Query 015017
Match_columns 414
No_of_seqs 323 out of 1225
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 02:17:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015017.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015017hhsearch_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 7.7E-55 1.7E-59 473.6 11.3 247 42-325 347-594 (1444)
2 TIGR01405 polC_Gram_pos DNA po 100.0 6.7E-41 1.5E-45 379.0 22.4 242 44-322 117-360 (1213)
3 KOG0542 Predicted exonuclease 100.0 2.5E-41 5.3E-46 320.3 12.6 220 133-357 53-278 (280)
4 PRK00448 polC DNA polymerase I 100.0 2.5E-38 5.4E-43 361.9 21.2 242 44-322 347-589 (1437)
5 PRK07748 sporulation inhibitor 100.0 6.6E-37 1.4E-41 288.1 19.6 177 136-321 4-184 (207)
6 PTZ00315 2'-phosphotransferase 100.0 3.4E-36 7.5E-41 316.9 25.7 196 132-327 52-265 (582)
7 PRK06722 exonuclease; Provisio 100.0 4.9E-34 1.1E-38 280.1 20.4 171 136-315 5-179 (281)
8 cd06133 ERI-1_3'hExo_like DEDD 100.0 8.2E-33 1.8E-37 250.2 20.4 172 138-314 1-176 (176)
9 TIGR01406 dnaQ_proteo DNA poly 100.0 4.6E-32 1E-36 258.9 19.6 170 137-319 1-174 (225)
10 PRK05711 DNA polymerase III su 100.0 5.8E-32 1.3E-36 260.6 19.5 173 136-322 4-181 (240)
11 smart00479 EXOIII exonuclease 100.0 3.6E-31 7.8E-36 237.0 22.0 166 137-317 1-167 (169)
12 PRK09146 DNA polymerase III su 100.0 1.9E-31 4.1E-36 256.9 21.3 174 123-319 39-229 (239)
13 cd06131 DNA_pol_III_epsilon_Ec 100.0 3.4E-31 7.3E-36 239.2 20.8 162 138-313 1-166 (167)
14 PRK08517 DNA polymerase III su 100.0 9.6E-31 2.1E-35 254.4 20.6 175 121-318 58-232 (257)
15 PRK06807 DNA polymerase III su 100.0 1.5E-30 3.2E-35 259.6 22.2 164 136-317 8-172 (313)
16 PRK06195 DNA polymerase III su 100.0 1.2E-30 2.7E-35 259.7 21.0 164 137-319 2-166 (309)
17 cd06130 DNA_pol_III_epsilon_li 100.0 1.6E-30 3.5E-35 231.1 19.3 154 138-311 1-155 (156)
18 PRK07740 hypothetical protein; 100.0 3.4E-30 7.5E-35 248.7 21.0 169 136-321 59-230 (244)
19 PRK06063 DNA polymerase III su 100.0 2E-30 4.3E-35 258.8 18.5 168 136-321 15-183 (313)
20 PRK07942 DNA polymerase III su 100.0 6.6E-30 1.4E-34 245.0 20.3 173 136-318 6-181 (232)
21 PRK06310 DNA polymerase III su 100.0 7.3E-30 1.6E-34 247.3 19.6 169 136-318 7-175 (250)
22 PRK05168 ribonuclease T; Provi 100.0 5.5E-30 1.2E-34 242.2 18.3 177 136-318 17-202 (211)
23 PRK09145 DNA polymerase III su 100.0 8.3E-30 1.8E-34 238.7 18.0 163 136-316 29-200 (202)
24 PRK07247 DNA polymerase III su 100.0 1.2E-29 2.7E-34 237.4 18.7 162 135-319 4-171 (195)
25 TIGR00573 dnaq exonuclease, DN 100.0 1.9E-29 4.1E-34 239.1 19.5 171 136-321 7-181 (217)
26 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 2E-29 4.3E-34 232.0 17.3 161 138-312 1-176 (177)
27 PRK06309 DNA polymerase III su 100.0 4.4E-29 9.6E-34 239.1 20.1 162 137-317 3-166 (232)
28 COG5018 KapD Inhibitor of the 100.0 7.9E-31 1.7E-35 235.9 7.4 187 136-324 4-192 (210)
29 cd06134 RNaseT DEDDh 3'-5' exo 100.0 4.3E-29 9.3E-34 232.2 18.7 174 137-316 6-188 (189)
30 PRK07883 hypothetical protein; 100.0 1.3E-28 2.7E-33 262.5 22.5 174 125-320 9-185 (557)
31 TIGR01298 RNaseT ribonuclease 100.0 8.9E-29 1.9E-33 232.1 18.0 177 136-318 8-193 (200)
32 PRK07246 bifunctional ATP-depe 100.0 3.1E-28 6.8E-33 269.6 19.6 165 136-319 7-172 (820)
33 PRK05601 DNA polymerase III su 100.0 1.5E-27 3.2E-32 240.2 19.9 163 136-314 46-246 (377)
34 cd06138 ExoI_N N-terminal DEDD 100.0 6.1E-28 1.3E-32 223.0 15.5 162 139-310 1-182 (183)
35 PRK08074 bifunctional ATP-depe 100.0 2.1E-27 4.6E-32 266.3 20.2 167 136-319 3-171 (928)
36 TIGR01407 dinG_rel DnaQ family 99.9 4.7E-27 1E-31 261.6 20.0 165 137-318 1-166 (850)
37 cd06127 DEDDh DEDDh 3'-5' exon 99.9 9.1E-27 2E-31 203.7 16.9 156 139-310 1-158 (159)
38 PRK07983 exodeoxyribonuclease 99.9 1.1E-26 2.5E-31 221.0 16.6 148 138-316 2-153 (219)
39 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 1.7E-27 3.7E-32 215.9 9.9 146 139-311 1-161 (161)
40 COG0847 DnaQ DNA polymerase II 99.9 2.5E-25 5.4E-30 212.8 17.7 165 136-316 13-181 (243)
41 cd06144 REX4_like DEDDh 3'-5' 99.9 7.8E-26 1.7E-30 203.1 11.7 149 139-311 1-152 (152)
42 cd06149 ISG20 DEDDh 3'-5' exon 99.9 8.5E-26 1.8E-30 204.3 10.9 147 139-311 1-157 (157)
43 PRK09182 DNA polymerase III su 99.9 3.8E-25 8.1E-30 219.1 16.0 200 136-362 37-241 (294)
44 PF00929 RNase_T: Exonuclease; 99.9 3E-27 6.5E-32 206.9 0.9 161 139-310 1-164 (164)
45 cd06145 REX1_like DEDDh 3'-5' 99.9 1.5E-25 3.3E-30 201.1 11.7 143 139-310 1-149 (150)
46 cd06135 Orn DEDDh 3'-5' exonuc 99.9 3.3E-25 7.2E-30 203.3 14.2 162 138-316 1-171 (173)
47 PRK05359 oligoribonuclease; Pr 99.9 2.3E-23 4.9E-28 192.9 16.5 164 136-317 3-175 (181)
48 PRK11779 sbcB exonuclease I; P 99.9 1E-22 2.2E-27 213.0 17.7 172 136-316 6-197 (476)
49 PF06839 zf-GRF: GRF zinc fing 99.3 9.4E-13 2E-17 95.5 3.0 44 366-412 1-44 (45)
50 KOG2249 3'-5' exonuclease [Rep 99.2 1E-10 2.2E-15 113.1 13.1 157 136-316 105-265 (280)
51 cd05160 DEDDy_DNA_polB_exo DED 99.2 6.4E-10 1.4E-14 103.4 18.0 139 139-292 2-162 (199)
52 cd06143 PAN2_exo DEDDh 3'-5' e 99.1 7.2E-10 1.6E-14 102.2 12.4 154 136-310 5-173 (174)
53 PHA02570 dexA exonuclease; Pro 99.0 5E-09 1.1E-13 99.4 11.4 165 138-318 3-200 (220)
54 cd06125 DnaQ_like_exo DnaQ-lik 98.9 1.4E-08 3.1E-13 84.7 11.5 83 139-269 1-83 (96)
55 COG2925 SbcB Exonuclease I [DN 98.8 3.3E-08 7.1E-13 99.9 12.2 166 136-313 9-197 (475)
56 COG1949 Orn Oligoribonuclease 98.8 3.1E-08 6.8E-13 89.8 10.2 160 135-312 5-173 (184)
57 KOG3242 Oligoribonuclease (3'- 98.7 1.7E-07 3.8E-12 85.8 10.2 163 136-315 26-197 (208)
58 cd05781 DNA_polB_B3_exo DEDDy 98.5 1.6E-06 3.5E-11 81.0 12.4 120 137-291 4-144 (188)
59 cd05780 DNA_polB_Kod1_like_exo 98.5 3E-06 6.4E-11 79.3 13.8 129 137-292 4-156 (195)
60 PF13482 RNase_H_2: RNase_H su 98.4 1E-06 2.2E-11 79.2 9.3 116 139-293 1-117 (164)
61 KOG2248 3'-5' exonuclease [Rep 98.4 9.6E-07 2.1E-11 90.7 9.3 157 136-321 216-379 (380)
62 cd05782 DNA_polB_like1_exo Unc 98.3 2.3E-05 5E-10 74.4 16.2 114 146-292 41-170 (208)
63 KOG0304 mRNA deadenylase subun 98.2 1.8E-05 3.8E-10 75.2 11.0 172 137-315 25-237 (239)
64 cd06139 DNA_polA_I_Ecoli_like_ 98.1 6.6E-05 1.4E-09 68.5 13.4 144 136-318 5-171 (193)
65 cd05779 DNA_polB_epsilon_exo D 98.0 0.0003 6.5E-09 66.7 15.6 145 137-292 3-169 (204)
66 cd05785 DNA_polB_like2_exo Unc 97.9 0.00033 7.1E-09 66.5 14.2 121 137-292 10-169 (207)
67 PF10108 DNA_pol_B_exo2: Predi 97.9 0.00044 9.5E-09 65.9 14.9 130 154-316 7-172 (209)
68 PF04857 CAF1: CAF1 family rib 97.9 0.00026 5.5E-09 69.4 13.7 172 136-312 22-262 (262)
69 PRK05755 DNA polymerase I; Pro 97.8 0.00018 3.8E-09 81.7 13.3 135 136-316 315-468 (880)
70 smart00481 POLIIIAc DNA polyme 97.8 9.3E-06 2E-10 62.9 1.8 52 45-104 13-64 (67)
71 KOG4793 Three prime repair exo 97.5 0.00018 3.8E-09 70.5 6.4 173 135-316 12-290 (318)
72 KOG1956 DNA topoisomerase III 97.4 0.00013 2.7E-09 78.4 4.0 41 365-410 718-758 (758)
73 cd05783 DNA_polB_B1_exo DEDDy 97.4 0.0074 1.6E-07 57.2 15.6 136 137-290 6-169 (204)
74 cd05777 DNA_polB_delta_exo DED 97.3 0.01 2.2E-07 57.0 16.0 135 137-290 8-181 (230)
75 PRK06920 dnaE DNA polymerase I 97.3 6.9E-05 1.5E-09 86.4 1.2 54 44-105 16-69 (1107)
76 PRK07279 dnaE DNA polymerase I 97.3 8.6E-05 1.9E-09 84.9 1.8 54 44-105 15-68 (1034)
77 TIGR03491 RecB family nuclease 97.3 0.0032 6.9E-08 66.6 12.7 123 136-293 284-411 (457)
78 PRK07135 dnaE DNA polymerase I 96.8 0.00047 1E-08 78.6 1.4 54 44-105 16-69 (973)
79 PF02811 PHP: PHP domain; Int 96.8 0.00044 9.6E-09 61.7 0.9 52 44-103 13-64 (175)
80 PTZ00166 DNA polymerase delta 96.7 0.023 5.1E-07 65.9 14.5 161 137-314 265-483 (1054)
81 COG3359 Predicted exonuclease 96.6 0.019 4.1E-07 56.0 10.8 118 136-293 98-220 (278)
82 cd05784 DNA_polB_II_exo DEDDy 96.6 0.016 3.4E-07 54.6 10.0 120 137-288 4-149 (193)
83 cd05778 DNA_polB_zeta_exo inac 96.6 0.084 1.8E-06 50.9 15.3 173 137-316 5-222 (231)
84 smart00486 POLBc DNA polymeras 96.6 0.18 4E-06 51.9 18.6 161 137-313 4-220 (471)
85 PRK05898 dnaE DNA polymerase I 96.6 0.00096 2.1E-08 75.9 1.8 54 44-105 15-68 (971)
86 PRK09532 DNA polymerase III su 96.5 0.00097 2.1E-08 75.6 1.5 54 44-105 16-69 (874)
87 PRK07374 dnaE DNA polymerase I 96.1 0.002 4.3E-08 75.0 1.3 54 44-105 16-69 (1170)
88 PRK05672 dnaE2 error-prone DNA 96.1 0.0021 4.5E-08 74.2 1.4 54 44-105 18-71 (1046)
89 COG0587 DnaE DNA polymerase II 96.0 0.0027 5.8E-08 73.5 1.7 54 44-105 17-70 (1139)
90 PRK05673 dnaE DNA polymerase I 95.7 0.0038 8.2E-08 72.7 1.3 54 44-105 15-68 (1135)
91 TIGR00594 polc DNA-directed DN 95.5 0.0054 1.2E-07 70.8 1.5 53 45-105 15-67 (1022)
92 PF01612 DNA_pol_A_exo1: 3'-5' 95.4 1 2.3E-05 39.8 15.7 91 213-316 65-174 (176)
93 PRK05762 DNA polymerase II; Re 95.4 0.3 6.6E-06 55.2 14.8 146 137-313 156-348 (786)
94 PF03104 DNA_pol_B_exo1: DNA p 95.3 0.23 5E-06 49.0 12.1 130 136-284 157-325 (325)
95 PF13017 Maelstrom: piRNA path 95.3 0.13 2.7E-06 49.2 9.7 156 156-316 8-196 (213)
96 PRK06826 dnaE DNA polymerase I 95.2 0.0073 1.6E-07 70.4 1.2 53 45-105 19-71 (1151)
97 KOG1798 DNA polymerase epsilon 94.3 0.81 1.8E-05 54.2 14.3 161 136-316 246-453 (2173)
98 cd05776 DNA_polB_alpha_exo ina 94.2 0.45 9.7E-06 45.9 10.5 149 137-291 4-186 (234)
99 KOG1365 RNA-binding protein Fu 94.0 0.028 6.1E-07 57.6 1.9 56 301-363 15-72 (508)
100 PHA02528 43 DNA polymerase; Pr 92.7 4.4 9.6E-05 46.6 16.8 160 137-312 107-323 (881)
101 COG5228 POP2 mRNA deadenylase 92.0 0.16 3.4E-06 48.9 3.7 160 155-323 79-259 (299)
102 PRK06361 hypothetical protein; 91.7 0.11 2.3E-06 48.9 2.2 53 45-105 8-68 (212)
103 TIGR00592 pol2 DNA polymerase 90.7 13 0.00027 44.3 18.2 143 137-287 505-677 (1172)
104 COG0349 Rnd Ribonuclease D [Tr 90.6 4.2 9.2E-05 42.0 12.6 132 136-316 17-165 (361)
105 COG0417 PolB DNA polymerase el 90.3 5.7 0.00012 45.2 14.5 130 136-289 154-305 (792)
106 cd06146 mut-7_like_exo DEDDy 3 89.6 5.4 0.00012 37.2 11.6 141 136-314 22-192 (193)
107 PHA03036 DNA polymerase; Provi 89.6 12 0.00026 43.6 16.4 180 135-324 159-399 (1004)
108 PHA02524 43A DNA polymerase su 89.4 2.2 4.7E-05 46.0 9.7 140 136-286 106-281 (498)
109 PRK09248 putative hydrolase; V 88.8 0.28 6E-06 47.4 2.3 60 45-105 17-77 (246)
110 cd00007 35EXOc 3'-5' exonuclea 88.6 4.3 9.3E-05 34.7 9.6 66 211-288 40-106 (155)
111 cd06141 WRN_exo DEDDy 3'-5' ex 87.5 15 0.00032 32.9 12.7 131 136-314 18-169 (170)
112 PRK05761 DNA polymerase I; Rev 84.8 9.4 0.0002 43.5 12.0 97 208-310 208-334 (787)
113 KOG1275 PAB-dependent poly(A) 84.5 0.45 9.8E-06 53.8 1.4 110 188-315 972-1090(1118)
114 TIGR01388 rnd ribonuclease D. 84.2 35 0.00077 35.2 15.0 131 136-316 18-165 (367)
115 PF01396 zf-C4_Topoisom: Topoi 79.2 2 4.4E-05 30.1 2.7 29 377-412 10-38 (39)
116 COG0613 Predicted metal-depend 78.2 1.4 3E-05 43.4 2.1 52 45-104 15-67 (258)
117 smart00474 35EXOc 3'-5' exonuc 75.6 34 0.00074 29.7 10.2 89 214-315 64-169 (172)
118 cd06148 Egl_like_exo DEDDy 3'- 74.7 40 0.00086 31.4 10.8 78 233-318 69-178 (197)
119 PRK07945 hypothetical protein; 61.7 5.7 0.00012 40.5 2.4 61 45-105 109-175 (335)
120 TIGR01856 hisJ_fam histidinol 59.8 6.1 0.00013 38.4 2.2 60 46-105 14-86 (253)
121 PRK08392 hypothetical protein; 58.9 5.2 0.00011 37.9 1.5 56 45-105 12-71 (215)
122 cd06129 RNaseD_like DEDDy 3'-5 56.2 38 0.00081 30.3 6.6 131 136-314 13-160 (161)
123 PRK00912 ribonuclease P protei 56.2 7 0.00015 37.5 1.9 50 45-104 14-64 (237)
124 TIGR00593 pola DNA polymerase 55.9 36 0.00078 39.4 7.8 96 209-316 362-476 (887)
125 PF04216 FdhE: Protein involve 54.3 4.5 9.7E-05 40.3 0.2 42 361-406 170-216 (290)
126 cd06142 RNaseD_exo DEDDy 3'-5' 51.2 1.7E+02 0.0037 25.7 10.2 92 213-317 52-160 (178)
127 COG0749 PolA DNA polymerase I 47.7 1.8E+02 0.0038 32.4 11.0 131 139-316 25-179 (593)
128 COG1387 HIS2 Histidinol phosph 47.4 13 0.00028 36.0 2.2 60 45-105 14-77 (237)
129 PRK07328 histidinol-phosphatas 45.3 12 0.00027 36.5 1.7 60 46-105 17-89 (269)
130 PRK06319 DNA topoisomerase I/S 44.4 16 0.00034 42.1 2.6 37 366-412 697-733 (860)
131 PHA02563 DNA polymerase; Provi 44.2 1.1E+02 0.0023 34.3 8.8 39 214-253 50-89 (630)
132 KOG0969 DNA polymerase delta, 42.0 12 0.00026 42.3 1.2 147 137-301 275-459 (1066)
133 PRK05588 histidinol-phosphatas 40.9 22 0.00047 34.4 2.6 59 46-105 15-75 (255)
134 PF11074 DUF2779: Domain of un 40.5 57 0.0012 28.8 5.0 57 207-272 54-117 (130)
135 TIGR01056 topB DNA topoisomera 40.2 19 0.00042 40.2 2.4 38 368-411 614-653 (660)
136 PRK10829 ribonuclease D; Provi 39.4 2.4E+02 0.0052 29.4 10.2 131 136-317 22-170 (373)
137 cd06140 DNA_polA_I_Bacillus_li 35.2 2.7E+02 0.0059 24.7 8.8 108 136-291 3-112 (178)
138 PRK08609 hypothetical protein; 32.8 30 0.00065 38.0 2.4 61 45-105 347-413 (570)
139 PRK07726 DNA topoisomerase III 30.7 30 0.00064 38.7 1.9 17 389-411 629-645 (658)
140 PRK06599 DNA topoisomerase I; 27.4 39 0.00084 37.8 2.2 26 378-410 596-621 (675)
141 TIGR01562 FdhE formate dehydro 22.2 58 0.0013 33.1 2.1 40 364-406 186-229 (305)
142 PF06777 DUF1227: Protein of u 21.7 3.7E+02 0.0081 24.4 7.0 100 187-310 41-140 (146)
143 PRK08123 histidinol-phosphatas 21.3 46 0.00099 32.6 1.1 58 48-105 20-92 (270)
No 1
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.7e-55 Score=473.57 Aligned_cols=247 Identities=18% Similarity=0.207 Sum_probs=228.2
Q ss_pred CCccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhccCCCCCCcccccccccc
Q 015017 42 DDTIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQFYPFPVENRFQFAPYNM 121 (414)
Q Consensus 42 ~~~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~y~~~v~d~~~~~~~~~ 121 (414)
.--++.++.+||++|++|||+|||||| |+++|+||++|.+++|.|+|+|||+|+| +|+|++ ||++
T Consensus 347 ~mDai~sv~~~vk~A~kwghkaIAITD--------h~~VqafP~~y~~akK~giK~IyG~Ean----lvdD~v---piv~ 411 (1444)
T COG2176 347 QMDAITSVEELVKQAKKWGHKAIAITD--------HGVVQAFPEAYKAAKKYGIKAIYGLEAN----LVDDGV---PIVY 411 (1444)
T ss_pred hhcccCCHHHHHHHHHHcCCceEEEec--------CcchhhchHHHHhhhhcCceEEEeeeee----eccCCC---ceec
Confidence 345678999999999999999999995 7777899999999999999999999999 599999 9999
Q ss_pred CCCCCCCCCCCCccccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCCh
Q 015017 122 LTPAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQ 201 (414)
Q Consensus 122 ~~~~~p~~~~~q~~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~ 201 (414)
|+.+..++ +.+|||||+||||| ++..++|||||||++ ++|+++|.|+.||+|.. +||.++++|||||+
T Consensus 412 N~~d~~l~-----datyVVfDiETTGL---s~~~d~iIE~aAvKi--kng~iId~f~~Fi~P~~--pl~~~~telTgITd 479 (1444)
T COG2176 412 NPDDQKLD-----DATYVVFDIETTGL---SPVYDEIIEIAAVKI--KNGRIIDKFQFFIKPGR--PLSATITELTGITD 479 (1444)
T ss_pred Cccccccc-----cccEEEEEeecCCc---Ccccchhhhheeeee--eCCcchHHHHHhcCCCC--cCchhhhhccccCH
Confidence 99999998 48999999999998 889999999999999 79999999999999995 59999999999999
Q ss_pred hhhhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCC
Q 015017 202 IQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCN 280 (414)
Q Consensus 202 e~V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~ 280 (414)
+||++|+++++||.+|.+|+++++||+||+ +||+ +||+..+++.++.. +.+++|||+.+.|.++| .++|+
T Consensus 480 eml~~a~~i~~vL~kf~~~~~d~IlVAHNa------sFD~-gFl~~~~~k~~~~~--~~~pvIDTL~lar~L~P~~ksh~ 550 (1444)
T COG2176 480 EMLENAPEIEEVLEKFREFIGDSILVAHNA------SFDM-GFLNTNYEKYGLEP--LTNPVIDTLELARALNPEFKSHR 550 (1444)
T ss_pred HHHcCCccHHHHHHHHHHHhcCcEEEeccC------ccch-hHHHHHHHHhCCcc--ccCchhhHHHHHHHhChhhhhcc
Confidence 999999999999999999999987666554 9998 89999999988764 78899999999999997 78999
Q ss_pred HHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcCCcccccc
Q 015017 281 LKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNS 325 (414)
Q Consensus 281 L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~~~i~e~ 325 (414)
|+.++++||+.++ +||||.+||.+|++||..|++...+.+|+..
T Consensus 551 Lg~l~kk~~v~le-~hHRA~yDaeat~~vf~~f~~~~ke~Gi~~l 594 (1444)
T COG2176 551 LGTLCKKLGVELE-RHHRADYDAEATAKVFFVFLKDLKEKGITNL 594 (1444)
T ss_pred hHHHHHHhCccHH-HhhhhhhhHHHHHHHHHHHHHHHHHhchhhH
Confidence 9999999999995 9999999999999999999998887777554
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=6.7e-41 Score=378.96 Aligned_cols=242 Identities=19% Similarity=0.235 Sum_probs=215.2
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhccCCCCCCccccccccccCC
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQFYPFPVENRFQFAPYNMLT 123 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~y~~~v~d~~~~~~~~~~~ 123 (414)
-++.++.++|++|++|||++||||| |+.+|+||+++.++++.++|+|||+|.+. ++|.+ ++++++
T Consensus 117 Dg~~~~~elv~~A~~~Gl~aiAITD--------H~~~~~~~~~~~~~~~~~ikvI~GvE~~~----~~d~~---~~v~n~ 181 (1213)
T TIGR01405 117 DAITSVQEYVKQAKKWGHKAIAITD--------HGVVQAFPEAYKAAKKDGIKIIYGMEANL----VDDRV---PIVYNP 181 (1213)
T ss_pred ccCCCHHHHHHHHHHCCCCEEEEec--------CCCccCHHHHHHHHHhcCCEEEEEEEEEe----ecccc---hhhcCc
Confidence 4567788999999999999999995 77778999999999999999999999984 78877 799999
Q ss_pred CCCCC-CCCCCccccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChh
Q 015017 124 PAHPY-DFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQI 202 (414)
Q Consensus 124 ~~~p~-~~~~q~~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e 202 (414)
.+.++ + ..+|||||+||||+ ++..++|||||||+++ +|+++++|++||+|.. +|+++++++||||++
T Consensus 182 ~~~~l~~-----~~~~VVfDiETTGL---~~~~d~IIEIGAVkv~--~g~iid~f~~~V~P~~--~I~~~~~~ltGIT~e 249 (1213)
T TIGR01405 182 DDQKLLD-----DATYVVFDIETTGL---SPQYDEIIEFGAVKVK--NGRIIDKFQFFIKPHE--PLSAFVTELTGITQD 249 (1213)
T ss_pred ccccccc-----CCcEEEEEeEecCC---CCCCCeEEEEEEEEEE--CCeEEEEEEEEECCCC--CCCHHHHHHhCCCHH
Confidence 88887 5 26999999999998 6788999999999996 7889999999999995 699999999999999
Q ss_pred hhhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCH
Q 015017 203 QVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNL 281 (414)
Q Consensus 203 ~V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L 281 (414)
||++||++++|+++|.+|+++.. .|.|++.||+ .||+.+++++|+.. +.++++|++.+++.+++ .++++|
T Consensus 250 ~L~~ap~~~evl~~f~~fl~~~i------LVaHNa~FD~-~fL~~~~~r~g~~~--~~~~~IDTl~lar~l~p~~k~~kL 320 (1213)
T TIGR01405 250 MLENAPEIEEVLEKFKEFFKDSI------LVAHNASFDI-GFLNTNFEKVGLEP--LENPVIDTLELARALNPEYKSHRL 320 (1213)
T ss_pred HHhCCCCHHHHHHHHHHHhCCCe------EEEEChHHHH-HHHHHHHHHcCCCc--cCCCEeEHHHHHHHHhccCCCCCH
Confidence 99999999999999999999854 4556669995 89999999998853 45689999999998885 578999
Q ss_pred HHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcCCccc
Q 015017 282 KEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSI 322 (414)
Q Consensus 282 ~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~~~i 322 (414)
++++++||++.+ ++|||++||.+|++||.+|+++..+.++
T Consensus 321 ~~Lak~lgi~~~-~~HrAl~DA~aTa~I~~~ll~~l~~~~i 360 (1213)
T TIGR01405 321 GNICKKLGVDLD-DHHRADYDAEATAKVFKVMVEQLKEKGI 360 (1213)
T ss_pred HHHHHHcCCCCC-CCcCHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 999999999996 5899999999999999999987655544
No 3
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.5e-41 Score=320.31 Aligned_cols=220 Identities=37% Similarity=0.673 Sum_probs=191.1
Q ss_pred CccccEEEEEEeeCCCCCCC-CCCCcEEEEcEEEEEc-CCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCH
Q 015017 133 QEFQYFVVIDFEATCDKDKN-PYPQEIIEFPSVIVSS-VTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL 210 (414)
Q Consensus 133 q~~~~~VV~D~ETTGl~~~~-~~~deIIEIgAV~vd~-~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f 210 (414)
|.+++++|||||+||.++.. .+..||||+.||.+|. ++++|.++|+.||||..||.||++|++||||+|++|+.||+|
T Consensus 53 q~fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f 132 (280)
T KOG0542|consen 53 QPFDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTF 132 (280)
T ss_pred CccceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCH
Confidence 44679999999999998755 5789999999996664 566676799999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCC--CCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHH
Q 015017 211 SEALLRHDKWLENKGIK--NTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEM 287 (414)
Q Consensus 211 ~eVl~~f~~fl~~~~lv--~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~ 287 (414)
.+||.+|.+||....+. .+|+++|+||++||+.||..+|++.+|..|.++++|||+++.|+..|.. .+.++..|+++
T Consensus 133 ~~vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mLe~ 212 (280)
T KOG0542|consen 133 PQVLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEH 212 (280)
T ss_pred HHHHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHHHH
Confidence 99999999999987664 3799999999999999999999999999999999999999999999876 67899999999
Q ss_pred cCCCCCCCCCcHHHHHHHHHHHHHHHHHhcCCcccccccc-cccCCCCCcccCCCCCCCCCCCcccchhcc
Q 015017 288 AGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLM-WQTNDGSLTWNQFPERIFLPPHQLHKQMDL 357 (414)
Q Consensus 288 ~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~~~i~e~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 357 (414)
+||+++|++|+|+|||+++|+|.++|++.|.++.||+.-. |+.++... +..|.+ .+.++.++.++
T Consensus 213 ~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~~~~~~~q~~~~----~~~~~~-~~~~~~~~~~~ 278 (280)
T KOG0542|consen 213 YGLQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINELCDLWERQPLVP----NRSWPS-EFADAGQIFER 278 (280)
T ss_pred hCCcccCCcccCchhHHHHHHHHHHHHhCCcEEEechhhhhcccCcccc----cccCCc-ccCCccccccc
Confidence 9999999999999999999999999999999999996533 44433333 234544 55666665544
No 4
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=100.00 E-value=2.5e-38 Score=361.95 Aligned_cols=242 Identities=18% Similarity=0.203 Sum_probs=214.5
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhccCCCCCCccccccccccCC
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQFYPFPVENRFQFAPYNMLT 123 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~y~~~v~d~~~~~~~~~~~ 123 (414)
-|+.++.++|++|++|||+|||||| |+++|+||+++.++++.++|+|||+|.+. ++|++ +++++.
T Consensus 347 Dg~~~~~elv~~A~~~G~~aIAITD--------H~~v~~~p~a~~~~k~~gikvI~GvE~~~----~~~~~---~iv~~~ 411 (1437)
T PRK00448 347 DAIPSVSELVKRAAKWGHKAIAITD--------HGVVQAFPEAYNAAKKAGIKVIYGVEANL----VDDGV---PIVYNE 411 (1437)
T ss_pred ccCCCHHHHHHHHHHCCCCEEEEec--------CCCCcCHHHHHHHHHhcCCceEeeeeEEE----eccce---eEEecC
Confidence 4678899999999999999999995 77778999999999999999999999994 78876 788887
Q ss_pred CCCCCCCCCCccccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhh
Q 015017 124 PAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQ 203 (414)
Q Consensus 124 ~~~p~~~~~q~~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~ 203 (414)
.+.++. ..++||||+||||+ ++..++|||||||+++ +|++.++|++||+|.. +++++++++||||+++
T Consensus 412 ~~~~L~-----~~~~VVfDLETTGL---~~~~deIIEIgAV~V~--~G~iie~F~~~V~P~~--~I~~~~~~LTGIT~e~ 479 (1437)
T PRK00448 412 VDRDLK-----DATYVVFDVETTGL---SAVYDEIIEIGAVKIK--NGEIIDKFEFFIKPGH--PLSAFTTELTGITDDM 479 (1437)
T ss_pred Cchhhc-----cCcEEEEEhhhcCC---CCchhhhheeeeEEEe--CCeEeeeEEEEECCCC--CCCHHHHHHhCCCHHH
Confidence 776665 26899999999998 6788999999999995 7899999999999995 5999999999999999
Q ss_pred hhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHH
Q 015017 204 VDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLK 282 (414)
Q Consensus 204 V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~ 282 (414)
|.+++++.+|+++|.+|+++. ++|+|++.||+ .||+..+++.|++. +...++|+..+++.+++ .++++|+
T Consensus 480 L~~aps~~EaL~~f~~figg~------vLVAHNa~FD~-~fL~~~l~rlgl~~--l~~~~IDTLelar~l~p~~k~~kL~ 550 (1437)
T PRK00448 480 VKDAPSIEEVLPKFKEFCGDS------ILVAHNASFDV-GFINTNYEKLGLEK--IKNPVIDTLELSRFLYPELKSHRLN 550 (1437)
T ss_pred HcCCCCHHHHHHHHHHHhCCC------EEEEeCccccH-HHHHHHHHHcCCcc--ccccceeHHHHHHHHcCccccccHH
Confidence 999999999999999999884 45677779995 89999999998864 35678999999988886 5678999
Q ss_pred HHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcCCccc
Q 015017 283 EAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSI 322 (414)
Q Consensus 283 ~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~~~i 322 (414)
+++++||++.. .+|||++||++||+||.+|+++..+.++
T Consensus 551 ~LAk~lGL~~~-~~HrAl~DA~aTa~lf~~ll~~l~~~gi 589 (1437)
T PRK00448 551 TLAKKFGVELE-HHHRADYDAEATAYLLIKFLKDLKEKGI 589 (1437)
T ss_pred HHHHHcCCCCC-CCcChHHHHHHHHHHHHHHHHHHHHcCC
Confidence 99999999986 6799999999999999999987655443
No 5
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=100.00 E-value=6.6e-37 Score=288.05 Aligned_cols=177 Identities=30% Similarity=0.499 Sum_probs=154.8
Q ss_pred ccEEEEEEeeCCCCC-CCC--CCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHH
Q 015017 136 QYFVVIDFEATCDKD-KNP--YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 212 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~-~~~--~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~e 212 (414)
.+|||||+||||++. .++ ..+||||||||+++ +|++.++|++||||..++.|+++++++||||++||++||+|++
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 479999999999854 233 25899999999996 6788899999999986556999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCC
Q 015017 213 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLA 291 (414)
Q Consensus 213 Vl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~~gI~ 291 (414)
|+++|.+|+++. +..++||++||+ .||+.+|+++|+++| +.+.|+|+..+++.+++. ..++|++++++|||+
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 357889999996 899999999999877 447899999888888874 468999999999999
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHhcCCcc
Q 015017 292 WQGRAHCGLDDAKNTARLLALLMHRGFKFS 321 (414)
Q Consensus 292 ~~g~~HrALdDA~aTA~Ll~~ll~~~~~~~ 321 (414)
..+++|||++||++||+||.+|++++..+.
T Consensus 155 ~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 184 (207)
T PRK07748 155 GTGKHHCALDDAMTTYNIFKLVEKDKEYLV 184 (207)
T ss_pred CCCCCcChHHHHHHHHHHHHHHHhCcceee
Confidence 877899999999999999999998875443
No 6
>PTZ00315 2'-phosphotransferase; Provisional
Probab=100.00 E-value=3.4e-36 Score=316.88 Aligned_cols=196 Identities=39% Similarity=0.624 Sum_probs=166.5
Q ss_pred CCccccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHH
Q 015017 132 PQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 211 (414)
Q Consensus 132 ~q~~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~ 211 (414)
.|.++.||||||||||++......+||||||||+||.++++++++|++||||..+|.|+++|++|||||++||++||+|.
T Consensus 52 ~q~~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~ 131 (582)
T PTZ00315 52 PQPFDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFP 131 (582)
T ss_pred cCCCCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHH
Confidence 34467999999999998532234689999999999988999999999999999777899999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCC----CCcEEEEEcCcchHHHHHHHHHHHcC-CCCCCCCCceeehHHHHH-HhcC----------
Q 015017 212 EALLRHDKWLENKGIK----NTNFAVVTWSNWDCRVMLESECRFKK-IWKPPYFNRWINLKVPFH-EVFG---------- 275 (414)
Q Consensus 212 eVl~~f~~fl~~~~lv----~hn~~vV~~g~fDir~fL~~~~~~~g-i~~P~~~~~~IDl~~l~r-~l~~---------- 275 (414)
+|+.+|.+|+++..++ .++++|+|||+||++.||..+|+..+ ..+|..+..|+|++..+. .+++
T Consensus 132 eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~ 211 (582)
T PTZ00315 132 VVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGAT 211 (582)
T ss_pred HHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccccc
Confidence 9999999999987532 24689999999998679999998432 123445678999865554 3444
Q ss_pred --CCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcCCcccccccc
Q 015017 276 --GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLM 327 (414)
Q Consensus 276 --~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~~~i~e~l~ 327 (414)
.++++|.+|++.+||+++|++|+|++||++||+||.+|+++|..+.+|..++
T Consensus 212 ~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~~~t~~~~ 265 (582)
T PTZ00315 212 PPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTA 265 (582)
T ss_pred cccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEEEecCCCC
Confidence 2457999999999999999999999999999999999999999999888776
No 7
>PRK06722 exonuclease; Provisional
Probab=100.00 E-value=4.9e-34 Score=280.08 Aligned_cols=171 Identities=26% Similarity=0.400 Sum_probs=146.1
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..||||||||||.+..+...++|||||||+|+..+++++++|++||||.. +|++++++|||||++||++||+|++|+.
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 68999999999753222456899999999997434488999999999995 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCC-CceeehHHHHHHhcCC---CCCCHHHHHHHcCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYF-NRWINLKVPFHEVFGG---VRCNLKEAVEMAGLA 291 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~-~~~IDl~~l~r~l~~~---~~~~L~~l~~~~gI~ 291 (414)
+|.+|+++. .+||||+.||+ .||+.+|++.|++.|.+. ..|+|+..+++..++. ..++|++++++|||+
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 999999873 46889999995 899999999999877543 4578988766554432 346899999999999
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHH
Q 015017 292 WQGRAHCGLDDAKNTARLLALLMH 315 (414)
Q Consensus 292 ~~g~~HrALdDA~aTA~Ll~~ll~ 315 (414)
..|++|||++||++||+|+.+|++
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=8.2e-33 Score=250.23 Aligned_cols=172 Identities=44% Similarity=0.785 Sum_probs=147.6
Q ss_pred EEEEEEeeCCCCCCC--CCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 138 FVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 138 ~VV~D~ETTGl~~~~--~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
|||||+||||+.... ...++|||||||+++...++++++|+++|||...+.++++++++||||+++|+++|++++|++
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 699999999984321 235899999999999655668999999999996456999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQ 293 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~-~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~~gI~~~ 293 (414)
+|.+|+++.. +..+|||+.||. .+|..++.+.+.. .|+.+.+|+|++.+++..++. +.++|++++++||++.+
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 9999999842 367899999996 6677777665543 455678999999999999885 47899999999999998
Q ss_pred CCCCcHHHHHHHHHHHHHHHH
Q 015017 294 GRAHCGLDDAKNTARLLALLM 314 (414)
Q Consensus 294 g~~HrALdDA~aTA~Ll~~ll 314 (414)
+++|+|++||++||+|+++|+
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=4.6e-32 Score=258.86 Aligned_cols=170 Identities=19% Similarity=0.137 Sum_probs=144.4
Q ss_pred cEEEEEEeeCCCCCCCCCC-CcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 137 YFVVIDFEATCDKDKNPYP-QEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~-deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
++||||+||||+ ++.. ++|||||||+++ ......++|++||+|.. .++++++++||||++||+++|+|++|+.
T Consensus 1 r~vvlD~ETTGl---~p~~~d~IIEIgav~~~-~~~~~~~~f~~~i~P~~--~i~~~a~~vhGIt~e~l~~~p~f~ev~~ 74 (225)
T TIGR01406 1 RQIILDTETTGL---DPKGGHRIVEIGAVELV-NRMLTGDNFHVYVNPER--DMPAEAAKVHGITDEFLADKPKFKEIAD 74 (225)
T ss_pred CEEEEEeeCCCc---CCCCCCeEEEEEEEEEE-CCcEecceEEEEECcCC--CCCHHHHhccCCCHHHHhCCCCHHHHHH
Confidence 479999999998 4543 899999999886 22334689999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCC--CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP--YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ 293 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~--~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~~ 293 (414)
+|.+|+++.. .|+||+.||+ .||+.++++.|..++. .+.+|+|+..+++..++..+++|+.++++|||+..
T Consensus 75 ~f~~fi~~~~------lVaHNa~FD~-~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~ 147 (225)
T TIGR01406 75 EFLDFIGGSE------LVIHNAAFDV-GFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNS 147 (225)
T ss_pred HHHHHhCCCE------EEEEecHHHH-HHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCCC
Confidence 9999999864 4556679996 8999999998853332 23689999999999998778899999999999976
Q ss_pred CC-CCcHHHHHHHHHHHHHHHHHhcCC
Q 015017 294 GR-AHCGLDDAKNTARLLALLMHRGFK 319 (414)
Q Consensus 294 g~-~HrALdDA~aTA~Ll~~ll~~~~~ 319 (414)
++ .|+|++||++||+||.+|......
T Consensus 148 ~r~~H~Al~DA~~~a~v~~~l~~~~~~ 174 (225)
T TIGR01406 148 HRTLHGALLDAHLLAEVYLALTGGQES 174 (225)
T ss_pred CCCCcCHHHHHHHHHHHHHHHHcCCcc
Confidence 43 699999999999999999875443
No 10
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=5.8e-32 Score=260.56 Aligned_cols=173 Identities=19% Similarity=0.205 Sum_probs=148.4
Q ss_pred ccEEEEEEeeCCCCCCCCC-CCcEEEEcEEEEEcCCCeE-eeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPY-PQEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 213 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~-~deIIEIgAV~vd~~~g~i-~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eV 213 (414)
..|||||+||||+ ++. .++|||||+|.++ ++.+ .++|++||+|.+ .++++++++||||++||.++|+|++|
T Consensus 4 ~r~vvlDtETTGl---dp~~~drIIEIGaV~v~--~~~~~~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev 76 (240)
T PRK05711 4 MRQIVLDTETTGL---NQREGHRIIEIGAVELI--NRRLTGRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEV 76 (240)
T ss_pred CeEEEEEeeCCCc---CCCCCCeEEEEEEEEEE--CCEEeccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHH
Confidence 4799999999998 454 7899999999996 4454 578999999986 59999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCC--CCceeehHHHHHHhcCCCCCCHHHHHHHcCCC
Q 015017 214 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPY--FNRWINLKVPFHEVFGGVRCNLKEAVEMAGLA 291 (414)
Q Consensus 214 l~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~--~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~ 291 (414)
+++|.+|+++.. .|+||+.||+ .||+.++++.|..+|.+ ..+++|+..+.+.+++.++++|+.++++|||+
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 999999999864 3566779996 89999999998666643 34689999999999887778999999999998
Q ss_pred CCCC-CCcHHHHHHHHHHHHHHHHHhcCCccc
Q 015017 292 WQGR-AHCGLDDAKNTARLLALLMHRGFKFSI 322 (414)
Q Consensus 292 ~~g~-~HrALdDA~aTA~Ll~~ll~~~~~~~i 322 (414)
...+ .|+|+.||++||+|+.+|+.....+..
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 699999999999999999876544443
No 11
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=100.00 E-value=3.6e-31 Score=236.98 Aligned_cols=166 Identities=34% Similarity=0.437 Sum_probs=148.0
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHH
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 216 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~ 216 (414)
.||+||+||||+ ++..++|||||+|+++ ++++.++|+++|+|.. +++++++++||||+++|.+++++.+|+.+
T Consensus 1 ~~v~~D~Ettg~---~~~~~~Iieig~v~~~--~~~~~~~f~~~v~p~~--~i~~~~~~~~Git~~~l~~~~~~~~~~~~ 73 (169)
T smart00479 1 TLVVIDCETTGL---DPGKDEIIEIAAVDVD--GGRIIVVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLEE 73 (169)
T ss_pred CEEEEEeeCCCC---CCCCCeEEEEEEEEEE--CCEeEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence 489999999997 4567999999999997 4568899999999974 69999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCC
Q 015017 217 HDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGR 295 (414)
Q Consensus 217 f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~~g~ 295 (414)
|.+|+++. .+|+||+ +||+ .||+..+.+.++..|. ..+|+|+..+++..++..+++|++++++||++..++
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 99999874 4677887 9995 8999999999988774 356999999998888766789999999999999765
Q ss_pred CCcHHHHHHHHHHHHHHHHHhc
Q 015017 296 AHCGLDDAKNTARLLALLMHRG 317 (414)
Q Consensus 296 ~HrALdDA~aTA~Ll~~ll~~~ 317 (414)
+|+|++||++|++|+.++++++
T Consensus 146 ~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 146 AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CcCcHHHHHHHHHHHHHHHHHh
Confidence 6999999999999999998765
No 12
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=1.9e-31 Score=256.85 Aligned_cols=174 Identities=21% Similarity=0.184 Sum_probs=148.6
Q ss_pred CCCCCCCCCCCccccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeE--eeEEEEeecCCCCCCCCcchhhhcCCC
Q 015017 123 TPAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQ 200 (414)
Q Consensus 123 ~~~~p~~~~~q~~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i--~d~F~~lVkP~~~p~Ls~~~~~LTGIT 200 (414)
..++|+.. ..|||||+||||+ ++..++|||||+|+++ ++++ .++|+++|+|.. +++++++.+||||
T Consensus 39 ~~~~~~~~-----~~~vviD~ETTGl---~p~~d~IieIg~v~v~--~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt 106 (239)
T PRK09146 39 SPDTPLSE-----VPFVALDFETTGL---DAEQDAIVSIGLVPFT--LQRIRCRQARHWVVKPRR--PLEEESVVIHGIT 106 (239)
T ss_pred CCCCCccc-----CCEEEEEeECCCC---CCCCCcEEEEEEEEEE--CCeEeecceEEEEECCCC--CCChhhhhhcCCC
Confidence 37788873 7999999999998 6778999999999996 4554 589999999996 5999999999999
Q ss_pred hhhhhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHc-CCCCCCCCCceeehHHHHHHhcCC---
Q 015017 201 QIQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFK-KIWKPPYFNRWINLKVPFHEVFGG--- 276 (414)
Q Consensus 201 ~e~V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~-gi~~P~~~~~~IDl~~l~r~l~~~--- 276 (414)
++||.+||+|++|+.+|.+|+++. ..|+|++.|| +.||++++++. +..+ ..+++|+..+++.+++.
T Consensus 107 ~e~l~~ap~~~evl~~l~~~~~~~------~lVaHna~FD-~~fL~~~l~~~~~~~~---~~~~iDTl~Lar~l~~~~~~ 176 (239)
T PRK09146 107 HSELQDAPDLERILDELLEALAGK------VVVVHYRRIE-RDFLDQALRNRIGEGI---EFPVIDTMEIEARIQRKQAG 176 (239)
T ss_pred HHHHhCCCCHHHHHHHHHHHhCCC------EEEEECHHHH-HHHHHHHHHHhcCCCC---CCceechHHHHHHHcccccc
Confidence 999999999999999999999875 4566677999 59999999875 3333 35789999998876532
Q ss_pred -----------CCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcCC
Q 015017 277 -----------VRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFK 319 (414)
Q Consensus 277 -----------~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~ 319 (414)
.+++|++++++|||+.+ ++|+|++||++||+||.+++++...
T Consensus 177 ~~~~~~~~~~~~~~~L~~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~~~ 229 (239)
T PRK09146 177 GLWNRLKGKKPESIRLADSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHHFS 229 (239)
T ss_pred cccchhccCCCCCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 35689999999999986 7899999999999999999987643
No 13
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.98 E-value=3.4e-31 Score=239.20 Aligned_cols=162 Identities=21% Similarity=0.213 Sum_probs=140.3
Q ss_pred EEEEEEeeCCCCCCCC-CCCcEEEEcEEEEEcCCCeE-eeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 138 FVVIDFEATCDKDKNP-YPQEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 138 ~VV~D~ETTGl~~~~~-~~deIIEIgAV~vd~~~g~i-~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
||+||+||||+ ++ ..++|||||||+++ ++.+ .++|+.+|+|.. .++++++++||||+++|+++|++.+|++
T Consensus 1 ~v~~D~ETTGl---~~~~~~~iieig~v~v~--~~~~~~~~~~~~v~P~~--~i~~~~~~ihGIt~e~l~~~~~~~~v~~ 73 (167)
T cd06131 1 QIVLDTETTGL---DPREGHRIIEIGCVELI--NRRLTGNTFHVYINPER--DIPEEAFKVHGITDEFLADKPKFAEIAD 73 (167)
T ss_pred CEEEEeeCCCC---CCCCCCeEEEEEEEEEE--CCcEeccEEEEEECCCC--CCCHHHHHHhCCCHHHHhcCCCHHHHHH
Confidence 68999999998 44 56899999999996 4444 569999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCC-CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP-YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQG 294 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~-~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~~g 294 (414)
+|.+|+++. ..|+||++||. .||++++++.|+..+. ....|+|+..+++..++..+++|++++++||++.++
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 999999885 35667789995 8999999998775432 345799999999888876778999999999999864
Q ss_pred -CCCcHHHHHHHHHHHHHHH
Q 015017 295 -RAHCGLDDAKNTARLLALL 313 (414)
Q Consensus 295 -~~HrALdDA~aTA~Ll~~l 313 (414)
++|+|++||++||+||.+|
T Consensus 147 ~~~H~Al~Da~~~a~l~~~l 166 (167)
T cd06131 147 RTLHGALLDAELLAEVYLEL 166 (167)
T ss_pred CCCCChHHHHHHHHHHHHHh
Confidence 4799999999999999876
No 14
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=9.6e-31 Score=254.44 Aligned_cols=175 Identities=20% Similarity=0.264 Sum_probs=153.2
Q ss_pred cCCCCCCCCCCCCccccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCC
Q 015017 121 MLTPAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQ 200 (414)
Q Consensus 121 ~~~~~~p~~~~~q~~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT 200 (414)
.....+|+. ...|||||+||||+ ++..++|||||||+++ +|+++++|+++|+|. .++++++++||||
T Consensus 58 l~~~~~~~~-----~~~~vv~DiETTG~---~~~~~~IIEIGAv~v~--~g~i~~~f~~~v~p~---~ip~~~~~itGIt 124 (257)
T PRK08517 58 LKTRFTPIK-----DQVFCFVDIETNGS---KPKKHQIIEIGAVKVK--NGEIIDRFESFVKAK---EVPEYITELTGIT 124 (257)
T ss_pred eccCCCCCC-----CCCEEEEEEeCCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECCC---CCChhhhhhcCcC
Confidence 334556665 36899999999997 5667899999999996 788999999999997 4899999999999
Q ss_pred hhhhhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCC
Q 015017 201 QIQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCN 280 (414)
Q Consensus 201 ~e~V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~ 280 (414)
++||.+||++.+|+.+|.+|++++ +.|+|+++||. .||+.++++.|+.. +.++++|+..+++++++..+++
T Consensus 125 ~e~l~~ap~~~evl~~f~~fl~~~------v~VaHNa~FD~-~fL~~~l~r~g~~~--~~~~~ldtl~la~~~~~~~~~~ 195 (257)
T PRK08517 125 YEDLENAPSLKEVLEEFRLFLGDS------VFVAHNVNFDY-NFISRSLEEIGLGP--LLNRKLCTIDLAKRTIESPRYG 195 (257)
T ss_pred HHHHcCCCCHHHHHHHHHHHHCCC------eEEEECHHHHH-HHHHHHHHHcCCCC--CCCCcEehHHHHHHHccCCCCC
Confidence 999999999999999999999875 45667779995 89999999998764 4678899999999888777889
Q ss_pred HHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcC
Q 015017 281 LKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 281 L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
|+++++++|++.+ ++|||++||++||+|+.+++.+..
T Consensus 196 L~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 196 LSFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred HHHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhH
Confidence 9999999999986 789999999999999999997653
No 15
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.5e-30 Score=259.63 Aligned_cols=164 Identities=26% Similarity=0.328 Sum_probs=148.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
.+|||||+||||+ ++..++|||||||+++ ++++.++|+++|+|.. .++++++.+||||++||.++|+|.+|+.
T Consensus 8 ~~~Vv~DlETTGl---~p~~~eIIEIgaV~v~--~g~i~~~f~~lVkP~~--~I~~~a~~ihGIT~e~l~~~~~~~evl~ 80 (313)
T PRK06807 8 LDYVVIDFETTGF---NPYNDKIIQVAAVKYR--NHELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPTIEEVLP 80 (313)
T ss_pred CCEEEEEEECCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHhhhccCCCCHHHHhCCCCHHHHHH
Confidence 5899999999998 5678999999999996 7899999999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQG 294 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g 294 (414)
+|.+|+++. ..|+||+.||+ .||.+++.+.|++.| ..++||+..+++.+++ .++++|++++++||++.
T Consensus 81 ~f~~fl~~~------~lVaHNa~FD~-~fL~~~~~~~gl~~~--~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~-- 149 (313)
T PRK06807 81 LFLAFLHTN------VIVAHNASFDM-RFLKSNVNMLGLPEP--KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL-- 149 (313)
T ss_pred HHHHHHcCC------eEEEEcHHHHH-HHHHHHHHHcCCCCC--CCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCC--
Confidence 999999874 46778889995 899999999998765 3579999999988886 45789999999999998
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhc
Q 015017 295 RAHCGLDDAKNTARLLALLMHRG 317 (414)
Q Consensus 295 ~~HrALdDA~aTA~Ll~~ll~~~ 317 (414)
++|+|++||++|++|+.+++...
T Consensus 150 ~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 150 SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CCcChHHHHHHHHHHHHHHHHhh
Confidence 68999999999999999998765
No 16
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.2e-30 Score=259.69 Aligned_cols=164 Identities=16% Similarity=0.232 Sum_probs=146.0
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHH
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 216 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~ 216 (414)
.|||||+||||. ..++|||||||+++ +|+++++|++||||.. ..++++++.|||||++||+++|+|.+|+++
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 699999999974 46899999999995 7899999999999984 358889999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 015017 217 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 295 (414)
Q Consensus 217 f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~ 295 (414)
|.+|+++. ..|+||++||+ .||+.+++++++++| .++|+|+..+++++++ .++++|.+++++||++. +
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 46677789995 899999999998876 3579999999999887 46789999999999985 5
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcCC
Q 015017 296 AHCGLDDAKNTARLLALLMHRGFK 319 (414)
Q Consensus 296 ~HrALdDA~aTA~Ll~~ll~~~~~ 319 (414)
+|+|++||++||+||.+|+++...
T Consensus 143 ~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 143 HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 899999999999999999987543
No 17
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.97 E-value=1.6e-30 Score=231.14 Aligned_cols=154 Identities=23% Similarity=0.286 Sum_probs=138.3
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHH
Q 015017 138 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 217 (414)
Q Consensus 138 ~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f 217 (414)
||+||+||||. ..++|||||||+++ ++++.++|+++|+|.. +++++++++||||+++|++++++.+|+.+|
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 69999999985 36899999999996 7888999999999996 699999999999999999999999999999
Q ss_pred HHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCCC
Q 015017 218 DKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGRA 296 (414)
Q Consensus 218 ~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~~ 296 (414)
.+|+++. ..|.|+++||+ .||+.++++.|+..| ..+++|+..+++..++ .++++|++++++||++.. +
T Consensus 72 ~~~l~~~------~lv~hn~~fD~-~~l~~~~~~~g~~~~--~~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~ 140 (156)
T cd06130 72 KPFLGGS------LVVAHNASFDR-SVLRAALEAYGLPPP--PYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--H 140 (156)
T ss_pred HHHhCCC------EEEEeChHHhH-HHHHHHHHHcCCCCC--CCCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--C
Confidence 9999874 45566679995 999999999998876 4579999999998887 467899999999999985 8
Q ss_pred CcHHHHHHHHHHHHH
Q 015017 297 HCGLDDAKNTARLLA 311 (414)
Q Consensus 297 HrALdDA~aTA~Ll~ 311 (414)
|+|++||++||+||.
T Consensus 141 H~Al~Da~~ta~l~~ 155 (156)
T cd06130 141 HDALEDARACAEILL 155 (156)
T ss_pred cCchHHHHHHHHHHh
Confidence 999999999999985
No 18
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=3.4e-30 Score=248.74 Aligned_cols=169 Identities=25% Similarity=0.307 Sum_probs=144.8
Q ss_pred ccEEEEEEeeCCCCCCCCCC-CcEEEEcEEEEEcCCCeE-eeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYP-QEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 213 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~-deIIEIgAV~vd~~~g~i-~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eV 213 (414)
.+|||||+||||+ ++.. ++|||||||+++ ++.+ .++|+++|+|.. +++++++++||||+++|++||++.+|
T Consensus 59 ~~~vv~D~ETTGl---~p~~~deIIeIgaV~~~--~~~i~~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev 131 (244)
T PRK07740 59 LPFVVFDLETTGF---SPQQGDEILSIGAVKTK--GGEVETDTFYSLVKPKR--PIPEHILELTGITAEDVAFAPPLAEV 131 (244)
T ss_pred CCEEEEEEeCCCC---CCCCCCeEEEEEEEEEE--CCEEEEEEEEEEeCcCC--CCChhheeccCCCHHHHhCCCCHHHH
Confidence 5899999999997 4544 899999999997 5666 899999999995 59999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCC
Q 015017 214 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAW 292 (414)
Q Consensus 214 l~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~~gI~~ 292 (414)
+.+|.+|+++. ..|+||+.|| ..||+.++.+... .| +..+++|+..+++.+++. ++++|++++++||++.
T Consensus 132 l~~f~~fi~~~------~lVahna~fD-~~fL~~~~~~~~~-~~-~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~ 202 (244)
T PRK07740 132 LHRFYAFIGAG------VLVAHHAGHD-KAFLRHALWRTYR-QP-FTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPI 202 (244)
T ss_pred HHHHHHHhCCC------EEEEeCHHHH-HHHHHHHHHHhcC-CC-cCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCC
Confidence 99999999885 4556677999 5899999876532 22 456899999999888764 4789999999999999
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcCCcc
Q 015017 293 QGRAHCGLDDAKNTARLLALLMHRGFKFS 321 (414)
Q Consensus 293 ~g~~HrALdDA~aTA~Ll~~ll~~~~~~~ 321 (414)
. .+|+|++||++||+||.+++.+....+
T Consensus 203 ~-~~H~Al~Da~ata~l~~~ll~~~~~~~ 230 (244)
T PRK07740 203 P-RRHHALGDALMTAKLWAILLVEAQQRG 230 (244)
T ss_pred C-CCCCcHHHHHHHHHHHHHHHHHHHHcC
Confidence 7 469999999999999999998755433
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=2e-30 Score=258.80 Aligned_cols=168 Identities=17% Similarity=0.156 Sum_probs=146.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..|||||+||||+ ++..++|||||+|+++ .+|++.++|+++|+|.. ++..+.+||||++||.++|+|+++++
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 5899999999998 6778999999999998 47889999999999984 24568999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQG 294 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g 294 (414)
+|.+|+++. .+|.||+.||+ .||+.++++.++.+| .+.++|++.+++++.+ ..+++|++++++|||+..
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 999999885 44566679995 899999999998876 3568999999988764 567899999999999975
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCCcc
Q 015017 295 RAHCGLDDAKNTARLLALLMHRGFKFS 321 (414)
Q Consensus 295 ~~HrALdDA~aTA~Ll~~ll~~~~~~~ 321 (414)
++|+|++||++||+||.+++++.....
T Consensus 157 ~~H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 157 RPHDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 789999999999999999998754443
No 20
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=6.6e-30 Score=244.96 Aligned_cols=173 Identities=20% Similarity=0.128 Sum_probs=146.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhC-CCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~-Ap~f~eVl 214 (414)
.+|||||+||||+ ++..++|||||+|+++ .+|+++++|+++|+|.. +|+++++++||||++|+.+ ++++.+|+
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 5899999999998 6778999999999997 45788899999999996 5999999999999999975 89999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC--CCCCHHHHHHHcCCCC
Q 015017 215 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG--VRCNLKEAVEMAGLAW 292 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~--~~~~L~~l~~~~gI~~ 292 (414)
.+|.+++.... .+...+|+||++||+ .||+.+++++|+..+ ....++|+..+.+.+.+. .+++|++++++||++.
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 122456778889995 899999999997643 235689998887766542 3579999999999998
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhcC
Q 015017 293 QGRAHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 293 ~g~~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
+ .+|+|++||++|++|+.+|+++..
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 689999999999999999987654
No 21
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=7.3e-30 Score=247.28 Aligned_cols=169 Identities=14% Similarity=0.132 Sum_probs=147.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..||+||+||||+ ++..++|||||+|+++ .+++.++|+++|+|.. +|+++++.+||||++||+++|++.+|+.
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 5899999999998 6778999999999997 4577899999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGR 295 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~~g~ 295 (414)
+|.+|+++. .++|.|+.+||+ .||..++.+.|++++.....+||+..+++.+.+..+++|..++++||++.. .
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 999999863 234556669995 899999999999876444689999999887544456899999999999986 6
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcC
Q 015017 296 AHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 296 ~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
+|+|++||++|++||.+|+++..
T Consensus 153 aH~Al~Da~at~~vl~~l~~~~~ 175 (250)
T PRK06310 153 NHRAMKDVEINIKVFKHLCKRFR 175 (250)
T ss_pred CcChHHHHHHHHHHHHHHHHhcc
Confidence 89999999999999999987643
No 22
>PRK05168 ribonuclease T; Provisional
Probab=99.97 E-value=5.5e-30 Score=242.16 Aligned_cols=177 Identities=21% Similarity=0.211 Sum_probs=144.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEc-CCCeE--eeEEEEeecCCCCCCCCcchhhhcCCChhh-hhCCCCHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS-VTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQIQ-VDRGVTLS 211 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~-~~g~i--~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~-V~~Ap~f~ 211 (414)
.++||||+||||+ ++..++|||||||++.. .+|.+ .++|+++|+|.....++++++++||||+++ +++++++.
T Consensus 17 ~~~vv~D~ETTGl---~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~~~~ 93 (211)
T PRK05168 17 FLPVVIDVETAGF---NAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAVSEK 93 (211)
T ss_pred CceEEEEeeCCCC---CCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCCChH
Confidence 6899999999998 66789999999999853 24553 589999999942236999999999999986 88999999
Q ss_pred HHHHHHHHHHhhcCC---CCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCC-CCceeehHHHHHHhcCCCCCCHHHHHHH
Q 015017 212 EALLRHDKWLENKGI---KNTNFAVVTWSNWDCRVMLESECRFKKIWKPPY-FNRWINLKVPFHEVFGGVRCNLKEAVEM 287 (414)
Q Consensus 212 eVl~~f~~fl~~~~l---v~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~-~~~~IDl~~l~r~l~~~~~~~L~~l~~~ 287 (414)
+++.+|.+|+.+... .+..+.|.|+++||+ .||+.++++.|+..+++ ..+++|+..+++.+++. .+|++++++
T Consensus 94 ~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~-~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~~--~~L~~l~~~ 170 (211)
T PRK05168 94 EALHEIFKMVRKGIKASGCNRAILVAHNAHFDL-SFLMAAAERAGLKRNPFHPFSTFDTATLSGLALGQ--TVLAKACQA 170 (211)
T ss_pred HHHHHHHHHHHHHHHhcccCCceEEEeccHHhH-HHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcCC--CCHHHHHHH
Confidence 999999999974210 112456667789996 89999999998753222 23689999999988764 589999999
Q ss_pred cCCCCCC-CCCcHHHHHHHHHHHHHHHHHhcC
Q 015017 288 AGLAWQG-RAHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 288 ~gI~~~g-~~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
+|++.++ .+|+|++||++||+||.+|+++..
T Consensus 171 ~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 171 AGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 9999742 589999999999999999998764
No 23
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=8.3e-30 Score=238.70 Aligned_cols=163 Identities=21% Similarity=0.261 Sum_probs=136.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeE--eeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 213 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i--~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eV 213 (414)
..|||||+||||+ ++..++|||||||+++ ++.+ .++|+++|+|.. .++++++++||||++||+++|++++|
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 5899999999998 5677999999999997 3444 378999999995 69999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHH-cCCCCCCCCCceeehHHHHHHh----cC--CCCCCHHHHHH
Q 015017 214 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRF-KKIWKPPYFNRWINLKVPFHEV----FG--GVRCNLKEAVE 286 (414)
Q Consensus 214 l~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~-~gi~~P~~~~~~IDl~~l~r~l----~~--~~~~~L~~l~~ 286 (414)
+++|.+|+++.. .|+|++.||+ .||+.++++ .+..+| ..++|+..++... ++ .++++|+++++
T Consensus 102 l~~~~~~i~~~~------lv~hn~~fD~-~fL~~~~~~~~~~~~~---~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~ 171 (202)
T PRK09145 102 LRQLLAFIGNRP------LVGYYLEFDV-AMLNRYVRPLLGIPLP---NPLIEVSALYYDKKERHLPDAYIDLRFDAILK 171 (202)
T ss_pred HHHHHHHHcCCe------EEEeCHHHHH-HHHHHHHHHhcCCCCC---CCeeeHHHHHHHHhhccCCCcccCCCHHHHHH
Confidence 999999998754 4455569995 999999987 465554 4689998766432 12 23579999999
Q ss_pred HcCCCCCCCCCcHHHHHHHHHHHHHHHHHh
Q 015017 287 MAGLAWQGRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 287 ~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
+||++.. .+|+|++||++||+||.+|++.
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 5799999999999999998764
No 24
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.2e-29 Score=237.45 Aligned_cols=162 Identities=19% Similarity=0.242 Sum_probs=131.9
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHH
Q 015017 135 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 214 (414)
Q Consensus 135 ~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl 214 (414)
..+|||||+||||++ ..++|||||||+++ +|+++++|++||+|.. +++++++++||||++||++||++.+|+
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 468999999999973 36899999999996 7888899999999995 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEcCc-chHHHHHHHHHHHcCCCCCCCCCceeehHHHH--HHh--c-CCCCCCHHHHHHHc
Q 015017 215 LRHDKWLENKGIKNTNFAVVTWSN-WDCRVMLESECRFKKIWKPPYFNRWINLKVPF--HEV--F-GGVRCNLKEAVEMA 288 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~~g~-fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~--r~l--~-~~~~~~L~~l~~~~ 288 (414)
++|.+|+++..+ |.|++. ||+ .||+ +.|+..+ ...++|+.... ++. + +.++++|.+++++|
T Consensus 76 ~~f~~f~~~~~l------VaHNa~~fD~-~fL~----~~g~~~~--~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~ 142 (195)
T PRK07247 76 AAFKEFVGELPL------IGYNAQKSDL-PILA----ENGLDLS--DQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL 142 (195)
T ss_pred HHHHHHHCCCeE------EEEeCcHhHH-HHHH----HcCCCcC--CCceeehHHHHHHhhccccCCCCCCCHHHHHHhc
Confidence 999999998654 444445 896 8885 3565543 22457764322 222 2 24578999999999
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHhcCC
Q 015017 289 GLAWQGRAHCGLDDAKNTARLLALLMHRGFK 319 (414)
Q Consensus 289 gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~ 319 (414)
||+. .+|||++||++||+||.++++.+..
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 4799999999999999999987653
No 25
>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=1.9e-29 Score=239.14 Aligned_cols=171 Identities=18% Similarity=0.131 Sum_probs=143.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..|||||+||||+ ++..+ |||||||++. .++.+.++|+++|+|.. ++++++.++||||++||.++|+|++|++
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 5899999999998 55566 9999999975 34556799999999995 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC---CCCCCHHHHHHHcCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG---GVRCNLKEAVEMAGLAW 292 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~---~~~~~L~~l~~~~gI~~ 292 (414)
+|.+|+++. .+|.||+.||+ .||+.++++.+...| ....++|++.+++.+++ ..+++|.+++++||++.
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 999999875 45566779995 899999998765433 34578999887776554 34678999999999986
Q ss_pred CC-CCCcHHHHHHHHHHHHHHHHHhcCCcc
Q 015017 293 QG-RAHCGLDDAKNTARLLALLMHRGFKFS 321 (414)
Q Consensus 293 ~g-~~HrALdDA~aTA~Ll~~ll~~~~~~~ 321 (414)
.. .+|+|++||++|++|+.+|+.+.....
T Consensus 152 ~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 152 SHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 42 479999999999999999998765544
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=2e-29 Score=232.03 Aligned_cols=161 Identities=17% Similarity=0.103 Sum_probs=131.7
Q ss_pred EEEEEEeeCCCCCCC-CCCCcEEEEcEEEEEcCC---C--------eEeeEEEEeecCCCCCCCCcchhhhcCCChhhhh
Q 015017 138 FVVIDFEATCDKDKN-PYPQEIIEFPSVIVSSVT---G--------QLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVD 205 (414)
Q Consensus 138 ~VV~D~ETTGl~~~~-~~~deIIEIgAV~vd~~~---g--------~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~ 205 (414)
|||||+||||+ + +..++|||||||+++... + ++.++|+++|||.. +|+++++.+||||++||.
T Consensus 1 ~vv~D~ETTGl---~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~--~I~~~a~~IhGIt~e~l~ 75 (177)
T cd06136 1 FVFLDLETTGL---PKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR--AISPGASEITGLSNDLLE 75 (177)
T ss_pred CeEEeeecCCC---CCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC--cCChhHHHHhCcCHHHHh
Confidence 69999999998 5 467999999999997311 1 36789999999996 599999999999999999
Q ss_pred CCCCHHH-HHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHH
Q 015017 206 RGVTLSE-ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKE 283 (414)
Q Consensus 206 ~Ap~f~e-Vl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~ 283 (414)
++|++++ +.+.+.+|++... +....|.||+ +||+ .||++++++.|+.+| ....++|++.+++++.+ +|++
T Consensus 76 ~~~~~~~~~~~~l~~f~~~~~--~~~~lVaHNa~~FD~-~fL~~~~~r~~~~~~-~~~~~iDtl~l~r~~~~----~L~~ 147 (177)
T cd06136 76 HKAPFDSDTANLIKLFLRRQP--KPICLVAHNGNRFDF-PILRSELERLGTKLP-DDILCVDSLPAFRELDQ----SLGS 147 (177)
T ss_pred cCCCccHHHHHHHHHHHHhcC--CCCEEEEcCCcccCH-HHHHHHHHHcCCCCC-CCCEEEEeHHHHhhhHh----hHHH
Confidence 9998874 5566666665320 1124566777 7996 899999999999876 45678999999988765 8999
Q ss_pred HHHH-cCCCCCCCCCcHHHHHHHHHHHHHH
Q 015017 284 AVEM-AGLAWQGRAHCGLDDAKNTARLLAL 312 (414)
Q Consensus 284 l~~~-~gI~~~g~~HrALdDA~aTA~Ll~~ 312 (414)
++++ ||++.. ++|+|++||.+|+++|.+
T Consensus 148 l~~~~~~~~~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 148 LYKRLFGQEPK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred HHHHHhCCCcc-cccchHHHHHHHHHHHhh
Confidence 9985 999986 789999999999999864
No 27
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=4.4e-29 Score=239.08 Aligned_cols=162 Identities=23% Similarity=0.261 Sum_probs=140.9
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHH
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 216 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~ 216 (414)
++||||+||||+ ++..++|||||++ + +...++|+++|+|.. +|+++++++||||++||+++|+|.+|+++
T Consensus 3 ~~vv~D~ETTGl---~~~~d~IIeig~v--~---~~~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~~ 72 (232)
T PRK06309 3 ALIFYDTETTGT---QIDKDRIIEIAAY--N---GVTSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQK 72 (232)
T ss_pred cEEEEEeeCCCC---CCCCCEEEEEEEE--c---CccccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 689999999998 5678999999995 3 234678999999996 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCCC
Q 015017 217 HDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQG 294 (414)
Q Consensus 217 f~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~~gI~~~g 294 (414)
|.+|+++. ...+.|+ ++||+ .||..++++.|+..|. ..++|+..+++.+++. .+++|..++++||++..
T Consensus 73 ~~~fi~~~-----~~lVaHN~~~FD~-~~L~~e~~r~g~~~~~--~~~iDt~~l~~~~~~~~~~~~L~~l~~~~~~~~~- 143 (232)
T PRK06309 73 FIEFCGTD-----NILVAHNNDAFDF-PLLRKECRRHGLEPPT--LRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEEN- 143 (232)
T ss_pred HHHHHcCC-----CEEEEeCCHHHHH-HHHHHHHHHcCCCCCC--CcEEeHHHHHHHHcCCCCCCCHHHHHHHcCCCCC-
Confidence 99999863 2345566 47995 8999999999998763 6899999999888763 56899999999999975
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhc
Q 015017 295 RAHCGLDDAKNTARLLALLMHRG 317 (414)
Q Consensus 295 ~~HrALdDA~aTA~Ll~~ll~~~ 317 (414)
++|+|++||.+|++||.+|+++.
T Consensus 144 ~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 144 QAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999764
No 28
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.97 E-value=7.9e-31 Score=235.90 Aligned_cols=187 Identities=32% Similarity=0.481 Sum_probs=164.8
Q ss_pred ccEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~-~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl 214 (414)
..++|||||+|+.+|+ ++.+.+||||+|.+|+..+.+++|+|++||||..+|.|+.+|+.+|||||..|++||-|..|+
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 4789999999999874 578899999999999888888999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCC-CCHHHHHHHcCCCCC
Q 015017 215 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVR-CNLKEAVEMAGLAWQ 293 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~-~~L~~l~~~~gI~~~ 293 (414)
++|..||....- ..+-++++||++|| ..|..++..+++.--++..+++|++..|...++..+ .+|+.+++.+|+.+.
T Consensus 84 E~f~r~L~~h~P-r~~~~wa~wG~~Dm-~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~~G~sf~ 161 (210)
T COG5018 84 EDFIRKLNEHDP-RKNSTWATWGNMDM-KVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEEYGDSFT 161 (210)
T ss_pred HHHHHHHHhcCc-ccCCccccccchhH-HHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHHHhccccC
Confidence 999999987632 22446899999997 567788888888722255688999999999998654 799999999999999
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCccccc
Q 015017 294 GRAHCGLDDAKNTARLLALLMHRGFKFSITN 324 (414)
Q Consensus 294 g~~HrALdDA~aTA~Ll~~ll~~~~~~~i~e 324 (414)
|.+||||+||+++++|+..+......++.+.
T Consensus 162 G~~HraldDArn~~rl~klv~~~~~~~e~~~ 192 (210)
T COG5018 162 GTHHRALDDARNAYRLFKLVEQDKQYLEKPK 192 (210)
T ss_pred CchhhhHHHHHHHHHHHHHHcchhhhccCCC
Confidence 9999999999999999999998887776654
No 29
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.96 E-value=4.3e-29 Score=232.16 Aligned_cols=174 Identities=22% Similarity=0.225 Sum_probs=139.6
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEc-CCCe--EeeEEEEeecCCCCCCCCcchhhhcCCChhh-hhCCCCHHH
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS-VTGQ--LEACFQTYVRPTCNQLLSDFCKDLTGIQQIQ-VDRGVTLSE 212 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~-~~g~--i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~-V~~Ap~f~e 212 (414)
.+||||+||||+ ++..++|||||||++.. ++|. +.++|+++|+|....+++++++++||||+++ +.++++..+
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 679999999998 66789999999999962 2454 4689999999931125999999999999986 678888888
Q ss_pred HHHHHHHHHhhcCC---CCCcEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc
Q 015017 213 ALLRHDKWLENKGI---KNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA 288 (414)
Q Consensus 213 Vl~~f~~fl~~~~l---v~hn~~vV~~g~fDir~fL~~~~~~~gi~-~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~ 288 (414)
++.+|.+++.+..- .+....|.|+++||+ .||+.++++.|+. .|....+++|+..+.+.+++ ..+|++++++|
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 88888888864210 112456777889996 8999999999883 22122368999999998876 35899999999
Q ss_pred CCCCC-CCCCcHHHHHHHHHHHHHHHHHh
Q 015017 289 GLAWQ-GRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 289 gI~~~-g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
||+.. .++|+|++||++||+||.+|+++
T Consensus 160 gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 160 GIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 99963 36899999999999999999874
No 30
>PRK07883 hypothetical protein; Validated
Probab=99.96 E-value=1.3e-28 Score=262.53 Aligned_cols=174 Identities=24% Similarity=0.226 Sum_probs=152.9
Q ss_pred CCCCCCCCCccccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhh
Q 015017 125 AHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQV 204 (414)
Q Consensus 125 ~~p~~~~~q~~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V 204 (414)
++|+.. ..|||||+||||+ ++..++|||||||+++ +|+++++|+++|+|.. .++++++++||||++||
T Consensus 9 ~~~~~~-----~~~Vv~D~ETTGl---~p~~~~IIEIgaV~v~--~g~iv~~f~~lV~P~~--~i~~~~~~itGIt~e~l 76 (557)
T PRK07883 9 GTPLRD-----VTFVVVDLETTGG---SPAGDAITEIGAVKVR--GGEVLGEFATLVNPGR--PIPPFITVLTGITTAMV 76 (557)
T ss_pred CCCCcC-----CCEEEEEEecCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECCCC--CCChhHHhhcCCCHHHH
Confidence 456652 6999999999998 6777999999999996 7889999999999985 59999999999999999
Q ss_pred hCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC---CCCCCH
Q 015017 205 DRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG---GVRCNL 281 (414)
Q Consensus 205 ~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~---~~~~~L 281 (414)
+++|++.+|+.+|.+|+++. ..|+||+.||+ .||+.++++.|+++| .+.++|+..+++.+++ ..+++|
T Consensus 77 ~~ap~~~evl~~f~~fl~~~------~lVaHNa~FD~-~fL~~~~~r~g~~~~--~~~~iDTl~lar~l~~~~~~~~~~L 147 (557)
T PRK07883 77 AGAPPIEEVLPAFLEFARGA------VLVAHNAPFDI-GFLRAAAARCGYPWP--GPPVLCTVRLARRVLPRDEAPNVRL 147 (557)
T ss_pred hCCCCHHHHHHHHHHHhcCC------EEEEeCcHHHH-HHHHHHHHHcCCCCC--CCCcEecHHHHHHhcccCCCCCCCH
Confidence 99999999999999999874 44566779995 899999999999876 3578999999988875 356899
Q ss_pred HHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcCCc
Q 015017 282 KEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKF 320 (414)
Q Consensus 282 ~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~~~ 320 (414)
++++++||++.+ .+|+|++||++|++||.+++.+....
T Consensus 148 ~~L~~~~gi~~~-~~H~Al~DA~ata~l~~~l~~~~~~~ 185 (557)
T PRK07883 148 STLARLFGATTT-PTHRALDDARATVDVLHGLIERLGNL 185 (557)
T ss_pred HHHHHHCCcccC-CCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999986 67999999999999999999876543
No 31
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.96 E-value=8.9e-29 Score=232.13 Aligned_cols=177 Identities=20% Similarity=0.179 Sum_probs=142.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEc-CCCeE--eeEEEEeecCCCCCCCCcchhhhcCCChh-hhhCCCCHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS-VTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQI-QVDRGVTLS 211 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~-~~g~i--~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e-~V~~Ap~f~ 211 (414)
..+||||+||||+ ++..++|||||||++.. .+|++ .++|+++|+|....+|++++.++||||++ |+.+++++.
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 4899999999998 66789999999999852 24665 47899999984222699999999999976 699999999
Q ss_pred HHHHHHHHHHhhcC---CCCCcEEEEEcCcchHHHHHHHHHHHcCCCC-CCCCCceeehHHHHHHhcCCCCCCHHHHHHH
Q 015017 212 EALLRHDKWLENKG---IKNTNFAVVTWSNWDCRVMLESECRFKKIWK-PPYFNRWINLKVPFHEVFGGVRCNLKEAVEM 287 (414)
Q Consensus 212 eVl~~f~~fl~~~~---lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~-P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~ 287 (414)
+++.+|.+|+.+.. +.+....|+|+++||+ .||+.++++.++.. |.....++|+..+.+..++. .+|++++++
T Consensus 85 ~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~-~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~~--~~L~~l~~~ 161 (200)
T TIGR01298 85 EALHEIFKVVRKAMKASGCQRAILVGHNANFDL-GFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYGQ--TVLAKACQA 161 (200)
T ss_pred HHHHHHHHHHHHHHHhcccCCCEEEEECchhhH-HHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcCc--ccHHHHHHH
Confidence 99999999885321 1123456777889996 89999999988742 21124689999999887763 579999999
Q ss_pred cCCCCC-CCCCcHHHHHHHHHHHHHHHHHhcC
Q 015017 288 AGLAWQ-GRAHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 288 ~gI~~~-g~~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
||++.. .++|||++||++||+||.+|+.+..
T Consensus 162 ~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 162 AGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred cCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 999863 2689999999999999999998764
No 32
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=3.1e-28 Score=269.58 Aligned_cols=165 Identities=22% Similarity=0.250 Sum_probs=146.8
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..|||||+||||+ ++ .++|||||||+++ +|+++++|+++|+|.. +|+++++.+||||++||++||+|++|++
T Consensus 7 ~~~vvvD~ETTGl---~~-~d~IIeIgaV~v~--~g~i~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~ 78 (820)
T PRK07246 7 RKYAVVDLEATGA---GP-NASIIQVGIVIIE--GGEIIDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFSQVAR 78 (820)
T ss_pred CCEEEEEEecCCc---CC-CCeEEEEEEEEEE--CCEEEEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHHHHHH
Confidence 6899999999997 33 4899999999995 7899999999999995 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQG 294 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g 294 (414)
+|.+|+++.. .|.||++||+ .||+.++.+.|+.++ ++++|+..+++.+++ ..+++|++++++||++..
T Consensus 79 ~~~~~l~~~~------lVaHN~~FD~-~fL~~~~~~~g~~~~---~~~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~- 147 (820)
T PRK07246 79 HIYDLIEDCI------FVAHNVKFDA-NLLAEALFLEGYELR---TPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLA- 147 (820)
T ss_pred HHHHHhCCCE------EEEECcHHHH-HHHHHHHHHcCCCCC---CCceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCC-
Confidence 9999999854 4556669995 899999988887653 568999999999887 457999999999999986
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhcCC
Q 015017 295 RAHCGLDDAKNTARLLALLMHRGFK 319 (414)
Q Consensus 295 ~~HrALdDA~aTA~Ll~~ll~~~~~ 319 (414)
++|+|++||++||+||.+|+++...
T Consensus 148 ~~H~Al~DA~ata~L~~~l~~~l~~ 172 (820)
T PRK07246 148 DAHTAIADARATAELFLKLLQKIES 172 (820)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 7899999999999999999987544
No 33
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.5e-27 Score=240.17 Aligned_cols=163 Identities=16% Similarity=0.161 Sum_probs=137.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..||||||||||+ ++..++|||||||+++ .+|++.++|++||+|.. + +.+ ..|||||++||++||+|.+|++
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 5899999999998 6788999999999996 47889999999999995 2 333 3799999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCC-------------------------CCCCCCCceeehHHHH
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKI-------------------------WKPPYFNRWINLKVPF 270 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi-------------------------~~P~~~~~~IDl~~l~ 270 (414)
+|.+||++.+ .|+|++.||+ .||..++++... ...+..+.++||+.+.
T Consensus 118 el~~fL~g~v------LVaHNA~FD~-~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LA 190 (377)
T PRK05601 118 PLDRLIDGRT------LILHNAPRTW-GFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATA 190 (377)
T ss_pred HHHHHhCCCE------EEEECcHHHH-HHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHH
Confidence 9999999864 4556669995 999999876411 0111346799999999
Q ss_pred HHhcC-CCCCCHHHHHHHcCCCC----------CCCCCcHH--HHHHHHHHHHHHHH
Q 015017 271 HEVFG-GVRCNLKEAVEMAGLAW----------QGRAHCGL--DDAKNTARLLALLM 314 (414)
Q Consensus 271 r~l~~-~~~~~L~~l~~~~gI~~----------~g~~HrAL--dDA~aTA~Ll~~ll 314 (414)
+++++ .++++|.+++++|||+. . ..|+|| +||+.+++|+.++.
T Consensus 191 Rrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~-~p~~~l~~~Da~ll~~l~~~~~ 246 (377)
T PRK05601 191 RRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQ-VPHRQLCREETLLVARLYFALR 246 (377)
T ss_pred HHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhc-CChhhhhhHHHHHHHHHHHHhh
Confidence 99986 57899999999999987 3 578998 69999999999873
No 34
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.95 E-value=6.1e-28 Score=222.97 Aligned_cols=162 Identities=19% Similarity=0.164 Sum_probs=129.5
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhC-CCCHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEALLRH 217 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~-Ap~f~eVl~~f 217 (414)
++||+||||+ ++..++|||||+|+++ .++.+.++|+++|+|.....+++.+..+||||++||.+ +|++.+++++|
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 5899999998 6778999999999997 34455699999999974224788999999999999999 99999999999
Q ss_pred HHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCCCCC----CCceeehHHHHHHhc--------------CCCC
Q 015017 218 DKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPY----FNRWINLKVPFHEVF--------------GGVR 278 (414)
Q Consensus 218 ~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~P~~----~~~~IDl~~l~r~l~--------------~~~~ 278 (414)
.+|+++. ..+.|+|+ ..||+ .||+.++++.++..+.. .+.++|+..+.+..+ +.++
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 9999642 12344555 48995 99999999988753211 234578877666542 1346
Q ss_pred CCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHH
Q 015017 279 CNLKEAVEMAGLAWQGRAHCGLDDAKNTARLL 310 (414)
Q Consensus 279 ~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll 310 (414)
++|++++++|||+.. ++|||++||++||+|+
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 789999999999985 7899999999999986
No 35
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.1e-27 Score=266.32 Aligned_cols=167 Identities=23% Similarity=0.291 Sum_probs=148.0
Q ss_pred ccEEEEEEeeCCCCCCCCC-CCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPY-PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~-~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl 214 (414)
..|||||+||||. ++. .++|||||||+++ +|+++++|+++|+|.. +|+++++++||||++||++||+|.+|+
T Consensus 3 ~~~vvvD~ETTG~---~p~~~d~IIeigav~v~--~~~i~~~f~~~v~P~~--~i~~~~~~ltGIt~~~l~~ap~f~ev~ 75 (928)
T PRK08074 3 KRFVVVDLETTGN---SPKKGDKIIQIAAVVVE--DGEILERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVA 75 (928)
T ss_pred CCEEEEEEeCCCC---CCCCCCcEEEEEEEEEE--CCEEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHhcCCCHHHHH
Confidence 4799999999997 443 4899999999995 8899999999999995 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCC
Q 015017 215 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQ 293 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~ 293 (414)
.+|.+|+++.. .|.|++.|| +.||+.++.+.|++.+ ..++||+..+.+.+++ ..+++|.+++++||++..
T Consensus 76 ~~l~~~l~~~~------~VaHN~~FD-~~fL~~~~~~~g~~~~--~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~~ 146 (928)
T PRK08074 76 PEIVELLEGAY------FVAHNVHFD-LNFLNEELERAGYTEI--HCPKLDTVELARILLPTAESYKLRDLSEELGLEHD 146 (928)
T ss_pred HHHHHHhCCCe------EEEEChHHH-HHHHHHHHHHcCCCCC--CCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCCC
Confidence 99999998854 455566999 5899999999998653 5689999999998887 467899999999999985
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCC
Q 015017 294 GRAHCGLDDAKNTARLLALLMHRGFK 319 (414)
Q Consensus 294 g~~HrALdDA~aTA~Ll~~ll~~~~~ 319 (414)
++|+|++||++||+||.+|+++...
T Consensus 147 -~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 147 -QPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHHh
Confidence 8899999999999999999987543
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=99.95 E-value=4.7e-27 Score=261.60 Aligned_cols=165 Identities=24% Similarity=0.246 Sum_probs=147.0
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHH
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 216 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~ 216 (414)
+|||||+||||+ ++..++|||||+|+++ +|+++++|+++|+|.. +++++++++||||++||++||+|.+|+.+
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 489999999997 5677999999999995 7899999999999995 69999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 015017 217 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 295 (414)
Q Consensus 217 f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~ 295 (414)
|.+|+++.. .|.|++.||+ .||+.++++.|++. +.+.++|+..+.+.+++ ..+++|.+++++||++.. +
T Consensus 74 l~~~l~~~~------~VahN~~fD~-~fL~~~~~~~g~~~--~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~ 143 (850)
T TIGR01407 74 IYDLLEDGI------FVAHNVHFDL-NFLAKALKDCGYEP--LPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHE-N 143 (850)
T ss_pred HHHHhCCCE------EEEeCcHHHH-HHHHHHHHHcCCCC--CCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-C
Confidence 999998753 4556669995 99999999999864 35678999999998887 467899999999999986 7
Q ss_pred CCcHHHHHHHHHHHHHHHHHhcC
Q 015017 296 AHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 296 ~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
+|+|++||++||+|+.+++++..
T Consensus 144 ~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 144 PHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred CCChHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999987643
No 37
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.95 E-value=9.1e-27 Score=203.67 Aligned_cols=156 Identities=28% Similarity=0.314 Sum_probs=137.0
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 218 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~ 218 (414)
|+||+||||+ ++..++|||||+|+++. ++++++.|+.+|+|.. .++++++++||||++++.+++++.+++.+|.
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 56789999999999984 4678899999999996 5999999999999999999999999999999
Q ss_pred HHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHH-HHHcCCCCCCCC
Q 015017 219 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEA-VEMAGLAWQGRA 296 (414)
Q Consensus 219 ~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l-~~~~gI~~~g~~ 296 (414)
+|+.+ ...|.|++.||+ .||+..+.+++. +.....|+|++.+++.+++. ..++|..+ ++.+|++.. ++
T Consensus 75 ~~l~~------~~~v~~n~~fD~-~~l~~~~~~~~~--~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~ 144 (159)
T cd06127 75 EFLGG------RVLVAHNASFDL-RFLNRELRRLGG--PPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE-GA 144 (159)
T ss_pred HHHCC------CEEEEeCcHhhH-HHHHHHHHHhCC--CCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC-CC
Confidence 99987 355667779995 899999999883 33567899999999998874 46789988 889999874 88
Q ss_pred CcHHHHHHHHHHHH
Q 015017 297 HCGLDDAKNTARLL 310 (414)
Q Consensus 297 HrALdDA~aTA~Ll 310 (414)
|+|++||++|++||
T Consensus 145 H~Al~Da~~t~~l~ 158 (159)
T cd06127 145 HRALADALATAELL 158 (159)
T ss_pred CCcHHHHHHHHHHh
Confidence 99999999999987
No 38
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=1.1e-26 Score=221.02 Aligned_cols=148 Identities=22% Similarity=0.232 Sum_probs=126.4
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHH
Q 015017 138 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 217 (414)
Q Consensus 138 ~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f 217 (414)
++|||+||||++ .+|||||+|++. +|++.++|+++|+|.. +|+++++++||||++||.+||++++|+++|
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 799999999973 249999999984 7899999999999996 599999999999999999999999999985
Q ss_pred HHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC----
Q 015017 218 DKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ---- 293 (414)
Q Consensus 218 ~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~~---- 293 (414)
+++. +.|.||+.|| +.||.. ....|+||..++|++++..+++|..++++||++..
T Consensus 72 ---~~~~------~lVaHNa~FD-~~~L~~-----------~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~ 130 (219)
T PRK07983 72 ---YGSE------WYVAHNASFD-RRVLPE-----------MPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPG 130 (219)
T ss_pred ---cCCC------EEEEeCcHhh-HHHHhC-----------cCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCC
Confidence 4443 4566667999 588851 23578999999999998656899999999998641
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHh
Q 015017 294 GRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 294 g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
.++|||++||++||+||+++++.
T Consensus 131 ~~aHrAl~Da~ata~ll~~l~~~ 153 (219)
T PRK07983 131 LHHHRALYDCYITAALLIDIMNT 153 (219)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999975
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=99.94 E-value=1.7e-27 Score=215.86 Aligned_cols=146 Identities=20% Similarity=0.278 Sum_probs=122.3
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCH-------H
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL-------S 211 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f-------~ 211 (414)
||||+||||+ ++..++|||||||++ ++|++. |++||||.. +++++++++||||++||++||++ +
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 6899999998 567899999999999 578875 999999985 69999999999999999999864 5
Q ss_pred HHHHHHHHHHhh-cCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC----CCCCHHHHHH
Q 015017 212 EALLRHDKWLEN-KGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG----VRCNLKEAVE 286 (414)
Q Consensus 212 eVl~~f~~fl~~-~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~----~~~~L~~l~~ 286 (414)
+|+++|.+|+++ .+++||| ..||+ .||+.. .++++||..+++.+++. .+++|+++++
T Consensus 72 ~~~~~~~~~i~~~~vlVgHn------~~fD~-~fL~~~-----------~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~ 133 (161)
T cd06137 72 AARAALWKFIDPDTILVGHS------LQNDL-DALRMI-----------HTRVVDTAILTREAVKGPLAKRQWSLRTLCR 133 (161)
T ss_pred HHHHHHHHhcCCCcEEEecc------HHHHH-HHHhCc-----------CCCeeEehhhhhhccCCCcCCCCccHHHHHH
Confidence 899999999987 5554444 49996 899731 24689999999988764 4789999998
Q ss_pred H-cCCCCC--CCCCcHHHHHHHHHHHHH
Q 015017 287 M-AGLAWQ--GRAHCGLDDAKNTARLLA 311 (414)
Q Consensus 287 ~-~gI~~~--g~~HrALdDA~aTA~Ll~ 311 (414)
+ ||++.. ..+|+|+.||++|++|++
T Consensus 134 ~~~~~~~~~~~~~H~A~~DA~at~~l~~ 161 (161)
T cd06137 134 DFLGLKIQGGGEGHDSLEDALAAREVVL 161 (161)
T ss_pred HHCCchhcCCCCCCCcHHHHHHHHHHhC
Confidence 6 798763 257999999999999974
No 40
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.93 E-value=2.5e-25 Score=212.81 Aligned_cols=165 Identities=25% Similarity=0.277 Sum_probs=145.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEee-EEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEA-CFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d-~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl 214 (414)
..+||||+||||+ ++..++|||||+|.+. ++++.+ .|+++|+|.. .+++++.++||||.+||.++|.|.+++
T Consensus 13 ~~~vv~D~ETtg~---~~~~~~iieIgav~~~--~~~i~~~~~~~~v~P~~--~i~~~~~~i~git~e~l~~~p~~~~v~ 85 (243)
T COG0847 13 TRFVVIDLETTGL---NPKKDRIIEIGAVTLE--DGRIVERSFHTLVNPER--PIPPEIFKIHGITDEMLADAPKFAEVL 85 (243)
T ss_pred CcEEEEecccCCC---CCCCCceEEEEeEEEE--CCeeecceeEEEECCCC--CCChhhhhhcCCCHHHHhcCCCHHHHH
Confidence 3899999999997 5678999999999995 777764 4999999964 599999999999999999999999999
Q ss_pred HHHHHHHhh-cCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCC
Q 015017 215 LRHDKWLEN-KGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAW 292 (414)
Q Consensus 215 ~~f~~fl~~-~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~~gI~~ 292 (414)
++|.+|+++ .. .|.|++.||+ .||..++.+.+...+ ...++|+..+.+..++. ..++|+.+++++|++.
T Consensus 86 ~~~~~~i~~~~~------~Vahna~fD~-~fl~~~~~~~~~~~~--~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~ 156 (243)
T COG0847 86 PEFLDFIGGLRL------LVAHNAAFDV-GFLRVESERLGIEIP--GDPVLDTLALARRHFPGFDRSSLDALAERLGIDR 156 (243)
T ss_pred HHHHHHHCCCCe------EEEEchhhcH-HHHHHHHHHcCCCcc--cCceehHHHHHHHHcCCCccchHHHHHHHcCCCc
Confidence 999999999 54 4556669995 999999999998875 55789999999998886 7889999999999994
Q ss_pred C-CCCCcHHHHHHHHHHHHHHHHHh
Q 015017 293 Q-GRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 293 ~-g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
. .++|+|+.||.++|+++.+++..
T Consensus 157 ~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 157 NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 2 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=99.93 E-value=7.8e-26 Score=203.06 Aligned_cols=149 Identities=20% Similarity=0.229 Sum_probs=114.2
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 218 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~ 218 (414)
||||+||||+ ++. ++++||++|.+...+|++. |++||+|.. .++++++.+||||++||++||+|.+++++|.
T Consensus 1 v~lD~EttGl---~~~-~~~~~i~~v~~v~~~~~~~--~~~~v~P~~--~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~ 72 (152)
T cd06144 1 VALDCEMVGV---GPD-GSESALARVSIVNEDGNVV--YDTYVKPQE--PVTDYRTAVSGIRPEHLKDAPDFEEVQKKVA 72 (152)
T ss_pred CEEEEEeecc---cCC-CCEEEEEEEEEEeCCCCEE--EEEEECCCC--CCCcccccCCCCCHHHHcCCCCHHHHHHHHH
Confidence 6899999998 332 3677776654422345543 999999985 5999999999999999999999999999999
Q ss_pred HHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHH-cCCCCCCC
Q 015017 219 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEM-AGLAWQGR 295 (414)
Q Consensus 219 ~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~--~~~~~L~~l~~~-~gI~~~g~ 295 (414)
+|+++.+ .|.||+.||+ .||+ +..| ...++|+..+.+.... .++++|++++++ +|++....
T Consensus 73 ~~l~~~v------lVgHn~~fD~-~~L~-------~~~~--~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~ 136 (152)
T cd06144 73 ELLKGRI------LVGHALKNDL-KVLK-------LDHP--KKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG 136 (152)
T ss_pred HHhCCCE------EEEcCcHHHH-HHhc-------CcCC--CccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCC
Confidence 9998854 4455669996 8986 2333 2357787554332222 357899999997 69987546
Q ss_pred CCcHHHHHHHHHHHHH
Q 015017 296 AHCGLDDAKNTARLLA 311 (414)
Q Consensus 296 ~HrALdDA~aTA~Ll~ 311 (414)
+|+|++||++|++||+
T Consensus 137 ~H~Al~DA~at~~l~~ 152 (152)
T cd06144 137 EHSSVEDARAAMRLYR 152 (152)
T ss_pred CcCcHHHHHHHHHHhC
Confidence 8999999999999984
No 42
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.93 E-value=8.5e-26 Score=204.34 Aligned_cols=147 Identities=20% Similarity=0.250 Sum_probs=117.9
Q ss_pred EEEEEeeCCCCCCCCC--CCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPY--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 216 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~--~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~ 216 (414)
||||+||||+ ++. .++|++|++|.+ +|+++ |++||||.. +++++++.+||||++||++||++++|+++
T Consensus 1 v~~D~EttGl---~~~~~~~~i~~i~~v~~---~g~~~--~~~lv~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~v~~~ 70 (157)
T cd06149 1 VAIDCEMVGT---GPGGRESELARCSIVNY---HGDVL--YDKYIRPEG--PVTDYRTRWSGIRRQHLVNATPFAVAQKE 70 (157)
T ss_pred CEEEeEeccc---cCCCCeEEEEEEEEEeC---CCCEE--EEEeECCCC--ccCccceECCCCCHHHHhcCCCHHHHHHH
Confidence 6899999998 343 588999988875 56664 999999995 69999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHH--HHHh--cC-CCCCCHHHHHHHc---
Q 015017 217 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVP--FHEV--FG-GVRCNLKEAVEMA--- 288 (414)
Q Consensus 217 f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l--~r~l--~~-~~~~~L~~l~~~~--- 288 (414)
|.+|+++.++++ |+..||+ .||+.. .| ...++|+..+ +++. ++ .++++|++++++|
T Consensus 71 l~~~l~~~vlV~------Hn~~~D~-~~l~~~-------~~--~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~ 134 (157)
T cd06149 71 ILKILKGKVVVG------HAIHNDF-KALKYF-------HP--KHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHR 134 (157)
T ss_pred HHHHcCCCEEEE------eCcHHHH-HHhccc-------CC--CcCEEECcccccchhhcCCcccCChhHHHHHHHHcCh
Confidence 999999865544 4459997 888732 22 2346787543 5443 44 3568999999999
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHH
Q 015017 289 GLAWQGRAHCGLDDAKNTARLLA 311 (414)
Q Consensus 289 gI~~~g~~HrALdDA~aTA~Ll~ 311 (414)
+++..++.|+|+.||++|++||+
T Consensus 135 ~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 135 DIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred hhcCCCCCcCcHHHHHHHHHHhC
Confidence 67764467999999999999973
No 43
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=3.8e-25 Score=219.06 Aligned_cols=200 Identities=19% Similarity=0.139 Sum_probs=144.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcC-CC---eEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSV-TG---QLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 211 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~-~g---~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~ 211 (414)
..+||||+||||+ ++..++|||||+|+++.. +| ++.++|+++|+|.. .|+++++.|||||++||.+++...
T Consensus 37 ~~~vvlD~ETTGL---d~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~--~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 37 RLGVILDTETTGL---DPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR--PIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CeEEEEEeeCCCC---CCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC--CCCHHHHHhcCCCHHHHhcCCCcH
Confidence 5899999999998 678899999999999732 44 45789999999995 599999999999999999998766
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHh-cCCCCCCHHHHHHHcCC
Q 015017 212 EALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEV-FGGVRCNLKEAVEMAGL 290 (414)
Q Consensus 212 eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l-~~~~~~~L~~l~~~~gI 290 (414)
+++. +|++.. .++|+||+.|| +.||++.+....- ..|.++....... .+..+++|.+++++||
T Consensus 112 ~~l~---~fl~~~-----~vlVAHNA~FD-~~fL~~~~~~~~~------~~~~ct~~~i~~~~~~~~~~kL~~La~~~g- 175 (294)
T PRK09182 112 AAVD---ALIAPA-----DLIIAHNAGFD-RPFLERFSPVFAT------KPWACSVSEIDWSARGFEGTKLGYLAGQAG- 175 (294)
T ss_pred HHHH---HHhcCC-----CEEEEeCHHHH-HHHHHHHHHhccC------CcccccHHHHhhccccCCCCCHHHHHHHcC-
Confidence 5554 445442 35677788999 5999987654321 2344444333221 2346789999999999
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHhcCCcccccccccccCCCCCcccCCCCCCCCCCCcccchhcccCCcc
Q 015017 291 AWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLMWQTNDGSLTWNQFPERIFLPPHQLHKQMDLQNSIF 362 (414)
Q Consensus 291 ~~~g~~HrALdDA~aTA~Ll~~ll~~~~~~~i~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lP~~ 362 (414)
+.. .+|||++||++|++||.+++.........+.+....+|.-..+ -...|++.....++||--|-
T Consensus 176 ~~~-~aHrAl~Da~Ata~ll~~~l~~~~~~~l~~Ll~~~~~~~~~~~-----a~~~p~~~k~~lk~rgyrw~ 241 (294)
T PRK09182 176 FFH-EGHRAVDDCQALLELLARPLPETGQPPLAELLEASRRSRVRIW-----AENSPFEMKDHLKARGYRWS 241 (294)
T ss_pred CCC-CCcChHHHHHHHHHHHHHHHhhcCCcCHHHHHHHhccCeeEEE-----cccCCccchHHHHhccCCCC
Confidence 443 6899999999999999998876544455555554332222221 01126777788888888875
No 44
>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=3e-27 Score=206.92 Aligned_cols=161 Identities=27% Similarity=0.352 Sum_probs=124.9
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 218 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~ 218 (414)
||||+||||+ ++..++|||||+|+++.....+.+.|+++|+|...+.+++.++++||||+++|++++++.+++.+|.
T Consensus 1 v~~D~Ettg~---~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~ 77 (164)
T PF00929_consen 1 VVFDTETTGL---DPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFE 77 (164)
T ss_dssp EEEEEEESSS---TTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHH
T ss_pred cEEEeEcCCC---CCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhh
Confidence 7999999998 4568999999999998554447899999999997445999999999999999999999999999999
Q ss_pred HHHhh-cCCCCCcEEEEEcCcchHHHHHHHHHHHc-CCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 015017 219 KWLEN-KGIKNTNFAVVTWSNWDCRVMLESECRFK-KIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 295 (414)
Q Consensus 219 ~fl~~-~~lv~hn~~vV~~g~fDir~fL~~~~~~~-gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~ 295 (414)
+|+.+ ..+++| +..||+ .++...+.+. +...| ....++|+..+.+..++ ...++|++++++||++..+.
T Consensus 78 ~~~~~~~~~v~~------n~~fd~-~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~ 149 (164)
T PF00929_consen 78 EFLKKNDILVGH------NASFDI-GFLRREDKRFLGKPIP-KPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGT 149 (164)
T ss_dssp HHHHHHTEEEET------TCCHEE-ESSHHHHHHHHHHHHH-HHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTST
T ss_pred hhhhcccccccc------cccchh-hHHHHhhhhccccccc-ccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCC
Confidence 99994 333333 358886 6777777665 33332 11234454333333322 11268999999999999866
Q ss_pred CCcHHHHHHHHHHHH
Q 015017 296 AHCGLDDAKNTARLL 310 (414)
Q Consensus 296 ~HrALdDA~aTA~Ll 310 (414)
+|+|++||++|++||
T Consensus 150 ~H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 150 AHDALDDARATAELF 164 (164)
T ss_dssp TTSHHHHHHHHHHHH
T ss_pred CcChHHHHHHHhCcC
Confidence 799999999999986
No 45
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.93 E-value=1.5e-25 Score=201.13 Aligned_cols=143 Identities=19% Similarity=0.232 Sum_probs=116.7
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCC-CHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV-TLSEALLRH 217 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap-~f~eVl~~f 217 (414)
|++|+||||... . ++|++|++|.+ +|++ .|++||+|.. +++++++++||||++||++|| ++++|+++|
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 99999999976 4554 4999999996 699999999999999999995 999999999
Q ss_pred HHHHh-hcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHc-CCCCC-
Q 015017 218 DKWLE-NKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMA-GLAWQ- 293 (414)
Q Consensus 218 ~~fl~-~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~-gI~~~- 293 (414)
.+|++ +.+++|| +.+||+ .||+. ..++++|+..+++..++ .++++|++++++| ++...
T Consensus 70 ~~fl~~~~vlVgH------n~~fD~-~fL~~-----------~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~ 131 (150)
T cd06145 70 LSLISPDTILVGH------SLENDL-KALKL-----------IHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQ 131 (150)
T ss_pred HHHhCCCCEEEEc------ChHHHH-HHhhc-----------cCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeC
Confidence 99997 5544444 459997 89863 12468999999887665 4468999999887 54332
Q ss_pred -CCCCcHHHHHHHHHHHH
Q 015017 294 -GRAHCGLDDAKNTARLL 310 (414)
Q Consensus 294 -g~~HrALdDA~aTA~Ll 310 (414)
+.+|||++||++|++||
T Consensus 132 ~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 132 GEGGHDSVEDARAALELV 149 (150)
T ss_pred CCCCCCcHHHHHHHHHHh
Confidence 36799999999999987
No 46
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.93 E-value=3.3e-25 Score=203.27 Aligned_cols=162 Identities=15% Similarity=0.165 Sum_probs=124.9
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCC--CCCCcchhhh---cCCChhhhhCCCCHHH
Q 015017 138 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCN--QLLSDFCKDL---TGIQQIQVDRGVTLSE 212 (414)
Q Consensus 138 ~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~--p~Ls~~~~~L---TGIT~e~V~~Ap~f~e 212 (414)
+|+||+||||+ ++..++|||||||+++...+++.++|+.+|+|... +.+++.+..+ ||||+++++++|++.+
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 58999999998 67789999999999986667888999999999851 1234556666 5999999999999999
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCCCCCCCceeeh---HHHHHHhcCCCCCCHHHHHHHc
Q 015017 213 ALLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPYFNRWINL---KVPFHEVFGGVRCNLKEAVEMA 288 (414)
Q Consensus 213 Vl~~f~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~P~~~~~~IDl---~~l~r~l~~~~~~~L~~l~~~~ 288 (414)
|+.+|.+|+++..- .....++++ .+||+ .||+.++++.+.. +.++.+|+ ..+.+++++. +. .+
T Consensus 78 vl~~~~~f~~~~~~-~~~~~lvgh~~~FD~-~fL~~~~~~~~~~---~~~~~~D~~~l~~l~~~l~p~----~~----~~ 144 (173)
T cd06135 78 AEAELLEFIKKYVP-KGKSPLAGNSVHQDR-RFLDKYMPELEEY---LHYRILDVSSIKELARRWYPE----IY----RK 144 (173)
T ss_pred HHHHHHHHHHHhcC-CCCCceeecchhhCH-HHHHHHHHHHhcc---CCcchhhHHHHHHHHHHhCcH----hh----hc
Confidence 99999999986310 112234454 49995 8999999988732 45667887 4566666652 11 15
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHHHHHh
Q 015017 289 GLAWQGRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 289 gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
+++. +..|||++||++|+.++.+.++.
T Consensus 145 ~~~~-~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 145 APKK-KGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred CCCC-CCCcchHHHHHHHHHHHHHHHHH
Confidence 6765 46899999999999999988753
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=99.91 E-value=2.3e-23 Score=192.91 Aligned_cols=164 Identities=14% Similarity=0.104 Sum_probs=128.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCC--CCCCcchhhhc---CCChhhhhCCCCH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCN--QLLSDFCKDLT---GIQQIQVDRGVTL 210 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~--p~Ls~~~~~LT---GIT~e~V~~Ap~f 210 (414)
+.||+||+||||+ ++..++|||||||+++.....+.+.|+.+|+|... ..+++.++.+| |||+++++++|++
T Consensus 3 ~~~vvlD~ETTGL---dp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~ 79 (181)
T PRK05359 3 DNLIWIDLEMTGL---DPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSE 79 (181)
T ss_pred CcEEEEEeecCCC---CCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCH
Confidence 5899999999998 77889999999999973223345789999999851 12577888887 8999999999999
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCCCCCCCceeeh--H-HHHHHhcCCCCCCHHHHHH
Q 015017 211 SEALLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPYFNRWINL--K-VPFHEVFGGVRCNLKEAVE 286 (414)
Q Consensus 211 ~eVl~~f~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~P~~~~~~IDl--~-~l~r~l~~~~~~~L~~l~~ 286 (414)
.+|+.+|++|+++..+ .|+..+|++ ..||+ .||++.+.+.+.. +.++++|+ . .+.++++|. +
T Consensus 80 ~e~~~~~l~fl~~~~~-~~~~~l~g~~v~FD~-~FL~~~~~~~~~~---l~~~~~Dv~tl~~l~r~~~P~----~----- 145 (181)
T PRK05359 80 AEAEAQTLEFLKQWVP-AGKSPLCGNSIGQDR-RFLARYMPELEAY---FHYRNLDVSTLKELARRWKPE----I----- 145 (181)
T ss_pred HHHHHHHHHHHHHhcC-CCCCceeecchhhCH-HHHHHHHHHhccc---CCCcccchhHHHHHHHHhChh----h-----
Confidence 9999999999987654 334455665 49994 9999999877654 34677884 3 577777762 2
Q ss_pred HcCCCCCCCCCcHHHHHHHHHHHHHHHHHhc
Q 015017 287 MAGLAWQGRAHCGLDDAKNTARLLALLMHRG 317 (414)
Q Consensus 287 ~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~ 317 (414)
.++++.. ..|||++||+++.+.+....+..
T Consensus 146 ~~~~~~~-~~HRal~D~~~s~~~~~~~~~~~ 175 (181)
T PRK05359 146 LNGFKKQ-GTHRALADIRESIAELKYYREHF 175 (181)
T ss_pred hhCCCCc-CCcccHHHHHHHHHHHHHHHHHh
Confidence 3578775 57999999999999988876643
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.89 E-value=1e-22 Score=212.96 Aligned_cols=172 Identities=16% Similarity=0.115 Sum_probs=130.1
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhC-CCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~-Ap~f~eVl 214 (414)
.+|||+|+||||+ ++..|+|||||||+++.....+.+.|+.+|+|.....+++.+..+||||++||.+ +.+..+++
T Consensus 6 ~~fvv~D~ETTGL---dP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~ 82 (476)
T PRK11779 6 PTFLWHDYETFGA---NPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFA 82 (476)
T ss_pred CcEEEEEEECCCC---CCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHH
Confidence 5899999999998 6788999999999998432355688999999985223577899999999999965 66799999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCC---C-CCCCceeehHHHHHHhc--------------C
Q 015017 215 LRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWK---P-PYFNRWINLKVPFHEVF--------------G 275 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~---P-~~~~~~IDl~~l~r~l~--------------~ 275 (414)
++|.+|+... ..++|.|+ .+||+ .||+.++.+..+.. . ...+..+|+..+.+..+ |
T Consensus 83 ~~i~~~l~~~----~~~lVGhNni~FD~-eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g 157 (476)
T PRK11779 83 ARIHAEFSQP----GTCILGYNNIRFDD-EVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDG 157 (476)
T ss_pred HHHHHHHhcC----CCEEEEeCchhhcH-HHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccC
Confidence 9999999621 13344444 48995 89999987654321 0 00122235544444322 2
Q ss_pred CCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHh
Q 015017 276 GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 276 ~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
..+++|+++++++||+.. ++|+|++||++|++|+.+|.++
T Consensus 158 ~~s~rLe~L~~~~gI~~~-~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 158 LPSFKLEHLTKANGIEHE-NAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CCCCcHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHh
Confidence 246899999999999985 7899999999999999988866
No 49
>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=99.31 E-value=9.4e-13 Score=95.46 Aligned_cols=44 Identities=34% Similarity=0.901 Sum_probs=40.5
Q ss_pred cceecCCCcCcceeccCCCCCCCceeecCCCcccCCCcccceeecCC
Q 015017 366 PSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 412 (414)
Q Consensus 366 ~~c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~~~ 412 (414)
|.|.||..+.+.|++|.|+|+||.||+|+++.. ..|+||+|.|+
T Consensus 1 p~C~Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~---~~C~fF~W~De 44 (45)
T PF06839_consen 1 PKCPCGEPAVRRTSKKTGPNPGRRFYKCPNYKD---KGCNFFQWEDE 44 (45)
T ss_pred CCCCCCCEeEEEEEeCCCCCCCCcceECCCCCC---CCcCCEEeccC
Confidence 689999999999999999999999999999754 67999999986
No 50
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.23 E-value=1e-10 Score=113.06 Aligned_cols=157 Identities=18% Similarity=0.252 Sum_probs=112.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..+|++|.|..|... +...+.+--++. || ..|.|+ |+.||||.. +++++.+..+||+.+.+.+|.+|+.|-.
T Consensus 105 ~r~vAmDCEMVG~Gp-~G~~s~lARvSI--VN-~~G~Vv--yDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~aQ~ 176 (280)
T KOG2249|consen 105 TRVVAMDCEMVGVGP-DGRESLLARVSI--VN-YHGHVV--YDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVAQK 176 (280)
T ss_pred ceEEEEeeeEeccCC-CccceeeeEEEE--ee-ccCcEe--eeeecCCCc--ccccceeeecccCHHHhccCccHHHHHH
Confidence 369999999999721 112344434433 34 567775 999999996 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehH--HHHHHhcC-CCCCCHHHHHH-HcCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLK--VPFHEVFG-GVRCNLKEAVE-MAGLA 291 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~--~l~r~l~~-~~~~~L~~l~~-~~gI~ 291 (414)
+++++|.+.+||||-. .-|+ .-|. +..|. ...-||. ..+++++. ....+|..|.+ .+|++
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-QALK-------LEHPR--SMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKD 240 (280)
T ss_pred HHHHHHhCCEEecccc------ccHH-HHHh-------hhCch--hhhcccccCchHHHHhhccCCccHHHHHHHHhchh
Confidence 9999999987776643 3354 2232 33442 1123553 23444433 34568999886 57877
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHh
Q 015017 292 WQGRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 292 ~~g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
...-.|+.+.||.+|.+|+.++-.+
T Consensus 241 IQ~GeHsSvEDA~AtM~LY~~vk~q 265 (280)
T KOG2249|consen 241 IQVGEHSSVEDARATMELYKRVKVQ 265 (280)
T ss_pred hhccccCcHHHHHHHHHHHHHHHHH
Confidence 6534599999999999999887543
No 51
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=99.23 E-value=6.4e-10 Score=103.39 Aligned_cols=139 Identities=15% Similarity=0.002 Sum_probs=100.8
Q ss_pred EEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHH
Q 015017 139 VVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 217 (414)
Q Consensus 139 VV~D~ETTGl~~~-~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f 217 (414)
++||+||||..+. ++..++||+||++.. .+|... .+.....+.. +..+ ||+..+|...++..++|..|
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 6899999997432 457899999999886 245432 2333333331 1111 89999999999999999999
Q ss_pred HHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCC-CC-------------------CCceeehHHHHHHhcCC
Q 015017 218 DKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKP-PY-------------------FNRWINLKVPFHEVFGG 276 (414)
Q Consensus 218 ~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P-~~-------------------~~~~IDl~~l~r~l~~~ 276 (414)
.++++.... .+++-+++ +||+ .||...++++|+... .. -..++|+..+++..+..
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 999987421 23444556 7996 899999999888651 11 12468999999888887
Q ss_pred CCCCHHHHHHHcCCCC
Q 015017 277 VRCNLKEAVEMAGLAW 292 (414)
Q Consensus 277 ~~~~L~~l~~~~gI~~ 292 (414)
.+++|+++++.++...
T Consensus 147 ~sy~L~~v~~~~l~~~ 162 (199)
T cd05160 147 KSYTLDAVAEELLGEG 162 (199)
T ss_pred ccCCHHHHHHHHhCCC
Confidence 7899999999876553
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=99.12 E-value=7.2e-10 Score=102.22 Aligned_cols=154 Identities=20% Similarity=0.227 Sum_probs=107.3
Q ss_pred ccEEEEEEeeCCCCCC-C-----CCCCcEEEEcEEEEEc-CCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCC
Q 015017 136 QYFVVIDFEATCDKDK-N-----PYPQEIIEFPSVIVSS-VTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV 208 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~-~-----~~~deIIEIgAV~vd~-~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap 208 (414)
.+||-+|.|+|++... . ....++.-+.+|-.+. .+|+++ +..||+|.. ++.++.+.++|||.+++++|.
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 5788888888876311 0 0123555665543110 356664 899999995 599999999999999999875
Q ss_pred ------CHHHHHHHHHHHHh-hcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCH
Q 015017 209 ------TLSEALLRHDKWLE-NKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNL 281 (414)
Q Consensus 209 ------~f~eVl~~f~~fl~-~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L 281 (414)
++++|..++.+++. +.+++||.. .-|+ . ..++..|. ...+||..+|+. .+.++.+|
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL------~nDL-~-------aL~l~hp~--~~viDTa~l~~~-~~~r~~sL 143 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGL------AKDF-R-------VINIQVPK--EQVIDTVELFHL-PGQRKLSL 143 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccc------hhHH-H-------HhcCcCCC--cceEEcHHhccC-CCCCChhH
Confidence 68999999999985 444444433 5564 2 33455552 357999877653 12235689
Q ss_pred HHHHH-HcCCCCCCCCCcHHHHHHHHHHHH
Q 015017 282 KEAVE-MAGLAWQGRAHCGLDDAKNTARLL 310 (414)
Q Consensus 282 ~~l~~-~~gI~~~g~~HrALdDA~aTA~Ll 310 (414)
..|++ ++|...+...|+.+.||+++.+|+
T Consensus 144 k~La~~~L~~~IQ~~~HdSvEDArAam~Ly 173 (174)
T cd06143 144 RFLAWYLLGEKIQSETHDSIEDARTALKLY 173 (174)
T ss_pred HHHHHHHcCCcccCCCcCcHHHHHHHHHHh
Confidence 99886 578776655799999999999987
No 53
>PHA02570 dexA exonuclease; Provisional
Probab=98.96 E-value=5e-09 Score=99.44 Aligned_cols=165 Identities=15% Similarity=0.118 Sum_probs=109.1
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCC----------CCcchhhhcCCChhh----
Q 015017 138 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQL----------LSDFCKDLTGIQQIQ---- 203 (414)
Q Consensus 138 ~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~----------Ls~~~~~LTGIT~e~---- 203 (414)
-++||+||.|. .....||+||||.+|...+ +..+|+.+|.....-+ ..+..+......|+.
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 4678899999999998666 6889999886422111 122223333333332
Q ss_pred -hh---CCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHc----C--CCCCCCCCceeehHHHHHH
Q 015017 204 -VD---RGVTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFK----K--IWKPPYFNRWINLKVPFHE 272 (414)
Q Consensus 204 -V~---~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~----g--i~~P~~~~~~IDl~~l~r~ 272 (414)
|. +..++.+++.+|.+||.....-.....+.++| +||+ .+|...+++. + ++.|..+..--|++.+...
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 35789999999999999764222234455665 7996 8999999887 7 5777766666788876654
Q ss_pred h-cCCC-------CCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHhcC
Q 015017 273 V-FGGV-------RCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 273 l-~~~~-------~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
. +.+. ...|+. + -+|+|+.||..=|..+..-.+...
T Consensus 157 ~~l~r~~~~cp~~~g~l~g--------f--v~H~sihDcakd~lml~y~~rya~ 200 (220)
T PHA02570 157 TLLTRGMTTCPLPKGTLDG--------F--VAHDSIHDCAKDILMLIYAKRYAL 200 (220)
T ss_pred hhccCCcccCCCcCccccc--------h--hhcccHHHHHHHHHHHHHHHHHhc
Confidence 3 2211 112211 1 579999999887776666555543
No 54
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.92 E-value=1.4e-08 Score=84.68 Aligned_cols=83 Identities=23% Similarity=0.237 Sum_probs=61.0
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 218 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~ 218 (414)
++||+||||+ ++..++|++|+....+ .+. .|. + . |.
T Consensus 1 ~~~DiEt~~~---~~~~~~i~~i~~~~~~--~~~---~~~--~-~---------------------------------f~ 36 (96)
T cd06125 1 IAIDTEATGL---DGAVHEIIEIALADVN--PED---TAV--I-D---------------------------------LK 36 (96)
T ss_pred CEEEEECCCC---CCCCCcEEEEEEEEcc--CCC---EEE--e-h---------------------------------HH
Confidence 4799999998 5688999999887532 111 111 0 0 88
Q ss_pred HHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHH
Q 015017 219 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVP 269 (414)
Q Consensus 219 ~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l 269 (414)
+|+++... ...|.|+++||+ .||++++++++++.|....+++|++.+
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 88887431 244556679996 899999999999988777899999865
No 55
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.82 E-value=3.3e-08 Score=99.94 Aligned_cols=166 Identities=16% Similarity=0.164 Sum_probs=127.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhh-CCCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVD-RGVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~-~Ap~f~eVl 214 (414)
-+|.+.|.||.|. +|..|++-+|++|.-|..=+.|.+--..|++|...---.+.+.-+||||+.... ++.+..+..
T Consensus 9 ~tF~~yDYETfG~---~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~ 85 (475)
T COG2925 9 PTFLFYDYETFGV---HPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFA 85 (475)
T ss_pred CcEEEEehhhcCC---CcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHH
Confidence 4899999999997 788999999999999865566788899999999532224778899999999876 789999989
Q ss_pred HHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCCCCCCC------ceeehHHHHHHhcCC----------
Q 015017 215 LRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPPYFN------RWINLKVPFHEVFGG---------- 276 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~P~~~~------~~IDl~~l~r~l~~~---------- 276 (414)
.++..-+... +.+++.+ -+|| ..+-+.-|-|+-+. | +.. +-.|++.+.|..+-.
T Consensus 86 ~~I~~~ls~P-----~Tcv~GYNniRFD-DEvtRy~fyRNF~D-P-Ya~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n 157 (475)
T COG2925 86 ARIHAELTQP-----NTCVLGYNNIRFD-DEVTRYIFYRNFYD-P-YAWSWQNGNSRWDLLDVVRACYALRPEGINWPEN 157 (475)
T ss_pred HHHHHHhCCC-----Ceeeecccccccc-hHHHHHHHHHhcCc-h-hhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcC
Confidence 8888877654 4566665 3788 57777777776554 2 333 335777777766522
Q ss_pred ----CCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHH
Q 015017 277 ----VRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALL 313 (414)
Q Consensus 277 ----~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~l 313 (414)
.+.+|+.+.+.-||+. +++|+|+.|++||..+-..+
T Consensus 158 ~dG~pSFkLEhLt~ANgieH-~nAHdAmsDVyATIamAklv 197 (475)
T COG2925 158 DDGLPSFKLEHLTKANGIEH-SNAHDAMSDVYATIAMAKLV 197 (475)
T ss_pred CCCCcchhhHHHhhcccccc-chhhHHHHHHHHHHHHHHHH
Confidence 1458999999999998 48999999999997654433
No 56
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.80 E-value=3.1e-08 Score=89.82 Aligned_cols=160 Identities=19% Similarity=0.181 Sum_probs=103.9
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCC--CCCCCcchhhhc---CCChhhhhCCCC
Q 015017 135 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTC--NQLLSDFCKDLT---GIQQIQVDRGVT 209 (414)
Q Consensus 135 ~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~--~p~Ls~~~~~LT---GIT~e~V~~Ap~ 209 (414)
.+++|=||+|.||+ ++..++||||++++-|..=+-+.+.+..-|.-.. -..+.+.+++.| |+++.-.+...+
T Consensus 5 ~~nLiWIDlEMTGL---d~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t 81 (184)
T COG1949 5 KNNLIWIDLEMTGL---DPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVT 81 (184)
T ss_pred CCceEEEeeeeccC---CcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhcc
Confidence 46899999999998 7899999999999988432223444444444332 112456677765 577777778899
Q ss_pred HHHHHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeeh---HHHHHHhcCCCCCCHHHHH
Q 015017 210 LSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINL---KVPFHEVFGGVRCNLKEAV 285 (414)
Q Consensus 210 f~eVl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~IDl---~~l~r~l~~~~~~~L~~l~ 285 (414)
..+|-.+.++||+.-+-. +...++.++ ..| |+||.+.+-+.--- +.++.+|+ +++.++..|. +
T Consensus 82 ~~~aE~~~l~flkkwvp~-~~spicGNSI~qD-RrFl~r~MP~Le~y---fHYR~lDVSTlKELa~RW~P~----i---- 148 (184)
T COG1949 82 EAEAEAQTLDFLKKWVPK-GVSPICGNSIAQD-RRFLFRYMPKLEAY---FHYRYLDVSTLKELARRWNPE----I---- 148 (184)
T ss_pred HHHHHHHHHHHHHHhCCC-CCCCCccchhhHH-HHHHHHHhhhHHHH---hhhHhhhHHHHHHHHHhhCcH----h----
Confidence 999999999999986544 223355553 468 89998764332111 23466775 4455555541 1
Q ss_pred HHcCCCCCCCCCcHHHHHHHHHHHHHH
Q 015017 286 EMAGLAWQGRAHCGLDDAKNTARLLAL 312 (414)
Q Consensus 286 ~~~gI~~~g~~HrALdDA~aTA~Ll~~ 312 (414)
..| +..+..|+||+|.+-...=++.
T Consensus 149 -~~~-~~K~~~H~Al~DI~ESI~EL~~ 173 (184)
T COG1949 149 -LAG-FKKGGTHRALDDIRESIAELRY 173 (184)
T ss_pred -hhc-cccccchhHHHHHHHHHHHHHH
Confidence 122 2345679999998765544443
No 57
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.65 E-value=1.7e-07 Score=85.82 Aligned_cols=163 Identities=17% Similarity=0.177 Sum_probs=111.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCC--CCCCCcchhhhcC---CChhhhhCCCCH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTC--NQLLSDFCKDLTG---IQQIQVDRGVTL 210 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~--~p~Ls~~~~~LTG---IT~e~V~~Ap~f 210 (414)
.++|=+|+|.||+ +-..+.||||++++-|..=..+.+.+...|+-.. -..+++.|.+-|| +|..-+....++
T Consensus 26 q~lVWiD~EMTGL---dvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl 102 (208)
T KOG3242|consen 26 QPLVWIDCEMTGL---DVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITL 102 (208)
T ss_pred CceEEEeeecccc---ccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccH
Confidence 5899999999998 5678999999999887544445666777776543 1236788888765 888888899999
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeeh---HHHHHHhcCCCCCCHHHHHH
Q 015017 211 SEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINL---KVPFHEVFGGVRCNLKEAVE 286 (414)
Q Consensus 211 ~eVl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~IDl---~~l~r~l~~~~~~~L~~l~~ 286 (414)
.+|-.++++|+......+ +..++.++ .-| +.||.+.+-+.--- +..+.+|+ +.+.++++|.- .
T Consensus 103 ~~aEnevl~yikk~ip~~-~~~laGNSV~~D-rlFl~k~mPk~~~~---lhyrivDVStIkeL~~Rw~P~~--------~ 169 (208)
T KOG3242|consen 103 ADAENEVLEYIKKHIPKG-KCPLAGNSVYMD-RLFLKKYMPKLIKH---LHYRIVDVSTIKELARRWYPDI--------K 169 (208)
T ss_pred HHHHHHHHHHHHHhCCCC-CCCccCcchhhH-HHHHHHHhHHHHHh---cceeeeeHHHHHHHHHHhCchh--------h
Confidence 999999999999875532 23344443 458 78998775432111 23567886 56777777621 1
Q ss_pred HcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 015017 287 MAGLAWQGRAHCGLDDAKNTARLLALLMH 315 (414)
Q Consensus 287 ~~gI~~~g~~HrALdDA~aTA~Ll~~ll~ 315 (414)
.+ -|-....|||++|.+-...=|+.-.+
T Consensus 170 ~~-aPkK~~~HrAldDI~ESI~ELq~Yr~ 197 (208)
T KOG3242|consen 170 AR-APKKKATHRALDDIRESIKELQYYRE 197 (208)
T ss_pred cc-CcccccccchHHHHHHHHHHHHHHHH
Confidence 11 12222469999998776555554443
No 58
>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=98.49 E-value=1.6e-06 Score=80.96 Aligned_cols=120 Identities=15% Similarity=0.120 Sum_probs=86.5
Q ss_pred cEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 137 YFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~-~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..+.||+||++..+. ++..+.||.||++.. +|.+ +.+. ....+..+.|.
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~---~g~~----~~~~-----------------------~~~~~E~~lL~ 53 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATS---NGDV----EFIL-----------------------AEGLDDRKIIR 53 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeC---CCCE----EEEE-----------------------ecCCCHHHHHH
Confidence 679999999965443 567899999998764 3331 1111 12357889999
Q ss_pred HHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCCCCCC------------------CceeehHHHHHHhcC
Q 015017 216 RHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPPYF------------------NRWINLKVPFHEVFG 275 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~P~~~------------------~~~IDl~~l~r~l~~ 275 (414)
.|.+++..... -++++| ..||+ .||..-++++|+.++.-. ...+|+....++...
T Consensus 54 ~F~~~i~~~dP----d~i~gyN~~~FDl-pyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~ 128 (188)
T cd05781 54 EFVKYVKEYDP----DIIVGYNSNAFDW-PYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPE 128 (188)
T ss_pred HHHHHHHHcCC----CEEEecCCCcCcH-HHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCC
Confidence 99999997521 145565 37997 899999999998764110 016898888888777
Q ss_pred CCCCCHHHHHHHcCCC
Q 015017 276 GVRCNLKEAVEMAGLA 291 (414)
Q Consensus 276 ~~~~~L~~l~~~~gI~ 291 (414)
..+++|+++++.+|+.
T Consensus 129 l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 129 VKVKTLENVAEYLGVM 144 (188)
T ss_pred CCCCCHHHHHHHHCCC
Confidence 7789999999999874
No 59
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.48 E-value=3e-06 Score=79.28 Aligned_cols=129 Identities=16% Similarity=0.102 Sum_probs=88.0
Q ss_pred cEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 137 YFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~-~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..+.||+|||+..+. ++..++||.||.+.. ..+.+. .+ ++. +. ..+..-.+..+.|.
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~--~~~~~~-~~----~~~-----~~----------~~v~~~~~E~~lL~ 61 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADE--GGNKVI-TW----KKF-----DL----------PFVEVVKTEKEMIK 61 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecC--CCceEE-Ee----cCC-----CC----------CeEEEeCCHHHHHH
Confidence 678999999965443 567899999998653 222332 11 121 10 12334567789999
Q ss_pred HHHHHHhhcCCCCCcEEEEEc-C-cchHHHHHHHHHHHcCCCCCCC--------------------CCceeehHHHHHHh
Q 015017 216 RHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKPPY--------------------FNRWINLKVPFHEV 273 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~-g-~fDir~fL~~~~~~~gi~~P~~--------------------~~~~IDl~~l~r~l 273 (414)
+|.+++..... . ++++| + .||+ .||..-+.++|+.+|.- -...+|+..++++.
T Consensus 62 ~F~~~i~~~dp---d-iivgyN~~~FD~-pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~ 136 (195)
T cd05780 62 RFIEIVKEKDP---D-VIYTYNGDNFDF-PYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT 136 (195)
T ss_pred HHHHHHHHcCC---C-EEEecCCCCCcH-HHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhh
Confidence 99999997311 2 34444 3 6996 89999999899876520 12368998888887
Q ss_pred cCCCCCCHHHHHH-HcCCCC
Q 015017 274 FGGVRCNLKEAVE-MAGLAW 292 (414)
Q Consensus 274 ~~~~~~~L~~l~~-~~gI~~ 292 (414)
+...+++|+++++ .+|.+.
T Consensus 137 ~~l~sy~L~~v~~~~Lg~~k 156 (195)
T cd05780 137 LNLTRYTLERVYEELFGIEK 156 (195)
T ss_pred CCCCcCcHHHHHHHHhCCCC
Confidence 7778899999876 677764
No 60
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.44 E-value=1e-06 Score=79.18 Aligned_cols=116 Identities=16% Similarity=0.117 Sum_probs=60.8
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 218 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~ 218 (414)
|+||+||||+ ++..+.|+-||++.++..... .|..+.-.. +..++.+.++.
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 6899999998 566788999999988732222 133333221 12344555555
Q ss_pred HHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC
Q 015017 219 KWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ 293 (414)
Q Consensus 219 ~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~~ 293 (414)
+++.+. +.++..+ ..||+ .||++.+.+++++. ...++|+...+++... .+++|+++.+.+|+...
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 777764 3344445 48996 99999997777654 4578999888765443 56799999999998764
No 61
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.41 E-value=9.6e-07 Score=90.69 Aligned_cols=157 Identities=20% Similarity=0.284 Sum_probs=111.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhh-CCCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVD-RGVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~-~Ap~f~eVl 214 (414)
.+.+++|.|....+. --|+..+++|=+ ++++ -+..||+|.. ++-++.+..+|||.+|++ ...++++|-
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 PNIFALDCEMVVTEN----GLELTRVTAVDR---DGKV--ILDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLEDVQ 284 (380)
T ss_pred CCeEEEEeeeeeecc----ceeeEEeeeeec---cCcE--EeEEeecCCC--cccccccccccccHHHHhcCccCHHHHH
Confidence 589999999886532 278888888755 4555 4889999995 599999999999999998 567799999
Q ss_pred HHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC--CCCCHHHHHH-HcCC
Q 015017 215 LRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG--VRCNLKEAVE-MAGL 290 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~--~~~~L~~l~~-~~gI 290 (414)
.+++.|+.. +.++|.++ .-|+ .-|+ +.. ..+||+..+|..-.|. .+.+|+.+++ ++|.
T Consensus 285 ~~l~~~~~~------~TILVGHSLenDL-~aLK-------l~H----~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~ 346 (380)
T KOG2248|consen 285 KELLELISK------NTILVGHSLENDL-KALK-------LDH----PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGK 346 (380)
T ss_pred HHHHhhcCc------CcEEEeechhhHH-HHHh-------hhC----CceeeeeEEEecCCCCccchHHHHHHHHHHHHH
Confidence 999999976 34566554 4565 2332 233 3578987555433331 2335777775 3443
Q ss_pred CCC-C-CCCcHHHHHHHHHHHHHHHHHhcCCcc
Q 015017 291 AWQ-G-RAHCGLDDAKNTARLLALLMHRGFKFS 321 (414)
Q Consensus 291 ~~~-g-~~HrALdDA~aTA~Ll~~ll~~~~~~~ 321 (414)
... + ..|+...||.++.+|+...+..+..++
T Consensus 347 ~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~~g 379 (380)
T KOG2248|consen 347 LIQEGVGGHDSVEDALACMKLVKLKIKNSESQG 379 (380)
T ss_pred HHhccCCCCccHHHHHHHHHHHHHHHhcccccC
Confidence 322 1 349999999999999998887765543
No 62
>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=98.33 E-value=2.3e-05 Score=74.38 Aligned_cols=114 Identities=18% Similarity=0.194 Sum_probs=77.2
Q ss_pred CCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHHHHHhhcC
Q 015017 146 TCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKG 225 (414)
Q Consensus 146 TGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~~fl~~~~ 225 (414)
+|.....+..+.||-||++..+..++.+ .++ .. ...+..+.|.+|.+++...
T Consensus 41 ~~~~~l~~~~~~Iv~Is~~~~~~~~~~~-----~~~--~~--------------------~~~~E~elL~~F~~~i~~~- 92 (208)
T cd05782 41 SGSDFLPLPFHKVVSISALYRDDDGGFL-----KVR--TL--------------------DGADEKELLEDFFQLIEKK- 92 (208)
T ss_pred cCCCCCccccCceEEEEEEEEecCCCeE-----EEe--ec--------------------CCCCHHHHHHHHHHHHHHh-
Confidence 3333335567999999999875333321 111 10 0123378999999999984
Q ss_pred CCCCcEEEEEc-C-cchHHHHHHHHHHHcCCCCCCCCC--------------ceeehHHHHHHhcCCCCCCHHHHHHHcC
Q 015017 226 IKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKPPYFN--------------RWINLKVPFHEVFGGVRCNLKEAVEMAG 289 (414)
Q Consensus 226 lv~hn~~vV~~-g-~fDir~fL~~~~~~~gi~~P~~~~--------------~~IDl~~l~r~l~~~~~~~L~~l~~~~g 289 (414)
+.++|+| | .||+ .||..-+..+|++.|..+. +.+|+..+++......+++|+++++.+|
T Consensus 93 ----~p~lv~yNg~~FDl-P~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~~~L~~va~~lG 167 (208)
T cd05782 93 ----NPRLVSFNGRGFDL-PVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARARASLDLLAKLLG 167 (208)
T ss_pred ----CCEEEecCCCcCCH-HHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCCCCHHHHHHHhC
Confidence 2246665 4 7997 8999999999998774321 2689888776533346789999999999
Q ss_pred CCC
Q 015017 290 LAW 292 (414)
Q Consensus 290 I~~ 292 (414)
++-
T Consensus 168 ~~~ 170 (208)
T cd05782 168 IPG 170 (208)
T ss_pred CCC
Confidence 964
No 63
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=98.16 E-value=1.8e-05 Score=75.15 Aligned_cols=172 Identities=19% Similarity=0.182 Sum_probs=114.4
Q ss_pred cEEEEEEeeCCCCC---C----C-----------CCCCcEEEEcEEEEEcCCCeEee----EEEEeec---CCCCCCCCc
Q 015017 137 YFVVIDFEATCDKD---K----N-----------PYPQEIIEFPSVIVSSVTGQLEA----CFQTYVR---PTCNQLLSD 191 (414)
Q Consensus 137 ~~VV~D~ETTGl~~---~----~-----------~~~deIIEIgAV~vd~~~g~i~d----~F~~lVk---P~~~p~Ls~ 191 (414)
+||++|.|.-|.-. + + -+.-.|||+|....| .+|++.+ +++.-.+ +.. .--++
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 67888888766410 0 1 134579999999998 5676654 5554444 221 13455
Q ss_pred chhhh---cCCChhhhh-CCCCHHHHHHHHHHHHhhcCCCC-CcEEEEE-cCcchHHHHHHHHHHHcCCCCC--------
Q 015017 192 FCKDL---TGIQQIQVD-RGVTLSEALLRHDKWLENKGIKN-TNFAVVT-WSNWDCRVMLESECRFKKIWKP-------- 257 (414)
Q Consensus 192 ~~~~L---TGIT~e~V~-~Ap~f~eVl~~f~~fl~~~~lv~-hn~~vV~-~g~fDir~fL~~~~~~~gi~~P-------- 257 (414)
.++++ +||.-+... .+.+.+ +|.+.+-..+++- .++.+|+ ++..|. ++|-+-+....++-.
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 56655 788877765 466655 5555555554443 4788888 588997 777666554433211
Q ss_pred -CCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 015017 258 -PYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMH 315 (414)
Q Consensus 258 -~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~ 315 (414)
.++..+.|++.+++..-+. ...+|.++++.++++..|..|.|-.|++.||..|.+|.+
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 1123556777776655342 245899999999999999999999999999999999864
No 64
>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=98.10 E-value=6.6e-05 Score=68.48 Aligned_cols=144 Identities=19% Similarity=0.139 Sum_probs=95.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..+++||+||||+ ++..++|+.++... ..++ .|..-+++. .. .+++++++++.
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 4789999999987 45567888876542 2221 222111211 01 14567889999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc-CCC--
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA-GLA-- 291 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~-~~~L~~l~~~~-gI~-- 291 (414)
+|.+++++.. ...++|++.||+ .+|. +.|+.++ ..++|+..+...+.+.. +++|+++++.| +..
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 9999998742 134677789995 6764 5677754 45789988777776654 67999998875 322
Q ss_pred --------------CCC-----CCCcHHHHHHHHHHHHHHHHHhcC
Q 015017 292 --------------WQG-----RAHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 292 --------------~~g-----~~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
+.. ..|.|..||.++.+|+..|..+..
T Consensus 126 ~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~ 171 (193)
T cd06139 126 SFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLK 171 (193)
T ss_pred cHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 000 124688899999999988877643
No 65
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=97.97 E-value=0.0003 Score=66.72 Aligned_cols=145 Identities=14% Similarity=0.056 Sum_probs=85.8
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCc-chhhhcCCChhhhhCCCCHHHH
Q 015017 137 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSD-FCKDLTGIQQIQVDRGVTLSEA 213 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~--~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~-~~~~LTGIT~e~V~~Ap~f~eV 213 (414)
..++||+||++.+++ ++..|.||+|+.+. + .+|...- ....+.+..+. +.. .+-.+-| .-.+..-.+..+.
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~-~-~~g~~~~-~~~~~~~~~~~-~~~~~~~~~~~--~~~v~~~~~E~~l 76 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMI-D-GQGYLIV-NREIVSEDIED-FEYTPKPEYEG--PFKVFNEPDEKAL 76 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEE-e-cCCEEEe-ccccccccccc-ccccCCCCCCC--ceEEecCCCHHHH
Confidence 578999999875443 46789999999775 3 3443210 00111110000 000 0000101 0122235788999
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCCCC-C---CC----------ceeehHHHHHHhc--C
Q 015017 214 LLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPP-Y---FN----------RWINLKVPFHEVF--G 275 (414)
Q Consensus 214 l~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~P~-~---~~----------~~IDl~~l~r~l~--~ 275 (414)
|.+|.+++..... -++++| -+||+ .||..-++.+|+.+.. + .. -.+|+..++++.. .
T Consensus 77 L~~f~~~i~~~~P----d~i~gyN~~~FD~-pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~ 151 (204)
T cd05779 77 LQRFFEHIREVKP----HIIVTYNGDFFDW-PFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLP 151 (204)
T ss_pred HHHHHHHHHHhCC----CEEEecCccccCH-HHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCC
Confidence 9999999998521 135555 37997 8999989988886531 0 00 1478888777532 3
Q ss_pred CCCCCHHHHHH-HcCCCC
Q 015017 276 GVRCNLKEAVE-MAGLAW 292 (414)
Q Consensus 276 ~~~~~L~~l~~-~~gI~~ 292 (414)
.++++|+.+++ .+|..-
T Consensus 152 ~~sysLd~Va~~~Lg~~K 169 (204)
T cd05779 152 QGSQGLKAVTKAKLGYDP 169 (204)
T ss_pred CCCccHHHHHHHHhCCCc
Confidence 45789999998 488743
No 66
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=97.88 E-value=0.00033 Score=66.50 Aligned_cols=121 Identities=15% Similarity=0.066 Sum_probs=81.4
Q ss_pred cEEEEEEeeCCCCCC-----CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHH
Q 015017 137 YFVVIDFEATCDKDK-----NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 211 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~-----~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~ 211 (414)
..+.||+||+...+. ++..+.||.||.. + .++. ... +. ....+..
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~--~-~~~~-----~~~--------~~--------------~~~~~E~ 59 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALR--D-NRGW-----EEV--------LH--------------AEDAAEK 59 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecc--c-CCCc-----eee--------ec--------------cCCCCHH
Confidence 789999999886542 2356899999874 2 1221 000 10 0157889
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEc-C-cchHHHHHHHHHHHcCCCCCC-------------C--------------C-C
Q 015017 212 EALLRHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKPP-------------Y--------------F-N 261 (414)
Q Consensus 212 eVl~~f~~fl~~~~lv~hn~~vV~~-g-~fDir~fL~~~~~~~gi~~P~-------------~--------------~-~ 261 (414)
++|..|++++..... . ++++| + .||+ .+|..-++++|+.++. . . +
T Consensus 60 ~lL~~f~~~i~~~dP---d-ii~g~N~~~FD~-pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr 134 (207)
T cd05785 60 ELLEELVAIIRERDP---D-VIEGHNIFRFDL-PYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGR 134 (207)
T ss_pred HHHHHHHHHHHHhCC---C-EEeccCCcccCH-HHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCE
Confidence 999999999998411 1 34443 4 7997 8999999999887631 0 0 1
Q ss_pred ceeehHHHHHHh----cCCCCCCHHHHHHHcCCCC
Q 015017 262 RWINLKVPFHEV----FGGVRCNLKEAVEMAGLAW 292 (414)
Q Consensus 262 ~~IDl~~l~r~l----~~~~~~~L~~l~~~~gI~~ 292 (414)
..+|+..++++. +...+++|+++++.+|+.-
T Consensus 135 ~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~ 169 (207)
T cd05785 135 HVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLAS 169 (207)
T ss_pred EEEEcHHHHHhhcccccCCCCCCHHHHHHHhcccC
Confidence 227888877753 3446789999999998744
No 67
>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=97.88 E-value=0.00044 Score=65.92 Aligned_cols=130 Identities=20% Similarity=0.209 Sum_probs=90.1
Q ss_pred CCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHHHHHhhcCCCCCcEEE
Q 015017 154 YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNFAV 233 (414)
Q Consensus 154 ~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~v 233 (414)
.-.+||.|+++.++ .++.+ .-.++-.+ .-+..+.+++|.++++.. +..+
T Consensus 7 ~f~kIV~Is~~~~~-~~~~~--~v~s~~~~-----------------------~~~E~~lL~~F~~~~~~~-----~p~L 55 (209)
T PF10108_consen 7 PFHKIVCISVVYAD-DDGQF--KVKSLGGP-----------------------DDDEKELLQDFFDLVEKY-----NPQL 55 (209)
T ss_pred cCCCeEEEEEEEEe-cCCcE--EEEeccCC-----------------------CCCHHHHHHHHHHHHHhC-----CCeE
Confidence 45889999999886 33433 12222111 123688999999999864 3346
Q ss_pred EEc--CcchHHHHHHHHHHHcCCCCCCCCC---------------ceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 015017 234 VTW--SNWDCRVMLESECRFKKIWKPPYFN---------------RWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 295 (414)
Q Consensus 234 V~~--g~fDir~fL~~~~~~~gi~~P~~~~---------------~~IDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~ 295 (414)
|+| ..||+ .||..-...+|++.|.++. +-+||..++.. ++ ....+|+.++..+|||-...
T Consensus 56 Vs~NG~~FDl-P~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~-~g~~~~~sLd~la~~lgiPgK~~ 133 (209)
T PF10108_consen 56 VSFNGRGFDL-PVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSF-YGAKARTSLDELAALLGIPGKDD 133 (209)
T ss_pred EecCCccCCH-HHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhc-cCccccCCHHHHHHHcCCCCCCC
Confidence 664 47997 8999999999999886432 24788776643 43 44679999999999985311
Q ss_pred C------------------CcHHHHHHHHHHHHHHHHHh
Q 015017 296 A------------------HCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 296 ~------------------HrALdDA~aTA~Ll~~ll~~ 316 (414)
- .--..|+++|+.|+.++..-
T Consensus 134 idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~~ 172 (209)
T PF10108_consen 134 IDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFELL 172 (209)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1 11267999999999998653
No 68
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=97.87 E-value=0.00026 Score=69.38 Aligned_cols=172 Identities=22% Similarity=0.174 Sum_probs=94.5
Q ss_pred ccEEEEEEeeCCCCCCCC------------------CCCcEEEEcEEEEEcCCCeEeeE-----EEEeecCCCCCCCCcc
Q 015017 136 QYFVVIDFEATCDKDKNP------------------YPQEIIEFPSVIVSSVTGQLEAC-----FQTYVRPTCNQLLSDF 192 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~------------------~~deIIEIgAV~vd~~~g~i~d~-----F~~lVkP~~~p~Ls~~ 192 (414)
..||+||+|.||+..... ..-.|||||...+...+++...+ |+-++-|......+..
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 489999999999854222 34689999999993256665433 3333333321111111
Q ss_pred hh---hhcCCChhhh-hCCCCHHHHHHH--HHHHHhhcCCC-----CCcEEEEEcCcchHHHHHHHHHHHcCCCCCCC--
Q 015017 193 CK---DLTGIQQIQV-DRGVTLSEALLR--HDKWLENKGIK-----NTNFAVVTWSNWDCRVMLESECRFKKIWKPPY-- 259 (414)
Q Consensus 193 ~~---~LTGIT~e~V-~~Ap~f~eVl~~--f~~fl~~~~lv-----~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~-- 259 (414)
+. .-+|+.=+.+ .++.++...-++ ..+.++-+.+. .+..+|.|++-+|+ .||-..+-. ++|.-
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-MYLYKKFIG---PLPETLE 177 (262)
T ss_dssp HHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHH-HHHHHHHTT---S--SSHH
T ss_pred hHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHH-HHHHHHhcC---CCCCCHH
Confidence 11 1245544433 244444333221 11344444332 23556667888997 676655433 44421
Q ss_pred ---------CCceeehHHHHHHhcCCCCCCHHHHHHHcCCCC-----------------------CCC-CCcHHHHHHHH
Q 015017 260 ---------FNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAW-----------------------QGR-AHCGLDDAKNT 306 (414)
Q Consensus 260 ---------~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~-----------------------~g~-~HrALdDA~aT 306 (414)
|...+||+-+..... ....+|+.+.+.+++.. .+. .|.|-.||..|
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 234678776664322 23468999999999764 344 89999999999
Q ss_pred HHHHHH
Q 015017 307 ARLLAL 312 (414)
Q Consensus 307 A~Ll~~ 312 (414)
+.+|.+
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 69
>PRK05755 DNA polymerase I; Provisional
Probab=97.83 E-value=0.00018 Score=81.74 Aligned_cols=135 Identities=21% Similarity=0.181 Sum_probs=93.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..+++||+||||+ ++...+|+.|++. . .++.. .+|.+. +|. .+++.
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 4689999999997 5678889988853 3 24431 233221 111 16888
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CCCC--
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GLAW-- 292 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~-gI~~-- 292 (414)
.|.+++++..+ ..|.|++.||+ .||. +.|+.++ ..++|+......+.+...++|++++++| |+..
T Consensus 361 ~l~~~L~d~~v----~kV~HNakfDl-~~L~----~~gi~~~---~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~ 428 (880)
T PRK05755 361 ALKPLLEDPAI----KKVGQNLKYDL-HVLA----RYGIELR---GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTIS 428 (880)
T ss_pred HHHHHHhCCCC----cEEEeccHhHH-HHHH----hCCCCcC---CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccc
Confidence 89999998532 24667789996 7876 3577654 4689998766665554348999999887 5541
Q ss_pred ----------------CCCCCcHHHHHHHHHHHHHHHHHh
Q 015017 293 ----------------QGRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 293 ----------------~g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
+...|.|..|+..|.+|+..|.+.
T Consensus 429 ~~~~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 429 FEEVAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred hHHhcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 012378999999999999988775
No 70
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=97.80 E-value=9.3e-06 Score=62.85 Aligned_cols=52 Identities=10% Similarity=0.098 Sum_probs=46.7
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQ 104 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~ 104 (414)
+..++.+++++|++.|.++++||| |..++++++++...++.++++++|+|.+
T Consensus 13 ~~~~~~~~~~~a~~~g~~~v~iTD--------h~~~~~~~~~~~~~~~~gi~~i~G~E~~ 64 (67)
T smart00481 13 GALSPEELVKRAKELGLKAIAITD--------HGNLFGAVEFYKAAKKAGIKPIIGLEAN 64 (67)
T ss_pred ccCCHHHHHHHHHHcCCCEEEEee--------CCcccCHHHHHHHHHHcCCeEEEEEEEE
Confidence 456788999999999999999995 7777899999998899999999999876
No 71
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=97.52 E-value=0.00018 Score=70.45 Aligned_cols=173 Identities=15% Similarity=0.125 Sum_probs=109.7
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEcEEEE-----EcC------C-------CeEeeEEEEeecCCCCCCCCcchhhh
Q 015017 135 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIV-----SSV------T-------GQLEACFQTYVRPTCNQLLSDFCKDL 196 (414)
Q Consensus 135 ~~~~VV~D~ETTGl~~~~~~~deIIEIgAV~v-----d~~------~-------g~i~d~F~~lVkP~~~p~Ls~~~~~L 196 (414)
..+|+++|+|+||+. ....+|-|+...-| +.+ + -++.+.-+-++-|.. ..++...++
T Consensus 12 ~~tf~fldleat~lp---~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~aeei 86 (318)
T KOG4793|consen 12 LRTFSFLDLEATGLP---GWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAEEI 86 (318)
T ss_pred eeEEEeeeeccccCC---cccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhhhh
Confidence 369999999999984 34556777643322 211 0 134566677777874 578888999
Q ss_pred cCCChhhh--hCCCCHHH-HHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehH-----
Q 015017 197 TGIQQIQV--DRGVTLSE-ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLK----- 267 (414)
Q Consensus 197 TGIT~e~V--~~Ap~f~e-Vl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~IDl~----- 267 (414)
||.++.-+ .+---|+. +.+-+..|+..-.- --..|+|+| .+|+ .+|..++++.|+..|. +-...|..
T Consensus 87 tgls~~~~~l~rr~~~D~dla~LL~afls~lp~--p~CLVaHng~~~df-pil~qela~lg~~lpq-~lvcvdslpa~~a 162 (318)
T KOG4793|consen 87 TGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPT--PGCLVAHNGNEYDF-PILAQELAGLGYSLPQ-DLVCVDSLPALNA 162 (318)
T ss_pred cccccHHHHHHHHhhhhHHHHHHHHHHHhcCCC--CceEEeecCCcccc-HHHHHHHHhcCccchh-hhcCcchhHHHHH
Confidence 99999654 33333443 44555666765321 112445665 5787 7899999988887762 11112211
Q ss_pred ------------------------------------------------------HHH-------------HHhcC-----
Q 015017 268 ------------------------------------------------------VPF-------------HEVFG----- 275 (414)
Q Consensus 268 ------------------------------------------------------~l~-------------r~l~~----- 275 (414)
++. +.+|+
T Consensus 163 ld~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a 242 (318)
T KOG4793|consen 163 LDRANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENA 242 (318)
T ss_pred HhhhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhc
Confidence 000 01111
Q ss_pred -------CCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHh
Q 015017 276 -------GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 276 -------~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
...++|+.++.++.+..++.+|||+.|...+.++++++-.+
T Consensus 243 ~~~~P~p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~~~k~~q~~~id 290 (318)
T KOG4793|consen 243 KSVEPTPKLVSSLEALATYYSLTPELDAHRALSDVLLLSKVFQKLTID 290 (318)
T ss_pred cccCCCCccchhHHHHHHHhhcCcccchhhhccccchhhhHHHHhhhh
Confidence 01246888888988877788999999999999999987443
No 72
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=97.40 E-value=0.00013 Score=78.36 Aligned_cols=41 Identities=34% Similarity=0.879 Sum_probs=36.8
Q ss_pred ccceecCCCcCcceeccCCCCCCCceeecCCCcccCCCcccceeec
Q 015017 365 HPSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWA 410 (414)
Q Consensus 365 ~~~c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~ 410 (414)
...|.||-++..++|+|.|||-||.||.|.. . ..|.||.|+
T Consensus 718 ~~~c~c~~ra~~l~v~k~~~nrGR~f~sc~~----~-k~c~ff~w~ 758 (758)
T KOG1956|consen 718 EVTCGCGTRAVKLLVAKTEPNRGRKFYSCLP----E-KSCNFFAWE 758 (758)
T ss_pred ccccCCcchhhhhhhhccCccCCCCCcccCC----C-CCcceEeeC
Confidence 5699999999999999999999999999984 2 349999996
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=97.39 E-value=0.0074 Score=57.19 Aligned_cols=136 Identities=18% Similarity=0.124 Sum_probs=80.5
Q ss_pred cEEEEEEeeCCCC-CCCC----CCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHH
Q 015017 137 YFVVIDFEATCDK-DKNP----YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 211 (414)
Q Consensus 137 ~~VV~D~ETTGl~-~~~~----~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~ 211 (414)
..+.||+||++.. +..| ..++||+|+.+ + .++. +.+ .++........+.... ....+..-.+..
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 7899999999643 2223 23789999875 2 1221 111 1222110000000000 112234446889
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCC---CCCC---------CCceeehHHHHHH-h---
Q 015017 212 EALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIW---KPPY---------FNRWINLKVPFHE-V--- 273 (414)
Q Consensus 212 eVl~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~---~P~~---------~~~~IDl~~l~r~-l--- 273 (414)
+.|.+|.+++... . ++++| ..||+ .+|..-++++|+. .|.. ....+|+...++. .
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 46676 37997 8999999999987 3211 1245788766543 1
Q ss_pred --c--CCCCCCHHHHHHHc-CC
Q 015017 274 --F--GGVRCNLKEAVEMA-GL 290 (414)
Q Consensus 274 --~--~~~~~~L~~l~~~~-gI 290 (414)
+ ...+++|+++++.+ |.
T Consensus 148 ~~~~~~~~~~~L~~Va~~~lg~ 169 (204)
T cd05783 148 YAFGNKYREYTLDAVAKALLGE 169 (204)
T ss_pred hhhccccccCcHHHHHHHhcCC
Confidence 2 23578999999865 54
No 74
>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=97.34 E-value=0.01 Score=57.01 Aligned_cols=135 Identities=15% Similarity=0.108 Sum_probs=84.1
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCe--EeeEEEEe-ecCCCCCCCCcchhhhcCCChhhhhCCCCHH
Q 015017 137 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQ--LEACFQTY-VRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 211 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~--~~~~deIIEIgAV~vd~~~g~--i~d~F~~l-VkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~ 211 (414)
..+.||+||+...+. ++..|+||.|+.+.-. ++. .... .-+ +++.. .++ ...|..-++..
T Consensus 8 ~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~--~~~~~~~~~-~~~~l~~~~--~~~----------~~~v~~~~~E~ 72 (230)
T cd05777 8 RILSFDIECAGRKGVFPEPEKDPVIQIANVVTR--QGEGEPFIR-NIFTLKTCA--PIV----------GAQVFSFETEE 72 (230)
T ss_pred eEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEe--CCCCCCcee-EEEEeCCCC--CCC----------CCEEEEECCHH
Confidence 689999999976542 4677999999988642 222 1111 112 22221 121 23344457899
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCCC-CC------------------------------
Q 015017 212 EALLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKP-PY------------------------------ 259 (414)
Q Consensus 212 eVl~~f~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~P-~~------------------------------ 259 (414)
+.|..|.+++..... .+++-++ -.||+ .+|..-+++.|+..- .+
T Consensus 73 eLL~~f~~~i~~~DP---Dii~GyN~~~FDl-~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i 148 (230)
T cd05777 73 ELLLAWRDFVQEVDP---DIITGYNICNFDL-PYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINI 148 (230)
T ss_pred HHHHHHHHHHHhcCC---CEEEEecCCCCCH-HHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEE
Confidence 999999999987421 2222223 37996 788888888776521 00
Q ss_pred -CCceeehHHHHHHhcCCCCCCHHHHHH-HcCC
Q 015017 260 -FNRWINLKVPFHEVFGGVRCNLKEAVE-MAGL 290 (414)
Q Consensus 260 -~~~~IDl~~l~r~l~~~~~~~L~~l~~-~~gI 290 (414)
-.-.+|+...+++.+...+++|+++++ .+|.
T Consensus 149 ~GR~~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~ 181 (230)
T cd05777 149 EGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLGE 181 (230)
T ss_pred cCEEeeeHHHHHHHhcCcccCcHHHHHHHHhCC
Confidence 012357777777776677899999987 4553
No 75
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=97.33 E-value=6.9e-05 Score=86.39 Aligned_cols=54 Identities=7% Similarity=0.027 Sum_probs=49.1
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|+..+.+||++|+++|++|||||| |++..+-+++|.+++++|+|+|.|+|.++
T Consensus 16 dg~~~i~~lv~~A~~~g~~alAlTD--------h~~m~Ga~~F~~~a~~~gIkPIiG~e~~v 69 (1107)
T PRK06920 16 KSACKIDELVVRAKELGYSSLAITD--------ENVMYGVIPFYKACKKHGIHPIIGLTASI 69 (1107)
T ss_pred ccCCCHHHHHHHHHHCCCCEEEEEe--------CChHhHHHHHHHHHHHcCCCEeeeeEEEE
Confidence 4677889999999999999999995 66768999999999999999999999884
No 76
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=97.32 E-value=8.6e-05 Score=84.87 Aligned_cols=54 Identities=11% Similarity=0.020 Sum_probs=49.2
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|+..+.++|++|+++|++|||||| |++..+-+++|.+.+++|||+|.|+|.++
T Consensus 15 dg~~~i~~lv~~A~~~g~~alAlTD--------~~~m~Ga~~F~~~a~~~gIkPIiG~e~~v 68 (1034)
T PRK07279 15 DSLIDLEKYVERAKELGYQTIGIMD--------KDNLYGAYHFIEGAQKNGLQPILGLELNI 68 (1034)
T ss_pred cccCCHHHHHHHHHHCCCCEEEEEc--------CCccccHHHHHHHHHHcCCcEEEEEEEEE
Confidence 4677889999999999999999995 77778999999999999999999999874
No 77
>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=97.27 E-value=0.0032 Score=66.56 Aligned_cols=123 Identities=12% Similarity=0.165 Sum_probs=86.8
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
...+.|||||+ |+..-.-.+|++..+ ++...+.|..|+-... ....+++.
T Consensus 284 ~~~~ffDiEt~------P~~~~~yL~G~~~~~--~~~~~~~~~~fla~~~----------------------~~E~~~~~ 333 (457)
T TIGR03491 284 PGELIFDIESD------PDENLDYLHGFLVVD--KGQENEKYRPFLAEDP----------------------NTEELAWQ 333 (457)
T ss_pred CccEEEEecCC------CCCCCceEEEEEEec--CCCCCcceeeeecCCc----------------------hHHHHHHH
Confidence 46789999998 344556788987654 3332234655553321 23567999
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCC---CCCceeehHHHHHHhc--CCCCCCHHHHHHHcCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP---YFNRWINLKVPFHEVF--GGVRCNLKEAVEMAGL 290 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~---~~~~~IDl~~l~r~l~--~~~~~~L~~l~~~~gI 290 (414)
+|.+|+... .+..|+||+.++ ...|++-+.+++..... +..+++|+....+..+ +..+++|++++..+|.
T Consensus 334 ~f~~~l~~~----~~~~i~hY~~~e-~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~ 408 (457)
T TIGR03491 334 QFLQLLQSY----PDAPIYHYGETE-KDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGF 408 (457)
T ss_pred HHHHHHHHC----CCCeEEeeCHHH-HHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCc
Confidence 999999874 245789999999 48899998888866321 2237899987776543 5668999999999999
Q ss_pred CCC
Q 015017 291 AWQ 293 (414)
Q Consensus 291 ~~~ 293 (414)
.+.
T Consensus 409 ~~~ 411 (457)
T TIGR03491 409 EWR 411 (457)
T ss_pred ccC
Confidence 775
No 78
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=96.79 E-value=0.00047 Score=78.63 Aligned_cols=54 Identities=6% Similarity=-0.002 Sum_probs=49.3
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|+.++.++|++|+++|.+|||||| |+++.+++++|.++++.|+|+|.|+|.++
T Consensus 16 Dg~~~~~elv~~Ak~~G~~avAITD--------h~~l~G~~~f~~~a~~~gIkpIiG~Ei~~ 69 (973)
T PRK07135 16 SSTIKLDSLIKYAKENNLKTLVLTD--------HNNMFGVPKFYKLCKKNNIKPIIGLDLEV 69 (973)
T ss_pred ccCCCHHHHHHHHHHcCCCEEEEec--------CCcHHhHHHHHHHHHHcCCeEEEeEEEEe
Confidence 4678899999999999999999995 77778999999999999999999999864
No 79
>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=96.79 E-value=0.00044 Score=61.68 Aligned_cols=52 Identities=12% Similarity=0.203 Sum_probs=46.7
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhh
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFES 103 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~ 103 (414)
.|..++.++|++|++.|.++||||| |....++|+.+...++.+++++.|+|.
T Consensus 13 dg~~~~~e~v~~A~~~Gl~~i~iTD--------H~~~~~~~~~~~~~~~~~i~vi~G~E~ 64 (175)
T PF02811_consen 13 DGKDSPEEYVEQAKEKGLDAIAITD--------HNNFAGYPDFYKEAKKKGIKVIPGVEI 64 (175)
T ss_dssp TSSSSHHHHHHHHHHTTESEEEEEE--------ETTTTTHHHHHHHHHHTTSEEEEEEEE
T ss_pred hhcCCHHHHHHHHHHcCCCEEEEcC--------CcccccchHHHHHHHhcCCceEEeEee
Confidence 3455888999999999999999995 777789999999999999999999986
No 80
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=96.73 E-value=0.023 Score=65.92 Aligned_cols=161 Identities=17% Similarity=0.130 Sum_probs=97.4
Q ss_pred cEEEEEEeeCCCCC-C--CCCCCcEEEEcEEEEEcCCCeEeeEEEEee-cCCCCCCCCcchhhhcCCChhhhhCCCCHHH
Q 015017 137 YFVVIDFEATCDKD-K--NPYPQEIIEFPSVIVSSVTGQLEACFQTYV-RPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 212 (414)
Q Consensus 137 ~~VV~D~ETTGl~~-~--~~~~deIIEIgAV~vd~~~g~i~d~F~~lV-kP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~e 212 (414)
..+.||+||++..+ + ++..|+||+|+.+... .|.-.+.+...| -+. .|..+.| ..|..-++..+
T Consensus 265 rilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~--~g~~~~~~~r~vftl~-------~c~~i~g---~~V~~f~sE~e 332 (1054)
T PTZ00166 265 RILSFDIECIKLKGLGFPEAENDPVIQISSVVTN--QGDEEEPLTKFIFTLK-------ECASIAG---ANVLSFETEKE 332 (1054)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEee--CCCccCCcceEEEecC-------ccccCCC---ceEEEeCCHHH
Confidence 68999999998653 1 3467999999998653 333211121111 111 1112222 34455678999
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCC-CCC-------------------C----------
Q 015017 213 ALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWK-PPY-------------------F---------- 260 (414)
Q Consensus 213 Vl~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~-P~~-------------------~---------- 260 (414)
.|..|.+++..... . ++++| ..||+ .+|..-++..|+.. +.+ +
T Consensus 333 LL~~f~~~I~~~DP---D-II~GYNi~~FDl-pYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i 407 (1054)
T PTZ00166 333 LLLAWAEFVIAVDP---D-FLTGYNIINFDL-PYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINI 407 (1054)
T ss_pred HHHHHHHHHHhcCC---C-EEEecCCcCCcH-HHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEe
Confidence 99999999987421 2 23333 37996 78877777766541 100 0
Q ss_pred --CceeehHHHHHHhcCCCCCCHHHHHHH-cCCCCCCCCC-------------------cHHHHHHHHHHHHHHHH
Q 015017 261 --NRWINLKVPFHEVFGGVRCNLKEAVEM-AGLAWQGRAH-------------------CGLDDAKNTARLLALLM 314 (414)
Q Consensus 261 --~~~IDl~~l~r~l~~~~~~~L~~l~~~-~gI~~~g~~H-------------------rALdDA~aTA~Ll~~ll 314 (414)
+-.+|+..++++.+...+++|++++.+ +|..-..-+| -.+.||..+.+|+.+|.
T Consensus 408 ~GR~~iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 408 EGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred eeEEEEEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 123678788887777788999999984 4532211111 13678888888887763
No 81
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=96.64 E-value=0.019 Score=55.96 Aligned_cols=118 Identities=16% Similarity=0.116 Sum_probs=70.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHH-HHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS-EAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~-eVl 214 (414)
.++++||+||||++ ...+.|+-+|...+ .+..+ +||-.. ++ ||.-+ -++
T Consensus 98 e~~~FFDiETTGL~---~ag~~I~~~g~a~~--~~~~~------~Vrq~~---lp----------------~p~~E~avl 147 (278)
T COG3359 98 EDVAFFDIETTGLD---RAGNTITLVGGARG--VDDTM------HVRQHF---LP----------------APEEEVAVL 147 (278)
T ss_pred cceEEEeeeccccC---CCCCeEEEEEEEEc--cCceE------EEEeec---CC----------------CcchhhHHH
Confidence 58999999999983 34566666665554 23332 344432 22 22222 245
Q ss_pred HHHHHHHhhcCCCCCcEEEEE-cC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHHcCC
Q 015017 215 LRHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEMAGL 290 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~vV~-~g-~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~--~~~~~L~~l~~~~gI 290 (414)
+.|+....- | .+|+ || .||. .|+++ +.+..+++. +.+.-+||.-..|++-+ +.+.+|++.=+.+|+
T Consensus 148 e~fl~~~~~------~-~lvsfNGkaFD~-PfikR-~v~~~~el~-l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi 217 (278)
T COG3359 148 ENFLHDPDF------N-MLVSFNGKAFDI-PFIKR-MVRDRLELS-LEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGI 217 (278)
T ss_pred HHHhcCCCc------c-eEEEecCcccCc-HHHHH-HHhcccccC-ccccchhhhhhhhhhhhccCCCCChhhHHHHhCc
Confidence 555544411 2 4666 44 7995 99995 666666552 33456888766666553 235689988888888
Q ss_pred CCC
Q 015017 291 AWQ 293 (414)
Q Consensus 291 ~~~ 293 (414)
..+
T Consensus 218 ~R~ 220 (278)
T COG3359 218 RRE 220 (278)
T ss_pred ccc
Confidence 653
No 82
>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=96.62 E-value=0.016 Score=54.58 Aligned_cols=120 Identities=12% Similarity=0.103 Sum_probs=76.9
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHH
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 216 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~ 216 (414)
..+.||+||++. .+|+.||.. +.++..++ .+=.+.. .. | ..+.--++..+.|..
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 679999999974 289999863 33333332 1111111 11 1 123344688899999
Q ss_pred HHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCCCCCC-----------------------CceeehHHHHH
Q 015017 217 HDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPPYF-----------------------NRWINLKVPFH 271 (414)
Q Consensus 217 f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~P~~~-----------------------~~~IDl~~l~r 271 (414)
|.+++..... . ++++| ..||+ .+|..-++++|+..+ +. .-.+|+..+.+
T Consensus 58 f~~~i~~~dP---D-vi~g~N~~~FD~-~yl~~R~~~~~i~~~-~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k 131 (193)
T cd05784 58 LIAWFAQYDP---D-IIIGWNVINFDL-RLLQRRAEAHGLPLR-LGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALK 131 (193)
T ss_pred HHHHHHhhCC---C-EEEECCCcCcCH-HHHHHHHHHhCCCcc-cccCCCccccccCCcCCcceEEEeeEEEEEhHHHHH
Confidence 9999988521 2 23333 37997 889888888887642 10 11568877776
Q ss_pred H-hcCCCCCCHHHHHHHc
Q 015017 272 E-VFGGVRCNLKEAVEMA 288 (414)
Q Consensus 272 ~-l~~~~~~~L~~l~~~~ 288 (414)
+ .+...+++|+++++++
T Consensus 132 ~~~~kl~sy~L~~Va~~~ 149 (193)
T cd05784 132 TATYHFESFSLENVAQEL 149 (193)
T ss_pred HccCCCCcCCHHHHHHHH
Confidence 5 4677789999999854
No 83
>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=96.61 E-value=0.084 Score=50.88 Aligned_cols=173 Identities=12% Similarity=0.009 Sum_probs=101.6
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeEe---eEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHH
Q 015017 137 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLE---ACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 211 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~--~~~~deIIEIgAV~vd~~~g~i~---d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~ 211 (414)
+.+.||+|+.+-.++ +|..|.||.|+.++-+...-... ...--++.+.... .+.. .....+....|.--++..
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~-~~~~~~~~~~v~~~~~E~ 82 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSN-ASNG-RIRSGLSGIPVEVVESEL 82 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccch-hhhh-ccccCCCCCeEEEeCCHH
Confidence 678999999865433 46789999999885532111111 1122334333210 1100 112244445667788999
Q ss_pred HHHHHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCCC--CC-----------------C----------
Q 015017 212 EALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKP--PY-----------------F---------- 260 (414)
Q Consensus 212 eVl~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~P--~~-----------------~---------- 260 (414)
+.|.+|.+++..... . ++++| -+||+ .+|..-++..++..- .+ +
T Consensus 83 ~LL~~f~~~i~~~DP---D-ii~GyNi~~fd~-~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i 157 (231)
T cd05778 83 ELFEELIDLVRRFDP---D-ILSGYEIQRSSW-GYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKI 157 (231)
T ss_pred HHHHHHHHHHHHhCC---C-EEEEeccccCcH-HHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEE
Confidence 999999999987521 1 23333 37996 777777766554320 00 0
Q ss_pred --CceeehHHHHHHhcCCCCCCHHHHHH-HcCCCCCCCCCcHHHHHH------HHHHHHHHHHHh
Q 015017 261 --NRWINLKVPFHEVFGGVRCNLKEAVE-MAGLAWQGRAHCGLDDAK------NTARLLALLMHR 316 (414)
Q Consensus 261 --~~~IDl~~l~r~l~~~~~~~L~~l~~-~~gI~~~g~~HrALdDA~------aTA~Ll~~ll~~ 316 (414)
.-.+|+..+.+..+...+++|++++. .+|-....-+|..+.+.. ...+++...+++
T Consensus 158 ~GRi~lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d 222 (231)
T cd05778 158 VGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKR 222 (231)
T ss_pred eeEEEeEhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHH
Confidence 01247777777777778899999997 567654333466666653 345566555554
No 84
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=96.56 E-value=0.18 Score=51.95 Aligned_cols=161 Identities=17% Similarity=0.060 Sum_probs=97.1
Q ss_pred cEEEEEEeeCCCCCCCC--C--CCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHH
Q 015017 137 YFVVIDFEATCDKDKNP--Y--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 212 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~--~--~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~e 212 (414)
..++||+||+...+..| . .++||.|+.+.-+...............+.. .+. ++ .+..-.+..+
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 68999999997543112 2 6899999988776332212222222333332 122 22 2332347889
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCC----------C---------------------C
Q 015017 213 ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPP----------Y---------------------F 260 (414)
Q Consensus 213 Vl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~----------~---------------------~ 260 (414)
.+..|.+++..... .+++.+++ .||+ .+|...+...++.... . -
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 99999999987532 34444554 6996 7888877766553320 0 0
Q ss_pred CceeehHHHHHHhcCCCCCCHHHHHHHcCCC-CCCCC-------------------CcHHHHHHHHHHHHHHH
Q 015017 261 NRWINLKVPFHEVFGGVRCNLKEAVEMAGLA-WQGRA-------------------HCGLDDAKNTARLLALL 313 (414)
Q Consensus 261 ~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~-~~g~~-------------------HrALdDA~aTA~Ll~~l 313 (414)
.-.+|+...++..+...+++|+.+++++.-. ...-. ..-+.||..+.+|+.++
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 2346888888888777788999988764321 11000 11256888888888775
No 85
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=96.56 E-value=0.00096 Score=75.91 Aligned_cols=54 Identities=9% Similarity=0.110 Sum_probs=48.4
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|..++.++|++|++.|.+|||||| |++..+=+++|.+.+++|+|+|.|+|.++
T Consensus 15 dg~~~~~~lv~~A~e~g~~alALTD--------~~nl~GaveF~~~ak~~gIkPIiG~e~~v 68 (971)
T PRK05898 15 SSTLSIDDIIKFALDNNQPYVCLTD--------LNNLYGCIEFYDKAKAHNLIPIIGLEIEY 68 (971)
T ss_pred cccCCHHHHHHHHHHCCCCEEEEEe--------CCccccHHHHHHHHHHcCCCEEEEEEEEE
Confidence 4567889999999999999999995 66667888999999999999999999874
No 86
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=96.52 E-value=0.00097 Score=75.63 Aligned_cols=54 Identities=4% Similarity=-0.168 Sum_probs=48.2
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|..++.++|++|++.|.+|||||| |+.+.+.++++.+.++.++++|.|+|.++
T Consensus 16 dg~~~~~elv~~A~~~G~~aiAiTD--------h~~~~g~~~f~~~~~~~gik~I~G~E~~~ 69 (874)
T PRK09532 16 DGASQLPALVDRAIELGMPAIALTD--------HGVMYGAIELLKVCRNKGIKPIIGNEMYV 69 (874)
T ss_pred hccCCHHHHHHHHHHCCCCEEEEec--------CCChhhHHHHHHHHHHcCCeEEEEEEEEe
Confidence 3567889999999999999999995 66667889999999999999999999885
No 87
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=96.14 E-value=0.002 Score=75.05 Aligned_cols=54 Identities=6% Similarity=-0.156 Sum_probs=48.1
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|..++.++|++|++.|.+|||||| |++..+.+++|.+.++.|+|+|.|+|.++
T Consensus 16 dg~~~i~elv~~A~~~G~~alAiTD--------h~~l~G~~~f~~~~~~~gIkpIiG~E~~v 69 (1170)
T PRK07374 16 DGASQLPKMVERAKELGMPAIALTD--------HGVMYGAIELLKLCKGKGIKPIIGNEMYV 69 (1170)
T ss_pred hccCCHHHHHHHHHHCCCCEEEEec--------CCchHHHHHHHHHHHHcCCeEEEEeEEEe
Confidence 4567889999999999999999995 66667889999999999999999999884
No 88
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=96.13 E-value=0.0021 Score=74.24 Aligned_cols=54 Identities=6% Similarity=-0.047 Sum_probs=48.6
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|+.++.++|++|++.|++|||||| |++..+.++++.+.++.|+++|.|+|.++
T Consensus 18 dg~~~~~elv~~A~~~G~~avAiTD--------h~~l~g~~~f~~~~~~~gIkpI~G~Ei~~ 71 (1046)
T PRK05672 18 DGASHPEELVERAARLGLRALAITD--------ECGLAGVVRAAEAAKELGLRLVIGAELSL 71 (1046)
T ss_pred ccCCCHHHHHHHHHHcCCCEEEEEe--------CCcchhHHHHHHHHHHCCCEEEEEEEEEE
Confidence 3678899999999999999999995 66668899999999999999999999874
No 89
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=96.04 E-value=0.0027 Score=73.47 Aligned_cols=54 Identities=9% Similarity=0.065 Sum_probs=48.0
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|+.++.+||++|++.|.+|||||| |++..+-.++|.++++.|+|+|.|+|.++
T Consensus 17 dga~~i~~Lv~~A~~~g~~AlaiTD--------~~nl~Gav~Fy~~ak~~gikpIiG~e~~v 70 (1139)
T COG0587 17 DGASKIEELVKKAKELGMPALALTD--------HNNLYGAVEFYKAAKKAGIKPIIGCEAYV 70 (1139)
T ss_pred ccccCHHHHHHHHHHcCCCeEEEec--------CCcceeHHHHHHHHHHcCCeEEeeeEEEE
Confidence 4678899999999999999999995 66667888899999999999999999883
No 90
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=95.73 E-value=0.0038 Score=72.69 Aligned_cols=54 Identities=9% Similarity=-0.010 Sum_probs=48.0
Q ss_pred ccccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 44 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 44 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
.|..++.++|++|++.|.+|||||| |++..+..++|.+.++.++++|.|+|.++
T Consensus 15 dg~~~i~elv~~A~e~G~~avAiTD--------H~~l~g~~~f~~~a~~~gIkpIiG~Ei~~ 68 (1135)
T PRK05673 15 DGAAKIKPLVKKAAELGMPAVALTD--------HGNLFGAVEFYKAAKGAGIKPIIGCEAYV 68 (1135)
T ss_pred hhcCCHHHHHHHHHHcCCCEEEEEc--------CCccHHHHHHHHHHHHcCCeEEEEEEEEe
Confidence 3567889999999999999999995 66667888999999999999999999875
No 91
>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=95.53 E-value=0.0054 Score=70.80 Aligned_cols=53 Identities=9% Similarity=0.006 Sum_probs=47.8
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
|..++.++|++|++.|.++||||| |+...+..+++.+.++.++++|.|+|.++
T Consensus 15 g~~~~~elv~~A~~~G~~alAiTD--------H~~l~g~~~f~~~~~~~gIkpI~G~Ei~~ 67 (1022)
T TIGR00594 15 GAAKIKPLVKKAKELGMPALALTD--------HGNMFGAVEFYKACKKAGIKPIIGCEAYV 67 (1022)
T ss_pred ccCCHHHHHHHHHHCCCCEEEEec--------CCCchhHHHHHHHHHHcCCeEEEEEEEEe
Confidence 677889999999999999999995 66667888999999999999999999885
No 92
>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=95.43 E-value=1 Score=39.84 Aligned_cols=91 Identities=20% Similarity=0.115 Sum_probs=56.2
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHH-cC-
Q 015017 213 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEM-AG- 289 (414)
Q Consensus 213 Vl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~-~g- 289 (414)
++..+.+++++..+ .-+.|+..||+ .+|... .|+.. ..++|+ .+...+.+. .+++|+++++. +|
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 66677777876522 23445668996 666644 67654 357899 555555553 34899999865 46
Q ss_pred CCC--C---CCC-----------CcHHHHHHHHHHHHHHHHHh
Q 015017 290 LAW--Q---GRA-----------HCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 290 I~~--~---g~~-----------HrALdDA~aTA~Ll~~ll~~ 316 (414)
++. . +.- .-|-.||..|.+|+..|.++
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 322 1 111 22667999999999888764
No 93
>PRK05762 DNA polymerase II; Reviewed
Probab=95.41 E-value=0.3 Score=55.19 Aligned_cols=146 Identities=11% Similarity=0.084 Sum_probs=91.3
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHH
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 216 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~ 216 (414)
..+.||+||++. .+|++|+..-. .+..+ ..|-+.. + .. .+.|..-++..+.|..
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 789999999863 36888886521 12222 1222221 1 10 1114556788999999
Q ss_pred HHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCCC-------------CCC----------CceeehHHHHH
Q 015017 217 HDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKP-------------PYF----------NRWINLKVPFH 271 (414)
Q Consensus 217 f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~P-------------~~~----------~~~IDl~~l~r 271 (414)
|.+++..... . ++++| .+||+ .+|..-++.+|+.+. ... .-.+|+..+.+
T Consensus 210 F~~~i~~~DP---D-IIvGyNi~~FDl-pyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k 284 (786)
T PRK05762 210 FNAWFAEHDP---D-VIIGWNVVQFDL-RLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALK 284 (786)
T ss_pred HHHHHHhcCC---C-EEEEeCCCCCcH-HHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHH
Confidence 9999988521 2 24443 37997 889888888888642 001 02568887777
Q ss_pred Hhc-CCCCCCHHHHHHHcCCCCCC--CCC-------------------cHHHHHHHHHHHHHHH
Q 015017 272 EVF-GGVRCNLKEAVEMAGLAWQG--RAH-------------------CGLDDAKNTARLLALL 313 (414)
Q Consensus 272 ~l~-~~~~~~L~~l~~~~gI~~~g--~~H-------------------rALdDA~aTA~Ll~~l 313 (414)
... ...+++|+++++++..+... ..| -.+.||..|.+|+.++
T Consensus 285 ~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 285 SATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 655 56789999999876543211 110 1378999999888743
No 94
>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=95.30 E-value=0.23 Score=48.96 Aligned_cols=130 Identities=15% Similarity=0.105 Sum_probs=80.3
Q ss_pred ccEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCe---EeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCH
Q 015017 136 QYFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQ---LEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL 210 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~--~~~~deIIEIgAV~vd~~~g~---i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f 210 (414)
-..+.||+||....+. ++..++|+.|+.+..+ .+. ..+.+.++..+.. ... ...|.--++.
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 3889999999986432 3577999999988764 221 1222333333331 211 4455566889
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHHcCCCC-----CCC-------------------C----
Q 015017 211 SEALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWK-----PPY-------------------F---- 260 (414)
Q Consensus 211 ~eVl~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~~gi~~-----P~~-------------------~---- 260 (414)
.+.|..|++++..... .+ +++| -.||+ .+|..-++..|+.. +.. .
T Consensus 223 ~~lL~~f~~~i~~~dP---Di-i~GyN~~~fD~-~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 297 (325)
T PF03104_consen 223 KELLEAFLDIIQEYDP---DI-ITGYNIDGFDL-PYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSRKFSRI 297 (325)
T ss_dssp HHHHHHHHHHHHHHS----SE-EEESSTTTTHH-HHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCTTEEEE
T ss_pred HHHHHHHHHHHHhcCC---cE-EEEecccCCCH-HHHHHHHHHhCccccccccccccceeEEeecccccccCCCcceeEE
Confidence 9999999999987522 23 3443 36996 78888888775442 000 0
Q ss_pred ----CceeehHHHHHHhcCCCCCCHHHH
Q 015017 261 ----NRWINLKVPFHEVFGGVRCNLKEA 284 (414)
Q Consensus 261 ----~~~IDl~~l~r~l~~~~~~~L~~l 284 (414)
.-.+|+..++++.+...+++|+++
T Consensus 298 ~~~Gr~~~D~~~~~~~~~~l~sY~L~~V 325 (325)
T PF03104_consen 298 DIPGRLVLDLYRLARKDYKLDSYSLDNV 325 (325)
T ss_dssp EETTSEEEEHHHHHHHHS--SS-SHHHH
T ss_pred EECCChHhHHHHHHHhhCCCCCCCCCCC
Confidence 023678888888887777888763
No 95
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=95.28 E-value=0.13 Score=49.23 Aligned_cols=156 Identities=14% Similarity=0.046 Sum_probs=91.9
Q ss_pred CcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCC------cchhhhcCCChhhhhCCC-CHHHHHHHHHHHHhhcCCCC
Q 015017 156 QEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLS------DFCKDLTGIQQIQVDRGV-TLSEALLRHDKWLENKGIKN 228 (414)
Q Consensus 156 deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls------~~~~~LTGIT~e~V~~Ap-~f~eVl~~f~~fl~~~~lv~ 228 (414)
--..|||++++.+++| |.+.||++|+|.. .++- ..+.+-|+|..+-...+. ++..++.++.+||+.....+
T Consensus 8 y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~-~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~~~ 85 (213)
T PF13017_consen 8 YVPAEIAICKFSLKEG-IIDSFHTFINPGQ-IPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNKGGE 85 (213)
T ss_pred EEeEEEEEEEEecCCc-cchhhhcccCCCC-CCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcCCCC
Confidence 3468999999999998 7899999999995 2232 233456778777666555 79999999999999864333
Q ss_pred CcEEEEEcCc-chH-HHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC----C----CCCCHHHHH-HHcC-------C
Q 015017 229 TNFAVVTWSN-WDC-RVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG----G----VRCNLKEAV-EMAG-------L 290 (414)
Q Consensus 229 hn~~vV~~g~-fDi-r~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~----~----~~~~L~~l~-~~~g-------I 290 (414)
....|++..+ +.+ ...|+.-+...+.... ....++..++-.+.. . ...-+...+ ..+. -
T Consensus 86 ~~~~i~~~~~~~~~V~~cl~~La~~a~~~~~---~~v~~~~~lf~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~ 162 (213)
T PF13017_consen 86 KMPPIFTKRDQIPRVQSCLKWLAKKAGEDND---FKVYDFEYLFFDLKNEKVDYRWDRQDFPSKTIADALFPKDFFEYSS 162 (213)
T ss_pred CcceEEEeHhHHHHHHHHHHHHHHhcCCCcc---eEeecHHHHHHHHHHHHhhcccccccCchHHHHHHHccchhhhccC
Confidence 3344555432 221 1234444444454432 234455444433321 1 111111111 1111 1
Q ss_pred C--------CCCCCCcHHHHHHHHHHHHHHHHHh
Q 015017 291 A--------WQGRAHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 291 ~--------~~g~~HrALdDA~aTA~Ll~~ll~~ 316 (414)
. .....++|+..+..+|..+...+..
T Consensus 163 ~~~C~~He~~d~~~~Ca~s~v~r~ay~i~d~~c~ 196 (213)
T PF13017_consen 163 NIRCDFHEEIDRSKYCALSTVKRWAYTISDYMCR 196 (213)
T ss_pred CCceeecccCCCcccchhHHHHHHHHHHHHHHHH
Confidence 1 1124689999999999887776643
No 96
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=95.21 E-value=0.0073 Score=70.41 Aligned_cols=53 Identities=11% Similarity=0.008 Sum_probs=47.3
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 105 (414)
+..++.++|++|++.|.+|||||| |++....+++|.++++.++++|.|+|.++
T Consensus 19 g~~~~~elv~~A~e~G~~avAITD--------H~~~~g~~~f~~~a~~~gIkpIiG~Ei~~ 71 (1151)
T PRK06826 19 GSARIKDLIKRAKELGMDSIAITD--------HGVMYGVVDFYKAAKKQGIKPIIGCEVYV 71 (1151)
T ss_pred hcCCHHHHHHHHHHCCCCEEEEec--------CCchHhHHHHHHHHHhCCCEEEEEEEEEe
Confidence 567888999999999999999995 66667888999999999999999999885
No 97
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=94.33 E-value=0.81 Score=54.20 Aligned_cols=161 Identities=17% Similarity=0.149 Sum_probs=99.3
Q ss_pred ccEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeE----------eeEEEEeecCCCCCCCCcchhhhcCCChhh
Q 015017 136 QYFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQL----------EACFQTYVRPTCNQLLSDFCKDLTGIQQIQ 203 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~--~~~~deIIEIgAV~vd~~~g~i----------~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~ 203 (414)
-..++||+|||-++-. ++..|+|.=|+ +.+|++ |.+ ++.|+.-=||+. .-+| -
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMIS-YMiDGq-GfLItNREiVs~DIedfEYTPKpE~---eG~F----------~ 310 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMIS-YMIDGQ-GFLITNREIVSEDIEDFEYTPKPEY---EGPF----------C 310 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEE-EEecCc-eEEEechhhhccchhhcccCCcccc---ccce----------E
Confidence 4788999999988633 24678998886 456653 322 233443333332 1112 1
Q ss_pred hhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEc-Cc-chHHHHHHHHHHHcCCCCCC-C-CC---------ceeehHHHH
Q 015017 204 VDRGVTLSEALLRHDKWLENKGIKNTNFAVVTW-SN-WDCRVMLESECRFKKIWKPP-Y-FN---------RWINLKVPF 270 (414)
Q Consensus 204 V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~-g~-fDir~fL~~~~~~~gi~~P~-~-~~---------~~IDl~~l~ 270 (414)
|-+-++....|++|.+-+... +.-++||+ |+ || +.|+++-+..+|+.+-. + |. +++--+.-|
T Consensus 311 v~Ne~dEv~Ll~RfFeHiq~~----kP~iivTyNGDFFD-WPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcf 385 (2173)
T KOG1798|consen 311 VFNEPDEVGLLQRFFEHIQEV----KPTIIVTYNGDFFD-WPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCF 385 (2173)
T ss_pred EecCCcHHHHHHHHHHHHHhc----CCcEEEEecCcccc-chhhHHHHHhcCCCcchhcCceecccccccccceeehhhh
Confidence 346778889999999999874 23467775 65 69 89999999999987631 1 10 222222233
Q ss_pred HH-----hcCCCCCCHHHHHH-HcCCCC-------------CCCCC---cHHHHHHHHHHHHHHHHHh
Q 015017 271 HE-----VFGGVRCNLKEAVE-MAGLAW-------------QGRAH---CGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 271 r~-----l~~~~~~~L~~l~~-~~gI~~-------------~g~~H---rALdDA~aTA~Ll~~ll~~ 316 (414)
|. ++|..+++|+.+.+ ++|-+. +...| -.+.||.||-.|+++-..-
T Consensus 386 rWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP 453 (2173)
T KOG1798|consen 386 RWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP 453 (2173)
T ss_pred hhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh
Confidence 32 23555778887764 455322 11123 3489999999999876654
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=94.15 E-value=0.45 Score=45.88 Aligned_cols=149 Identities=13% Similarity=0.075 Sum_probs=90.0
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcC--C-----CeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCC
Q 015017 137 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSV--T-----GQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVT 209 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~--~-----g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~ 209 (414)
+.+.|-+-|+--. .....||+.|+++....- + ......+.++++|......+..-...-.-....|.--++
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 4556666675310 123699999999875310 1 112346677888875311222222333333344667888
Q ss_pred HHHHHHHHHHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCC------------CCCC-------------Cce
Q 015017 210 LSEALLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWK------------PPYF-------------NRW 263 (414)
Q Consensus 210 f~eVl~~f~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~------------P~~~-------------~~~ 263 (414)
..+.|..|.+++..... .+++-|+ -.||+ .+|-.-++..|++. |... +-.
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 99999999999987521 2222233 27997 77777777666642 1100 123
Q ss_pred eehHHHHHHhcCCCCCCHHHHHH-HcCCC
Q 015017 264 INLKVPFHEVFGGVRCNLKEAVE-MAGLA 291 (414)
Q Consensus 264 IDl~~l~r~l~~~~~~~L~~l~~-~~gI~ 291 (414)
+|+...++.+....+++|+++++ .+|..
T Consensus 158 ~D~~~~~k~~~~~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 158 CDTYLSAKELIRCKSYDLTELSQQVLGIE 186 (234)
T ss_pred hccHHHHHHHhCCCCCChHHHHHHHhCcC
Confidence 57777777777777899999997 67753
No 99
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=93.99 E-value=0.028 Score=57.62 Aligned_cols=56 Identities=5% Similarity=-0.046 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHhc--CCcccccccccccCCCCCcccCCCCCCCCCCCcccchhcccCCccc
Q 015017 301 DDAKNTARLLALLMHRG--FKFSITNSLMWQTNDGSLTWNQFPERIFLPPHQLHKQMDLQNSIFQ 363 (414)
Q Consensus 301 dDA~aTA~Ll~~ll~~~--~~~~i~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lP~~~ 363 (414)
++.+.+..|..+|+++- ..|+..+.++.++ ++++| ++....++++++|+|++|||.
T Consensus 15 ~eved~vai~~a~l~~~~~~l~~~~e~vn~~y--~~gt~-----s~~~~~~~~vvvRaRglpwq~ 72 (508)
T KOG1365|consen 15 EEVEDMVAIILAILDEPDELLFSTPEFVNIKY--EAGTC-----SKNHSADDNVVVRARGLPWQS 72 (508)
T ss_pred HHHHHHHHHHHHHHcCcHhhhhcchhhheeee--cccch-----hhccccCcceEEEecCCCCCc
Confidence 46677777888888764 4578899999888 99998 778899999999999999985
No 100
>PHA02528 43 DNA polymerase; Provisional
Probab=92.65 E-value=4.4 Score=46.61 Aligned_cols=160 Identities=14% Similarity=0.123 Sum_probs=89.3
Q ss_pred cEEEEEEeeCCCCCC-CCC--CCcEEEEcEEEEEcCCCeEeeEEEEeecCCC------CCCCCcchhhhcCCChhhhhCC
Q 015017 137 YFVVIDFEATCDKDK-NPY--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTC------NQLLSDFCKDLTGIQQIQVDRG 207 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~-~~~--~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~------~p~Ls~~~~~LTGIT~e~V~~A 207 (414)
..+.||+||+...+. +|. .++||.||.. +..+. .+..+.-+.. .+..++. -.....+..-
T Consensus 107 rv~s~DIE~~~~~gfP~p~~~~d~IisIsl~--~~~~~----~~~v~~~~~~~~~~~~~~~~~~~-----~~~~v~~~~~ 175 (881)
T PHA02528 107 RIANLDIEVTAEDGFPDPEEAKYEIDAITHY--DSIDD----RFYVFDLGSVEEWDAKGDEVPQE-----ILDKVVYMPF 175 (881)
T ss_pred cEEEEEEEECCCCCCCCcccCCCcEEEEEEe--cCCCC----EEEEEEecCcccccccCCccccc-----ccCCeeEEEc
Confidence 889999999864331 233 5699999972 32222 2222221110 0001100 0111122235
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHHH-cCCCC----CCC-----------C---------
Q 015017 208 VTLSEALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRF-KKIWK----PPY-----------F--------- 260 (414)
Q Consensus 208 p~f~eVl~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~~-~gi~~----P~~-----------~--------- 260 (414)
++..+.|..|.+|+..... . +++.| -+||+ .+|..-+++ .|+.+ +.+ +
T Consensus 176 ~sE~eLL~~F~~~i~~~DP---D-II~GyNi~~FDl-pYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i 250 (881)
T PHA02528 176 DTEREMLLEYINFWEENTP---V-IFTGWNVELFDV-PYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDI 250 (881)
T ss_pred CCHHHHHHHHHHHHHHhCC---c-EEEecCCccCCH-HHHHHHHHHHcCcccccccccccccccccccccccccceeEEE
Confidence 6889999999999976421 1 33434 37997 777776664 35331 100 0
Q ss_pred --CceeehHHHHHHh-c-CCCCCCHHHHHHH-cCCCCCCC----------------CCcHHHHHHHHHHHHHH
Q 015017 261 --NRWINLKVPFHEV-F-GGVRCNLKEAVEM-AGLAWQGR----------------AHCGLDDAKNTARLLAL 312 (414)
Q Consensus 261 --~~~IDl~~l~r~l-~-~~~~~~L~~l~~~-~gI~~~g~----------------~HrALdDA~aTA~Ll~~ 312 (414)
.-.+|+..+++.+ + ...+++|++++++ +|..-... .+-.+.||..+.+|+.+
T Consensus 251 ~GRv~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 251 SGISILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred cceEEEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 0135666777764 2 3567899999984 77643210 12237889999998877
No 101
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=92.04 E-value=0.16 Score=48.94 Aligned_cols=160 Identities=19% Similarity=0.166 Sum_probs=96.3
Q ss_pred CCcEEEEcEEEEEcCCCeE----eeEEEEeecCCCCCCCCcchhhh---cCCChhhhh-CCCCHHHHHHHHHHHHhhcCC
Q 015017 155 PQEIIEFPSVIVSSVTGQL----EACFQTYVRPTCNQLLSDFCKDL---TGIQQIQVD-RGVTLSEALLRHDKWLENKGI 226 (414)
Q Consensus 155 ~deIIEIgAV~vd~~~g~i----~d~F~~lVkP~~~p~Ls~~~~~L---TGIT~e~V~-~Ap~f~eVl~~f~~fl~~~~l 226 (414)
.=.||++|...-|.+.++- .=.|+.-..|.. .-.+.++.+| .||.-+.-+ -+.. ..+|-+.|-+++|
T Consensus 79 ~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~-dmya~ESieLL~ksgIdFkkHe~~GI~----v~eF~elLm~SGL 153 (299)
T COG5228 79 FLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKK-DMYATESIELLRKSGIDFKKHENLGID----VFEFSELLMDSGL 153 (299)
T ss_pred hhhhhheeeeeccccCCCCCCCceeEEEEEecchh-hhcchHHHHHHHHcCCChhhHhhcCCC----HHHHHHHHhccCc
Confidence 3479999999887432222 235666677774 3356666666 455544332 1222 3467777777766
Q ss_pred CC-CcEEEEE-cCcchHHHHHHHHHHHcCCCCCCC-----------CCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC
Q 015017 227 KN-TNFAVVT-WSNWDCRVMLESECRFKKIWKPPY-----------FNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ 293 (414)
Q Consensus 227 v~-hn~~vV~-~g~fDir~fL~~~~~~~gi~~P~~-----------~~~~IDl~~l~r~l~~~~~~~L~~l~~~~gI~~~ 293 (414)
+- ..+++++ ++..|+ ++|-+.+.. .++|.- +..+.|+.-+++..... +..|.+...-++|...
T Consensus 154 vm~e~VtWitfHsaYDf-gyLikilt~--~plP~~~EdFy~~l~~yfP~fYDik~v~ks~~~~-~KglQei~ndlql~r~ 229 (299)
T COG5228 154 VMDESVTWITFHSAYDF-GYLIKILTN--DPLPNNKEDFYWWLHQYFPNFYDIKLVYKSVLNN-SKGLQEIKNDLQLQRS 229 (299)
T ss_pred eeccceEEEEeecchhH-HHHHHHHhc--CCCCccHHHHHHHHHHHCccccchHHHHHhhhhh-hhHHHHhcCcHhhhcc
Confidence 53 4566776 477897 777665443 344421 12344555444333221 1257777777888888
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHhcCCcccc
Q 015017 294 GRAHCGLDDAKNTARLLALLMHRGFKFSIT 323 (414)
Q Consensus 294 g~~HrALdDA~aTA~Ll~~ll~~~~~~~i~ 323 (414)
|..|.|-.||+.||+.|...-..-..-+|.
T Consensus 230 g~QhQagsdaLlTa~~ff~~R~~~F~~sig 259 (299)
T COG5228 230 GQQHQAGSDALLTADEFFLPRFSIFTTSIG 259 (299)
T ss_pred chhhhccchhhhhhHHhcchhhheeccccc
Confidence 889999999999999887654443333443
No 102
>PRK06361 hypothetical protein; Provisional
Probab=91.73 E-value=0.11 Score=48.88 Aligned_cols=53 Identities=4% Similarity=-0.157 Sum_probs=38.1
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcc--------hhhhccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYP--------DSQKVHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~--------~~~k~~~~~~~g~e~~~ 105 (414)
+..++.++|++|.+.|.++|+||||+.. .+....+. ..++.+++++.|+|..+
T Consensus 8 g~~~~~e~v~~A~~~Gl~~i~iTDH~~~--------~~~~~~~~~~~~~~~~~~~~~~i~v~~GiE~~~ 68 (212)
T PRK06361 8 GELIPSELVRRARVLGYRAIAITDHADA--------SNLEEILEKLVRAAEELELYWDIEVIPGVELTH 68 (212)
T ss_pred CCCCHHHHHHHHHHcCCCEEEEecCCCC--------ccHHHHHHHHHHHHHHHhhcCCCEEEEEEEEcc
Confidence 5567889999999999999999975543 33332211 12345899999999874
No 103
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.65 E-value=13 Score=44.34 Aligned_cols=143 Identities=15% Similarity=0.111 Sum_probs=90.5
Q ss_pred cEEEEEEe--eCCCCCCCCCCCcEEEEcEEEEEcCC-----C--eEeeEEEEeecCCCCCCCC-cchhhhcCCChhhhhC
Q 015017 137 YFVVIDFE--ATCDKDKNPYPQEIIEFPSVIVSSVT-----G--QLEACFQTYVRPTCNQLLS-DFCKDLTGIQQIQVDR 206 (414)
Q Consensus 137 ~~VV~D~E--TTGl~~~~~~~deIIEIgAV~vd~~~-----g--~i~d~F~~lVkP~~~p~Ls-~~~~~LTGIT~e~V~~ 206 (414)
+++++||- +.-. +...++||.|+.+..+... . .....|...++|... .++ .+.....|+....|..
T Consensus 505 Pl~vLdFsi~SlyP---si~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~~-~~p~~~~~~~~~~~~~~L~~ 580 (1172)
T TIGR00592 505 PLVVLDFSMKSLNP---SIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDC-SFPLDLKGEFPGKKPSLVED 580 (1172)
T ss_pred CeEEEEeeeEEecC---ccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCCC-CCCchhhhhhhccCCcEEEE
Confidence 47777666 5422 3456889999888764200 1 122345566777321 122 2334566777778888
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCcEEEEEc-CcchHHHHHHHHHHHcCCCC----------CC---------CCCceeeh
Q 015017 207 GVTLSEALLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWK----------PP---------YFNRWINL 266 (414)
Q Consensus 207 Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~-g~fDir~fL~~~~~~~gi~~----------P~---------~~~~~IDl 266 (414)
-.+..+.+..|++++....- ..++.++ .+||+ .+|-.-+.+.+++. |. .-+-.+|+
T Consensus 581 ~~sEr~lL~~fl~~~~~~DP---Dii~g~n~~qfdl-kvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~ 656 (1172)
T TIGR00592 581 LATERALIKKFMAKVKKIDP---DEIVGHDYQQRAL-KVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDV 656 (1172)
T ss_pred ecCHHHHHHHHHHHHHhcCC---CEEEEEcccCccH-HHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEH
Confidence 89999999999999984311 2344555 47997 56666666666542 00 01235788
Q ss_pred HHHHHHhcCCCCCCHHHHHHH
Q 015017 267 KVPFHEVFGGVRCNLKEAVEM 287 (414)
Q Consensus 267 ~~l~r~l~~~~~~~L~~l~~~ 287 (414)
...++..+...+++|+++++.
T Consensus 657 ~~~~k~~~~~~sy~L~~v~~~ 677 (1172)
T TIGR00592 657 EISAKELIRCKSYDLSELVQQ 677 (1172)
T ss_pred HHHHHHHhCcCCCCHHHHHHH
Confidence 888888887788999998874
No 104
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=90.63 E-value=4.2 Score=42.01 Aligned_cols=132 Identities=14% Similarity=0.140 Sum_probs=78.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
..+|+||+||.+. .++++++.-| .+.+ .++ -.+|+|-. + .. +.++|
T Consensus 17 ~~~iAiDTEf~r~---~t~~p~LcLI--Qi~~-~e~------~~lIdpl~-~-~~---------------d~~~l----- 62 (361)
T COG0349 17 SKAIAIDTEFMRL---RTYYPRLCLI--QISD-GEG------ASLIDPLA-G-IL---------------DLPPL----- 62 (361)
T ss_pred CCceEEecccccc---cccCCceEEE--EEec-CCC------ceEecccc-c-cc---------------ccchH-----
Confidence 4689999999997 5565544322 1222 122 35777763 1 11 23333
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHH-HcCCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVE-MAGLAWQ 293 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~-~~~L~~l~~-~~gI~~~ 293 (414)
...+.+..++ -|.|.++||+ .+|...+ |+.. .+.+||.- ..++.|.. +++|++|++ .+|+...
T Consensus 63 --~~Ll~d~~v~----KIfHaa~~DL-~~l~~~~---g~~p----~plfdTqi-Aa~l~g~~~~~gl~~Lv~~ll~v~ld 127 (361)
T COG0349 63 --VALLADPNVV----KIFHAARFDL-EVLLNLF---GLLP----TPLFDTQI-AAKLAGFGTSHGLADLVEELLGVELD 127 (361)
T ss_pred --HHHhcCCcee----eeeccccccH-HHHHHhc---CCCC----CchhHHHH-HHHHhCCcccccHHHHHHHHhCCccc
Confidence 3344444322 2678899998 4554332 4432 24568764 44566643 889999996 4677653
Q ss_pred CCC---------------CcHHHHHHHHHHHHHHHHHh
Q 015017 294 GRA---------------HCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 294 g~~---------------HrALdDA~aTA~Ll~~ll~~ 316 (414)
..+ --|..|+..+..|..+|.+.
T Consensus 128 K~~q~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~ 165 (361)
T COG0349 128 KSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEE 165 (361)
T ss_pred ccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 111 23688999999998887654
No 105
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=90.25 E-value=5.7 Score=45.16 Aligned_cols=130 Identities=17% Similarity=0.111 Sum_probs=82.2
Q ss_pred ccEEEEEEeeCCCCCCCC--CCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHH
Q 015017 136 QYFVVIDFEATCDKDKNP--YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 213 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~--~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eV 213 (414)
-..++||+||+...+..+ ..+.|+.|+...-. .++.. ..+.. +...|. .|..-.+-.+.
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 478999999999765433 47888888766432 22222 11110 000111 15566778899
Q ss_pred HHHHHHHHhhcCCCCCcEEEEE-cC-cchHHHHHHHHHHHcCCCCCC-------------C----CCceeehHHHHH-Hh
Q 015017 214 LLRHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIWKPP-------------Y----FNRWINLKVPFH-EV 273 (414)
Q Consensus 214 l~~f~~fl~~~~lv~hn~~vV~-~g-~fDir~fL~~~~~~~gi~~P~-------------~----~~~~IDl~~l~r-~l 273 (414)
+.+|.+++....- . ++++ ++ +||+ .+|..-+.+.|++... + ...-+|+...++ +.
T Consensus 215 l~~~~~~i~~~dP---d-VIvgyn~~~fd~-pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~ 289 (792)
T COG0417 215 LERFVELIREYDP---D-VIVGYNGDNFDW-PYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRP 289 (792)
T ss_pred HHHHHHHHHhcCC---C-EEEeccCCcCCh-HHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhh
Confidence 9999999987521 2 3444 44 5995 8999999998887640 0 123468877777 46
Q ss_pred cCCCCCCHHHHHHHcC
Q 015017 274 FGGVRCNLKEAVEMAG 289 (414)
Q Consensus 274 ~~~~~~~L~~l~~~~g 289 (414)
+....++|...++.+.
T Consensus 290 ~~~~~ysl~~v~~~~l 305 (792)
T COG0417 290 LNLKSYSLEAVSEALL 305 (792)
T ss_pred cccccccHHHHHHHhc
Confidence 6666788998876544
No 106
>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=89.64 E-value=5.4 Score=37.19 Aligned_cols=141 Identities=14% Similarity=0.035 Sum_probs=79.7
Q ss_pred ccEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHH
Q 015017 136 QYFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~-~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl 214 (414)
...|.||+|++..... ....-.+|||+. . +.+ .+|.+.. +.. -+ .+.+
T Consensus 22 ~~vig~D~Ew~~~~~~~~~~~v~LiQiat-----~-~~~-----~lid~~~---~~~----------------~~-~~~~ 70 (193)
T cd06146 22 GRVVGIDSEWKPSFLGDSDPRVAILQLAT-----E-DEV-----FLLDLLA---LEN----------------LE-SEDW 70 (193)
T ss_pred CCEEEEECccCCCccCCCCCCceEEEEec-----C-CCE-----EEEEchh---ccc----------------cc-hHHH
Confidence 5889999999865321 134567888862 1 221 2444431 111 01 2223
Q ss_pred -HHHHHHHhhcCCCCCcEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-----------CCCCCH
Q 015017 215 -LRHDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-----------GVRCNL 281 (414)
Q Consensus 215 -~~f~~fl~~~~lv~hn~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-----------~~~~~L 281 (414)
+.+.+++.+. +++ |.|+...|+ .+|.+.+...+-. +.....++||..+++.+.+ ..+.+|
T Consensus 71 ~~~L~~ll~d~-----~i~KVg~~~~~D~-~~L~~~~~~~~~~-~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL 143 (193)
T cd06146 71 DRLLKRLFEDP-----DVLKLGFGFKQDL-KALSASYPALKCM-FERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGL 143 (193)
T ss_pred HHHHHHHhCCC-----CeeEEEechHHHH-HHHHHhcCccccc-cccCCceEEHHHHHHHHhhccccccccccCcccCCH
Confidence 3344556654 233 445568896 6776543321100 0012468999887776542 235689
Q ss_pred HHHHHHc-CCCCC---------C------CCCcHHHHHHHHHHHHHHHH
Q 015017 282 KEAVEMA-GLAWQ---------G------RAHCGLDDAKNTARLLALLM 314 (414)
Q Consensus 282 ~~l~~~~-gI~~~---------g------~~HrALdDA~aTA~Ll~~ll 314 (414)
.++++.+ |.+.. . +-+-|..||..+..|+.+|.
T Consensus 144 ~~l~~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 144 ADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHHHHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999764 54321 1 22678999999999999875
No 107
>PHA03036 DNA polymerase; Provisional
Probab=89.59 E-value=12 Score=43.55 Aligned_cols=180 Identities=15% Similarity=0.088 Sum_probs=104.7
Q ss_pred cccEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCC---------Chhh
Q 015017 135 FQYFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGI---------QQIQ 203 (414)
Q Consensus 135 ~~~~VV~D~ETTGl~~~--~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGI---------T~e~ 203 (414)
...|+.||+|+-. .+. ++..+-|+.|+...++. .|. +.--++++...-+.-...-..+-|. .-..
T Consensus 159 ~~~~lsfDIEC~~-~g~FPs~~~~pvshIs~~~~~~-~~~--~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (1004)
T PHA03036 159 PRSYLFLDIECHF-DKKFPSVFINPVSHISCCYIDL-SGK--EKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSK 234 (1004)
T ss_pred cceeEEEEEEecc-CCCCCCcccCcceEEEEEEEec-CCC--eeEEEEeccccccccccccceeeeeeccccccccCCce
Confidence 3589999999985 332 35679999999877773 443 2334566664310011111111222 1111
Q ss_pred hhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEc-C-cchHHHHHHHHHHHc---CCCCCC--------------------
Q 015017 204 VDRGVTLSEALLRHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFK---KIWKPP-------------------- 258 (414)
Q Consensus 204 V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~-g-~fDir~fL~~~~~~~---gi~~P~-------------------- 258 (414)
+---++..+ +.+|.+++..... . +|+++ + +||++ .|..-++.. ++.++.
T Consensus 235 ~~~~~sE~~-ml~~~~~i~~~d~---D-~i~~yNg~nFD~~-Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~ 308 (1004)
T PHA03036 235 ELILCSEIV-LLRIAKKLLELEF---D-YVVTFNGHNFDLR-YISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHK 308 (1004)
T ss_pred eeecCCHHH-HHHHHHHHHhcCC---C-EEEeccCCCcchH-HHHHHHHHhccCceeeccCCCcccccceeecccccccc
Confidence 122345555 5577888876532 3 34554 3 79984 555544442 111100
Q ss_pred -----------CC----CceeehHHHHHHhcCCCCCCHHHHHHH-cCCCC-----CCCC-C---cHHHHHHHHHHHHHHH
Q 015017 259 -----------YF----NRWINLKVPFHEVFGGVRCNLKEAVEM-AGLAW-----QGRA-H---CGLDDAKNTARLLALL 313 (414)
Q Consensus 259 -----------~~----~~~IDl~~l~r~l~~~~~~~L~~l~~~-~gI~~-----~g~~-H---rALdDA~aTA~Ll~~l 313 (414)
+. .-++|+....++-+.+.+++|+++++. |+... .... + .-..|+...+.||...
T Consensus 309 ~~gg~~~~t~~i~~~~G~i~fDLy~~i~k~~~L~sYkL~~Vsk~~f~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~f~~v 388 (1004)
T PHA03036 309 GVGGVANTTYHINNNNGTIFFDLYTFIQKTEKLDSYKLDSISKNAFNCNAKVLSENNNEVTFIGDNTTDAKGKASIFSEV 388 (1004)
T ss_pred ccCccccceEEecccCCeEEEEhHHHHhhhcCcccccHHHHHHHhhccceeeeecCCceeEEccCcccccccchhhhhhh
Confidence 00 135688888998888889999999986 43200 0000 0 1135889999999999
Q ss_pred HHhcCCccccc
Q 015017 314 MHRGFKFSITN 324 (414)
Q Consensus 314 l~~~~~~~i~e 324 (414)
|+.|.-.+|++
T Consensus 389 l~t~ny~~i~~ 399 (1004)
T PHA03036 389 LSTGNYVTIND 399 (1004)
T ss_pred hcccceeeecc
Confidence 99888777777
No 108
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=89.37 E-value=2.2 Score=45.96 Aligned_cols=140 Identities=13% Similarity=0.043 Sum_probs=75.8
Q ss_pred ccEEEEEEeeCCCCCCCC----CCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcc--hhhhcCCChhhhhCCCC
Q 015017 136 QYFVVIDFEATCDKDKNP----YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDF--CKDLTGIQQIQVDRGVT 209 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~----~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~--~~~LTGIT~e~V~~Ap~ 209 (414)
-....||+|+|+.+ .| ..-+|..|.-.-. .++ .++|..+.-+.......+. .....-+..-.+-.=++
T Consensus 106 i~~~~~DIEv~~~~--fp~~~~a~~~i~~i~~~d~--~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~s 179 (498)
T PHA02524 106 VVIDVVDIEVTAPE--FPEPKYAKYEIDMISHVRL--HNG--KKTYYIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFED 179 (498)
T ss_pred ceEEEEEEEecCCC--CCChhhcCCceEEEEeeec--ccC--CccEEEEeccccccCCCcccccccccccCCeEEEEeCC
Confidence 37889999999852 22 2346666644322 211 2344444211100011111 11111122234456788
Q ss_pred HHHHHHHHHHHHhhcCCCCCcEEEEEc--CcchHHHHHHHHHH-HcCCCC----CCCC---------------------C
Q 015017 210 LSEALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECR-FKKIWK----PPYF---------------------N 261 (414)
Q Consensus 210 f~eVl~~f~~fl~~~~lv~hn~~vV~~--g~fDir~fL~~~~~-~~gi~~----P~~~---------------------~ 261 (414)
..+.|.+|.+|+..... . ++.+| -+||+ .+|..-++ ..|+.. +.+. .
T Consensus 180 E~eLL~~F~~~i~~~DP---D-IItGYNi~nFDl-PYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GR 254 (498)
T PHA02524 180 EVDLLLNYIQLWKANTP---D-LVFGWNSEGFDI-PYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGI 254 (498)
T ss_pred HHHHHHHHHHHHHHhCC---C-EEEeCCCcccCH-HHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeE
Confidence 99999999999988421 1 23333 37997 67776665 356531 1110 0
Q ss_pred ceeehHHHHHHh--cCCCCCCHHHHHH
Q 015017 262 RWINLKVPFHEV--FGGVRCNLKEAVE 286 (414)
Q Consensus 262 ~~IDl~~l~r~l--~~~~~~~L~~l~~ 286 (414)
-.+|+..++++. ....+++|+++++
T Consensus 255 v~iDl~~l~kk~s~~~l~sYsL~~Vs~ 281 (498)
T PHA02524 255 ALMDYMDVFKKFSFTPMPDYKLGNVGY 281 (498)
T ss_pred EEeEHHHHHHHhhhccCCCCCHHHHHH
Confidence 135777888875 4567899999876
No 109
>PRK09248 putative hydrolase; Validated
Probab=88.77 E-value=0.28 Score=47.36 Aligned_cols=60 Identities=5% Similarity=-0.001 Sum_probs=37.4
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcc-hhhhccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYP-DSQKVHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~-~~~k~~~~~~~g~e~~~ 105 (414)
+..++.++|++|.++|.++|+||||....|.. .....+...-. ..++.+++++.|+|..+
T Consensus 17 ~~~~~~e~v~~A~~~G~~~i~iTdH~~~~~~~-~~~~~~~~~~~~~~~~~~i~il~GiE~~~ 77 (246)
T PRK09248 17 AYSTLHENAAEAKQKGLKLFAITDHGPDMPGA-PHYWHFGNLRVLPRKVDGVGILRGIEANI 77 (246)
T ss_pred CCCCHHHHHHHHHHCCCCEEEECCCCCCcCCC-CCHHHHHHHHHHHHhhcCCeEEEEEEecc
Confidence 55678899999999999999999764321100 00001111100 12446899999999864
No 110
>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=88.63 E-value=4.3 Score=34.73 Aligned_cols=66 Identities=20% Similarity=0.143 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc
Q 015017 211 SEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA 288 (414)
Q Consensus 211 ~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~-~~~L~~l~~~~ 288 (414)
.++++.|.+|+++..+ ..++|+..+|+ .+|. ..++..+ ..++|+..+...+.+.. +++|++++++|
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 5677778888887521 23556678895 6664 4455443 35689987776666644 57999999887
No 111
>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=87.48 E-value=15 Score=32.89 Aligned_cols=131 Identities=16% Similarity=0.043 Sum_probs=77.6
Q ss_pred ccEEEEEEeeCCCCC-CCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHH
Q 015017 136 QYFVVIDFEATCDKD-KNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 214 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~-~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl 214 (414)
...|.||+|++.... +....-.+|+|+. .+ ...+|++.. + ....
T Consensus 18 ~~~ig~D~E~~~~~~~~~~~~~~liQl~~-----~~------~~~l~~~~~---~---------------------~~~~ 62 (170)
T cd06141 18 EKVVGFDTEWRPSFRKGKRNKVALLQLAT-----ES------RCLLFQLAH---M---------------------DKLP 62 (170)
T ss_pred CCEEEEeCccCCccCCCCCCCceEEEEec-----CC------cEEEEEhhh---h---------------------hccc
Confidence 588999999997521 0123456777761 11 123444442 1 1112
Q ss_pred HHHHHHHhhcCCCCCcEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHc-CCC
Q 015017 215 LRHDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMA-GLA 291 (414)
Q Consensus 215 ~~f~~fl~~~~lv~hn~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~-~~~~L~~l~~~~-gI~ 291 (414)
+.|.+++.+. ++. +.|+...|+ .+|. +..|+.. ...+|+..++..+.+. ...+|.++++.+ |+.
T Consensus 63 ~~l~~ll~~~-----~i~kv~~~~k~D~-~~L~---~~~g~~~----~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~ 129 (170)
T cd06141 63 PSLKQLLEDP-----SILKVGVGIKGDA-RKLA---RDFGIEV----RGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLP 129 (170)
T ss_pred HHHHHHhcCC-----CeeEEEeeeHHHH-HHHH---hHcCCCC----CCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcc
Confidence 3455566654 222 445567885 4553 2456653 2458998777665554 346899999875 654
Q ss_pred CC-----------C------CCCcHHHHHHHHHHHHHHHH
Q 015017 292 WQ-----------G------RAHCGLDDAKNTARLLALLM 314 (414)
Q Consensus 292 ~~-----------g------~~HrALdDA~aTA~Ll~~ll 314 (414)
.. . +-|-|..||..+.+|+.+|.
T Consensus 130 ~~k~k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 130 LSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred cCCCCCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 32 1 12668899999999888775
No 112
>PRK05761 DNA polymerase I; Reviewed
Probab=84.78 E-value=9.4 Score=43.49 Aligned_cols=97 Identities=20% Similarity=0.084 Sum_probs=62.3
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCc------eeehHHHHHHh----c--
Q 015017 208 VTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNR------WINLKVPFHEV----F-- 274 (414)
Q Consensus 208 p~f~eVl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~------~IDl~~l~r~l----~-- 274 (414)
++..+.|.+|.+|+.... ..|.-|+ +||+ .+|..-++++|+....+... .+|+...++.. +
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 778999999999999852 3333343 7997 88988888899875422111 26664444311 1
Q ss_pred -C---CCCCCHHHHHH-HcCCCCCCC------------CCcHHHHHHHHHHHH
Q 015017 275 -G---GVRCNLKEAVE-MAGLAWQGR------------AHCGLDDAKNTARLL 310 (414)
Q Consensus 275 -~---~~~~~L~~l~~-~~gI~~~g~------------~HrALdDA~aTA~Ll 310 (414)
+ .++++|+..++ .+|..-... ..-.+.||..|.+|+
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 1 12578999887 677543110 123588999998874
No 113
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=84.46 E-value=0.45 Score=53.75 Aligned_cols=110 Identities=21% Similarity=0.271 Sum_probs=71.6
Q ss_pred CCCcchhhhcCCChhhhhCC------CCHHHHHHHHHHHHhhcCCCCCcEEEEEcC-cchHHHHHHHHHHHcCCCCCCCC
Q 015017 188 LLSDFCKDLTGIQQIQVDRG------VTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYF 260 (414)
Q Consensus 188 ~Ls~~~~~LTGIT~e~V~~A------p~f~eVl~~f~~fl~~~~lv~hn~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~ 260 (414)
++.++-++..||...||+-- -++..++.++.=.+ +. -+++|.|| +-|. +-.++..| -
T Consensus 972 ~VvDYLTqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li-~~-----GviFVGHGL~nDF--------rvINi~Vp--~ 1035 (1118)
T KOG1275|consen 972 KVVDYLTQYSGIKPGDLDPTTSEKRLTTLKVLYLKLRLLI-QR-----GVIFVGHGLQNDF--------RVINIHVP--E 1035 (1118)
T ss_pred HHHHHHHHhcCCCccccCCccCcceehhHHHHHHHHHHHH-Hc-----CcEEEcccccccc--------eEEEEecC--h
Confidence 57788899999999999632 23555555554333 33 24667665 3343 33445554 2
Q ss_pred CceeehHHHHHHhcCCC-CCCHHHHHH-HcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Q 015017 261 NRWINLKVPFHEVFGGV-RCNLKEAVE-MAGLAWQGRAHCGLDDAKNTARLLALLMH 315 (414)
Q Consensus 261 ~~~IDl~~l~r~l~~~~-~~~L~~l~~-~~gI~~~g~~HrALdDA~aTA~Ll~~ll~ 315 (414)
.+.+|+..+|+ .|.+ -.+|.-|+. .+|-......|+.+.||+.+.+|+.+-++
T Consensus 1036 ~QiiDTv~lf~--~~s~R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1036 EQIIDTVTLFR--LGSQRMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred hhheeeeEEEe--cccccEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHH
Confidence 45778776653 3432 247888875 46766655689999999999999887764
No 114
>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=84.18 E-value=35 Score=35.22 Aligned_cols=131 Identities=17% Similarity=0.162 Sum_probs=73.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
...|.||+|++..... ...-.+|+|+. .+. ..+|.|-. +.+ +.
T Consensus 18 ~~~ia~DtE~~~~~~y-~~~l~LiQia~------~~~-----~~liD~~~---~~~----------------------~~ 60 (367)
T TIGR01388 18 FPFVALDTEFVRERTF-WPQLGLIQVAD------GEQ-----LALIDPLV---IID----------------------WS 60 (367)
T ss_pred CCEEEEeccccCCCCC-CCcceEEEEee------CCe-----EEEEeCCC---ccc----------------------HH
Confidence 4799999999876311 11235566642 111 24666642 110 23
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHc-CCCCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMA-GLAWQ 293 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~-~~~~~L~~l~~~~-gI~~~ 293 (414)
.|.+++.+..+ ..|.|+...|+ .+|. +.+...| ..++||.-.. .+++ ..+.+|.++++.| |+...
T Consensus 61 ~L~~lL~d~~i----~KV~h~~k~Dl-~~L~----~~~~~~~---~~~fDtqlAa-~lL~~~~~~~l~~Lv~~~Lg~~l~ 127 (367)
T TIGR01388 61 PLKELLRDESV----VKVLHAASEDL-EVFL----NLFGELP---QPLFDTQIAA-AFCGFGMSMGYAKLVQEVLGVELD 127 (367)
T ss_pred HHHHHHCCCCc----eEEEeecHHHH-HHHH----HHhCCCC---CCcccHHHHH-HHhCCCCCccHHHHHHHHcCCCCC
Confidence 34556665321 23567778886 5554 3333343 3467986544 4444 3356899998765 66442
Q ss_pred CCC------C---------cHHHHHHHHHHHHHHHHHh
Q 015017 294 GRA------H---------CGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 294 g~~------H---------rALdDA~aTA~Ll~~ll~~ 316 (414)
..+ . -|..||..+..|+..|.++
T Consensus 128 K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~ 165 (367)
T TIGR01388 128 KSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMER 165 (367)
T ss_pred cccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 100 1 3788888888888877554
No 115
>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=79.24 E-value=2 Score=30.10 Aligned_cols=29 Identities=31% Similarity=0.638 Sum_probs=22.1
Q ss_pred ceeccCCCCCCCceeecCCCcccCCCcccceeecCC
Q 015017 377 GMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 412 (414)
Q Consensus 377 ~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~~~ 412 (414)
.+|.|-|..- .||||.|+ +.|.|-+|..+
T Consensus 10 ~lv~r~~k~g--~F~~Cs~y-----P~C~~~~~~~~ 38 (39)
T PF01396_consen 10 PLVLRRGKKG--KFLGCSNY-----PECKYTEPLPK 38 (39)
T ss_pred eeEEEECCCC--CEEECCCC-----CCcCCeEeCCC
Confidence 3566666654 99999986 67999999754
No 116
>COG0613 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]
Probab=78.23 E-value=1.4 Score=43.36 Aligned_cols=52 Identities=4% Similarity=-0.048 Sum_probs=42.4
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhc-chhhhccccccchhhhc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFY-PDSQKVHHCQMNSFESQ 104 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~-~~~~k~~~~~~~g~e~~ 104 (414)
++-++.++|++|++-|-..+|||| |-.+...+++- .+....++..+.|+|-.
T Consensus 15 g~~~p~~vv~~A~~~g~~vlAiTD--------Hdt~~g~~~a~~~~~~~l~i~vipG~Ei~ 67 (258)
T COG0613 15 GGLTPREVVERAKAKGVDVLAITD--------HDTVRGLLEARRAAGLRLGITVIPGIEIS 67 (258)
T ss_pred CCCCHHHHHHHHHHcCCCEEEECC--------cccccccHHHHHHhhcCCCceeeccEEee
Confidence 344588999999999999999995 77777888885 66667788898888755
No 117
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=75.56 E-value=34 Score=29.65 Aligned_cols=89 Identities=20% Similarity=0.175 Sum_probs=53.5
Q ss_pred HHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCC-CCHHHHHHHc-CCC
Q 015017 214 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVR-CNLKEAVEMA-GLA 291 (414)
Q Consensus 214 l~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~-~~L~~l~~~~-gI~ 291 (414)
+..+.+|+.+... ..++|+..+|+ .+|. +.|+.++ + ++|+.-.+..+.+..+ ++|.++++.| |+.
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---N-IFDTMLAAYLLLGGPSKHGLATLLKEYLGVE 130 (172)
T ss_pred HHHHHHHhcCCCc----eEEEechHHHH-HHHH----HCCCccc---c-hhHHHHHHHHHcCCCCcCCHHHHHHHHhCCC
Confidence 4556677776421 24567778885 5664 4787754 2 3898766655556443 6999998775 554
Q ss_pred CC---CC--------CC----cHHHHHHHHHHHHHHHHH
Q 015017 292 WQ---GR--------AH----CGLDDAKNTARLLALLMH 315 (414)
Q Consensus 292 ~~---g~--------~H----rALdDA~aTA~Ll~~ll~ 315 (414)
.+ +. .. .|..||.++.+|+..|.+
T Consensus 131 ~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~ 169 (172)
T smart00474 131 LDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEK 169 (172)
T ss_pred CCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 21 10 01 256667777777666654
No 118
>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=74.66 E-value=40 Score=31.41 Aligned_cols=78 Identities=10% Similarity=-0.105 Sum_probs=46.5
Q ss_pred EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC--------CCCCHHHHHHHc-CCCC-----------
Q 015017 233 VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG--------VRCNLKEAVEMA-GLAW----------- 292 (414)
Q Consensus 233 vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~--------~~~~L~~l~~~~-gI~~----------- 292 (414)
+.|+...|+ .+|. +..|+... .++||...+..+.+. ...+|.++++.| |++.
T Consensus 69 v~h~~k~D~-~~L~---~~~gi~~~----~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~ 140 (197)
T cd06148 69 VIHDCRRDS-DALY---HQYGIKLN----NVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMR 140 (197)
T ss_pred EEEechhHH-HHHH---HhcCcccc----ceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHh
Confidence 556677885 4542 35576532 347886543322211 124788877764 5432
Q ss_pred ------CC------CCCcHHHHHHHHHHHHHHHHHhcC
Q 015017 293 ------QG------RAHCGLDDAKNTARLLALLMHRGF 318 (414)
Q Consensus 293 ------~g------~~HrALdDA~aTA~Ll~~ll~~~~ 318 (414)
.. +-.-|..||..+..|+..|+....
T Consensus 141 ~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~ 178 (197)
T cd06148 141 EDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALI 178 (197)
T ss_pred cCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 11 125578999999999999887654
No 119
>PRK07945 hypothetical protein; Provisional
Probab=61.69 E-value=5.7 Score=40.51 Aligned_cols=61 Identities=7% Similarity=-0.019 Sum_probs=38.7
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCC-cCCchhhcch----hhh-ccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHD-FGSWSTFYPD----SQK-VHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~-~q~~p~~~~~----~~k-~~~~~~~g~e~~~ 105 (414)
+..++.++|++|.+-|.+.|+||||+-.-+...+. .+.++..+.. .++ .+++++.|+|..+
T Consensus 109 g~~~~ee~v~~Ai~~Gl~~i~~TDH~p~~~~~~~~~~~~l~~y~~~i~~l~~ky~~I~Il~GiE~d~ 175 (335)
T PRK07945 109 GGSPIEEMARTAAALGHEYCALTDHSPRLTVANGLSAERLRKQLDVVAELNEELAPFRILTGIEVDI 175 (335)
T ss_pred CCCCHHHHHHHHHHCCCCEEEEeCCCCCccCCCCCCHHHHHHHHHHHHHHHHhcCCceEEEEeEecc
Confidence 56778999999999999999999876542111111 1112222211 122 3589999999875
No 120
>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=59.85 E-value=6.1 Score=38.36 Aligned_cols=60 Identities=10% Similarity=0.110 Sum_probs=38.6
Q ss_pred ccCcchhhhhhhhcCCceeeecccCCCC-CCCCCC------cCCchhhcch----hhh--ccccccchhhhcc
Q 015017 46 VHPGGDAGESIHQLSSEFVEYSNEFYNN-PTYQHD------FGSWSTFYPD----SQK--VHHCQMNSFESQF 105 (414)
Q Consensus 46 ~~~~~~~i~~~~~~g~~aiait~~~~~~-~~~h~~------~q~~p~~~~~----~~k--~~~~~~~g~e~~~ 105 (414)
..+..++|++|.+-|-+.|+||||+... +..... ...+|..... .+| .++++..|+|..+
T Consensus 14 ~~~~ee~v~~A~~~Gl~~i~~TdH~p~~~~~~~~~~~~~~~~~~~~~Y~~~i~~l~~~y~~~i~I~~GiE~~~ 86 (253)
T TIGR01856 14 TDTLEEVVQEAIQLGFEEICFTEHAPLPFEYPEETALDKMAFSSLPEYFKEINRLKKEYADKLKILIGLEVDY 86 (253)
T ss_pred CCCHHHHHHHHHHcCCCEEEecCCCCcccCCCccccccchhHHHHHHHHHHHHHHHHHhhCCCeEEEEEEecc
Confidence 3457799999999999999999987631 110110 1224433321 122 3689999999985
No 121
>PRK08392 hypothetical protein; Provisional
Probab=58.87 E-value=5.2 Score=37.86 Aligned_cols=56 Identities=7% Similarity=0.028 Sum_probs=38.1
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhc----chhhhccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFY----PDSQKVHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~----~~~~k~~~~~~~g~e~~~ 105 (414)
+..++.++|+.|.+-|-+.|+||||.... ....++... ...++.+++++.|+|..+
T Consensus 12 ~~~~~~e~v~~A~~~Gl~~i~iTdH~~~~-----~~~~~~~y~~~i~~l~~~~~i~il~GiE~~~ 71 (215)
T PRK08392 12 GIGSVRDNIAEAERKGLRLVGISDHIHYF-----TPSKFNAYINEIRQWGEESEIVVLAGIEANI 71 (215)
T ss_pred CcCCHHHHHHHHHHcCCCEEEEccCCCcc-----chhhHHHHHHHHHHHhhccCceEEEeEEeee
Confidence 44568899999999999999999765331 001233222 223445788899999874
No 122
>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=56.24 E-value=38 Score=30.31 Aligned_cols=131 Identities=15% Similarity=0.004 Sum_probs=75.0
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
...|.||+|+..... ...+-.+|||+. .++.+ .+|++.. +.. ..+
T Consensus 13 ~~~ig~D~E~~~~~~-~~~~~~liQl~~-----~~~~~-----~l~d~~~---~~~---------------------~~~ 57 (161)
T cd06129 13 GDVIAFDMEWPPGRR-YYGEVALIQLCV-----SEEKC-----YLFDPLS---LSV---------------------DWQ 57 (161)
T ss_pred CCEEEEECCccCCCC-CCCceEEEEEEE-----CCCCE-----EEEeccc---Ccc---------------------CHH
Confidence 578999999997521 113455666643 11222 3444442 111 123
Q ss_pred HHHHHHhhcCCCCCcEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CCCCC
Q 015017 216 RHDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GLAWQ 293 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~-gI~~~ 293 (414)
.+.+++++. ++. |.|+...|+ ..|. +..|+.. ...+|+...+..+-+..+.+|.+++++| |+...
T Consensus 58 ~L~~lL~d~-----~i~Kvg~~~k~D~-~~L~---~~~gi~~----~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~ 124 (161)
T cd06129 58 GLKMLLENP-----SIVKALHGIEGDL-WKLL---RDFGEKL----QRLFDTTIAANLKGLPERWSLASLVEHFLGKTLD 124 (161)
T ss_pred HHHHHhCCC-----CEEEEEeccHHHH-HHHH---HHcCCCc----ccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCC
Confidence 344556653 233 445567785 4443 2356653 2347987655543323356899999875 66431
Q ss_pred ---------------CCCCcHHHHHHHHHHHHHHHH
Q 015017 294 ---------------GRAHCGLDDAKNTARLLALLM 314 (414)
Q Consensus 294 ---------------g~~HrALdDA~aTA~Ll~~ll 314 (414)
.+-|-|..||..+.+|+.+|.
T Consensus 125 K~~~~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 125 KSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred ccceeccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 123678999999999988874
No 123
>PRK00912 ribonuclease P protein component 3; Provisional
Probab=56.19 E-value=7 Score=37.50 Aligned_cols=50 Identities=12% Similarity=-0.005 Sum_probs=34.0
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhh-ccccccchhhhc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQK-VHHCQMNSFESQ 104 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k-~~~~~~~g~e~~ 104 (414)
+..++.+++++|.+.|-+.|+||| |... +|......+. .+++++.|+|-.
T Consensus 14 ~~~~~~e~i~~A~~~Gl~~i~itd--------H~~~--~~~~~~~~~~~~~i~Il~GiEi~ 64 (237)
T PRK00912 14 GYDTVLRLISEASHLGYSGIALSN--------HSDK--YPESKPELEDLLGFEIFRGVEIV 64 (237)
T ss_pred CcchHHHHHHHHHHCCCCEEEEec--------Cccc--ccchhHHHHHhcCCcEEeeEEEe
Confidence 345788999999999999999996 4432 2221111111 278899999875
No 124
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.95 E-value=36 Score=39.43 Aligned_cols=96 Identities=14% Similarity=0.008 Sum_probs=60.7
Q ss_pred CHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc
Q 015017 209 TLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA 288 (414)
Q Consensus 209 ~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~ 288 (414)
+...++..|.+|+++..+ ..+.|+..||+ .+|. ++|+.++. .+.|+.-....+-+..+++|++++++|
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----REGIELGG---VIFDTMLAAYLLDPAQVSTLDTLARRY 429 (887)
T ss_pred hhHHHHHHHHHHHhCCCC----cEEEeeHHHHH-HHHH----hCCCCCCC---cchhHHHHHHHcCCCCCCCHHHHHHHH
Confidence 355677788888887532 24667789995 6664 67887642 457887554444444456899998775
Q ss_pred -CCCC---C---CC------------CCcHHHHHHHHHHHHHHHHHh
Q 015017 289 -GLAW---Q---GR------------AHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 289 -gI~~---~---g~------------~HrALdDA~aTA~Ll~~ll~~ 316 (414)
+... + |. ...|..||..|.+|+..|..+
T Consensus 430 l~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 430 LVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred cCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3110 0 10 013667888888888777554
No 125
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=54.27 E-value=4.5 Score=40.26 Aligned_cols=42 Identities=24% Similarity=0.688 Sum_probs=22.4
Q ss_pred cc-ccccceecCCCcCcceeccCCCCCCCceeecC----CCcccCCCcccc
Q 015017 361 IF-QYHPSCFCGVKSSKGMVRKPGPKQGSVFFGCG----NWTVTRGARCHF 406 (414)
Q Consensus 361 ~~-~~~~~c~cg~~~~~~~~~~~gp~qg~~f~~c~----~~~~~~~~~c~~ 406 (414)
|+ +++|+ ||-....++++..++ +|+.|.-|+ -|...| .+|+|
T Consensus 170 w~~g~CPv--CGs~P~~s~l~~~~~-~G~R~L~Cs~C~t~W~~~R-~~Cp~ 216 (290)
T PF04216_consen 170 WQRGYCPV--CGSPPVLSVLRGGER-EGKRYLHCSLCGTEWRFVR-IKCPY 216 (290)
T ss_dssp TT-SS-TT--T---EEEEEEE-------EEEEEETTT--EEE--T-TS-TT
T ss_pred ccCCcCCC--CCCcCceEEEecCCC-CccEEEEcCCCCCeeeecC-CCCcC
Confidence 54 56776 899999999999999 999999998 477665 56775
No 126
>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=51.23 E-value=1.7e+02 Score=25.72 Aligned_cols=92 Identities=17% Similarity=0.125 Sum_probs=52.2
Q ss_pred HHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHc-CCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CC
Q 015017 213 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFK-KIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GL 290 (414)
Q Consensus 213 Vl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~-gi~~P~~~~~~IDl~~l~r~l~~~~~~~L~~l~~~~-gI 290 (414)
+...|.+++++..+ ..++|+...|+ .+|. ++ |+. + +.++|+.-....+-+..+++|+++++.| |+
T Consensus 52 ~~~~l~~ll~~~~i----~kv~~d~K~~~-~~L~----~~~gi~-~---~~~~D~~laayLl~p~~~~~l~~l~~~~l~~ 118 (178)
T cd06142 52 DLSPLKELLADPNI----VKVFHAAREDL-ELLK----RDFGIL-P---QNLFDTQIAARLLGLGDSVGLAALVEELLGV 118 (178)
T ss_pred cHHHHHHHHcCCCc----eEEEeccHHHH-HHHH----HHcCCC-C---CCcccHHHHHHHhCCCccccHHHHHHHHhCC
Confidence 34445666776421 23556667774 4443 44 766 2 2457986544433344446999998764 65
Q ss_pred CCC-----CC----------CCcHHHHHHHHHHHHHHHHHhc
Q 015017 291 AWQ-----GR----------AHCGLDDAKNTARLLALLMHRG 317 (414)
Q Consensus 291 ~~~-----g~----------~HrALdDA~aTA~Ll~~ll~~~ 317 (414)
... +. .+.|..||.++.+|+..|.++.
T Consensus 119 ~~~~~~~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L 160 (178)
T cd06142 119 ELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160 (178)
T ss_pred CCCcccccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 421 00 0136677888888877776543
No 127
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=47.74 E-value=1.8e+02 Score=32.40 Aligned_cols=131 Identities=21% Similarity=0.243 Sum_probs=72.4
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHHHHH
Q 015017 139 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 218 (414)
Q Consensus 139 VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~ 218 (414)
+.+|+||+|+ ++....++-++...- . . ..|| |..+. +..-+++..+.
T Consensus 25 ~a~~~et~~l---~~~~~~lvg~s~~~~---~----~--~~yi-~~~~~--------------------~~~~~~~~~l~ 71 (593)
T COG0749 25 IAFDTETDGL---DPHGADLVGLSVASE---E----E--AAYI-PLLHG--------------------PEQLNVLAALK 71 (593)
T ss_pred ceeecccccc---CcccCCeeEEEeecc---c----c--ceeE-eeccc--------------------hhhhhhHHHHH
Confidence 9999999998 455666776644321 1 1 1122 22110 11112888999
Q ss_pred HHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc--CCCCCCHHHHHHHc-CCCCC--
Q 015017 219 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVF--GGVRCNLKEAVEMA-GLAWQ-- 293 (414)
Q Consensus 219 ~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~--~~~~~~L~~l~~~~-gI~~~-- 293 (414)
.|+.+... ..+.++..+|+ .+| .++|+. + ....|+.- +.-+. +...+.|++++++| +....
T Consensus 72 ~~l~~~~~----~kv~~~~K~d~-~~l----~~~Gi~-~---~~~~Dtml-asYll~~~~~~~~~~~l~~r~l~~~~~~~ 137 (593)
T COG0749 72 PLLEDEGI----KKVGQNLKYDY-KVL----ANLGIE-P---GVAFDTML-ASYLLNPGAGAHNLDDLAKRYLGLETITF 137 (593)
T ss_pred HHhhCccc----chhccccchhH-HHH----HHcCCc-c---cchHHHHH-HHhccCcCcCcCCHHHHHHHhcCCccchh
Confidence 99998641 12334447884 444 467754 2 12457653 32222 33467899888877 22211
Q ss_pred ------CC-------------CCcHHHHHHHHHHHHHHHHHh
Q 015017 294 ------GR-------------AHCGLDDAKNTARLLALLMHR 316 (414)
Q Consensus 294 ------g~-------------~HrALdDA~aTA~Ll~~ll~~ 316 (414)
|. .-.+-.||.+|.+|...|..+
T Consensus 138 ~~i~~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~ 179 (593)
T COG0749 138 EDIAGKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPE 179 (593)
T ss_pred HHhhccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00 123567888888887777643
No 128
>COG1387 HIS2 Histidinol phosphatase and related hydrolases of the PHP family [Amino acid transport and metabolism / General function prediction only]
Probab=47.36 E-value=13 Score=35.98 Aligned_cols=60 Identities=10% Similarity=-0.027 Sum_probs=36.1
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcc----hhhhccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYP----DSQKVHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~----~~~k~~~~~~~g~e~~~ 105 (414)
+..++.+++++|.+-|.+.++||||+-..+. .....-++.... ..++..++++-|+|..+
T Consensus 14 g~~~~~e~~~~A~~~g~~~~~iTdH~~~~~~-~~~~~~~~~~~~~~~~~~~~~~i~i~~G~E~~~ 77 (237)
T COG1387 14 GEATPEEMVEAAIELGLEYIAITDHAPFLRV-GLDAELLKYFIEEIRELKKEYDIKILIGIEVDI 77 (237)
T ss_pred CCCCHHHHHHHHHHcCCeEEEEecccccccc-CCCHHHHHHHHHHHHHHHHhcCceEEEeEEEEe
Confidence 4456778999999999999999964433211 000000222211 12334588888998885
No 129
>PRK07328 histidinol-phosphatase; Provisional
Probab=45.26 E-value=12 Score=36.52 Aligned_cols=60 Identities=3% Similarity=0.026 Sum_probs=37.6
Q ss_pred ccCcchhhhhhhhcCCceeeecccCCCCCCC----CCC----cCCchhhcch----hhh-ccccccchhhhcc
Q 015017 46 VHPGGDAGESIHQLSSEFVEYSNEFYNNPTY----QHD----FGSWSTFYPD----SQK-VHHCQMNSFESQF 105 (414)
Q Consensus 46 ~~~~~~~i~~~~~~g~~aiait~~~~~~~~~----h~~----~q~~p~~~~~----~~k-~~~~~~~g~e~~~ 105 (414)
..+..++|++|.+-|-+.|+||||+-.-..+ +.. ...+++.... .+| .+++++.|+|..+
T Consensus 17 ~~~~ee~v~~A~~~Gl~~i~~TdH~~~~~~~~~~~~~~~~~~~~~~~~y~~~i~~l~~~y~~i~Il~GiE~~~ 89 (269)
T PRK07328 17 VGTPEEYVQAARRAGLKEIGFTDHLPMYFLPPEWRDPGLAMRLEELPFYVSEVERLRARFPDLYVRLGIEADY 89 (269)
T ss_pred CCCHHHHHHHHHHCCCCEEEEecCCCCCCcCcccccccccccHHHHHHHHHHHHHHHHHcCCCeEEEEEEecc
Confidence 4457899999999999999999876541000 000 0123333221 122 3689999999875
No 130
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=44.38 E-value=16 Score=42.14 Aligned_cols=37 Identities=16% Similarity=0.512 Sum_probs=23.9
Q ss_pred cceecCCCcCcceeccCCCCCCCceeecCCCcccCCCcccceeecCC
Q 015017 366 PSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 412 (414)
Q Consensus 366 ~~c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~~~ 412 (414)
|-|-||- .++.+-|. -|+.||+|+++ +.|.|..|.-+
T Consensus 697 P~~~C~g----~l~~r~gr-~G~~f~~Cs~y-----p~C~~~~~~~~ 733 (860)
T PRK06319 697 PAIGCTG----HIVKRRSR-FNKMFYSCSEY-----PACSVIGNSID 733 (860)
T ss_pred CCcCCCC----cEEEEecC-CCCeeeccCCC-----CCCceeeccCC
Confidence 3344763 24445554 37789999986 56998876643
No 131
>PHA02563 DNA polymerase; Provisional
Probab=44.17 E-value=1.1e+02 Score=34.31 Aligned_cols=39 Identities=13% Similarity=0.114 Sum_probs=26.6
Q ss_pred HHHHHHHHhhcCCCCCcE-EEEEcCcchHHHHHHHHHHHcC
Q 015017 214 LLRHDKWLENKGIKNTNF-AVVTWSNWDCRVMLESECRFKK 253 (414)
Q Consensus 214 l~~f~~fl~~~~lv~hn~-~vV~~g~fDir~fL~~~~~~~g 253 (414)
+++|++|+....-..+++ +.+|++.|| ..||-+.+.+++
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN~~FD-~~Fil~~L~~~~ 89 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHNLKFD-GSFILKWLLRNG 89 (630)
T ss_pred HHHHHHHHhhccccccceEEEEecCCcc-HHHHHHHHHhhc
Confidence 448888888422222233 456889999 589999888765
No 132
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=42.00 E-value=12 Score=42.28 Aligned_cols=147 Identities=17% Similarity=0.128 Sum_probs=81.8
Q ss_pred cEEEEEEeeCCCCCCC--CCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHH
Q 015017 137 YFVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 214 (414)
Q Consensus 137 ~~VV~D~ETTGl~~~~--~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl 214 (414)
..+-||+|+.|-.+.. +..|.||+|+-+.. .-|+- +-||+-.. .|.+ .++|.-.+|-.-....++|
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--TLKT----CAPIVGSNVHSYETEKELL 342 (1066)
T ss_pred cccceeEEeccCCCCCCccccChHHHHHHHHH--HhcCC----chHHHhhh--cccC----cCCCCCceeEEeccHHHHH
Confidence 4577999999976543 45689999987654 22321 11222221 1222 3566667776666666666
Q ss_pred HHHHHHHhh---cCCCCCcEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCC-----ce----------------------
Q 015017 215 LRHDKWLEN---KGIKNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFN-----RW---------------------- 263 (414)
Q Consensus 215 ~~f~~fl~~---~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~-~P~~~~-----~~---------------------- 263 (414)
+.-.+|+.. .++.|.|+. +||+ .+|-.-++-.|++ ||.+-+ .+
T Consensus 343 ~~W~~firevDPDvI~GYNi~-----nFDi-PYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~ 416 (1066)
T KOG0969|consen 343 ESWRKFIREVDPDVIIGYNIC-----NFDI-PYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNID 416 (1066)
T ss_pred HHHHHHHHhcCCCeEeccccc-----cccc-ceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeec
Confidence 666666654 455666653 7896 4444434444443 332110 11
Q ss_pred ----eehHHHHHHhcCCCCCCHHHHHHHc-CCCCCCCCCcHHH
Q 015017 264 ----INLKVPFHEVFGGVRCNLKEAVEMA-GLAWQGRAHCGLD 301 (414)
Q Consensus 264 ----IDl~~l~r~l~~~~~~~L~~l~~~~-gI~~~g~~HrALd 301 (414)
+|++....+-|.+++|+|+...-+| |=.-++-||+-+.
T Consensus 417 GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siIt 459 (1066)
T KOG0969|consen 417 GRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIIT 459 (1066)
T ss_pred ceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchh
Confidence 2444455555666788898877654 3333334565543
No 133
>PRK05588 histidinol-phosphatase; Provisional
Probab=40.91 E-value=22 Score=34.40 Aligned_cols=59 Identities=7% Similarity=-0.032 Sum_probs=37.5
Q ss_pred ccCcchhhhhhhhcCCceeeecccCCCCCCCCC-CcCCchhhcchhhhc-cccccchhhhcc
Q 015017 46 VHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQH-DFGSWSTFYPDSQKV-HHCQMNSFESQF 105 (414)
Q Consensus 46 ~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~-~~q~~p~~~~~~~k~-~~~~~~g~e~~~ 105 (414)
..+..++|++|.+-|-+.+ ||||+-.-..++. .....+.+....++. ++++..|+|..+
T Consensus 15 ~~~~ee~v~~A~~~Gl~~~-~TdH~~~~~~~~~~~~~~~~~y~~~i~~~~~~~I~~GiE~~~ 75 (255)
T PRK05588 15 KMKIEEAIKKAKENNLGII-ITEHMDLNLPDKNKFCFDVDSYFNKYSKYRNNKLLLGIELGM 75 (255)
T ss_pred ccCHHHHHHHHHHcCCCEE-EeCCCCCCCCCccccccCHHHHHHHHHHHhcCCcceEEEecc
Confidence 3457799999999999988 9988633100111 112344444333433 478888999874
No 134
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=40.46 E-value=57 Score=28.84 Aligned_cols=57 Identities=18% Similarity=0.147 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCC-------CCCceeehHHHHHH
Q 015017 207 GVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP-------YFNRWINLKVPFHE 272 (414)
Q Consensus 207 Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~-------~~~~~IDl~~l~r~ 272 (414)
..+-.+.++.+.+.++... ..+||.+.+|+ +..|+.-++. +|. +..+.+||..+|+.
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 5566778888888887641 24566667799 5777655443 221 22356777777765
No 135
>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=40.16 E-value=19 Score=40.16 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=24.9
Q ss_pred eecCCCcCcceeccCCCCCCCceeecCCCcccCC--CcccceeecC
Q 015017 368 CFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRG--ARCHFFEWAF 411 (414)
Q Consensus 368 c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~--~~c~~f~w~~ 411 (414)
|-||- .++. +=|.+ || |.+|+|++.-++ ++|.|=+|..
T Consensus 614 cpcg~---~l~~-~~~~~-g~-f~~c~~~p~C~~~~~~c~~~~~~~ 653 (660)
T TIGR01056 614 VSCGG---IAKC-PAKDN-GR-LIDCKKFPECTEYGNGCEFTIPKK 653 (660)
T ss_pred CCCCC---ceee-eecCC-Ce-eecCCCCCCccCcCCCCeEEccHH
Confidence 44873 2233 34444 54 999999866653 7899999863
No 136
>PRK10829 ribonuclease D; Provisional
Probab=39.44 E-value=2.4e+02 Score=29.37 Aligned_cols=131 Identities=15% Similarity=0.145 Sum_probs=79.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
...|+||+|+...... ...-.+|+|+ + ... ..+|.|-. +.+ +.
T Consensus 22 ~~~lalDtEf~~~~ty-~~~l~LiQl~----~--~~~-----~~LiD~l~---~~d----------------------~~ 64 (373)
T PRK10829 22 FPAIALDTEFVRTRTY-YPQLGLIQLY----D--GEQ-----LSLIDPLG---ITD----------------------WS 64 (373)
T ss_pred CCeEEEecccccCccC-CCceeEEEEe----c--CCc-----eEEEecCC---ccc----------------------hH
Confidence 4789999999975211 1224556664 2 111 24666652 221 23
Q ss_pred HHHHHHhhcCCCCCcEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHH-HcCCCC
Q 015017 216 RHDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVE-MAGLAW 292 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~-~~~L~~l~~-~~gI~~ 292 (414)
.|.+.+.+. +++ |.|.+.+|+ .+|.. ..|+. | .+++||.-.+ .+.|.. +.+|..+++ .+|+..
T Consensus 65 ~L~~ll~~~-----~ivKV~H~~~~Dl-~~l~~---~~g~~-p---~~~fDTqiaa-~~lg~~~~~gl~~Lv~~~lgv~l 130 (373)
T PRK10829 65 PFKALLRDP-----QVTKFLHAGSEDL-EVFLN---AFGEL-P---QPLIDTQILA-AFCGRPLSCGFASMVEEYTGVTL 130 (373)
T ss_pred HHHHHHcCC-----CeEEEEeChHhHH-HHHHH---HcCCC-c---CCeeeHHHHH-HHcCCCccccHHHHHHHHhCCcc
Confidence 355566664 333 567789997 56643 45663 2 3578996544 466644 579999886 577753
Q ss_pred CC---------------CCCcHHHHHHHHHHHHHHHHHhc
Q 015017 293 QG---------------RAHCGLDDAKNTARLLALLMHRG 317 (414)
Q Consensus 293 ~g---------------~~HrALdDA~aTA~Ll~~ll~~~ 317 (414)
.. +-+-|..|+..+..|+.+|.++.
T Consensus 131 dK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L 170 (373)
T PRK10829 131 DKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAET 170 (373)
T ss_pred CcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 21 12568999999999988877643
No 137
>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=35.15 E-value=2.7e+02 Score=24.67 Aligned_cols=108 Identities=17% Similarity=0.094 Sum_probs=60.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEeecCCCCCCCCcchhhhcCCChhhhhCCCCHHHHHH
Q 015017 136 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 215 (414)
Q Consensus 136 ~~~VV~D~ETTGl~~~~~~~deIIEIgAV~vd~~~g~i~d~F~~lVkP~~~p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~ 215 (414)
...+.||+|++|. ++...+|+-|+.. . +++ ..||.+.. . + .+..
T Consensus 3 ~~~~~~~~~~~~~---~~~~~~l~~i~l~--~--~~~-----~~~i~~~~--~----------~------------~~~~ 46 (178)
T cd06140 3 ADEVALYVELLGE---NYHTADIIGLALA--N--GGG-----AYYIPLEL--A----------L------------LDLA 46 (178)
T ss_pred CCceEEEEEEcCC---CcceeeEEEEEEE--e--CCc-----EEEEeccc--h----------H------------HHHH
Confidence 3678999999986 3445666544322 2 111 23454331 1 0 1455
Q ss_pred HHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc-CCC
Q 015017 216 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA-GLA 291 (414)
Q Consensus 216 ~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl~~l~r~l~~~~-~~~L~~l~~~~-gI~ 291 (414)
.|.+++++..+ ..++|+..+|+ .+| .+.|+.++ ..+.|+.-...-+-+.. +++|++++++| ++.
T Consensus 47 ~l~~~l~~~~~----~ki~~d~K~~~-~~l----~~~gi~~~---~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~ 112 (178)
T cd06140 47 ALKEWLEDEKI----PKVGHDAKRAY-VAL----KRHGIELA---GVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRE 112 (178)
T ss_pred HHHHHHhCCCC----ceeccchhHHH-HHH----HHCCCcCC---CcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 56677776421 13455667774 444 46788765 23578865444433443 37999998765 443
No 138
>PRK08609 hypothetical protein; Provisional
Probab=32.79 E-value=30 Score=37.97 Aligned_cols=61 Identities=7% Similarity=-0.122 Sum_probs=38.1
Q ss_pred cccCcchhhhhhhhcCCceeeecccCCCCCCCCCC-cCCchhhcc---h-hhh-ccccccchhhhcc
Q 015017 45 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHD-FGSWSTFYP---D-SQK-VHHCQMNSFESQF 105 (414)
Q Consensus 45 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~-~q~~p~~~~---~-~~k-~~~~~~~g~e~~~ 105 (414)
+..+..++++.|.+-|-+.|+||||.-..+..++. ...++..+. . .++ .++++..|+|..+
T Consensus 347 g~~sleemv~~A~~~Gl~~i~iTdH~~~~~~~~~~~~~~l~~~~~ei~~l~~~~~~i~Il~GiEv~i 413 (570)
T PRK08609 347 GAFSIEEMVEACIAKGYEYMAITDHSQYLKVANGLTEERLLEQAEEIKALNEKYPEIDILSGIEMDI 413 (570)
T ss_pred CCCCHHHHHHHHHHCCCCEEEEeCCCCCccccCCCCHHHHHHHHHHHHHHHHhcCCCeEEEEEEEee
Confidence 44567889999999999999999876432211111 111222221 1 111 3688999999885
No 139
>PRK07726 DNA topoisomerase III; Provisional
Probab=30.68 E-value=30 Score=38.66 Aligned_cols=17 Identities=12% Similarity=0.161 Sum_probs=12.2
Q ss_pred ceeecCCCcccCCCcccceeecC
Q 015017 389 VFFGCGNWTVTRGARCHFFEWAF 411 (414)
Q Consensus 389 ~f~~c~~~~~~~~~~c~~f~w~~ 411 (414)
.||||.||+ |.|+.|..
T Consensus 629 ~f~~Cs~~~------~~~~~~~~ 645 (658)
T PRK07726 629 KMLVCQDRE------CGKRKNVS 645 (658)
T ss_pred eeEecCCCc------cccccccc
Confidence 499999952 66668743
No 140
>PRK06599 DNA topoisomerase I; Validated
Probab=27.43 E-value=39 Score=37.82 Aligned_cols=26 Identities=31% Similarity=0.806 Sum_probs=18.3
Q ss_pred eeccCCCCCCCceeecCCCcccCCCcccceeec
Q 015017 378 MVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWA 410 (414)
Q Consensus 378 ~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~ 410 (414)
++.+-|.. |+ ||+|.|| ..|.|..|.
T Consensus 596 l~~k~~k~-g~-F~~Cs~~-----p~C~~~~~~ 621 (675)
T PRK06599 596 LVLKLGKN-GK-FLGCSGY-----PECKYTKNI 621 (675)
T ss_pred ceEEecCC-Cc-eeeCCCC-----CccCCCCCC
Confidence 45566654 54 9999998 348888774
No 141
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=22.20 E-value=58 Score=33.08 Aligned_cols=40 Identities=30% Similarity=0.809 Sum_probs=31.8
Q ss_pred cccceecCCCcCcceeccCCCCCCCceeecC----CCcccCCCcccc
Q 015017 364 YHPSCFCGVKSSKGMVRKPGPKQGSVFFGCG----NWTVTRGARCHF 406 (414)
Q Consensus 364 ~~~~c~cg~~~~~~~~~~~gp~qg~~f~~c~----~~~~~~~~~c~~ 406 (414)
++|+ ||-....++|+.-|+.+|..|.-|+ .|...| .+|.|
T Consensus 186 ~CPv--CGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R-~~C~~ 229 (305)
T TIGR01562 186 LCPA--CGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVR-VKCSH 229 (305)
T ss_pred cCCC--CCChhhhhhhcccCCCCCceEEEcCCCCCcccccC-ccCCC
Confidence 5665 7888888888887888999999998 587775 77765
No 142
>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases.; GO: 0005634 nucleus
Probab=21.68 E-value=3.7e+02 Score=24.44 Aligned_cols=100 Identities=15% Similarity=0.031 Sum_probs=63.0
Q ss_pred CCCCcchhhhcCCChhhhhCCCCHHHHHHHHHHHHhhcCCCCCcEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeeh
Q 015017 187 QLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINL 266 (414)
Q Consensus 187 p~Ls~~~~~LTGIT~e~V~~Ap~f~eVl~~f~~fl~~~~lv~hn~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~IDl 266 (414)
|.|++.+.+- -| +-.+.+|.-|-..+++|.+|+....-+.| ++..++ ..||..-....+|+ .
T Consensus 41 pvLp~dil~e-aV-PGnIR~AeHFv~flkR~veylk~rlrv~~---v~~e~P---~sFL~~~~~~~~id----------~ 102 (146)
T PF06777_consen 41 PVLPDDILKE-AV-PGNIRRAEHFVAFLKRFVEYLKTRLRVQH---VISESP---LSFLQHLKDETFID----------R 102 (146)
T ss_pred CCCchhhhhh-cC-CchHHhHHHHHHHHHHHHHHHHHHhhhcc---eeecCH---HHHHHHHHHHhCCC----------c
Confidence 3466554322 22 55678899999999999999998642221 233332 36887666655544 2
Q ss_pred HHHHHHhcCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHH
Q 015017 267 KVPFHEVFGGVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLL 310 (414)
Q Consensus 267 ~~l~r~l~~~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll 310 (414)
+. .+.+. -+|..++.-++|.-. ..-++|.++-.-|-|+
T Consensus 103 k~-LrFc~----eRL~sLl~TLei~d~-~df~~L~~Va~FaTLv 140 (146)
T PF06777_consen 103 KP-LRFCS----ERLSSLLRTLEITDI-DDFSALQLVADFATLV 140 (146)
T ss_pred HH-HHHHH----HHHHHHHHHHCCCcH-hhhhHHHHHHHHHHHH
Confidence 22 22222 279999999998753 3467888877766654
No 143
>PRK08123 histidinol-phosphatase; Reviewed
Probab=21.25 E-value=46 Score=32.60 Aligned_cols=58 Identities=10% Similarity=0.008 Sum_probs=36.9
Q ss_pred CcchhhhhhhhcCCceeeecccCCCC-----CC---CCCC-cCCchhhcch----hhh--ccccccchhhhcc
Q 015017 48 PGGDAGESIHQLSSEFVEYSNEFYNN-----PT---YQHD-FGSWSTFYPD----SQK--VHHCQMNSFESQF 105 (414)
Q Consensus 48 ~~~~~i~~~~~~g~~aiait~~~~~~-----~~---~h~~-~q~~p~~~~~----~~k--~~~~~~~g~e~~~ 105 (414)
+..++|++|.+-|-+.|+||||.-.. |. +.+. ..+++..+.. .+| .++++..|+|..+
T Consensus 20 ~~e~~v~~Ai~~Gl~~i~~tdH~p~~~~~~~~~~~~~~~~~~~~~~~Y~~~i~~l~~ky~~~i~i~~GiE~~~ 92 (270)
T PRK08123 20 DLEAYIERAIELGFTEITFTEHAPLPPGFIDPTPRQDSAMAIEQLERYLKELNELKKKYAGQIDIRIGLEVDY 92 (270)
T ss_pred CHHHHHHHHHHcCCcEEEEeccCCCccccCCcccCcccccCHHHHHHHHHHHHHHHHHccCCCeEEEEEEeec
Confidence 45799999999999999999876542 10 0000 1134433322 222 3588899999875
Done!