+....
T Consensus 17 dga~~i~~Lv~~A~~~g~~AlaiTD~~nl~Gav~Fy~~ak~~gikpIiG~e~~v~~~~ 74 (1139)
T COG0587 17 DGASKIEELVKKAKELGMPALALTDHNNLYGAVEFYKAAKKAGIKPIIGCEAYVANGD 74 (1139)
T ss_pred ccccCHHHHHHHHHHcCCCeEEEecCCcceeHHHHHHHHHHcCCeEEeeeEEEEeccc
Confidence 467889999999999999999999994 5999999999887543
No 90
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=95.04 E-value=0.011 Score=66.59 Aligned_cols=39 Identities=5% Similarity=-0.093 Sum_probs=35.1
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCcccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGS 82 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~ 82 (375)
-++.+++++|++|+++|.+|||||||. +||||.|+|++.
T Consensus 16 Dg~~~~~elv~~Ak~~G~~avAITDh~~l~G~~~f~~~a~~~gIkpIiG~Ei~~ 69 (973)
T PRK07135 16 SSTIKLDSLIKYAKENNLKTLVLTDHNNMFGVPKFYKLCKKNNIKPIIGLDLEV 69 (973)
T ss_pred ccCCCHHHHHHHHHHcCCCEEEEecCCcHHhHHHHHHHHHHcCCeEEEeEEEEe
Confidence 467889999999999999999999993 589999999975
No 91
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=94.84 E-value=0.19 Score=47.18 Aligned_cols=157 Identities=14% Similarity=0.054 Sum_probs=91.4
Q ss_pred CCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCC------cchHhhhCCChHHHhCCC-CHHHHHHHHHHHHhhCCCC
Q 017210 116 PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLS------DFCKDLTGIQQIQVDRGV-TLSEALLRHDKWLENKGIK 188 (375)
Q Consensus 116 ~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is------~~~~~LTGIt~e~l~~ap-~~~evl~~f~~fl~~~~lv 188 (375)
..-..|||+++++.++| |++.||++|+|...+ +- ..+.+-|+|..+-...+. .+.+++.++.+||+.....
T Consensus 7 ~y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~p-~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~~ 84 (213)
T PF13017_consen 7 EYVPAEIAICKFSLKEG-IIDSFHTFINPGQIP-LGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNKGG 84 (213)
T ss_pred cEEeEEEEEEEEecCCc-cchhhhcccCCCCCC-cHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcCCC
Confidence 34579999999998888 889999999998522 22 122344677766555544 7999999999999986432
Q ss_pred CccEEEEEcC-cchH-HHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc----CC----CCCCHHHHH-HHcC-------
Q 017210 189 NTNFAVVTWS-NWDC-RVMLESECRFKKIWKPPYFNRWINLKVPFHEVF----GG----VRCNLKEAV-EMAG------- 250 (375)
Q Consensus 189 ~~n~~vv~~a-~FD~-~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~----~~----~~~~L~~l~-~~lg------- 250 (375)
+.-..|++.. ..+. ...|+.-+...+.... ..+.++..++-.+. .. ...-+..++ ..+.
T Consensus 85 ~~~~~i~~~~~~~~~V~~cl~~La~~a~~~~~---~~v~~~~~lf~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 161 (213)
T PF13017_consen 85 EKMPPIFTKRDQIPRVQSCLKWLAKKAGEDND---FKVYDFEYLFFDLKNEKVDYRWDRQDFPSKTIADALFPKDFFEYS 161 (213)
T ss_pred CCcceEEEeHhHHHHHHHHHHHHHHhcCCCcc---eEeecHHHHHHHHHHHHhhcccccccCchHHHHHHHccchhhhcc
Confidence 2223344432 2332 2355555555555432 13445544443322 11 111112222 1111
Q ss_pred --C------CCCCCCCcHHHHHHHHHHHHHHHHHh
Q 017210 251 --L------AWQGRAHCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 251 --I------~~~g~~HrALdDA~atA~L~~~ll~~ 277 (375)
+ +.+...++|+..+..+|..+...+-.
T Consensus 162 ~~~~C~~He~~d~~~~Ca~s~v~r~ay~i~d~~c~ 196 (213)
T PF13017_consen 162 SNIRCDFHEEIDRSKYCALSTVKRWAYTISDYMCR 196 (213)
T ss_pred CCCceeecccCCCcccchhHHHHHHHHHHHHHHHH
Confidence 1 11224699999999999887776633
No 92
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=94.84 E-value=0.03 Score=52.77 Aligned_cols=180 Identities=21% Similarity=0.219 Sum_probs=111.6
Q ss_pred cEEEEEEeeCCCCCCCC-------------------CCCcEEEEceEEEEcCCCeE-----eeEEEEeecCCCCCCCCcc
Q 017210 98 YFVVIDFEATCDKDKNP-------------------YPQEIIEFPSVIVSSVTGQL-----EACFQTYVRPTCNQLLSDF 153 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~-------------------~~~eIIEIGAV~vd~~~g~i-----~d~F~~lVkP~~~p~Is~~ 153 (375)
.+|.+|.|..|.-. .| ..=.||++|..+-| ++|.- .=.|..-.+|+. .-...+
T Consensus 43 n~vSmdTEFpGvvA-rPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSD-e~GN~P~~~sTWQFNF~F~l~~-dmya~E 119 (299)
T COG5228 43 NHVSMDTEFPGVVA-RPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSD-ENGNKPNGPSTWQFNFEFDLKK-DMYATE 119 (299)
T ss_pred CceeeccccCceee-cccccccccchHHHHHHhcccchhhhhheeeeecc-ccCCCCCCCceeEEEEEecchh-hhcchH
Confidence 47889999887621 11 12379999999988 44432 235666777765 223444
Q ss_pred hHhh---hCCChHHHhC-CCCHHHHHHHHHHHHhhCCCC-CccEEEEE-cCcchHHHHHHHHHHHcCCCCCC--------
Q 017210 154 CKDL---TGIQQIQVDR-GVTLSEALLRHDKWLENKGIK-NTNFAVVT-WSNWDCRVMLESECRFKKIWKPP-------- 219 (375)
Q Consensus 154 ~~~L---TGIt~e~l~~-ap~~~evl~~f~~fl~~~~lv-~~n~~vv~-~a~FD~~~fL~~~~~~~gi~~P~-------- 219 (375)
..+| .||+-+.-++ +... .+|-+.|-+++|+ ...+.+++ ++.+|+ .+|-+.+.. .+.|.
T Consensus 120 SieLL~ksgIdFkkHe~~GI~v----~eF~elLm~SGLvm~e~VtWitfHsaYDf-gyLikilt~--~plP~~~EdFy~~ 192 (299)
T COG5228 120 SIELLRKSGIDFKKHENLGIDV----FEFSELLMDSGLVMDESVTWITFHSAYDF-GYLIKILTN--DPLPNNKEDFYWW 192 (299)
T ss_pred HHHHHHHcCCChhhHhhcCCCH----HHHHHHHhccCceeccceEEEEeecchhH-HHHHHHHhc--CCCCccHHHHHHH
Confidence 4444 5666555443 4433 4577777787765 34445555 577897 788765543 33331
Q ss_pred ---CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhccccccccccc
Q 017210 220 ---YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLM 288 (375)
Q Consensus 220 ---~~~~~iDt~~l~~~~~~~~~~~L~~l~~~lgI~~~g~~HrALdDA~atA~L~~~ll~~~~~~~i~~~l~ 288 (375)
++..+.|+.-+++..... +-.|.+...-++|...|..|.|-.||..||+.|-........-+|..+|.
T Consensus 193 l~~yfP~fYDik~v~ks~~~~-~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F~~sig~~ll 263 (299)
T COG5228 193 LHQYFPNFYDIKLVYKSVLNN-SKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTSIGQSLL 263 (299)
T ss_pred HHHHCccccchHHHHHhhhhh-hhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhheecccccHHHH
Confidence 122345665555433221 34688888888888888899999999999999876655555555555544
No 93
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=94.76 E-value=0.015 Score=65.18 Aligned_cols=40 Identities=5% Similarity=-0.108 Sum_probs=35.6
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCC---------------CCCCcccccccccc
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSWS 84 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~~ 84 (375)
+..+++++|++|++.|++|||||||+ +||||.|+|+++..
T Consensus 17 g~~~~~elv~~A~~~G~~aiAiTDh~~~~g~~~f~~~~~~~gik~I~G~E~~~~~ 71 (874)
T PRK09532 17 GASQLPALVDRAIELGMPAIALTDHGVMYGAIELLKVCRNKGIKPIIGNEMYVIN 71 (874)
T ss_pred ccCCHHHHHHHHHHCCCCEEEEecCCChhhHHHHHHHHHHcCCeEEEEEEEEecC
Confidence 56789999999999999999999994 58999999998753
No 94
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=94.66 E-value=0.55 Score=47.52 Aligned_cols=132 Identities=14% Similarity=0.134 Sum_probs=80.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCc--EEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQE--IIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~e--IIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ev 174 (375)
..+|.||+||.+. .++.++ +|+| . +|+ . -.+|+|-. + +. +.++
T Consensus 17 ~~~iAiDTEf~r~---~t~~p~LcLIQi-----~--~~e---~-~~lIdpl~-~-~~---------------d~~~---- 61 (361)
T COG0349 17 SKAIAIDTEFMRL---RTYYPRLCLIQI-----S--DGE---G-ASLIDPLA-G-IL---------------DLPP---- 61 (361)
T ss_pred CCceEEecccccc---cccCCceEEEEE-----e--cCC---C-ceEecccc-c-cc---------------ccch----
Confidence 4599999999986 344443 4444 2 222 1 36777753 1 11 1222
Q ss_pred HHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHH-HcCCC
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVE-MAGLA 252 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~-~~~L~~l~~-~lgI~ 252 (375)
|...+.+..++ -|.|.++||+ .+|... .|+.. .+.+||+. ...+.|.. +++|++|++ .+|++
T Consensus 62 ---l~~Ll~d~~v~----KIfHaa~~DL-~~l~~~---~g~~p----~plfdTqi-Aa~l~g~~~~~gl~~Lv~~ll~v~ 125 (361)
T COG0349 62 ---LVALLADPNVV----KIFHAARFDL-EVLLNL---FGLLP----TPLFDTQI-AAKLAGFGTSHGLADLVEELLGVE 125 (361)
T ss_pred ---HHHHhcCCcee----eeeccccccH-HHHHHh---cCCCC----CchhHHHH-HHHHhCCcccccHHHHHHHHhCCc
Confidence 33444444322 2678899998 455433 35543 35789974 44555543 899999995 56887
Q ss_pred CCCCC---------------CcHHHHHHHHHHHHHHHHHhcc
Q 017210 253 WQGRA---------------HCGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 253 ~~g~~---------------HrALdDA~atA~L~~~ll~~~~ 279 (375)
.+..+ --|..|+..+..|+.+|.++..
T Consensus 126 ldK~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 126 LDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELA 167 (361)
T ss_pred ccccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 65211 2368899999999998876543
No 95
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=94.39 E-value=0.9 Score=48.01 Aligned_cols=189 Identities=11% Similarity=-0.021 Sum_probs=101.0
Q ss_pred eccCCccccCchhHhHHHhhcCCcceeeCcC--CCCCCccccccccccccCCCCCCCCCcccEEEEEEeeCCCCCCCC--
Q 017210 39 ELKDDTIVHPGGDAGESIHQLSSEFVEYSNE--FYNNPTYQHDFGSWSTFYPDSQKPQEFQYFVVIDFEATCDKDKNP-- 114 (375)
Q Consensus 39 ~~~~~~~~~~~~~~v~~a~~~g~~aiaitd~--~~~kpiyg~e~~~~~~~~~~~~~~~~~~~fVVfDlETTGl~g~~~-- 114 (375)
.-+.-.++-.+.+++|+-+..|.++.+-.|- .+|--.|+.| +..+..+ -....||+|+|+.+ .|
T Consensus 56 ~~~~f~~~~~a~~~~~~~~~~~~~~~g~~~~~~~yi~~~y~~~------~~~d~~~----i~~~~~DIEv~~~~--fp~~ 123 (498)
T PHA02524 56 VPKKHENIWEAKQWIKRMEEVGMDAMGMDDYGISYISDTYRGV------IDFDRDD----VVIDVVDIEVTAPE--FPEP 123 (498)
T ss_pred cccCCCCHHHHHHHHHHHhhcChhhccchHHHHHHHHHhcCCc------cccchhh----ceEEEEEEEecCCC--CCCh
Confidence 3344445566778888877777777665553 1222223322 1222211 25889999998752 23
Q ss_pred --CCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcc--hHhhhCCChHHHhCCCCHHHHHHHHHHHHhhCCCCCc
Q 017210 115 --YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDF--CKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNT 190 (375)
Q Consensus 115 --~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~--~~~LTGIt~e~l~~ap~~~evl~~f~~fl~~~~lv~~ 190 (375)
-..+|.-|.-... .+ ..++|..+.=......+.+. +....-+..-.+-.=++-.+.|.+|.+|+....-
T Consensus 124 ~~a~~~i~~i~~~d~--~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~sE~eLL~~F~~~i~~~DP--- 196 (498)
T PHA02524 124 KYAKYEIDMISHVRL--HN--GKKTYYIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFEDEVDLLLNYIQLWKANTP--- 196 (498)
T ss_pred hhcCCceEEEEeeec--cc--CCccEEEEeccccccCCCcccccccccccCCeEEEEeCCHHHHHHHHHHHHHHhCC---
Confidence 2345666643322 21 13445555311100111111 1111112222334567888999999999998421
Q ss_pred cEEEEEc-CcchHHHHHHHHHHH-cCCCC----CCCC---------------------CceeehHHHHHHh--cCCCCCC
Q 017210 191 NFAVVTW-SNWDCRVMLESECRF-KKIWK----PPYF---------------------NRWINLKVPFHEV--FGGVRCN 241 (375)
Q Consensus 191 n~~vv~~-a~FD~~~fL~~~~~~-~gi~~----P~~~---------------------~~~iDt~~l~~~~--~~~~~~~ 241 (375)
.+++..| .+||+ .+|..-+++ +|+.. +++. ...+|+..+++.. ..+++|+
T Consensus 197 DIItGYNi~nFDl-PYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl~~l~kk~s~~~l~sYs 275 (498)
T PHA02524 197 DLVFGWNSEGFDI-PYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDYMDVFKKFSFTPMPDYK 275 (498)
T ss_pred CEEEeCCCcccCH-HHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeEHHHHHHHhhhccCCCCC
Confidence 2233334 38998 777777753 66531 1110 0135778888765 4678999
Q ss_pred HHHHHH
Q 017210 242 LKEAVE 247 (375)
Q Consensus 242 L~~l~~ 247 (375)
|+++++
T Consensus 276 L~~Vs~ 281 (498)
T PHA02524 276 LGNVGY 281 (498)
T ss_pred HHHHHH
Confidence 999986
No 96
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=94.13 E-value=0.023 Score=64.75 Aligned_cols=40 Identities=8% Similarity=-0.090 Sum_probs=35.5
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSW 83 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~ 83 (375)
-+..++++++++|++.|++|||||||+ +||||.|+|++..
T Consensus 18 dg~~~~~elv~~A~~~G~~avAiTDh~~l~g~~~f~~~~~~~gIkpI~G~Ei~~~ 72 (1046)
T PRK05672 18 DGASHPEELVERAARLGLRALAITDECGLAGVVRAAEAAKELGLRLVIGAELSLG 72 (1046)
T ss_pred ccCCCHHHHHHHHHHcCCCEEEEEeCCcchhHHHHHHHHHHCCCEEEEEEEEEEe
Confidence 367789999999999999999999993 5899999999874
No 97
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=94.11 E-value=0.025 Score=65.12 Aligned_cols=40 Identities=8% Similarity=-0.074 Sum_probs=35.4
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSW 83 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~ 83 (375)
.+...++++|++|++.|++|||||||+ +||||.|+|.++.
T Consensus 16 dg~~~i~elv~~A~~~G~~alAiTDh~~l~G~~~f~~~~~~~gIkpIiG~E~~v~ 70 (1170)
T PRK07374 16 DGASQLPKMVERAKELGMPAIALTDHGVMYGAIELLKLCKGKGIKPIIGNEMYVI 70 (1170)
T ss_pred hccCCHHHHHHHHHHCCCCEEEEecCCchHHHHHHHHHHHHcCCeEEEEeEEEec
Confidence 356788999999999999999999993 5899999999875
No 98
>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=94.10 E-value=1 Score=42.65 Aligned_cols=148 Identities=14% Similarity=0.067 Sum_probs=92.0
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcC--C-----CeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCC
Q 017210 98 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSV--T-----GQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVT 170 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~--~-----g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~ 170 (375)
+.+.|-+-|.--. .....||+.|+++....- + ......+.++++|......+......-......|.--.+
T Consensus 4 ~v~sls~~T~~n~--k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~ 81 (234)
T cd05776 4 TVMSLSIKTVLNS--KTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFEN 81 (234)
T ss_pred EEEEEEeEEEecC--cCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCC
Confidence 3566777776311 123589999999876311 1 112346677788875211233323333333344666778
Q ss_pred HHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCC------------CCC-------------CCce
Q 017210 171 LSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWK------------PPY-------------FNRW 224 (375)
Q Consensus 171 ~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~------------P~~-------------~~~~ 224 (375)
-.+-|..|.+++....- ++++.||. .||+ .+|-.-++..|++. |.. ..-.
T Consensus 82 E~~LL~~f~~~i~~~DP---DiivG~Ni~~fdl-~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~ 157 (234)
T cd05776 82 ERALLNFFLAKLQKIDP---DVLVGHDLEGFDL-DVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLL 157 (234)
T ss_pred HHHHHHHHHHHHhhcCC---CEEEeeccCCCCH-HHHHHHHHHhCCCccccccccccccCccccccccccccccccCchh
Confidence 88999999999987532 34555554 7998 78888787777652 100 0114
Q ss_pred eehHHHHHHhcCCCCCCHHHHHH-HcCC
Q 017210 225 INLKVPFHEVFGGVRCNLKEAVE-MAGL 251 (375)
Q Consensus 225 iDt~~l~~~~~~~~~~~L~~l~~-~lgI 251 (375)
+|+...++.+....+|+|+++++ .+|.
T Consensus 158 ~D~~~~~k~~~~~~sY~L~~va~~~Lg~ 185 (234)
T cd05776 158 CDTYLSAKELIRCKSYDLTELSQQVLGI 185 (234)
T ss_pred hccHHHHHHHhCCCCCChHHHHHHHhCc
Confidence 67877787777778999999997 6675
No 99
>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=93.64 E-value=1.3 Score=40.72 Aligned_cols=142 Identities=14% Similarity=0.021 Sum_probs=80.9
Q ss_pred ccEEEEEEeeCCCCCC-CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 97 QYFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~-~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
...|.||+|++..... ....-.+|+|+. . +. -.+|.+.. +.. .-.+.+
T Consensus 22 ~~vig~D~Ew~~~~~~~~~~~v~LiQiat-----~-~~-----~~lid~~~---~~~-----------------~~~~~~ 70 (193)
T cd06146 22 GRVVGIDSEWKPSFLGDSDPRVAILQLAT-----E-DE-----VFLLDLLA---LEN-----------------LESEDW 70 (193)
T ss_pred CCEEEEECccCCCccCCCCCCceEEEEec-----C-CC-----EEEEEchh---ccc-----------------cchHHH
Confidence 4689999999865321 123457788852 1 11 13444432 111 011222
Q ss_pred -HHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-----------CCCCCHH
Q 017210 176 -LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-----------GVRCNLK 243 (375)
Q Consensus 176 -~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-----------~~~~~L~ 243 (375)
+.+.+++.+..+ .-|.|+..+|+ .+|.+.+...+- .+.....++||..++..+.. ..+++|.
T Consensus 71 ~~~L~~ll~d~~i----~KVg~~~~~D~-~~L~~~~~~~~~-~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~ 144 (193)
T cd06146 71 DRLLKRLFEDPDV----LKLGFGFKQDL-KALSASYPALKC-MFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLA 144 (193)
T ss_pred HHHHHHHhCCCCe----eEEEechHHHH-HHHHHhcCcccc-ccccCCceEEHHHHHHHHhhccccccccccCcccCCHH
Confidence 334555666422 12556778897 677654432110 00012478999887775532 2367999
Q ss_pred HHHHHc-CCCCC---------C------CCCcHHHHHHHHHHHHHHHH
Q 017210 244 EAVEMA-GLAWQ---------G------RAHCGLDDAKNTARLLALLM 275 (375)
Q Consensus 244 ~l~~~l-gI~~~---------g------~~HrALdDA~atA~L~~~ll 275 (375)
++++.+ |.+.+ . +-+-|..||..+..|+.+|.
T Consensus 145 ~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 145 DLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999765 54321 1 22779999999999999885
No 100
>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=93.64 E-value=0.7 Score=39.10 Aligned_cols=66 Identities=20% Similarity=0.143 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc
Q 017210 172 SEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA 249 (375)
Q Consensus 172 ~evl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~-~~~L~~l~~~l 249 (375)
.++++.+.+|+.+..+ ..|+|++.+|+ .+|. ..++..+ ..++||..++..+.+.. +++|++++++|
T Consensus 40 ~~~~~~l~~~l~~~~~----~~v~~~~k~d~-~~L~----~~~~~~~---~~~~D~~~~ayll~~~~~~~~l~~l~~~~ 106 (155)
T cd00007 40 EEDLEALKELLEDEDI----TKVGHDAKFDL-VVLA----RDGIELP---GNIFDTMLAAYLLNPGEGSHSLDDLAKEY 106 (155)
T ss_pred HHHHHHHHHHHcCCCC----cEEeccHHHHH-HHHH----HCCCCCC---CCcccHHHHHHHhCCCCCcCCHHHHHHHH
Confidence 5677778888887532 24678889996 6764 3444443 35789976665555544 67999999887
No 101
>PF02811 PHP: PHP domain; InterPro: IPR004013 The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. This family is often associated with an N-terminal region IPR003141 from INTERPRO.; GO: 0003824 catalytic activity; PDB: 2WJE_A 3QY8_A 2WJD_A 2WJF_A 1PB0_B 1M68_A 1M65_A 3E38_B 2W9M_A 3E0F_A ....
Probab=93.56 E-value=0.029 Score=49.16 Aligned_cols=26 Identities=4% Similarity=-0.065 Sum_probs=23.7
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEF 70 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~ 70 (375)
+..++++++++|++.|.++||||||.
T Consensus 14 g~~~~~e~v~~A~~~Gl~~i~iTDH~ 39 (175)
T PF02811_consen 14 GKDSPEEYVEQAKEKGLDAIAITDHN 39 (175)
T ss_dssp SSSSHHHHHHHHHHTTESEEEEEEET
T ss_pred hcCCHHHHHHHHHHcCCCEEEEcCCc
Confidence 45588999999999999999999994
No 102
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=93.35 E-value=0.039 Score=63.44 Aligned_cols=41 Identities=7% Similarity=-0.180 Sum_probs=35.6
Q ss_pred ccccCchhHhHHHhhcCCcceeeCcCC---------------CCCCcccccccccc
Q 017210 44 TIVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSWS 84 (375)
Q Consensus 44 ~~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~~ 84 (375)
-+...++++|++|++.|++|||||||+ +||||.|+|.+...
T Consensus 15 dg~~~i~elv~~A~e~G~~avAiTDH~~l~g~~~f~~~a~~~gIkpIiG~Ei~~~~ 70 (1135)
T PRK05673 15 DGAAKIKPLVKKAAELGMPAVALTDHGNLFGAVEFYKAAKGAGIKPIIGCEAYVAP 70 (1135)
T ss_pred hhcCCHHHHHHHHHHcCCCEEEEEcCCccHHHHHHHHHHHHcCCeEEEEEEEEecC
Confidence 356788999999999999999999993 58999999988653
No 103
>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=93.28 E-value=2.4 Score=37.48 Aligned_cols=132 Identities=17% Similarity=0.051 Sum_probs=79.0
Q ss_pred ccEEEEEEeeCCCCCC-CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 97 QYFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~-~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
...|.||+|++..... ....-.+|+|+ . .+ .-.+|++.. + ....
T Consensus 18 ~~~ig~D~E~~~~~~~~~~~~~~liQl~---~--~~------~~~l~~~~~---~---------------------~~~~ 62 (170)
T cd06141 18 EKVVGFDTEWRPSFRKGKRNKVALLQLA---T--ES------RCLLFQLAH---M---------------------DKLP 62 (170)
T ss_pred CCEEEEeCccCCccCCCCCCCceEEEEe---c--CC------cEEEEEhhh---h---------------------hccc
Confidence 4689999999975310 12345677774 1 11 124444432 1 1122
Q ss_pred HHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHc-CCCC
Q 017210 176 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMA-GLAW 253 (375)
Q Consensus 176 ~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~~l-gI~~ 253 (375)
+.|.+++.+..+ ..+.|+...|+ .+|.+ .+|+.. ..++|+..++..+.+. .+.+|.++++.+ |+..
T Consensus 63 ~~l~~ll~~~~i----~kv~~~~k~D~-~~L~~---~~g~~~----~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~ 130 (170)
T cd06141 63 PSLKQLLEDPSI----LKVGVGIKGDA-RKLAR---DFGIEV----RGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPL 130 (170)
T ss_pred HHHHHHhcCCCe----eEEEeeeHHHH-HHHHh---HcCCCC----CCeeeHHHHHHHhCCCcCCccHHHHHHHHcCccc
Confidence 345566665422 23566778886 55542 456653 3468998766555443 346999999876 6543
Q ss_pred C-----------C------CCCcHHHHHHHHHHHHHHHH
Q 017210 254 Q-----------G------RAHCGLDDAKNTARLLALLM 275 (375)
Q Consensus 254 ~-----------g------~~HrALdDA~atA~L~~~ll 275 (375)
. . +-|-|..||..+.+|+.+|.
T Consensus 131 ~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 131 SKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 2 1 12678999999999998875
No 104
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.13 E-value=3.8 Score=47.77 Aligned_cols=143 Identities=13% Similarity=0.082 Sum_probs=90.6
Q ss_pred EEEE--EEeeCCCCCCCCCCCcEEEEceEEEEcCC-----Ce--EeeEEEEeecCCCCCCCCc-chHhhhCCChHHHhCC
Q 017210 99 FVVI--DFEATCDKDKNPYPQEIIEFPSVIVSSVT-----GQ--LEACFQTYVRPTCNQLLSD-FCKDLTGIQQIQVDRG 168 (375)
Q Consensus 99 fVVf--DlETTGl~g~~~~~~eIIEIGAV~vd~~~-----g~--i~d~F~~lVkP~~~p~Is~-~~~~LTGIt~e~l~~a 168 (375)
++|+ ++|+.- .+...++||.|.++..+..+ +. ....|...++|... .+|. +.....|+....|..-
T Consensus 506 l~vLdFsi~Sly---Psi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~-~~p~~~~~~~~~~~~~~L~~~ 581 (1172)
T TIGR00592 506 LVVLDFSMKSLN---PSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDC-SFPLDLKGEFPGKKPSLVEDL 581 (1172)
T ss_pred eEEEEeeeEEec---CccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCC-CCCchhhhhhhccCCcEEEEe
Confidence 5555 555542 23456899999888764200 11 22345566677321 1332 3335667777778888
Q ss_pred CCHHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCC----------CC---------CCCceeehH
Q 017210 169 VTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWK----------PP---------YFNRWINLK 228 (375)
Q Consensus 169 p~~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~----------P~---------~~~~~iDt~ 228 (375)
.+-.+.+..|++++.... -..++.||. +||+ .+|-.-+...+++. +. ...-.+|+.
T Consensus 582 ~sEr~lL~~fl~~~~~~D---PDii~g~n~~qfdl-kvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~ 657 (1172)
T TIGR00592 582 ATERALIKKFMAKVKKID---PDEIVGHDYQQRAL-KVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVE 657 (1172)
T ss_pred cCHHHHHHHHHHHHHhcC---CCEEEEEcccCccH-HHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHH
Confidence 888999999999998431 134566664 7998 66666666666642 00 012357888
Q ss_pred HHHHHhcCCCCCCHHHHHHHc
Q 017210 229 VPFHEVFGGVRCNLKEAVEMA 249 (375)
Q Consensus 229 ~l~~~~~~~~~~~L~~l~~~l 249 (375)
..++..+..++|+|+++++++
T Consensus 658 ~~~k~~~~~~sy~L~~v~~~~ 678 (1172)
T TIGR00592 658 ISAKELIRCKSYDLSELVQQI 678 (1172)
T ss_pred HHHHHHhCcCCCCHHHHHHHH
Confidence 888888888899999999644
No 105
>PHA03036 DNA polymerase; Provisional
Probab=92.92 E-value=2.3 Score=48.39 Aligned_cols=181 Identities=12% Similarity=0.038 Sum_probs=106.6
Q ss_pred cccEEEEEEeeCCCCCC--CCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCC---------ChHH
Q 017210 96 FQYFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGI---------QQIQ 164 (375)
Q Consensus 96 ~~~fVVfDlETTGl~g~--~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGI---------t~e~ 164 (375)
...|+.||+|.-. ++. ++..+-|+.|..+.++ ..|. +.--++++....+.-...-..+-|. .-..
T Consensus 159 ~~~~lsfDIEC~~-~g~FPs~~~~pvshIs~~~~~-~~~~--~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (1004)
T PHA03036 159 PRSYLFLDIECHF-DKKFPSVFINPVSHISCCYID-LSGK--EKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSK 234 (1004)
T ss_pred cceeEEEEEEecc-CCCCCCcccCcceEEEEEEEe-cCCC--eeEEEEeccccccccccccceeeeeeccccccccCCce
Confidence 3579999999995 443 3467899999987777 3443 2345677764311011111222222 1111
Q ss_pred HhCCCCHHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCC---CCC----------------------
Q 017210 165 VDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKI---WKP---------------------- 218 (375)
Q Consensus 165 l~~ap~~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi---~~P---------------------- 218 (375)
.---++-.+ |-+|.+++..... .+++-.|+ +||+ .+|..-++.... .++
T Consensus 235 ~~~~~sE~~-ml~~~~~i~~~d~---D~i~~yNg~nFD~-~Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~ 309 (1004)
T PHA03036 235 ELILCSEIV-LLRIAKKLLELEF---DYVVTFNGHNFDL-RYISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKG 309 (1004)
T ss_pred eeecCCHHH-HHHHHHHHHhcCC---CEEEeccCCCcch-HHHHHHHHHhccCceeeccCCCcccccceeeccccccccc
Confidence 111233334 6678888876432 34333455 7998 666665555311 000
Q ss_pred -------------CCCCceeehHHHHHHhcCCCCCCHHHHHHH-cCCC-----CCCCC-C---cHHHHHHHHHHHHHHHH
Q 017210 219 -------------PYFNRWINLKVPFHEVFGGVRCNLKEAVEM-AGLA-----WQGRA-H---CGLDDAKNTARLLALLM 275 (375)
Q Consensus 219 -------------~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~-lgI~-----~~g~~-H---rALdDA~atA~L~~~ll 275 (375)
....-++|+....++-+.+.+|+|+++.+. |+.. ..++. + .-..||...+.||.+.+
T Consensus 310 ~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~vl 389 (1004)
T PHA03036 310 VGGVANTTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEVL 389 (1004)
T ss_pred cCccccceEEecccCCeEEEEhHHHHhhhcCcccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhhh
Confidence 001125688888888888899999999987 3320 00010 0 11368899999999999
Q ss_pred Hhcccccccc
Q 017210 276 HRGFKFSITN 285 (375)
Q Consensus 276 ~~~~~~~i~~ 285 (375)
+-|.-.+|.+
T Consensus 390 ~t~ny~~i~~ 399 (1004)
T PHA03036 390 STGNYVTIND 399 (1004)
T ss_pred cccceeeecc
Confidence 9998888877
No 106
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=92.84 E-value=2.2 Score=47.69 Aligned_cols=131 Identities=17% Similarity=0.099 Sum_probs=83.8
Q ss_pred ccEEEEEEeeCCCCCCCC--CCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHH
Q 017210 97 QYFVVIDFEATCDKDKNP--YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 174 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~--~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~ev 174 (375)
-..++||+||....+..+ ..+.|+.|+...-. .++.+ ..+.. +...|. .+....+-.+.
T Consensus 154 l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~-~~~~~-------~~~~~--------~~~~~~---~v~~~~~e~e~ 214 (792)
T COG0417 154 LRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEA-EGGLI-------EVFIY--------TSGEGF---SVEVVISEAEL 214 (792)
T ss_pred ceEEEEEEEEecCCCCCCCccCCceEEEEEEecc-CCCcc-------ccccc--------cCCCCc---eeEEecCHHHH
Confidence 368999999998865443 36788888655432 12221 11111 011111 15556678899
Q ss_pred HHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCC-------------CC----CCceeehHHHHH-Hhc
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKP-------------PY----FNRWINLKVPFH-EVF 235 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P-------------~~----~~~~iDt~~l~~-~~~ 235 (375)
+.+|.+++.... -.+++.+|+ +||+ .+|..-+.++|++.. .+ ....+|+...++ +.+
T Consensus 215 l~~~~~~i~~~d---PdVIvgyn~~~fd~-pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~ 290 (792)
T COG0417 215 LERFVELIREYD---PDVIVGYNGDNFDW-PYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPL 290 (792)
T ss_pred HHHHHHHHHhcC---CCEEEeccCCcCCh-HHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhc
Confidence 999999998753 234444565 5996 899999999988753 00 123578877777 466
Q ss_pred CCCCCCHHHHHHHcC
Q 017210 236 GGVRCNLKEAVEMAG 250 (375)
Q Consensus 236 ~~~~~~L~~l~~~lg 250 (375)
...+++|..+++.+.
T Consensus 291 ~~~~ysl~~v~~~~l 305 (792)
T COG0417 291 NLKSYSLEAVSEALL 305 (792)
T ss_pred ccccccHHHHHHHhc
Confidence 677899999876554
No 107
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.72 E-value=0.057 Score=61.56 Aligned_cols=39 Identities=5% Similarity=-0.194 Sum_probs=34.6
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCC---------------CCCCccccccccc
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSW 83 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~ 83 (375)
+..+++++|++|++.|.++||||||. +||||.|+|.+..
T Consensus 15 g~~~~~elv~~A~~~G~~alAiTDH~~l~g~~~f~~~~~~~gIkpI~G~Ei~~~ 68 (1022)
T TIGR00594 15 GAAKIKPLVKKAKELGMPALALTDHGNMFGAVEFYKACKKAGIKPIIGCEAYVA 68 (1022)
T ss_pred ccCCHHHHHHHHHHCCCCEEEEecCCCchhHHHHHHHHHHcCCeEEEEEEEEee
Confidence 57789999999999999999999993 5889999998764
No 108
>PRK05761 DNA polymerase I; Reviewed
Probab=92.30 E-value=1.3 Score=49.49 Aligned_cols=97 Identities=19% Similarity=0.058 Sum_probs=63.8
Q ss_pred CCHHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCc------eeehHHHHHHh-------
Q 017210 169 VTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNR------WINLKVPFHEV------- 234 (375)
Q Consensus 169 p~~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~------~iDt~~l~~~~------- 234 (375)
.+-.+.|.+|.+|+.... ..|.-|+ +||+ .+|..-++++|++...+... .+|+...++..
T Consensus 208 ~~E~eLL~~f~~~i~~~d-----Pdi~yN~~~FDl-PYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~ 281 (787)
T PRK05761 208 DSEKELLAELFDIILEYP-----PVVTFNGDNFDL-PYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAF 281 (787)
T ss_pred CCHHHHHHHHHHHHHhcC-----CEEEEcCCcchH-HHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeec
Confidence 678899999999999863 3444565 7998 89999999999875322111 15664443211
Q ss_pred ---cCCCCCCHHHHHH-HcCCCCCCC------------CCcHHHHHHHHHHHH
Q 017210 235 ---FGGVRCNLKEAVE-MAGLAWQGR------------AHCGLDDAKNTARLL 271 (375)
Q Consensus 235 ---~~~~~~~L~~l~~-~lgI~~~g~------------~HrALdDA~atA~L~ 271 (375)
+..++++|+.+++ .+|..-... ..-.+.||..|.+|+
T Consensus 282 ~~~~~~~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 282 YGKYRHREARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred cceeecccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 1123689999997 667543100 123589999999874
No 109
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=91.65 E-value=0.09 Score=60.60 Aligned_cols=40 Identities=8% Similarity=-0.118 Sum_probs=34.9
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCC---------------CCCCcccccccccc
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEF---------------YNNPTYQHDFGSWS 84 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~---------------~~kpiyg~e~~~~~ 84 (375)
+...++++|++|++.|.+|||||||+ +||||.|+|.+...
T Consensus 19 g~~~~~elv~~A~e~G~~avAITDH~~~~g~~~f~~~a~~~gIkpIiG~Ei~~~~ 73 (1151)
T PRK06826 19 GSARIKDLIKRAKELGMDSIAITDHGVMYGVVDFYKAAKKQGIKPIIGCEVYVAP 73 (1151)
T ss_pred hcCCHHHHHHHHHHCCCCEEEEecCCchHhHHHHHHHHHhCCCEEEEEEEEEecC
Confidence 56788999999999999999999993 57899999987653
No 110
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=91.47 E-value=0.068 Score=59.09 Aligned_cols=117 Identities=22% Similarity=0.294 Sum_probs=76.6
Q ss_pred EeecCCCCCCCCcchHhhhCCChHHHhCCC------CHHHHHHHHHHHHhhCCCCCccEEEEEcC-cchHHHHHHHHHHH
Q 017210 140 TYVRPTCNQLLSDFCKDLTGIQQIQVDRGV------TLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRF 212 (375)
Q Consensus 140 ~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap------~~~evl~~f~~fl~~~~lv~~n~~vv~~a-~FD~~~fL~~~~~~ 212 (375)
-||--.. ++.++-++..||...||+-.. ++.-++.++.=.+ +.+ +++|.|| .-|+ +.
T Consensus 965 DYv~T~d--~VvDYLTqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li-~~G-----viFVGHGL~nDF--------rv 1028 (1118)
T KOG1275|consen 965 DYVSTDD--KVVDYLTQYSGIKPGDLDPTTSEKRLTTLKVLYLKLRLLI-QRG-----VIFVGHGLQNDF--------RV 1028 (1118)
T ss_pred ceecchh--HHHHHHHHhcCCCccccCCccCcceehhHHHHHHHHHHHH-HcC-----cEEEcccccccc--------eE
Confidence 4444443 577889999999999997422 3445555554333 432 4677765 4454 23
Q ss_pred cCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHH-HcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 017210 213 KKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVE-MAGLAWQGRAHCGLDDAKNTARLLALLMH 276 (375)
Q Consensus 213 ~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~-~lgI~~~g~~HrALdDA~atA~L~~~ll~ 276 (375)
.++..| ..+.+||..+++ .+. +..+|..|+. .+|-.....+|+.+.||+.+.+||.+.++
T Consensus 1029 INi~Vp--~~QiiDTv~lf~--~~s~R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1029 INIHVP--EEQIIDTVTLFR--LGSQRMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred EEEecC--hhhheeeeEEEe--cccccEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHH
Confidence 456555 346889876553 233 3458999985 45665554679999999999999887654
No 111
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=90.38 E-value=0.24 Score=48.16 Aligned_cols=165 Identities=10% Similarity=-0.080 Sum_probs=102.0
Q ss_pred EEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCC--CHHHHHHHH
Q 017210 101 VIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV--TLSEALLRH 178 (375)
Q Consensus 101 VfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap--~~~evl~~f 178 (375)
+=|++|+|-=........+++|-+.-+. .+. ...++++|.+.. ++..-.-.+ +++|+..++ .-.+-..-|
T Consensus 114 ls~lp~p~CLVaHng~~~dfpil~qela--~lg-~~lpq~lvcvds---lpa~~ald~--a~s~~tr~~~~~~~~l~~If 185 (318)
T KOG4793|consen 114 LSRLPTPGCLVAHNGNEYDFPILAQELA--GLG-YSLPQDLVCVDS---LPALNALDR--ANSMVTRPEVRRMYSLGSIF 185 (318)
T ss_pred HhcCCCCceEEeecCCccccHHHHHHHH--hcC-ccchhhhcCcch---hHHHHHHhh--hcCcccCCCCCcccccchHH
Confidence 3477777610011234567777766552 222 467899999985 443221112 677776543 333333445
Q ss_pred HHHHhh-CCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHH------hcC--CCCCCHHHHHHH
Q 017210 179 DKWLEN-KGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHE------VFG--GVRCNLKEAVEM 248 (375)
Q Consensus 179 ~~fl~~-~~lv~~n~~vv~~a-~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~------~~~--~~~~~L~~l~~~ 248 (375)
..+.+. ..-.+|+.-+.+++ .|++ .|..+++-+.+-+.+ .+|.-++.+|.. .++ ...++|..|+.+
T Consensus 186 ~ry~~q~eppa~~~~e~d~~~l~~~f-qf~~~ellR~~deqa---~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~ 261 (318)
T KOG4793|consen 186 LRYVEQREPPAGHVAEGDVNGLLFIF-QFRINELLRWSDEQA---RPWLLIRPLYLARENAKSVEPTPKLVSSLEALATY 261 (318)
T ss_pred HhhhcccCCCcceeeecccchhHHHH-HHHHHHHHhhHhhcC---CCcccccchhhhhhhccccCCCCccchhHHHHHHH
Confidence 566665 23334555555555 5786 888888888766553 346555555521 122 124789999999
Q ss_pred cCCCCCCCCCcHHHHHHHHHHHHHHHHHh
Q 017210 249 AGLAWQGRAHCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 249 lgI~~~g~~HrALdDA~atA~L~~~ll~~ 277 (375)
+....++.+|||+.|...+.++++++-.+
T Consensus 262 ~~~~p~l~ahra~~Dv~~~~k~~q~~~id 290 (318)
T KOG4793|consen 262 YSLTPELDAHRALSDVLLLSKVFQKLTID 290 (318)
T ss_pred hhcCcccchhhhccccchhhhHHHHhhhh
Confidence 99887888999999999999999987543
No 112
>PRK06361 hypothetical protein; Provisional
Probab=89.80 E-value=0.21 Score=46.09 Aligned_cols=29 Identities=3% Similarity=-0.144 Sum_probs=25.5
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCCCCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNN 73 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~~~k 73 (375)
+..++++++++|.+.|.++|+||||....
T Consensus 8 g~~~~~e~v~~A~~~Gl~~i~iTDH~~~~ 36 (212)
T PRK06361 8 GELIPSELVRRARVLGYRAIAITDHADAS 36 (212)
T ss_pred CCCCHHHHHHHHHHcCCCEEEEecCCCCc
Confidence 55678999999999999999999997643
No 113
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=88.45 E-value=5.6 Score=34.16 Aligned_cols=90 Identities=19% Similarity=0.162 Sum_probs=55.2
Q ss_pred HHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCC-CCHHHHHHHc-CCC
Q 017210 175 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVR-CNLKEAVEMA-GLA 252 (375)
Q Consensus 175 l~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~-~~L~~l~~~l-gI~ 252 (375)
+..+.+|+.+..+ ..++|+..+|+ .+|. ++|+..+ .++|+...+..+.+..+ ++|..+++.| ++.
T Consensus 64 ~~~l~~~l~~~~~----~kv~~d~k~~~-~~L~----~~gi~~~----~~~D~~laayll~p~~~~~~l~~l~~~~l~~~ 130 (172)
T smart00474 64 LEILKDLLEDETI----TKVGHNAKFDL-HVLA----RFGIELE----NIFDTMLAAYLLLGGPSKHGLATLLKEYLGVE 130 (172)
T ss_pred HHHHHHHhcCCCc----eEEEechHHHH-HHHH----HCCCccc----chhHHHHHHHHHcCCCCcCCHHHHHHHHhCCC
Confidence 4556677776432 25677888896 6664 3687753 24899765544444333 7999998765 554
Q ss_pred CC---CC--------CC----cHHHHHHHHHHHHHHHHHh
Q 017210 253 WQ---GR--------AH----CGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 253 ~~---g~--------~H----rALdDA~atA~L~~~ll~~ 277 (375)
.+ +. .. .|..||.++.+|+..|.++
T Consensus 131 ~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 131 LDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22 10 01 2566777777777776654
No 114
>PRK09248 putative hydrolase; Validated
Probab=88.18 E-value=0.34 Score=46.00 Aligned_cols=27 Identities=4% Similarity=-0.091 Sum_probs=24.4
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEFY 71 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~~ 71 (375)
+..++++++++|.++|.++|+||||..
T Consensus 17 ~~~~~~e~v~~A~~~G~~~i~iTdH~~ 43 (246)
T PRK09248 17 AYSTLHENAAEAKQKGLKLFAITDHGP 43 (246)
T ss_pred CCCCHHHHHHHHHHCCCCEEEECCCCC
Confidence 556789999999999999999999974
No 115
>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=86.08 E-value=13 Score=34.10 Aligned_cols=93 Identities=14% Similarity=-0.038 Sum_probs=55.7
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC--------CCCCHHHHHHH
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG--------VRCNLKEAVEM 248 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~--------~~~~L~~l~~~ 248 (375)
.+.+++++..+ .-|.|++..|+ .+|. +.+|+.. ..+.||...+..+... ...+|.+++++
T Consensus 56 ~L~~iLe~~~i----~Kv~h~~k~D~-~~L~---~~~gi~~----~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~ 123 (197)
T cd06148 56 GLKDILESKKI----LKVIHDCRRDS-DALY---HQYGIKL----NNVFDTQVADALLQEQETGGFNPDRVISLVQLLDK 123 (197)
T ss_pred HHHHHhcCCCc----cEEEEechhHH-HHHH---HhcCccc----cceeeHHHHHHHHHHHhcCCccccccccHHHHHHH
Confidence 34455655422 23667788886 5553 3557653 2458987544322211 13588888876
Q ss_pred c-CCCC-----------------CC------CCCcHHHHHHHHHHHHHHHHHhcccc
Q 017210 249 A-GLAW-----------------QG------RAHCGLDDAKNTARLLALLMHRGFKF 281 (375)
Q Consensus 249 l-gI~~-----------------~g------~~HrALdDA~atA~L~~~ll~~~~~~ 281 (375)
| |++. .- +-+-|..||..+..|+..|+....+.
T Consensus 124 ~l~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 124 YLYISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred hhCCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 4 5532 10 12568899999999999998776543
No 116
>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=82.85 E-value=8.7 Score=33.86 Aligned_cols=87 Identities=16% Similarity=-0.027 Sum_probs=54.4
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CCCCC-
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GLAWQ- 254 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~l-gI~~~- 254 (375)
.+.+++.+..+ ..|.|+...|+ ..|.+ .+|+.. ...+||...+..+-...+.+|.++++++ |+..+
T Consensus 58 ~L~~lL~d~~i----~Kvg~~~k~D~-~~L~~---~~gi~~----~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K 125 (161)
T cd06129 58 GLKMLLENPSI----VKALHGIEGDL-WKLLR---DFGEKL----QRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDK 125 (161)
T ss_pred HHHHHhCCCCE----EEEEeccHHHH-HHHHH---HcCCCc----ccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCc
Confidence 34556665421 23556677886 55532 256653 2458997655433222467999999875 76431
Q ss_pred --------------CCCCcHHHHHHHHHHHHHHHH
Q 017210 255 --------------GRAHCGLDDAKNTARLLALLM 275 (375)
Q Consensus 255 --------------g~~HrALdDA~atA~L~~~ll 275 (375)
.+-|-|..||..+.+|+.+|.
T Consensus 126 ~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 126 SISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred cceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 123779999999999998874
No 117
>PRK10829 ribonuclease D; Provisional
Probab=82.52 E-value=9.1 Score=39.09 Aligned_cols=134 Identities=13% Similarity=0.136 Sum_probs=82.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHH
Q 017210 97 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 176 (375)
Q Consensus 97 ~~fVVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~ 176 (375)
...|.||+|+....... ..--+|+|+ ++. --.+|.|-. +++ +.
T Consensus 22 ~~~lalDtEf~~~~ty~-~~l~LiQl~-------~~~----~~~LiD~l~---~~d----------------------~~ 64 (373)
T PRK10829 22 FPAIALDTEFVRTRTYY-PQLGLIQLY-------DGE----QLSLIDPLG---ITD----------------------WS 64 (373)
T ss_pred CCeEEEecccccCccCC-CceeEEEEe-------cCC----ceEEEecCC---ccc----------------------hH
Confidence 46899999998753211 123456663 121 125667752 211 13
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHH-HcCCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVE-MAGLAWQ 254 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~-~~~L~~l~~-~lgI~~~ 254 (375)
.|.+++.+..+ .-|.|.+.+|+ .+|.+ ..|+.. .+++||.. +..+.|.. +.+|..|++ .+|+..+
T Consensus 65 ~L~~ll~~~~i----vKV~H~~~~Dl-~~l~~---~~g~~p----~~~fDTqi-aa~~lg~~~~~gl~~Lv~~~lgv~ld 131 (373)
T PRK10829 65 PFKALLRDPQV----TKFLHAGSEDL-EVFLN---AFGELP----QPLIDTQI-LAAFCGRPLSCGFASMVEEYTGVTLD 131 (373)
T ss_pred HHHHHHcCCCe----EEEEeChHhHH-HHHHH---HcCCCc----CCeeeHHH-HHHHcCCCccccHHHHHHHHhCCccC
Confidence 35556666432 12568889998 66643 456642 36889964 44556654 689999885 5687542
Q ss_pred C---------------CCCcHHHHHHHHHHHHHHHHHhccc
Q 017210 255 G---------------RAHCGLDDAKNTARLLALLMHRGFK 280 (375)
Q Consensus 255 g---------------~~HrALdDA~atA~L~~~ll~~~~~ 280 (375)
. +-+-|..|+..+..|+.+|..+..+
T Consensus 132 K~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~ 172 (373)
T PRK10829 132 KSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEA 172 (373)
T ss_pred cccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 1266899999999999998766543
No 118
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=81.91 E-value=3.3 Score=46.93 Aligned_cols=97 Identities=13% Similarity=0.000 Sum_probs=62.5
Q ss_pred CHHHHHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc
Q 017210 170 TLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA 249 (375)
Q Consensus 170 ~~~evl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~l 249 (375)
..++++..|.+|+.+..+ ..+.||+.||+ .+|. ++|+..+ ..+.||.-...-+-+..+++|++++++|
T Consensus 362 ~~~~~~~~l~~~l~~~~~----~~v~~n~K~d~-~~l~----~~gi~~~---~~~~Dt~la~yll~~~~~~~l~~la~~y 429 (887)
T TIGR00593 362 LTILTDDKFARWLLNEQI----KKIGHDAKFLM-HLLK----REGIELG---GVIFDTMLAAYLLDPAQVSTLDTLARRY 429 (887)
T ss_pred hhHHHHHHHHHHHhCCCC----cEEEeeHHHHH-HHHH----hCCCCCC---CcchhHHHHHHHcCCCCCCCHHHHHHHH
Confidence 355677888889987532 25788999996 6664 6788764 2467986443333333457999998765
Q ss_pred -CCCC---C---CC------------CCcHHHHHHHHHHHHHHHHHhc
Q 017210 250 -GLAW---Q---GR------------AHCGLDDAKNTARLLALLMHRG 278 (375)
Q Consensus 250 -gI~~---~---g~------------~HrALdDA~atA~L~~~ll~~~ 278 (375)
+... . |. ...|..||.+|.+|+..+..+.
T Consensus 430 l~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l 477 (887)
T TIGR00593 430 LVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKEL 477 (887)
T ss_pred cCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3210 0 10 0246778999999988776554
No 119
>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=77.99 E-value=18 Score=36.69 Aligned_cols=90 Identities=14% Similarity=0.100 Sum_probs=55.0
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHc-CCCCC
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMA-GLAWQ 254 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~-~~~~L~~l~~~l-gI~~~ 254 (375)
.|.+++.+..+ ..|.|++..|+ .+|.+ .+...| ..++||... ..+.+. .+++|..+++.| |+..+
T Consensus 61 ~L~~lL~d~~i----~KV~h~~k~Dl-~~L~~----~~~~~~---~~~fDtqlA-a~lL~~~~~~~l~~Lv~~~Lg~~l~ 127 (367)
T TIGR01388 61 PLKELLRDESV----VKVLHAASEDL-EVFLN----LFGELP---QPLFDTQIA-AAFCGFGMSMGYAKLVQEVLGVELD 127 (367)
T ss_pred HHHHHHCCCCc----eEEEeecHHHH-HHHHH----HhCCCC---CCcccHHHH-HHHhCCCCCccHHHHHHHHcCCCCC
Confidence 44556665422 23677788897 56643 333333 357899753 344443 357999998765 66543
Q ss_pred CCC------C---------cHHHHHHHHHHHHHHHHHhcc
Q 017210 255 GRA------H---------CGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 255 g~~------H---------rALdDA~atA~L~~~ll~~~~ 279 (375)
..+ . -|..||..+..|+..|..+..
T Consensus 128 K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 128 KSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLE 167 (367)
T ss_pred cccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 110 2 378899999999888866543
No 120
>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=77.60 E-value=18 Score=31.54 Aligned_cols=95 Identities=18% Similarity=0.148 Sum_probs=56.1
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHc-CC
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMA-GL 251 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~-~~~~~L~~l~~~l-gI 251 (375)
+.+.|.+++.+..+ ..++|+..+|+ ..|.+ .+|+. + +.+.|+.. +..+.+ ..+++|+++++.| ++
T Consensus 52 ~~~~l~~ll~~~~i----~kv~~d~K~~~-~~L~~---~~gi~-~---~~~~D~~l-aayLl~p~~~~~l~~l~~~~l~~ 118 (178)
T cd06142 52 DLSPLKELLADPNI----VKVFHAAREDL-ELLKR---DFGIL-P---QNLFDTQI-AARLLGLGDSVGLAALVEELLGV 118 (178)
T ss_pred cHHHHHHHHcCCCc----eEEEeccHHHH-HHHHH---HcCCC-C---CCcccHHH-HHHHhCCCccccHHHHHHHHhCC
Confidence 34446667776422 24667778886 55532 22766 2 34689964 334443 3456999998764 65
Q ss_pred CCC-----CC----------CCcHHHHHHHHHHHHHHHHHhcccc
Q 017210 252 AWQ-----GR----------AHCGLDDAKNTARLLALLMHRGFKF 281 (375)
Q Consensus 252 ~~~-----g~----------~HrALdDA~atA~L~~~ll~~~~~~ 281 (375)
... ++ .+.|..||.++.+|+..|.++..+.
T Consensus 119 ~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~ 163 (178)
T cd06142 119 ELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEE 163 (178)
T ss_pred CCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHc
Confidence 421 11 0136777888888888887665443
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=66.25 E-value=46 Score=29.20 Aligned_cols=93 Identities=18% Similarity=0.103 Sum_probs=52.8
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc-CCC-CCCHHHHHHHc-C
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVF-GGV-RCNLKEAVEMA-G 250 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~-~~~-~~~L~~l~~~l-g 250 (375)
+...+.+|+.+..+ ..+.|++.+|+ .+| .++|++.+ ..+.||.- +..+. +.. +++|+++++.| +
T Consensus 44 ~~~~l~~~l~~~~~----~ki~~d~K~~~-~~l----~~~gi~~~---~~~fDt~l-aaYLL~p~~~~~~l~~l~~~yl~ 110 (178)
T cd06140 44 DLAALKEWLEDEKI----PKVGHDAKRAY-VAL----KRHGIELA---GVAFDTML-AAYLLDPTRSSYDLADLAKRYLG 110 (178)
T ss_pred HHHHHHHHHhCCCC----ceeccchhHHH-HHH----HHCCCcCC---CcchhHHH-HHHHcCCCCCCCCHHHHHHHHcC
Confidence 45556677776422 24566777775 454 45788764 34679864 33444 333 47999998765 5
Q ss_pred CCCC------CC-----C--C-----cHHHHHHHHHHHHHHHHHhcc
Q 017210 251 LAWQ------GR-----A--H-----CGLDDAKNTARLLALLMHRGF 279 (375)
Q Consensus 251 I~~~------g~-----~--H-----rALdDA~atA~L~~~ll~~~~ 279 (375)
+... +. . . .+..||..+.+|+..|.++..
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~a~~l~~l~~~l~~~L~ 157 (178)
T cd06140 111 RELPSDEEVYGKGAKFAVPDEEVLAEHLARKAAAIARLAPKLEEELE 157 (178)
T ss_pred CCCcchHHhcCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4321 00 0 0 144456667777666655543
No 122
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=64.12 E-value=57 Score=35.47 Aligned_cols=90 Identities=24% Similarity=0.249 Sum_probs=55.8
Q ss_pred HHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc--CCCCCCHHHHHHHc-C
Q 017210 174 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVF--GGVRCNLKEAVEMA-G 250 (375)
Q Consensus 174 vl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~--~~~~~~L~~l~~~l-g 250 (375)
++..+..|+.+... ..+.++..+|+ .+| .++|+. + ....|+.- +.-+. +...+.|+++++++ +
T Consensus 66 ~~~~l~~~l~~~~~----~kv~~~~K~d~-~~l----~~~Gi~-~---~~~~Dtml-asYll~~~~~~~~~~~l~~r~l~ 131 (593)
T COG0749 66 VLAALKPLLEDEGI----KKVGQNLKYDY-KVL----ANLGIE-P---GVAFDTML-ASYLLNPGAGAHNLDDLAKRYLG 131 (593)
T ss_pred hHHHHHHHhhCccc----chhccccchhH-HHH----HHcCCc-c---cchHHHHH-HHhccCcCcCcCCHHHHHHHhcC
Confidence 88899999998642 23566778886 444 467754 2 23568753 33333 34468999999877 3
Q ss_pred CCCC--------CC-------------CCcHHHHHHHHHHHHHHHHHh
Q 017210 251 LAWQ--------GR-------------AHCGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 251 I~~~--------g~-------------~HrALdDA~atA~L~~~ll~~ 277 (375)
.... |. .-.+-.||.+|.+|...|..+
T Consensus 132 ~~~~~~~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~ 179 (593)
T COG0749 132 LETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPE 179 (593)
T ss_pred CccchhHHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2211 00 123567888888888777643
No 123
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=62.97 E-value=5 Score=44.44 Aligned_cols=146 Identities=18% Similarity=0.135 Sum_probs=82.3
Q ss_pred cEEEEEEeeCCCCCCC--CCCCcEEEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHH
Q 017210 98 YFVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 175 (375)
Q Consensus 98 ~fVVfDlETTGl~g~~--~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl 175 (375)
....||+|+.|-.|.. +..|-||+|+-+.. .-|+- +-||+-.. .+. .-++|...+|-.-..-+|.|
T Consensus 275 rvlSfDIECagrkg~FPe~~~DPvIQIan~v~--~~Ge~----~pf~rnvf--~l~----~capI~G~~V~~~~~e~elL 342 (1066)
T KOG0969|consen 275 RVLSFDIECAGRKGVFPEAKIDPVIQIANLVT--LQGEN----EPFVRNVF--TLK----TCAPIVGSNVHSYETEKELL 342 (1066)
T ss_pred cccceeEEeccCCCCCCccccChHHHHHHHHH--HhcCC----chHHHhhh--ccc----CcCCCCCceeEEeccHHHHH
Confidence 4788999999976644 36688999987755 22321 12222221 122 12556666676555666777
Q ss_pred HHHHHHHhh---CCCCCccEEEEEcCcchHHHHHHHHHHHcCCC-CCCCC---C--c-----------------------
Q 017210 176 LRHDKWLEN---KGIKNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYF---N--R----------------------- 223 (375)
Q Consensus 176 ~~f~~fl~~---~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~-~P~~~---~--~----------------------- 223 (375)
+.-.+|+.+ +++.|.|+ -+||+ .+|-.-.+-.|++ +|.+. + .
T Consensus 343 ~~W~~firevDPDvI~GYNi-----~nFDi-PYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~ 416 (1066)
T KOG0969|consen 343 ESWRKFIREVDPDVIIGYNI-----CNFDI-PYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNID 416 (1066)
T ss_pred HHHHHHHHhcCCCeEecccc-----ccccc-ceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeec
Confidence 666666665 33333332 37997 6665555555654 23111 0 1
Q ss_pred ---eeehHHHHHHhcCCCCCCHHHHHHHc-CCCCCCCCCcHH
Q 017210 224 ---WINLKVPFHEVFGGVRCNLKEAVEMA-GLAWQGRAHCGL 261 (375)
Q Consensus 224 ---~iDt~~l~~~~~~~~~~~L~~l~~~l-gI~~~g~~HrAL 261 (375)
-+|+.....+-|.+++|+|+.+..+| +=.-+..||+-+
T Consensus 417 GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siI 458 (1066)
T KOG0969|consen 417 GRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSII 458 (1066)
T ss_pred ceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccch
Confidence 12444444555667789999888655 333334566543
No 124
>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=53.61 E-value=1.3e+02 Score=25.08 Aligned_cols=63 Identities=16% Similarity=-0.007 Sum_probs=36.6
Q ss_pred HHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc-CCC
Q 017210 178 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA-GLA 252 (375)
Q Consensus 178 f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~-~~~L~~l~~~l-gI~ 252 (375)
+.+++.+..+ ..++|+...|+ .+| .+.|+..+ ..+.|+...+..+-+.+ +.+|.++++.| ++.
T Consensus 45 l~~~l~~~~~----~kv~~d~K~~~-~~L----~~~~~~~~---~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKA----LKVGQNLKYDR-GIL----LNYFIELR---GIAFDTMLEAYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCC----ceeeecHHHHH-HHH----HHcCCccC---CcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence 5566665422 23556666675 444 45666653 34689975544333433 56999998775 554
No 125
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=49.18 E-value=14 Score=25.33 Aligned_cols=28 Identities=36% Similarity=0.770 Sum_probs=18.9
Q ss_pred ccccCCCCCCCCcccCCCCcccCCCCcCcccccCC
Q 017210 339 MVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 373 (375)
Q Consensus 339 ~v~k~Gpn~Gr~fy~C~~~~~~~~~~c~ff~W~~~ 373 (375)
+|.|.|.. | .||+|.++ ..|.|..|..+
T Consensus 11 lv~r~~k~-g-~F~~Cs~y-----P~C~~~~~~~~ 38 (39)
T PF01396_consen 11 LVLRRGKK-G-KFLGCSNY-----PECKYTEPLPK 38 (39)
T ss_pred eEEEECCC-C-CEEECCCC-----CCcCCeEeCCC
Confidence 33444443 3 99999664 46999998764
No 126
>PF06373 CART: Cocaine and amphetamine regulated transcript protein (CART); InterPro: IPR009106 The cocaine and amphetamine regulated transcript (CART) is a brain-localised peptide that acts as a satiety factor in appetite regulation. CART was found to inhibit both normal and starvation-induced feeding, and completely blocks the feeding response induced by neuropeptide Y. CART is regulated by leptin in the hypothalamus, and can be transcriptionally induced after cocaine or amphetamine administration []. Posttranslational processing of CART produces an N-terminal CART peptide and a C-terminal CART peptide. The C-terminal CART peptide has been isolated from the hypothalamus, nucleus accumbens, and the anterior pituitary lobe in rats. C-terminal CART is the biologically active part of the molecule affecting food intake. The structure of C-terminal CART consists of a disulphide-bound fold containing a beta-hairpin and two adjacent disulphide bridges [].; GO: 0000186 activation of MAPKK activity, 0001678 cellular glucose homeostasis, 0007186 G-protein coupled receptor protein signaling pathway, 0008343 adult feeding behavior, 0009267 cellular response to starvation, 0032099 negative regulation of appetite, 0005615 extracellular space; PDB: 1HY9_A.
Probab=48.69 E-value=5.5 Score=31.07 Aligned_cols=37 Identities=35% Similarity=0.855 Sum_probs=16.0
Q ss_pred ccccccccCCCCCCccccccCCCCCCCCcccCCCCcccCCCCcCccc
Q 017210 323 FQYHPSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFE 369 (375)
Q Consensus 323 ~~~~~~c~cg~~a~~~~v~k~Gpn~Gr~fy~C~~~~~~~~~~c~ff~ 369 (375)
.|..|+|.=|...-. +.||.-||.= .| ++|+.|+||.
T Consensus 33 ~g~vP~Cd~GE~CAv----rkG~RIGklC-dC-----~rG~~CN~fl 69 (73)
T PF06373_consen 33 YGQVPSCDVGEQCAV----RKGPRIGKLC-DC-----PRGTSCNFFL 69 (73)
T ss_dssp -----B--SSS-SEE----E-SSSEEE---B-------TT--B-TTT
T ss_pred cCcCCCCCCCchhhh----cccccccccc-CC-----CCCCchhhhH
Confidence 445678877776543 6789889872 45 5899999996
No 127
>COG0613 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]
Probab=45.17 E-value=18 Score=34.93 Aligned_cols=29 Identities=3% Similarity=-0.110 Sum_probs=25.1
Q ss_pred ccCchhHhHHHhhcCCcceeeCcCCCCCC
Q 017210 46 VHPGGDAGESIHQLSSEFVEYSNEFYNNP 74 (375)
Q Consensus 46 ~~~~~~~v~~a~~~g~~aiaitd~~~~kp 74 (375)
+-++.+++++|++-|...+|||||.-+..
T Consensus 16 ~~~p~~vv~~A~~~g~~vlAiTDHdt~~g 44 (258)
T COG0613 16 GLTPREVVERAKAKGVDVLAITDHDTVRG 44 (258)
T ss_pred CCCHHHHHHHHHHcCCCEEEECCcccccc
Confidence 33488999999999999999999987655
No 128
>PRK00912 ribonuclease P protein component 3; Provisional
Probab=44.93 E-value=15 Score=34.68 Aligned_cols=28 Identities=11% Similarity=-0.187 Sum_probs=24.6
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCCCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEFYN 72 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~~~ 72 (375)
+..++++++++|.+.|-+.|+||||...
T Consensus 14 ~~~~~~e~i~~A~~~Gl~~i~itdH~~~ 41 (237)
T PRK00912 14 GYDTVLRLISEASHLGYSGIALSNHSDK 41 (237)
T ss_pred CcchHHHHHHHHHHCCCCEEEEecCccc
Confidence 4567899999999999999999999753
No 129
>COG1387 HIS2 Histidinol phosphatase and related hydrolases of the PHP family [Amino acid transport and metabolism / General function prediction only]
Probab=38.46 E-value=21 Score=33.94 Aligned_cols=29 Identities=10% Similarity=-0.013 Sum_probs=24.8
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCCCCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNN 73 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~~~k 73 (375)
+..++.+++++|.+.|++.+++|||...-
T Consensus 14 g~~~~~e~~~~A~~~g~~~~~iTdH~~~~ 42 (237)
T COG1387 14 GEATPEEMVEAAIELGLEYIAITDHAPFL 42 (237)
T ss_pred CCCCHHHHHHHHHHcCCeEEEEecccccc
Confidence 45677888999999999999999997643
No 130
>PRK08392 hypothetical protein; Provisional
Probab=36.64 E-value=25 Score=32.56 Aligned_cols=28 Identities=11% Similarity=-0.031 Sum_probs=24.7
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCCCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEFYN 72 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~~~ 72 (375)
+..+++++++.|.+-|-+.+++|||...
T Consensus 12 ~~~~~~e~v~~A~~~Gl~~i~iTdH~~~ 39 (215)
T PRK08392 12 GIGSVRDNIAEAERKGLRLVGISDHIHY 39 (215)
T ss_pred CcCCHHHHHHHHHHcCCCEEEEccCCCc
Confidence 4556899999999999999999999854
No 131
>PRK07945 hypothetical protein; Provisional
Probab=36.53 E-value=25 Score=35.25 Aligned_cols=28 Identities=11% Similarity=0.101 Sum_probs=25.3
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCCCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEFYN 72 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~~~ 72 (375)
+..+++++|++|.+-|.+.+++|||...
T Consensus 109 g~~~~ee~v~~Ai~~Gl~~i~~TDH~p~ 136 (335)
T PRK07945 109 GGSPIEEMARTAAALGHEYCALTDHSPR 136 (335)
T ss_pred CCCCHHHHHHHHHHCCCCEEEEeCCCCC
Confidence 6677899999999999999999999753
No 132
>TIGR01856 hisJ_fam histidinol phosphate phosphatase HisJ family. This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.
Probab=36.30 E-value=32 Score=32.69 Aligned_cols=27 Identities=11% Similarity=-0.031 Sum_probs=24.1
Q ss_pred ccCchhHhHHHhhcCCcceeeCcCCCC
Q 017210 46 VHPGGDAGESIHQLSSEFVEYSNEFYN 72 (375)
Q Consensus 46 ~~~~~~~v~~a~~~g~~aiaitd~~~~ 72 (375)
..+.+++|++|.+-|-+.++||||...
T Consensus 14 ~~~~ee~v~~A~~~Gl~~i~~TdH~p~ 40 (253)
T TIGR01856 14 TDTLEEVVQEAIQLGFEEICFTEHAPL 40 (253)
T ss_pred CCCHHHHHHHHHHcCCCEEEecCCCCc
Confidence 456789999999999999999999864
No 133
>PRK07328 histidinol-phosphatase; Provisional
Probab=35.61 E-value=26 Score=33.64 Aligned_cols=28 Identities=4% Similarity=0.036 Sum_probs=24.2
Q ss_pred cccCchhHhHHHhhcCCcceeeCcCCCC
Q 017210 45 IVHPGGDAGESIHQLSSEFVEYSNEFYN 72 (375)
Q Consensus 45 ~~~~~~~~v~~a~~~g~~aiaitd~~~~ 72 (375)
+..+++++|++|.+-|.+.+++|||...
T Consensus 16 ~~~~~ee~v~~A~~~Gl~~i~~TdH~~~ 43 (269)
T PRK07328 16 AVGTPEEYVQAARRAGLKEIGFTDHLPM 43 (269)
T ss_pred CCCCHHHHHHHHHHCCCCEEEEecCCCC
Confidence 3446889999999999999999999754
No 134
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=34.01 E-value=1.6e+02 Score=25.44 Aligned_cols=57 Identities=18% Similarity=0.147 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCC-------CCCceeehHHHHHH
Q 017210 168 GVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP-------YFNRWINLKVPFHE 233 (375)
Q Consensus 168 ap~~~evl~~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~-------~~~~~iDt~~l~~~ 233 (375)
..+-.+.+..|.+-++... ..+||.|..|. +..|++-++. +|. +..+.+|+..+++.
T Consensus 54 ~DPr~~~~~~L~~~i~~~~----g~ivvyN~sfE-~~rL~ela~~----~p~~~~~l~~I~~r~vDL~~~f~~ 117 (130)
T PF11074_consen 54 EDPRRELIEALIKAIGSIY----GSIVVYNKSFE-KTRLKELAEL----FPDYAEKLNSIIERTVDLLDPFKN 117 (130)
T ss_pred CCchHHHHHHHHHHhhhhc----CeEEEechHHH-HHHHHHHHHH----hHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4456667778888777641 25788888898 5777665543 221 11245666666655
No 135
>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=29.56 E-value=2e+02 Score=25.73 Aligned_cols=88 Identities=13% Similarity=0.110 Sum_probs=47.0
Q ss_pred HHHHHHhhCCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CCC---
Q 017210 177 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GLA--- 252 (375)
Q Consensus 177 ~f~~fl~~~~lv~~n~~vv~~a~FD~~~fL~~~~~~~gi~~P~~~~~~iDt~~l~~~~~~~~~~~L~~l~~~l-gI~--- 252 (375)
.|.+|+.+..+ ..++|+...|+ ..|.. .+|+..+ .. .|+.....-+-+. +++|+.+++.| +..
T Consensus 68 ~L~~~L~~~~i----~kv~~d~K~~~-~~L~~---~~gi~~~---~~-fD~~laaYLL~p~-~~~l~~l~~~yl~~~~~k 134 (192)
T cd06147 68 ILNEVFTDPNI----LKVFHGADSDI-IWLQR---DFGLYVV---NL-FDTGQAARVLNLP-RHSLAYLLQKYCNVDADK 134 (192)
T ss_pred HHHHHhcCCCc----eEEEechHHHH-HHHHH---HhCCCcC---ch-HHHHHHHHHhCCC-cccHHHHHHHHhCCCcch
Confidence 46667766422 24555666564 44321 6687653 23 7886544433333 46999998776 443
Q ss_pred ------CCCC--CC----cHHHHHHHHHHHHHHHHHh
Q 017210 253 ------WQGR--AH----CGLDDAKNTARLLALLMHR 277 (375)
Q Consensus 253 ------~~g~--~H----rALdDA~atA~L~~~ll~~ 277 (375)
++.. .. .+..||.++.+|+..|..+
T Consensus 135 ~~~~~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~ 171 (192)
T cd06147 135 KYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNE 171 (192)
T ss_pred hhhccccccCCCCHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 1110 00 1445566666666666544
No 136
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=29.13 E-value=38 Score=28.19 Aligned_cols=44 Identities=23% Similarity=0.503 Sum_probs=28.7
Q ss_pred ccccCCCCCCccccccCCCCCCCCcccCCCC-cccCCCCcCccccc
Q 017210 327 PSCFCGVKSSKGMVRKPGPKQGSVFFGCGNW-TVTRGARCHFFEWA 371 (375)
Q Consensus 327 ~~c~cg~~a~~~~v~k~Gpn~Gr~fy~C~~~-~~~~~~~c~ff~W~ 371 (375)
+-|.|+..-...| +.+--..|..||.|+-- ....+.+|+|=.|-
T Consensus 21 ie~dcnakvvvat-s~dpvts~klyfscpyeisdg~g~~~gfkrww 65 (122)
T PF05325_consen 21 IECDCNAKVVVAT-SRDPVTSGKLYFSCPYEISDGPGRGCGFKRWW 65 (122)
T ss_pred eeccCCceEEEEe-ccCCcccceeeecCccccccCCCCCccceeEE
Confidence 5788876544433 24445789999999532 22246789998884
No 137
>TIGR01685 MDP-1 magnesium-dependent phosphatase-1. This model represents two closely related clades of sequences from eukaryotes and archaea. The mouse enzyme has been characterized as a phosphatase and has been positively identified as a member of the haloacid dehalogenase (HAD) superfamily by site-directed mutagenesis of the active site residues.
Probab=27.78 E-value=2.1e+02 Score=25.99 Aligned_cols=12 Identities=25% Similarity=0.321 Sum_probs=10.4
Q ss_pred cEEEEEEeeCCC
Q 017210 98 YFVVIDFEATCD 109 (375)
Q Consensus 98 ~fVVfDlETTGl 109 (375)
+.||||++.|-+
T Consensus 3 ~~~~~~~~~~~~ 14 (174)
T TIGR01685 3 RVIVFDLDGTLW 14 (174)
T ss_pred cEEEEeCCCCCc
Confidence 589999999965
No 138
>PF12860 PAS_7: PAS fold
Probab=23.98 E-value=1.5e+02 Score=23.89 Aligned_cols=46 Identities=15% Similarity=0.300 Sum_probs=35.7
Q ss_pred EEEceEEEEcCCCeEeeEEEEeecCCCCCCCCcchHhhhCCChHHHhCCCCHHHHHHHHH
Q 017210 120 IEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 179 (375)
Q Consensus 120 IEIGAV~vd~~~g~i~d~F~~lVkP~~~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f~ 179 (375)
+..|.+++| .+|+++ + .++...++.|+..+++.-+.++.+++....
T Consensus 4 l~~Gv~v~D-~~~rl~-----~--------~N~~~~~l~~~~~~~~~~G~~~~~l~~~~~ 49 (115)
T PF12860_consen 4 LPQGVAVFD-SDGRLV-----F--------WNQRFRELFGLPPEMLRPGASFRDLLRRLA 49 (115)
T ss_pred cCceEEEEc-CCCeEE-----e--------EcHHHHHHhCCCHHHhcCCCCHHHHHHHHH
Confidence 346788888 577774 2 455678999999999999999988888763
No 139
>PF11079 YqhG: Bacterial protein YqhG of unknown function; InterPro: IPR024562 This family of putative proteins appears to be restricted to Firmicutes. Their function is not known.
Probab=22.82 E-value=45 Score=32.49 Aligned_cols=71 Identities=21% Similarity=0.400 Sum_probs=51.8
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEceEEEEcCCCeEeeEEEEeecCCC-CCCCCcchHhhhCCChHHHhCCCCHHHHHHHH
Q 017210 100 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTC-NQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 178 (375)
Q Consensus 100 VVfDlETTGl~g~~~~~~eIIEIGAV~vd~~~g~i~d~F~~lVkP~~-~p~Is~~~~~LTGIt~e~l~~ap~~~evl~~f 178 (375)
|-+-++-.|. -.+|++.++|.-++ +|++++.|+..+.... .|+||+.+--++- -.++..++.++
T Consensus 124 vN~KVsy~cD----~KkDel~SlGi~Li---~G~ive~F~~~L~~~~LtpkiPdy~ftlsp--------~i~~~sa~~rl 188 (260)
T PF11079_consen 124 VNVKVSYQCD----RKKDELLSLGINLI---SGQIVENFHERLQGRQLTPKIPDYCFTLSP--------IIKPKSALKRL 188 (260)
T ss_pred EeEEEEEeec----cchHHHhhheeecc---CCcchhhHHHHHhcCCCCCCCCcceeecCC--------cCCHHHHHHHH
Confidence 3466677763 46899999999887 8999999999998864 3445555444333 34688899998
Q ss_pred HHHHhhC
Q 017210 179 DKWLENK 185 (375)
Q Consensus 179 ~~fl~~~ 185 (375)
..+|.+.
T Consensus 189 E~~l~~~ 195 (260)
T PF11079_consen 189 EQYLEQY 195 (260)
T ss_pred HHHHHHH
Confidence 8888774
No 140
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=22.61 E-value=54 Score=37.23 Aligned_cols=36 Identities=17% Similarity=0.544 Sum_probs=22.0
Q ss_pred ccccCCCCCCccccccCCCCCCCCcccCCCCcccCCCCcCcccccC
Q 017210 327 PSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAF 372 (375)
Q Consensus 327 ~~c~cg~~a~~~~v~k~Gpn~Gr~fy~C~~~~~~~~~~c~ff~W~~ 372 (375)
+-|.||.. ++.+.|. .|+.||+|.++ ..|.|..|.-
T Consensus 697 P~~~C~g~----l~~r~gr-~G~~f~~Cs~y-----p~C~~~~~~~ 732 (860)
T PRK06319 697 PAIGCTGH----IVKRRSR-FNKMFYSCSEY-----PACSVIGNSI 732 (860)
T ss_pred CCcCCCCc----EEEEecC-CCCeeeccCCC-----CCCceeeccC
Confidence 33457642 3334443 47789999765 3699886654
No 141
>PRK08123 histidinol-phosphatase; Reviewed
Probab=22.38 E-value=56 Score=31.41 Aligned_cols=25 Identities=8% Similarity=-0.140 Sum_probs=22.5
Q ss_pred CchhHhHHHhhcCCcceeeCcCCCC
Q 017210 48 PGGDAGESIHQLSSEFVEYSNEFYN 72 (375)
Q Consensus 48 ~~~~~v~~a~~~g~~aiaitd~~~~ 72 (375)
.++++|++|.+-|-+.+++|||...
T Consensus 20 ~~e~~v~~Ai~~Gl~~i~~tdH~p~ 44 (270)
T PRK08123 20 DLEAYIERAIELGFTEITFTEHAPL 44 (270)
T ss_pred CHHHHHHHHHHcCCcEEEEeccCCC
Confidence 4689999999999999999999654
No 142
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=22.17 E-value=54 Score=36.07 Aligned_cols=39 Identities=15% Similarity=0.268 Sum_probs=24.1
Q ss_pred cccCCCCCCccccccCCCCCCCCcccCCCCcccCC--CCcCcccccC
Q 017210 328 SCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRG--ARCHFFEWAF 372 (375)
Q Consensus 328 ~c~cg~~a~~~~v~k~Gpn~Gr~fy~C~~~~~~~~--~~c~ff~W~~ 372 (375)
.|-||... |.+.|.+ |+ |.+|.++..-++ .+|+|=.|.+
T Consensus 613 ~cpcg~~l----~~~~~~~-g~-f~~c~~~p~C~~~~~~c~~~~~~~ 653 (660)
T TIGR01056 613 PVSCGGIA----KCPAKDN-GR-LIDCKKFPECTEYGNGCEFTIPKK 653 (660)
T ss_pred cCCCCCce----eeeecCC-Ce-eecCCCCCCccCcCCCCeEEccHH
Confidence 35577433 2344443 54 999988744433 6899998864
Done!