Query 015078
Match_columns 413
No_of_seqs 327 out of 1209
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 02:52:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015078.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015078hhsearch_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 1.8E-54 3.9E-59 470.5 11.2 248 40-324 346-594 (1444)
2 TIGR01405 polC_Gram_pos DNA po 100.0 1E-40 2.2E-45 377.4 22.0 242 43-321 117-360 (1213)
3 KOG0542 Predicted exonuclease 100.0 3.8E-41 8.1E-46 318.9 12.5 220 132-356 53-278 (280)
4 PRK00448 polC DNA polymerase I 100.0 2.6E-38 5.7E-43 361.6 20.9 242 43-321 347-589 (1437)
5 PRK07748 sporulation inhibitor 100.0 6.4E-37 1.4E-41 288.0 19.5 175 135-318 4-182 (207)
6 PTZ00315 2'-phosphotransferase 100.0 4.1E-36 8.9E-41 316.2 25.5 194 131-326 52-265 (582)
7 PRK06722 exonuclease; Provisio 100.0 5.1E-34 1.1E-38 279.9 20.3 172 134-314 4-179 (281)
8 cd06133 ERI-1_3'hExo_like DEDD 100.0 9.4E-33 2E-37 249.8 19.9 172 137-313 1-176 (176)
9 TIGR01406 dnaQ_proteo DNA poly 100.0 5.2E-32 1.1E-36 258.4 19.5 169 136-317 1-173 (225)
10 PRK09146 DNA polymerase III su 100.0 9.2E-32 2E-36 259.0 21.1 172 123-317 40-228 (239)
11 PRK05711 DNA polymerase III su 100.0 6.1E-32 1.3E-36 260.3 19.8 172 135-320 4-180 (240)
12 smart00479 EXOIII exonuclease 100.0 4.3E-31 9.4E-36 236.4 21.9 166 136-316 1-167 (169)
13 cd06131 DNA_pol_III_epsilon_Ec 100.0 2.7E-31 5.9E-36 239.7 20.6 162 137-312 1-166 (167)
14 PRK08517 DNA polymerase III su 100.0 1.5E-30 3.2E-35 253.0 22.3 174 121-317 59-232 (257)
15 PRK06807 DNA polymerase III su 100.0 1.3E-30 2.8E-35 260.0 22.1 164 135-316 8-172 (313)
16 cd06130 DNA_pol_III_epsilon_li 100.0 1.4E-30 3.1E-35 231.4 19.2 154 137-310 1-155 (156)
17 PRK06195 DNA polymerase III su 100.0 1.3E-30 2.7E-35 259.5 20.6 164 136-318 2-166 (309)
18 PRK07740 hypothetical protein; 100.0 2.3E-30 5E-35 249.9 21.1 168 135-319 59-229 (244)
19 PRK06063 DNA polymerase III su 100.0 4E-30 8.7E-35 256.5 20.5 168 135-320 15-183 (313)
20 PRK07942 DNA polymerase III su 100.0 5.1E-30 1.1E-34 245.6 20.3 173 135-317 6-181 (232)
21 PRK06310 DNA polymerase III su 100.0 1.3E-29 2.7E-34 245.5 21.7 168 135-316 7-174 (250)
22 PRK09145 DNA polymerase III su 100.0 4.9E-30 1.1E-34 240.2 17.9 163 135-315 29-200 (202)
23 PRK05168 ribonuclease T; Provi 100.0 5.7E-30 1.2E-34 242.0 18.5 178 135-318 17-203 (211)
24 TIGR00573 dnaq exonuclease, DN 100.0 2.9E-29 6.2E-34 237.8 21.4 171 135-320 7-181 (217)
25 PRK07247 DNA polymerase III su 100.0 1.4E-29 3E-34 237.0 18.3 162 134-318 4-171 (195)
26 PRK06309 DNA polymerase III su 100.0 2.4E-29 5.3E-34 240.8 20.0 162 136-316 3-166 (232)
27 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 1.3E-29 2.9E-34 233.1 17.2 161 137-311 1-176 (177)
28 cd06134 RNaseT DEDDh 3'-5' exo 100.0 3.3E-29 7.1E-34 232.9 18.8 174 136-315 6-188 (189)
29 PRK07883 hypothetical protein; 100.0 7.5E-29 1.6E-33 264.2 22.4 174 124-319 9-185 (557)
30 COG5018 KapD Inhibitor of the 100.0 1.5E-30 3.2E-35 234.1 7.6 186 135-323 4-192 (210)
31 TIGR01298 RNaseT ribonuclease 100.0 8.3E-29 1.8E-33 232.3 18.2 178 135-318 8-194 (200)
32 PRK07246 bifunctional ATP-depe 100.0 2.6E-28 5.6E-33 270.1 19.2 165 135-318 7-172 (820)
33 PRK05601 DNA polymerase III su 100.0 1.4E-27 2.9E-32 240.3 19.9 164 135-314 46-247 (377)
34 cd06138 ExoI_N N-terminal DEDD 100.0 7E-28 1.5E-32 222.5 15.4 162 138-309 1-182 (183)
35 PRK08074 bifunctional ATP-depe 100.0 2E-27 4.3E-32 266.5 19.7 167 135-318 3-171 (928)
36 TIGR01407 dinG_rel DnaQ family 99.9 4.8E-27 1E-31 261.5 19.5 165 136-317 1-166 (850)
37 cd06127 DEDDh DEDDh 3'-5' exon 99.9 8E-27 1.7E-31 204.0 16.7 157 138-310 1-159 (159)
38 PRK07983 exodeoxyribonuclease 99.9 1.1E-26 2.3E-31 221.1 16.6 159 137-327 2-164 (219)
39 cd06137 DEDDh_RNase DEDDh 3'-5 99.9 1.7E-27 3.7E-32 215.8 9.8 146 138-310 1-161 (161)
40 COG0847 DnaQ DNA polymerase II 99.9 2.1E-25 4.4E-30 213.3 17.6 165 135-315 13-181 (243)
41 PRK09182 DNA polymerase III su 99.9 2.4E-25 5.2E-30 220.4 17.8 200 135-361 37-241 (294)
42 cd06144 REX4_like DEDDh 3'-5' 99.9 8E-26 1.7E-30 202.9 11.7 149 138-310 1-152 (152)
43 cd06135 Orn DEDDh 3'-5' exonuc 99.9 3.1E-25 6.8E-30 203.3 14.8 161 137-314 1-170 (173)
44 cd06149 ISG20 DEDDh 3'-5' exon 99.9 8.9E-26 1.9E-30 204.1 11.0 147 138-310 1-157 (157)
45 PF00929 RNase_T: Exonuclease; 99.9 3.3E-27 7.1E-32 206.6 0.6 162 138-309 1-164 (164)
46 cd06145 REX1_like DEDDh 3'-5' 99.9 2.4E-25 5.3E-30 199.7 11.9 143 138-309 1-149 (150)
47 PRK05359 oligoribonuclease; Pr 99.9 1.6E-23 3.5E-28 193.9 16.5 164 135-316 3-175 (181)
48 PRK11779 sbcB exonuclease I; P 99.9 7.9E-23 1.7E-27 213.8 17.7 172 135-315 6-197 (476)
49 PF06839 zf-GRF: GRF zinc fing 99.3 9.2E-13 2E-17 95.5 3.0 44 365-411 1-44 (45)
50 cd05160 DEDDy_DNA_polB_exo DED 99.3 4.1E-10 9E-15 104.6 18.3 139 138-291 2-162 (199)
51 KOG2249 3'-5' exonuclease [Rep 99.2 1.1E-10 2.3E-15 112.8 13.3 157 135-315 105-265 (280)
52 cd06143 PAN2_exo DEDDh 3'-5' e 99.1 1.5E-09 3.2E-14 100.1 12.8 154 135-309 5-173 (174)
53 cd06125 DnaQ_like_exo DnaQ-lik 98.9 1.4E-08 3.1E-13 84.6 11.5 83 138-268 1-83 (96)
54 PHA02570 dexA exonuclease; Pro 98.9 1.2E-08 2.7E-13 96.8 11.2 162 138-315 4-198 (220)
55 COG1949 Orn Oligoribonuclease 98.8 1.9E-08 4.2E-13 91.1 10.0 160 134-312 5-174 (184)
56 COG2925 SbcB Exonuclease I [DN 98.8 3.3E-08 7.2E-13 99.8 12.1 165 135-312 9-197 (475)
57 KOG3242 Oligoribonuclease (3'- 98.7 7.9E-08 1.7E-12 88.0 9.8 163 135-314 26-197 (208)
58 cd05780 DNA_polB_Kod1_like_exo 98.5 4E-06 8.8E-11 78.3 16.1 129 136-291 4-156 (195)
59 cd05781 DNA_polB_B3_exo DEDDy 98.5 2.9E-06 6.2E-11 79.2 14.7 120 136-290 4-144 (188)
60 PF13482 RNase_H_2: RNase_H su 98.5 6.8E-07 1.5E-11 80.2 9.2 116 138-292 1-117 (164)
61 cd05782 DNA_polB_like1_exo Unc 98.4 1.8E-05 3.9E-10 75.1 16.2 114 145-291 41-170 (208)
62 KOG2248 3'-5' exonuclease [Rep 98.3 2.1E-06 4.7E-11 88.1 9.3 157 135-320 216-379 (380)
63 cd06139 DNA_polA_I_Ecoli_like_ 98.2 4.7E-05 1E-09 69.4 13.5 145 135-318 5-172 (193)
64 KOG0304 mRNA deadenylase subun 98.1 2E-05 4.4E-10 74.7 10.7 172 136-314 25-237 (239)
65 cd05779 DNA_polB_epsilon_exo D 98.1 0.00026 5.6E-09 67.1 17.6 145 136-291 3-169 (204)
66 PF04857 CAF1: CAF1 family rib 98.0 0.00012 2.6E-09 71.7 12.9 172 135-311 22-262 (262)
67 cd05785 DNA_polB_like2_exo Unc 97.9 0.00036 7.8E-09 66.2 14.3 121 136-291 10-169 (207)
68 PF10108 DNA_pol_B_exo2: Predi 97.9 0.00047 1E-08 65.7 14.8 130 153-315 7-172 (209)
69 PRK05755 DNA polymerase I; Pro 97.8 0.00017 3.7E-09 81.9 13.4 135 135-315 315-468 (880)
70 smart00481 POLIIIAc DNA polyme 97.7 1.3E-05 2.9E-10 62.0 1.8 52 44-103 13-64 (67)
71 cd05777 DNA_polB_delta_exo DED 97.6 0.0058 1.3E-07 58.6 18.8 137 136-289 8-181 (230)
72 KOG4793 Three prime repair exo 97.6 7.9E-05 1.7E-09 72.8 5.8 171 135-315 13-290 (318)
73 cd05783 DNA_polB_B1_exo DEDDy 97.5 0.0056 1.2E-07 58.0 15.9 136 136-289 6-169 (204)
74 KOG1956 DNA topoisomerase III 97.4 0.00012 2.6E-09 78.5 4.0 41 364-409 718-758 (758)
75 PRK06920 dnaE DNA polymerase I 97.2 9.6E-05 2.1E-09 85.2 1.1 54 43-104 16-69 (1107)
76 TIGR03491 RecB family nuclease 97.2 0.0035 7.6E-08 66.2 12.7 123 135-292 284-411 (457)
77 PRK07279 dnaE DNA polymerase I 97.2 0.00012 2.6E-09 83.7 1.8 54 43-104 15-68 (1034)
78 cd05784 DNA_polB_II_exo DEDDy 97.0 0.025 5.4E-07 53.2 14.6 120 136-287 4-149 (193)
79 smart00486 POLBc DNA polymeras 96.9 0.092 2E-06 54.2 19.0 162 135-312 3-220 (471)
80 COG3359 Predicted exonuclease 96.8 0.0084 1.8E-07 58.3 10.0 118 135-292 98-220 (278)
81 cd05778 DNA_polB_zeta_exo inac 96.7 0.068 1.5E-06 51.5 15.7 173 136-315 5-222 (231)
82 PF02811 PHP: PHP domain; Int 96.7 0.00051 1.1E-08 61.3 0.9 52 43-102 13-64 (175)
83 PTZ00166 DNA polymerase delta 96.7 0.026 5.7E-07 65.5 14.9 162 136-313 265-483 (1054)
84 PRK07135 dnaE DNA polymerase I 96.7 0.0006 1.3E-08 77.7 1.3 54 43-104 16-69 (973)
85 PRK05898 dnaE DNA polymerase I 96.4 0.0013 2.9E-08 74.8 1.8 54 43-104 15-68 (971)
86 PRK09532 DNA polymerase III su 96.4 0.0013 2.7E-08 74.7 1.5 53 44-104 17-69 (874)
87 PF03104 DNA_pol_B_exo1: DNA p 96.0 0.092 2E-06 51.8 12.4 130 135-283 157-325 (325)
88 PRK05672 dnaE2 error-prone DNA 96.0 0.0028 6E-08 73.2 1.4 54 43-104 18-71 (1046)
89 PRK07374 dnaE DNA polymerase I 96.0 0.0027 5.9E-08 73.9 1.2 54 43-104 16-69 (1170)
90 COG0587 DnaE DNA polymerase II 95.8 0.0037 8.1E-08 72.3 1.7 54 43-104 17-70 (1139)
91 PRK05762 DNA polymerase II; Re 95.8 0.27 5.7E-06 55.6 15.9 147 135-312 155-348 (786)
92 PF01612 DNA_pol_A_exo1: 3'-5' 95.5 0.91 2E-05 40.2 15.7 91 212-315 65-174 (176)
93 PRK05673 dnaE DNA polymerase I 95.5 0.0051 1.1E-07 71.6 1.2 54 43-104 15-68 (1135)
94 TIGR00594 polc DNA-directed DN 95.3 0.0071 1.5E-07 69.8 1.5 53 44-104 15-67 (1022)
95 PF13017 Maelstrom: piRNA path 95.3 0.13 2.9E-06 49.1 9.8 157 154-315 7-196 (213)
96 PRK06826 dnaE DNA polymerase I 95.0 0.0096 2.1E-07 69.4 1.2 53 44-104 19-71 (1151)
97 cd05776 DNA_polB_alpha_exo ina 94.9 0.26 5.7E-06 47.5 10.9 149 136-290 4-186 (234)
98 KOG1798 DNA polymerase epsilon 94.9 0.41 8.9E-06 56.5 13.7 161 135-315 246-453 (2173)
99 KOG1365 RNA-binding protein Fu 94.2 0.025 5.4E-07 58.0 1.9 56 300-362 15-72 (508)
100 PRK06361 hypothetical protein; 93.4 0.02 4.4E-07 53.8 -0.3 53 44-104 8-68 (212)
101 PHA02528 43 DNA polymerase; Pr 93.3 3.5 7.6E-05 47.4 17.2 166 135-311 106-323 (881)
102 COG5228 POP2 mRNA deadenylase 93.2 0.1 2.2E-06 50.2 4.0 153 154-315 79-252 (299)
103 TIGR00592 pol2 DNA polymerase 92.3 7.4 0.00016 46.2 18.5 144 136-287 505-678 (1172)
104 COG0417 PolB DNA polymerase el 91.5 4.8 0.0001 45.8 15.3 153 135-311 154-349 (792)
105 cd06146 mut-7_like_exo DEDDy 3 91.1 3.6 7.8E-05 38.4 11.8 141 135-313 22-192 (193)
106 COG0349 Rnd Ribonuclease D [Tr 90.4 4.4 9.6E-05 41.8 12.5 132 135-315 17-165 (361)
107 PHA03036 DNA polymerase; Provi 90.0 12 0.00026 43.7 16.7 180 134-323 159-399 (1004)
108 cd00007 35EXOc 3'-5' exonuclea 88.9 3.9 8.5E-05 35.0 9.5 67 210-288 40-107 (155)
109 PRK09248 putative hydrolase; V 87.8 0.35 7.5E-06 46.7 2.3 60 44-104 17-77 (246)
110 PRK05761 DNA polymerase I; Rev 86.8 5.8 0.00013 45.1 11.6 97 207-309 208-334 (787)
111 cd06141 WRN_exo DEDDy 3'-5' ex 86.5 17 0.00036 32.6 12.4 131 135-313 18-169 (170)
112 PHA02524 43A DNA polymerase su 84.5 10 0.00022 40.9 11.5 140 135-285 106-281 (498)
113 TIGR01388 rnd ribonuclease D. 84.2 35 0.00077 35.2 15.0 129 135-315 18-165 (367)
114 cd06129 RNaseD_like DEDDy 3'-5 84.0 18 0.00039 32.4 11.4 131 135-313 13-160 (161)
115 PF01396 zf-C4_Topoisom: Topoi 79.4 2 4.4E-05 30.1 2.7 29 376-411 10-38 (39)
116 KOG1275 PAB-dependent poly(A) 78.1 1.1 2.4E-05 50.8 1.6 110 187-314 972-1090(1118)
117 COG0613 Predicted metal-depend 77.3 1.5 3.2E-05 43.1 2.1 52 44-103 15-67 (258)
118 smart00474 35EXOc 3'-5' exonuc 74.5 37 0.00081 29.4 10.2 90 213-315 64-170 (172)
119 cd06148 Egl_like_exo DEDDy 3'- 72.8 49 0.0011 30.8 11.0 78 232-317 69-178 (197)
120 TIGR01856 hisJ_fam histidinol 58.4 6.7 0.00014 38.0 2.2 60 45-104 14-86 (253)
121 PRK07945 hypothetical protein; 57.4 7.5 0.00016 39.6 2.4 61 44-104 109-175 (335)
122 TIGR00593 pola DNA polymerase 57.2 33 0.00071 39.7 7.7 96 208-315 362-476 (887)
123 KOG0969 DNA polymerase delta, 55.8 5.5 0.00012 44.8 1.2 160 136-313 275-491 (1066)
124 COG0749 PolA DNA polymerase I 55.1 1.1E+02 0.0024 33.9 10.9 131 138-315 25-179 (593)
125 PF04216 FdhE: Protein involve 54.5 4.4 9.5E-05 40.3 0.2 42 360-405 170-216 (290)
126 PRK08392 hypothetical protein; 54.4 6.8 0.00015 37.1 1.4 56 44-104 12-71 (215)
127 PHA02563 DNA polymerase; Provi 54.3 1.6E+02 0.0034 33.0 12.1 39 213-252 50-89 (630)
128 cd06142 RNaseD_exo DEDDy 3'-5' 53.4 1.6E+02 0.0034 26.0 10.1 92 212-316 52-160 (178)
129 PRK00912 ribonuclease P protei 52.0 8.9 0.00019 36.8 1.9 50 44-103 14-64 (237)
130 PRK06319 DNA topoisomerase I/S 44.4 16 0.00034 42.1 2.6 37 365-411 697-733 (860)
131 COG1387 HIS2 Histidinol phosph 43.2 16 0.00036 35.3 2.2 60 44-104 14-77 (237)
132 PRK07328 histidinol-phosphatas 43.0 14 0.0003 36.1 1.7 60 45-104 17-89 (269)
133 PRK10829 ribonuclease D; Provi 41.1 2.2E+02 0.0047 29.7 10.1 129 135-316 22-170 (373)
134 TIGR01056 topB DNA topoisomera 40.1 19 0.00042 40.1 2.4 38 367-410 614-653 (660)
135 PRK05588 histidinol-phosphatas 39.0 24 0.00053 34.0 2.7 59 45-104 15-75 (255)
136 PF11074 DUF2779: Domain of un 37.1 66 0.0014 28.4 4.9 57 206-271 54-117 (130)
137 cd06140 DNA_polA_I_Bacillus_li 37.0 2.5E+02 0.0054 24.9 8.8 108 135-290 3-112 (178)
138 PRK07726 DNA topoisomerase III 30.6 30 0.00064 38.6 1.9 17 388-410 629-645 (658)
139 PRK08609 hypothetical protein; 29.7 36 0.00078 37.3 2.4 61 44-104 347-413 (570)
140 PRK06599 DNA topoisomerase I; 27.3 39 0.00085 37.8 2.2 26 377-409 596-621 (675)
141 PF06777 DUF1227: Protein of u 24.2 3.1E+02 0.0068 24.9 7.0 101 186-310 41-141 (146)
142 TIGR01562 FdhE formate dehydro 22.3 57 0.0012 33.1 2.1 40 363-405 186-229 (305)
143 PF04244 DPRP: Deoxyribodipyri 21.1 2E+02 0.0044 27.7 5.5 83 204-291 74-162 (224)
144 TIGR01685 MDP-1 magnesium-depe 20.8 3.3E+02 0.0072 25.1 6.7 12 136-147 3-14 (174)
No 1
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.8e-54 Score=470.55 Aligned_cols=248 Identities=18% Similarity=0.211 Sum_probs=228.1
Q ss_pred cCCccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcccCCCcCccccccccc
Q 015078 40 KDDTIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQFYPFPVENRFQFAPYN 119 (413)
Q Consensus 40 ~~~~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~y~~~v~d~~~~~~~~ 119 (413)
+.--++.++.+||++|++|||+|||||| |+++|+||++|.+++|+|+|.|||+|++ +++|++ ||+
T Consensus 346 S~mDai~sv~~~vk~A~kwghkaIAITD--------h~~VqafP~~y~~akK~giK~IyG~Ean----lvdD~v---piv 410 (1444)
T COG2176 346 SQMDAITSVEELVKQAKKWGHKAIAITD--------HGVVQAFPEAYKAAKKYGIKAIYGLEAN----LVDDGV---PIV 410 (1444)
T ss_pred hhhcccCCHHHHHHHHHHcCCceEEEec--------CcchhhchHHHHhhhhcCceEEEeeeee----eccCCC---cee
Confidence 3445779999999999999999999995 7777899999999999999999999999 699998 999
Q ss_pred cCCCCCCCCCCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCC
Q 015078 120 MLTPAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQ 199 (413)
Q Consensus 120 ~~~~~~p~~~~~q~~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT 199 (413)
+|+.+..+++ .+|||||+||||| ++..++|||||||++ ++|++++.|+.||+|.. +||.++++|||||
T Consensus 411 ~N~~d~~l~d-----atyVVfDiETTGL---s~~~d~iIE~aAvKi--kng~iId~f~~Fi~P~~--pl~~~~telTgIT 478 (1444)
T COG2176 411 YNPDDQKLDD-----ATYVVFDIETTGL---SPVYDEIIEIAAVKI--KNGRIIDKFQFFIKPGR--PLSATITELTGIT 478 (1444)
T ss_pred cCcccccccc-----ccEEEEEeecCCc---Ccccchhhhheeeee--eCCcchHHHHHhcCCCC--cCchhhhhccccC
Confidence 9999999984 8999999999998 889999999999999 79999999999999996 5999999999999
Q ss_pred hhhhcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCC
Q 015078 200 QIQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRC 278 (413)
Q Consensus 200 ~edV~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~ 278 (413)
++||++|+++.+||.+|.+|++++++|+|| ++||| +||+..+.+.++.. +.+++|||+.+.|.++| .++|
T Consensus 479 deml~~a~~i~~vL~kf~~~~~d~IlVAHN------asFD~-gFl~~~~~k~~~~~--~~~pvIDTL~lar~L~P~~ksh 549 (1444)
T COG2176 479 DEMLENAPEIEEVLEKFREFIGDSILVAHN------ASFDM-GFLNTNYEKYGLEP--LTNPVIDTLELARALNPEFKSH 549 (1444)
T ss_pred HHHHcCCccHHHHHHHHHHHhcCcEEEecc------Cccch-hHHHHHHHHhCCcc--ccCchhhHHHHHHHhChhhhhc
Confidence 999999999999999999999997665555 59998 89999999988753 78899999999999997 7899
Q ss_pred CHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHhccccccccc
Q 015078 279 NLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNS 324 (413)
Q Consensus 279 ~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~~~~i~e~ 324 (413)
+|+.++++||+.++ +||||.+||.+|++||..++++..+.+|+.+
T Consensus 550 ~Lg~l~kk~~v~le-~hHRA~yDaeat~~vf~~f~~~~ke~Gi~~l 594 (1444)
T COG2176 550 RLGTLCKKLGVELE-RHHRADYDAEATAKVFFVFLKDLKEKGITNL 594 (1444)
T ss_pred chHHHHHHhCccHH-HhhhhhhhHHHHHHHHHHHHHHHHHhchhhH
Confidence 99999999999995 9999999999999999999998877777554
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=1e-40 Score=377.38 Aligned_cols=242 Identities=19% Similarity=0.236 Sum_probs=215.4
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcccCCCcCccccccccccCC
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQFYPFPVENRFQFAPYNMLT 122 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~y~~~v~d~~~~~~~~~~~ 122 (413)
-|+.++.++|++|++|||++||||| |+.+|+||+++.++++.++++|||+|.+ .++|.+ ++++++
T Consensus 117 Dg~~~~~elv~~A~~~Gl~aiAITD--------H~~~~~~~~~~~~~~~~~ikvI~GvE~~----~~~d~~---~~v~n~ 181 (1213)
T TIGR01405 117 DAITSVQEYVKQAKKWGHKAIAITD--------HGVVQAFPEAYKAAKKDGIKIIYGMEAN----LVDDRV---PIVYNP 181 (1213)
T ss_pred ccCCCHHHHHHHHHHCCCCEEEEec--------CCCccCHHHHHHHHHhcCCEEEEEEEEE----eecccc---hhhcCc
Confidence 4567788999999999999999995 7777899999999999999999999998 478877 799999
Q ss_pred CCCCC-CCCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChh
Q 015078 123 PAHPY-DFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQI 201 (413)
Q Consensus 123 ~~~p~-~~~~q~~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~e 201 (413)
.+.++ + ..+|||||+||||+ ++..++|||||||+++ +|+++++|++||+|.. +|++.++++||||++
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 6889999999999995 699999999999999
Q ss_pred hhcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCH
Q 015078 202 QVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNL 280 (413)
Q Consensus 202 dV~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L 280 (413)
||++||++++|+++|.+|+++. +.|+|++.||+ .||+.+++++|++. +.++++|++.+++.+++ .++++|
T Consensus 250 ~L~~ap~~~evl~~f~~fl~~~------iLVaHNa~FD~-~fL~~~~~r~g~~~--~~~~~IDTl~lar~l~p~~k~~kL 320 (1213)
T TIGR01405 250 MLENAPEIEEVLEKFKEFFKDS------ILVAHNASFDI-GFLNTNFEKVGLEP--LENPVIDTLELARALNPEYKSHRL 320 (1213)
T ss_pred HHhCCCCHHHHHHHHHHHhCCC------eEEEEChHHHH-HHHHHHHHHcCCCc--cCCCEeEHHHHHHHHhccCCCCCH
Confidence 9999999999999999999875 45566679995 89999999998752 45689999999998886 578999
Q ss_pred HHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHhcccccc
Q 015078 281 KEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSI 321 (413)
Q Consensus 281 ~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~~~~i 321 (413)
++++++||++.. ++|||++||.+|++||.+|+++..+..+
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 999999999997 5899999999999999999987655544
No 3
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=3.8e-41 Score=318.93 Aligned_cols=220 Identities=36% Similarity=0.674 Sum_probs=191.5
Q ss_pred CCcccEEEEEEeeCCCCCCC-CCCCcEEEEcEEEEEc-CCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCH
Q 015078 132 QEFQYFVVIDFEATCDKDKN-PYPQEIIEFPSVIVSS-VTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL 209 (413)
Q Consensus 132 q~~~~fVV~D~ETTGl~~~~-~~~deIIEIGAV~vd~-~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f 209 (413)
|.+++++|+|||+||.++.. .+..||||+.||.+|. ++++|.++|+.||||..||.||++|+++|||.|++|+.||+|
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 55689999999999998755 4789999999996664 566666699999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCC-C-ccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHH
Q 015078 210 SEALLRHDKWLENKGIK-N-TNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEM 286 (413)
Q Consensus 210 ~eVl~~f~~fL~~~~lv-~-~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~ 286 (413)
.+||.+|..||....+. . +++++|+||++||+.||..+|++.+|..|.++++|||+++.|+..+.. .+.++..|+++
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 99999999999887665 2 689999999999999999999999999999999999999999999976 57899999999
Q ss_pred cCCCCCCCCCchHHHHHHHHHHHHHHHHhccccccccccc-cccCCCCCcccCCCCCCCCCCCcccchhcc
Q 015078 287 AGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLM-WQTNDGSLTWNQFPERIFLPPHQLHKQMDL 356 (413)
Q Consensus 287 ~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~~~~i~e~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (413)
|||+++|++|+|+|||.++|+|.++|+++|.++.||+.-. |+.++.... ..|.+ .+.++.++.++
T Consensus 213 ~gL~f~Gr~HsGiDDa~Nia~I~~kM~~dg~~~~In~~~~~~~~q~~~~~----~~~~~-~~~~~~~~~~~ 278 (280)
T KOG0542|consen 213 YGLQFEGRAHSGIDDARNIARIAQKMIRDGAEFRINELCDLWERQPLVPN----RSWPS-EFADAGQIFER 278 (280)
T ss_pred hCCcccCCcccCchhHHHHHHHHHHHHhCCcEEEechhhhhcccCccccc----ccCCc-ccCCccccccc
Confidence 9999999999999999999999999999999999996533 544433332 34544 55666665544
No 4
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=100.00 E-value=2.6e-38 Score=361.61 Aligned_cols=242 Identities=18% Similarity=0.203 Sum_probs=214.7
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcccCCCcCccccccccccCC
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQFYPFPVENRFQFAPYNMLT 122 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~y~~~v~d~~~~~~~~~~~ 122 (413)
-|+.++.++|++|++|||+|||||| |+++|+||+++.++++.++|+|||+|.+. ++|++ +++++.
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 77778999999999999999999999983 77776 788887
Q ss_pred CCCCCCCCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhh
Q 015078 123 PAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQ 202 (413)
Q Consensus 123 ~~~p~~~~~q~~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~ed 202 (413)
.+.++.. ..+||||+||||+ ++..++|||||||+++ +|++.++|++||+|.. +++++++++||||+++
T Consensus 412 ~~~~L~~-----~~~VVfDLETTGL---~~~~deIIEIgAV~V~--~G~iie~F~~~V~P~~--~I~~~~~~LTGIT~e~ 479 (1437)
T PRK00448 412 VDRDLKD-----ATYVVFDVETTGL---SAVYDEIIEIGAVKIK--NGEIIDKFEFFIKPGH--PLSAFTTELTGITDDM 479 (1437)
T ss_pred Cchhhcc-----CcEEEEEhhhcCC---CCchhhhheeeeEEEe--CCeEeeeEEEEECCCC--CCCHHHHHHhCCCHHH
Confidence 7766662 6899999999998 6788999999999995 7899999999999996 6999999999999999
Q ss_pred hcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHH
Q 015078 203 VDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLK 281 (413)
Q Consensus 203 V~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~ 281 (413)
|.+++++.+|+++|.+|+++. ++|+|++.||+ .||+..+++.|++. +...++|+..+++.+++ .++++|+
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 999999999999999999874 56777889995 89999999998754 35678999999998886 5678999
Q ss_pred HHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHhcccccc
Q 015078 282 EAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSI 321 (413)
Q Consensus 282 ~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~~~~i 321 (413)
+++++||++.. .+|||++||++||+||.+|+++..+.++
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=6.4e-37 Score=288.01 Aligned_cols=175 Identities=30% Similarity=0.489 Sum_probs=153.7
Q ss_pred ccEEEEEEeeCCCCC-CCCC--CCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHH
Q 015078 135 QYFVVIDFEATCDKD-KNPY--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSE 211 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~-~~~~--~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~e 211 (413)
.+||||||||||++. .++. .+||||||||+++ ++++.++|++||||..++.|+++++++||||++||++||+|++
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 479999999999853 2332 5899999999996 6788899999999986556999999999999999999999999
Q ss_pred HHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCC
Q 015078 212 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLA 290 (413)
Q Consensus 212 Vl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~~gI~ 290 (413)
|+++|.+|+++. +.+++||++||+ .||+.+|+++|+++| +.+.|+|+..+++.+++. ..++|++++++|||+
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 999999999862 357889999996 899999999999877 447899999888888763 468999999999999
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHhccc
Q 015078 291 WQGRAHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 291 ~~g~~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
..+++|||++||++||+||.+|++++.-
T Consensus 155 ~~~~~H~Al~DA~~ta~l~~~l~~~~~~ 182 (207)
T PRK07748 155 GTGKHHCALDDAMTTYNIFKLVEKDKEY 182 (207)
T ss_pred CCCCCcChHHHHHHHHHHHHHHHhCcce
Confidence 8778999999999999999999988643
No 6
>PTZ00315 2'-phosphotransferase; Provisional
Probab=100.00 E-value=4.1e-36 Score=316.20 Aligned_cols=194 Identities=39% Similarity=0.642 Sum_probs=166.3
Q ss_pred CCCcccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHH
Q 015078 131 PQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 210 (413)
Q Consensus 131 ~q~~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~ 210 (413)
.|.++.||||||||||++......+||||||||+||.++++++++|++||||..+|.|+++|++|||||++||++||+|.
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 34567999999999998532234689999999999988999999999999999777799999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCC----CccEEEEEcCcchHHHHHHHHHHH---cCCCCCCCCCceeehHHHHH-HhcC--------
Q 015078 211 EALLRHDKWLENKGIK----NTNFAVVTWSNWDCRVMLESECRF---KKIWKPPYFNRWINLKVPFH-EVFG-------- 274 (413)
Q Consensus 211 eVl~~f~~fL~~~~lv----~~n~~vV~~g~fDir~fL~~~~~~---~gi~~P~~~~~~iDl~~l~r-~l~~-------- 274 (413)
+|+.+|.+|+++..++ .++++|+||++||++.||..+|+. .++ |..+..|+|++..+. .+++
T Consensus 132 eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~--p~~f~~widLk~~lar~l~p~~~~~~~~ 209 (582)
T PTZ00315 132 VVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGT--PLSFQRWCNLKKYMSQLGFGNGSGCGGG 209 (582)
T ss_pred HHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCC--CcccceEEEhHHHHHHHhCccccccccc
Confidence 9999999999987532 246899999999986799999984 454 435678999865444 4444
Q ss_pred ----CCCCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHhccccccccccc
Q 015078 275 ----GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLM 326 (413)
Q Consensus 275 ----~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~~~~i~e~l~ 326 (413)
.++++|.+|++.+||+++|++|+|++||++||+||.+|+++|..+.+|..++
T Consensus 210 ~~~~~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~g~~~~~t~~~~ 265 (582)
T PTZ00315 210 ATPPLGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRRGLVIDPTFDTA 265 (582)
T ss_pred cccccCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHcCCEEEecCCCC
Confidence 2457999999999999999999999999999999999999999999888776
No 7
>PRK06722 exonuclease; Provisional
Probab=100.00 E-value=5.1e-34 Score=279.85 Aligned_cols=172 Identities=26% Similarity=0.394 Sum_probs=146.4
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 134 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 134 ~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
...||||||||||....+...++|||||||+|+..+++++++|++||||.. +|++++++|||||++||++||+|++|+
T Consensus 4 ~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--~I~~~i~~LTGIT~emV~~AP~f~eVl 81 (281)
T PRK06722 4 ATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--RLTRHTTKLTGITKKDLIGVEKFPQII 81 (281)
T ss_pred CCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--cCCHhHhhhcCCCHHHHcCCCCHHHHH
Confidence 368999999999743222355899999999997434588999999999996 699999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCC-CceeehHHHHHHhcCC---CCCCHHHHHHHcCC
Q 015078 214 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYF-NRWINLKVPFHEVFGG---VRCNLKEAVEMAGL 289 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~-~~~iDl~~l~r~l~~~---~~~~L~~l~~~~gI 289 (413)
.+|.+|+++. .+||||+.||+ .||+.++++.|++.|.+. ..++|+..+++..++. ..++|++++++|||
T Consensus 82 ~ef~~fig~~------~lvahna~FD~-~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL 154 (281)
T PRK06722 82 EKFIQFIGED------SIFVTWGKEDY-RFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGL 154 (281)
T ss_pred HHHHHHHCCC------cEEEEEeHHHH-HHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCC
Confidence 9999999863 46889999995 899999999998877543 3578988776555432 34689999999999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHH
Q 015078 290 AWQGRAHCGLDDAKNTARLLALLMH 314 (413)
Q Consensus 290 ~~~g~~HrALdDA~aTA~Ll~~ll~ 314 (413)
+..|++|||++||++||+||.+|++
T Consensus 155 ~~~g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 155 IWEGKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCCCCcCcHHHHHHHHHHHHHHhc
Confidence 9888899999999999999999984
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=9.4e-33 Score=249.76 Aligned_cols=172 Identities=44% Similarity=0.785 Sum_probs=147.4
Q ss_pred EEEEEEeeCCCCCCC--CCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 137 FVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 137 fVV~D~ETTGl~~~~--~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
|||||+||||+.... ...++|||||||+++..+++++++|+++|||...+.+++++.++||||+++|+++|++++|++
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 699999999984211 235899999999999666668999999999996456999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQ 292 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~-~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~~gI~~~ 292 (413)
+|.+|+++.. +..+|||+.||. .+|..++.+.+.. .|+.+.+++|++.+++..++. +.++|++++++||++..
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 6666777665543 455678999999999999885 47899999999999998
Q ss_pred CCCCchHHHHHHHHHHHHHHH
Q 015078 293 GRAHCGLDDAKNTARLLALLM 313 (413)
Q Consensus 293 g~~HrALdDA~aTA~Ll~~ll 313 (413)
+++|+||+||++||+|+++|+
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=5.2e-32 Score=258.43 Aligned_cols=169 Identities=20% Similarity=0.137 Sum_probs=144.1
Q ss_pred cEEEEEEeeCCCCCCCCCC-CcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 136 YFVVIDFEATCDKDKNPYP-QEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~-deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
.+||||+||||+ ++.. ++|||||||.++ .+....++|++||+|.. .++++++++||||++||+++|+|++|+.
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 5544 899999999886 22334689999999996 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCC--CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP--YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ 292 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~--~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~~ 292 (413)
+|.+|+++.. .|+||+.||+ .||+.++++.|..++. .+.+|+|+..+++..++..+++|++++++|||+..
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 4566779995 8999999998843332 23689999999999998778899999999999976
Q ss_pred CC-CCchHHHHHHHHHHHHHHHHhcc
Q 015078 293 GR-AHCGLDDAKNTARLLALLMHRGF 317 (413)
Q Consensus 293 g~-~HrALdDA~aTA~Ll~~ll~~g~ 317 (413)
++ .|+|++||++||+||.+|.....
T Consensus 148 ~r~~H~Al~DA~~~a~v~~~l~~~~~ 173 (225)
T TIGR01406 148 HRTLHGALLDAHLLAEVYLALTGGQE 173 (225)
T ss_pred CCCCcCHHHHHHHHHHHHHHHHcCCc
Confidence 43 69999999999999999976543
No 10
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=9.2e-32 Score=258.95 Aligned_cols=172 Identities=22% Similarity=0.183 Sum_probs=148.0
Q ss_pred CCCCCCCCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeE--eeEEEEEEeCCCCCCCCcchhhhcCCCh
Q 015078 123 PAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQ 200 (413)
Q Consensus 123 ~~~p~~~~~q~~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i--~dsF~~~VkP~~~p~Ls~~~~~LTGIT~ 200 (413)
.++|+.+ ..|||||+||||+ ++..++|||||+|+++ ++++ .++|+++|+|.. +|+++++.+||||+
T Consensus 40 ~~~~~~~-----~~~vviD~ETTGl---~p~~d~IieIg~v~v~--~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt~ 107 (239)
T PRK09146 40 PDTPLSE-----VPFVALDFETTGL---DAEQDAIVSIGLVPFT--LQRIRCRQARHWVVKPRR--PLEEESVVIHGITH 107 (239)
T ss_pred CCCCccc-----CCEEEEEeECCCC---CCCCCcEEEEEEEEEE--CCeEeecceEEEEECCCC--CCChhhhhhcCCCH
Confidence 7788873 7999999999998 6788999999999996 4554 589999999996 59999999999999
Q ss_pred hhhcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHc-CCCCCCCCCceeehHHHHHHhcCC----
Q 015078 201 IQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFK-KIWKPPYFNRWINLKVPFHEVFGG---- 275 (413)
Q Consensus 201 edV~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~-gi~~P~~~~~~iDl~~l~r~l~~~---- 275 (413)
+||.+||++++|+.+|.+|+++. ..|+|+..|| +.||++++++. +..+ ..+++|+..+++.+++.
T Consensus 108 e~l~~ap~~~evl~~l~~~~~~~------~lVaHna~FD-~~fL~~~l~~~~~~~~---~~~~iDTl~Lar~l~~~~~~~ 177 (239)
T PRK09146 108 SELQDAPDLERILDELLEALAGK------VVVVHYRRIE-RDFLDQALRNRIGEGI---EFPVIDTMEIEARIQRKQAGG 177 (239)
T ss_pred HHHhCCCCHHHHHHHHHHHhCCC------EEEEECHHHH-HHHHHHHHHHhcCCCC---CCceechHHHHHHHccccccc
Confidence 99999999999999999999874 4566777999 59999999875 3332 35689999998887542
Q ss_pred ----------CCCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHhcc
Q 015078 276 ----------VRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGF 317 (413)
Q Consensus 276 ----------~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~ 317 (413)
.+++|++++++|||+.+ ++|+|++||++||+||.+++++..
T Consensus 178 ~~~~~~~~~~~~~~L~~l~~~~gl~~~-~~H~Al~DA~ata~l~~~~~~~~~ 228 (239)
T PRK09146 178 LWNRLKGKKPESIRLADSRLRYGLPAY-SPHHALTDAIATAELLQAQIAHHF 228 (239)
T ss_pred ccchhccCCCCCCCHHHHHHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHHHc
Confidence 35689999999999986 789999999999999999997754
No 11
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=6.1e-32 Score=260.31 Aligned_cols=172 Identities=19% Similarity=0.204 Sum_probs=148.1
Q ss_pred ccEEEEEEeeCCCCCCCCC-CCcEEEEcEEEEEcCCCeE-eeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPY-PQEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~-~deIIEIGAV~vd~~~g~i-~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
..|||||+||||+ ++. .++|||||+|.++ ++.+ .++|++||+|.+ .+++++.++||||++||.++|+|++|
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 555 7999999999996 4454 578999999986 69999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCC--CCceeehHHHHHHhcCCCCCCHHHHHHHcCCC
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPY--FNRWINLKVPFHEVFGGVRCNLKEAVEMAGLA 290 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~--~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~ 290 (413)
+++|.+|+++.. .|+||+.||+ .||+.++++.|..+|.+ ...++|+..+++.+++.++++|+.++++|||+
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 999999998864 4567779996 89999999988666643 34699999999999987778999999999998
Q ss_pred CCCC-CCchHHHHHHHHHHHHHHHHhccccc
Q 015078 291 WQGR-AHCGLDDAKNTARLLALLMHRGFKFS 320 (413)
Q Consensus 291 ~~g~-~HrALdDA~aTA~Ll~~ll~~g~~~~ 320 (413)
...+ .|+||.||++||+||.+|+.....+.
T Consensus 150 ~~~r~~H~AL~DA~~~A~v~~~l~~~~~~l~ 180 (240)
T PRK05711 150 NSHRTLHGALLDAEILAEVYLAMTGGQTSLG 180 (240)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCcccccc
Confidence 7543 69999999999999999986644443
No 12
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.98 E-value=4.3e-31 Score=236.37 Aligned_cols=166 Identities=34% Similarity=0.437 Sum_probs=147.9
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHH
Q 015078 136 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 215 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~ 215 (413)
.||+||+||||+ ++..++|||||+|+++ ++++.++|+++|+|.. +++++++++||||+++|++++++.+|+.+
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 489999999998 5667999999999997 4558899999999974 69999999999999999999999999999
Q ss_pred HHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCC
Q 015078 216 HDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGR 294 (413)
Q Consensus 216 f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~~g~ 294 (413)
|.+|+++. .+++||+ +||+ .||+.++.+.|+..|. ..+++|+..+++..++..+++|++++++||++..++
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 4678887 9995 8999999999988773 356999999998888766789999999999999765
Q ss_pred CCchHHHHHHHHHHHHHHHHhc
Q 015078 295 AHCGLDDAKNTARLLALLMHRG 316 (413)
Q Consensus 295 ~HrALdDA~aTA~Ll~~ll~~g 316 (413)
+|+|++||++|++|+.+++++.
T Consensus 146 ~H~A~~Da~~t~~l~~~~~~~~ 167 (169)
T smart00479 146 AHRALDDARATAKLFKKLVERL 167 (169)
T ss_pred CcCcHHHHHHHHHHHHHHHHHh
Confidence 6999999999999999998764
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=2.7e-31 Score=239.74 Aligned_cols=162 Identities=21% Similarity=0.209 Sum_probs=140.4
Q ss_pred EEEEEEeeCCCCCCCC-CCCcEEEEcEEEEEcCCCeE-eeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 137 FVVIDFEATCDKDKNP-YPQEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 137 fVV~D~ETTGl~~~~~-~~deIIEIGAV~vd~~~g~i-~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
||+||+||||+ ++ ..++|||||||+++ ++.+ .++|+.+|+|.. .++++++++||||+++|+++|++.+|++
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 55 57899999999996 3443 569999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCC-CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP-YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQG 293 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~-~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~~g 293 (413)
+|.+|+++. .+|+||+.|| +.||+++++++|+..+. ....|+|+..+++..++..+++|++++++||++.++
T Consensus 74 ~l~~~l~~~------~lv~hn~~fD-~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~ 146 (167)
T cd06131 74 EFLDFIRGA------ELVIHNASFD-VGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSH 146 (167)
T ss_pred HHHHHHCCC------eEEEeChHHh-HHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCC
Confidence 999999874 3567788999 48999999998775432 345799999999988876778999999999999864
Q ss_pred -CCCchHHHHHHHHHHHHHH
Q 015078 294 -RAHCGLDDAKNTARLLALL 312 (413)
Q Consensus 294 -~~HrALdDA~aTA~Ll~~l 312 (413)
++|+|++||++||+||.+|
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=1.5e-30 Score=253.04 Aligned_cols=174 Identities=20% Similarity=0.257 Sum_probs=153.0
Q ss_pred CCCCCCCCCCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCCh
Q 015078 121 LTPAHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQ 200 (413)
Q Consensus 121 ~~~~~p~~~~~q~~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~ 200 (413)
....+|+.+ ..|||||+||||+ ++..++|||||||+++ +|++.++|+++|+|. .++++++++||||+
T Consensus 59 ~~~~~~~~~-----~~~vv~DiETTG~---~~~~~~IIEIGAv~v~--~g~i~~~f~~~v~p~---~ip~~~~~itGIt~ 125 (257)
T PRK08517 59 KTRFTPIKD-----QVFCFVDIETNGS---KPKKHQIIEIGAVKVK--NGEIIDRFESFVKAK---EVPEYITELTGITY 125 (257)
T ss_pred ccCCCCCCC-----CCEEEEEEeCCCC---CCCCCeEEEEEEEEEE--CCEEEEEEEEEECCC---CCChhhhhhcCcCH
Confidence 345566653 6899999999997 5677899999999996 788999999999996 48999999999999
Q ss_pred hhhcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCH
Q 015078 201 IQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNL 280 (413)
Q Consensus 201 edV~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L 280 (413)
+||++||++.+|+.+|.+|++++ +.|+|+++|| ..||++++++.|+.. +.++++|+..+++++++..+++|
T Consensus 126 e~l~~ap~~~evl~~f~~fl~~~------v~VaHNa~FD-~~fL~~~l~r~g~~~--~~~~~ldtl~la~~~~~~~~~~L 196 (257)
T PRK08517 126 EDLENAPSLKEVLEEFRLFLGDS------VFVAHNVNFD-YNFISRSLEEIGLGP--LLNRKLCTIDLAKRTIESPRYGL 196 (257)
T ss_pred HHHcCCCCHHHHHHHHHHHHCCC------eEEEECHHHH-HHHHHHHHHHcCCCC--CCCCcEehHHHHHHHccCCCCCH
Confidence 99999999999999999999874 4566777999 589999999998754 46788999999998887778899
Q ss_pred HHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHhcc
Q 015078 281 KEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGF 317 (413)
Q Consensus 281 ~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~ 317 (413)
+++++++|++.+ ++|||++||++||+||.+++.+..
T Consensus 197 ~~L~~~lgi~~~-~~HrAl~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 197 SFLKELLGIEIE-VHHRAYADALAAYEIFKICLLNLP 232 (257)
T ss_pred HHHHHHcCcCCC-CCCChHHHHHHHHHHHHHHHHHhH
Confidence 999999999986 789999999999999999997653
No 15
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.3e-30 Score=259.97 Aligned_cols=164 Identities=26% Similarity=0.328 Sum_probs=149.1
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
.+|||||+||||+ ++..++|||||||+++ ++++.++|+++|+|.. .|+++++.+||||++||.++|+|.+|+.
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 6778999999999996 7899999999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQG 293 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g 293 (413)
+|++|+++. ..|+||++||+ .||.+++.+.|++.| ..+++|+..+++.+++ .++++|++++++||++.
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 46788899995 899999999998765 3579999999998886 45789999999999998
Q ss_pred CCCchHHHHHHHHHHHHHHHHhc
Q 015078 294 RAHCGLDDAKNTARLLALLMHRG 316 (413)
Q Consensus 294 ~~HrALdDA~aTA~Ll~~ll~~g 316 (413)
++|+|++||++|++||.+++...
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
>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=1.4e-30 Score=231.41 Aligned_cols=154 Identities=23% Similarity=0.301 Sum_probs=138.5
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHH
Q 015078 137 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 216 (413)
Q Consensus 137 fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f 216 (413)
||+||+||||. ..++|||||||+++ ++++.++|+++|+|.. +++++++++||||+++|++++++.+|+.+|
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 6888999999999996 699999999999999999999999999999
Q ss_pred HHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCCC
Q 015078 217 DKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGRA 295 (413)
Q Consensus 217 ~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~~ 295 (413)
.+|+++. +.|.|+++|| +.||++++++.|+..| ..+++|+..+++..++ .++++|++++++||++.. +
T Consensus 72 ~~~l~~~------~lv~hn~~fD-~~~l~~~~~~~g~~~~--~~~~idt~~~~~~~~~~~~~~~L~~l~~~~g~~~~--~ 140 (156)
T cd06130 72 KPFLGGS------LVVAHNASFD-RSVLRAALEAYGLPPP--PYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELN--H 140 (156)
T ss_pred HHHhCCC------EEEEeChHHh-HHHHHHHHHHcCCCCC--CCCEEEHHHHHHHHhccCCCCCHHHHHHHcCCCcc--C
Confidence 9999873 4566677999 4899999999998876 3579999999998887 467899999999999986 8
Q ss_pred CchHHHHHHHHHHHH
Q 015078 296 HCGLDDAKNTARLLA 310 (413)
Q Consensus 296 HrALdDA~aTA~Ll~ 310 (413)
|+|++||++||+||.
T Consensus 141 H~Al~Da~~ta~l~~ 155 (156)
T cd06130 141 HDALEDARACAEILL 155 (156)
T ss_pred cCchHHHHHHHHHHh
Confidence 999999999999985
No 17
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.3e-30 Score=259.55 Aligned_cols=164 Identities=16% Similarity=0.232 Sum_probs=146.1
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHH
Q 015078 136 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 215 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~ 215 (413)
+|||||+||||. ..++|||||||+++ +++++++|+++|||.. ..++++++.|||||++||+++|+|.+|+++
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 015078 216 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 294 (413)
Q Consensus 216 f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~ 294 (413)
|.+|+++. .+|+||++||+ .||+++++++++++| .++|+|+..+++++++ .++++|++++++||++. +
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 56778889995 899999999998876 3579999999999887 46789999999999985 5
Q ss_pred CCchHHHHHHHHHHHHHHHHhccc
Q 015078 295 AHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 295 ~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
+|+|++||++||+||.+|+++...
T Consensus 143 ~H~Al~DA~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 143 HHDALADAMACSNILLNISKELNS 166 (309)
T ss_pred ccCCHHHHHHHHHHHHHHHHHhcc
Confidence 899999999999999999987543
No 18
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=2.3e-30 Score=249.88 Aligned_cols=168 Identities=25% Similarity=0.308 Sum_probs=144.8
Q ss_pred ccEEEEEEeeCCCCCCCCCC-CcEEEEcEEEEEcCCCeE-eeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYP-QEIIEFPSVIVSSVTGQL-EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~-deIIEIGAV~vd~~~g~i-~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
.+|||||+||||+ ++.. ++|||||||+++ ++.+ .++|+++|+|.. +++++++++||||+++|++||++.+|
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 5899999999998 5554 899999999997 5666 899999999996 59999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCC
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAW 291 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~~gI~~ 291 (413)
+.+|.+|+++. ..|+|++.|| +.||+.++.+... .| +..+++|+..+++.+++. ++++|++++++||++.
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 99999999875 4566777999 5899998876532 22 456899999999888874 5789999999999999
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHhcccc
Q 015078 292 QGRAHCGLDDAKNTARLLALLMHRGFKF 319 (413)
Q Consensus 292 ~g~~HrALdDA~aTA~Ll~~ll~~g~~~ 319 (413)
. .+|+|++||++||+||.+++.+..+.
T Consensus 203 ~-~~H~Al~Da~ata~l~~~ll~~~~~~ 229 (244)
T PRK07740 203 P-RRHHALGDALMTAKLWAILLVEAQQR 229 (244)
T ss_pred C-CCCCcHHHHHHHHHHHHHHHHHHHHc
Confidence 7 46999999999999999999875543
No 19
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=4e-30 Score=256.48 Aligned_cols=168 Identities=17% Similarity=0.156 Sum_probs=147.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..|||||+||||+ ++..++|||||+|+++ .+|++.++|+++|+|.. ++..+.+||||++||.++|+|.++++
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 47889999999999985 24568899999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQG 293 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g 293 (413)
+|.+|+++. ++|+||..||+ .||++++++.|+.+| .+.++|+..+++.+.+ ..+++|++++++|||+..
T Consensus 87 ~l~~~l~~~------~lVaHNa~FD~-~fL~~~~~r~g~~~~--~~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~- 156 (313)
T PRK06063 87 EVAELLRGR------TLVAHNVAFDY-SFLAAEAERAGAELP--VDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQ- 156 (313)
T ss_pred HHHHHcCCC------EEEEeCHHHHH-HHHHHHHHHcCCCCC--CCCEEehHHHHHHhccCCCCCCHHHHHHHcCCCCC-
Confidence 999999875 45666779995 899999999998876 3568999999988764 568899999999999975
Q ss_pred CCCchHHHHHHHHHHHHHHHHhccccc
Q 015078 294 RAHCGLDDAKNTARLLALLMHRGFKFS 320 (413)
Q Consensus 294 ~~HrALdDA~aTA~Ll~~ll~~g~~~~ 320 (413)
++|+|++||++||+||.+++++.....
T Consensus 157 ~~H~Al~DA~ata~l~~~ll~~~~~~~ 183 (313)
T PRK06063 157 RPHDALDDARVLAGILRPSLERARERD 183 (313)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 789999999999999999998755443
No 20
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=5.1e-30 Score=245.62 Aligned_cols=173 Identities=20% Similarity=0.133 Sum_probs=146.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcC-CCCHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~-Ap~f~eVl 213 (413)
.+|||||+||||+ ++..++|||||+|+++ .+|+++++|+++|+|.. +|+++++++||||++|+.+ ++++.+|+
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 45788899999999986 5999999999999999975 89999999
Q ss_pred HHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHHcCCCC
Q 015078 214 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEMAGLAW 291 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~--~~~~~L~~l~~~~gI~~ 291 (413)
.+|.+++.+.. .+...+|+||++||+ .||+++++++|+..+ ....++|+..+.+.+.+ ..+++|++++++||++.
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 122456888899995 899999999987543 23568999888776654 24679999999999998
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHhcc
Q 015078 292 QGRAHCGLDDAKNTARLLALLMHRGF 317 (413)
Q Consensus 292 ~g~~HrALdDA~aTA~Ll~~ll~~g~ 317 (413)
+ .+|+|++||++|++||.+|+++..
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 689999999999999999987644
No 21
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.3e-29 Score=245.54 Aligned_cols=168 Identities=14% Similarity=0.139 Sum_probs=147.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..||+||+||||+ ++..++|||||+|+++ .+++.++|+++|+|.. +|++++..+||||++||+++|++.+|+.
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 6788999999999997 4577899999999996 5999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQGR 294 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~~g~ 294 (413)
+|.+|+++. .++|.|+.+||+ .||..++.+.|++++.....+||+..+++.+.+..+++|..++++||++.. .
T Consensus 80 ~~~~fl~~~-----~~lvghn~~FD~-~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~-~ 152 (250)
T PRK06310 80 QIKGFFKEG-----DYIVGHSVGFDL-QVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYD-G 152 (250)
T ss_pred HHHHHhCCC-----CEEEEECHHHHH-HHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCC-C
Confidence 999999763 345666679995 899999999999876444689999999887544456899999999999986 6
Q ss_pred CCchHHHHHHHHHHHHHHHHhc
Q 015078 295 AHCGLDDAKNTARLLALLMHRG 316 (413)
Q Consensus 295 ~HrALdDA~aTA~Ll~~ll~~g 316 (413)
+|+|++||++|++||.+|+++.
T Consensus 153 aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 153 NHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CcChHHHHHHHHHHHHHHHHhc
Confidence 8999999999999999998754
No 22
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=4.9e-30 Score=240.17 Aligned_cols=163 Identities=21% Similarity=0.261 Sum_probs=136.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeE--eeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i--~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
..|||||+||||+ ++..++|||||||+++ ++.+ .++|+++|+|.. .++++++++||||++||+++|++++|
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 6778999999999997 3444 378999999995 69999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHH-cCCCCCCCCCceeehHHHHHHh----cC--CCCCCHHHHHH
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRF-KKIWKPPYFNRWINLKVPFHEV----FG--GVRCNLKEAVE 285 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~-~gi~~P~~~~~~iDl~~l~r~l----~~--~~~~~L~~l~~ 285 (413)
+++|.+|+++.. .++|+..||+ .||++++++ .+.++| ..++|+..++... ++ .++++|+++++
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 999999998753 4556669994 899999986 465554 4689998766432 12 23579999999
Q ss_pred HcCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 015078 286 MAGLAWQGRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 286 ~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
+||++.. .+|+|++||++||+||.+|++.
T Consensus 172 ~~gi~~~-~~H~Al~DA~ata~l~~~l~~~ 200 (202)
T PRK09145 172 HLDLPVL-GRHDALNDAIMAALIFLRLRKG 200 (202)
T ss_pred HcCCCCC-CCCCcHHHHHHHHHHHHHHHhc
Confidence 9999986 5799999999999999998753
No 23
>PRK05168 ribonuclease T; Provisional
Probab=99.97 E-value=5.7e-30 Score=241.99 Aligned_cols=178 Identities=21% Similarity=0.213 Sum_probs=145.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcC-CCeE--eeEEEEEEeCCCCCCCCcchhhhcCCChhh-hcCCCCHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSV-TGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQIQ-VDRGVTLS 210 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~-~g~i--~dsF~~~VkP~~~p~Ls~~~~~LTGIT~ed-V~~Ap~f~ 210 (413)
.++||||+||||+ ++..++|||||||++... +|.+ .++|+++|+|.....|+++++++||||+++ +++++++.
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 677899999999999532 4553 589999999942236999999999999986 88999999
Q ss_pred HHHHHHHHHHhhcCC---CCccEEEEEcCcchHHHHHHHHHHHcCCCCCCC-CCceeehHHHHHHhcCCCCCCHHHHHHH
Q 015078 211 EALLRHDKWLENKGI---KNTNFAVVTWSNWDCRVMLESECRFKKIWKPPY-FNRWINLKVPFHEVFGGVRCNLKEAVEM 286 (413)
Q Consensus 211 eVl~~f~~fL~~~~l---v~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~-~~~~iDl~~l~r~l~~~~~~~L~~l~~~ 286 (413)
+++.+|.+|+.+... .+..+.|+|+.+||+ .||++++++.|+..+++ ..+++|+..+++.+++. .+|++++++
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 999999999974211 112456777789996 89999999998753222 23689999999988763 589999999
Q ss_pred cCCCCCC-CCCchHHHHHHHHHHHHHHHHhccc
Q 015078 287 AGLAWQG-RAHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 287 ~gI~~~g-~~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
||++... ++|+|++||++||+||.+|+++..+
T Consensus 171 ~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~~ 203 (211)
T PRK05168 171 AGIEFDNKEAHSALYDTEKTAELFCEIVNRWKR 203 (211)
T ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 9999742 5899999999999999999987643
No 24
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.97 E-value=2.9e-29 Score=237.83 Aligned_cols=171 Identities=18% Similarity=0.131 Sum_probs=143.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..|||||+||||+ ++..+ |||||||+++ .++.+.++|+++|+|.. ++++++..+||||++||.++|++++|++
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 56667 9999999975 34566799999999996 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC---CCCCCHHHHHHHcCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG---GVRCNLKEAVEMAGLAW 291 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~---~~~~~L~~l~~~~gI~~ 291 (413)
+|.+|+++. .+|+|++.||+ .||++++++.+...| ....++|+..+++.+++ ..+++|.+++++||++.
T Consensus 80 ~~~~~~~~~------~lVaHNa~FD~-~fL~~~~~r~~~~~~-~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~ 151 (217)
T TIGR00573 80 DFADYIRGA------ELVIHNASFDV-GFLNYEFSKLYKVEP-KTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITN 151 (217)
T ss_pred HHHHHhCCC------EEEEeccHHHH-HHHHHHHHHhcCCCC-CccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCC
Confidence 999999874 45667779995 899999998765433 34578999887776654 24678999999999987
Q ss_pred CC-CCCchHHHHHHHHHHHHHHHHhccccc
Q 015078 292 QG-RAHCGLDDAKNTARLLALLMHRGFKFS 320 (413)
Q Consensus 292 ~g-~~HrALdDA~aTA~Ll~~ll~~g~~~~ 320 (413)
.. .+|+|++||++|++||.+|+++.....
T Consensus 152 ~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 152 SHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 42 479999999999999999998765543
No 25
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.4e-29 Score=237.05 Aligned_cols=162 Identities=19% Similarity=0.257 Sum_probs=131.8
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 134 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 134 ~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
..+|||||+||||+ + ..++|||||||+++ +|+++++|++||+|.. +++++++++||||++||++||++.+|+
T Consensus 4 ~~~~vvlD~EtTGl---~-~~~eIIeIgaV~v~--~g~~~~~f~~lv~P~~--~i~~~~~~lhGIt~~~v~~ap~~~evl 75 (195)
T PRK07247 4 LETYIAFDLEFNTV---N-GVSHIIQVSAVKYD--DHKEVDSFDSYVYTDV--PLQSFINGLTGITADKIADAPKVEEVL 75 (195)
T ss_pred CCeEEEEEeeCCCC---C-CCCeEEEEEEEEEE--CCEEEEEEEEEECCCC--CCCccceecCCCCHHHHhCCCCHHHHH
Confidence 35899999999998 3 36899999999996 6888899999999995 599999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCccEEEEEcCc-chHHHHHHHHHHHcCCCCCCCCCceeehHHHH--HHh--c-CCCCCCHHHHHHHc
Q 015078 214 LRHDKWLENKGIKNTNFAVVTWSN-WDCRVMLESECRFKKIWKPPYFNRWINLKVPF--HEV--F-GGVRCNLKEAVEMA 287 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~~g~-fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~--r~l--~-~~~~~~L~~l~~~~ 287 (413)
++|.+|+++..+ |.|+.. ||+ .||+. .|+..+ ...++|+.... ++. + +.++++|++++++|
T Consensus 76 ~~f~~f~~~~~l------VaHNa~~fD~-~fL~~----~g~~~~--~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~ 142 (195)
T PRK07247 76 AAFKEFVGELPL------IGYNAQKSDL-PILAE----NGLDLS--DQYQVDLYDEAFERRSSDLNGIANLKLQTVADFL 142 (195)
T ss_pred HHHHHHHCCCeE------EEEeCcHhHH-HHHHH----cCCCcC--CCceeehHHHHHHhhccccCCCCCCCHHHHHHhc
Confidence 999999998644 455555 896 88853 465543 22457764322 222 2 24578999999999
Q ss_pred CCCCCCCCCchHHHHHHHHHHHHHHHHhccc
Q 015078 288 GLAWQGRAHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 288 gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
||+. .+|||++||++||+||.++++.+..
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 5799999999999999999987653
No 26
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.4e-29 Score=240.81 Aligned_cols=162 Identities=23% Similarity=0.261 Sum_probs=141.4
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHH
Q 015078 136 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 215 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~ 215 (413)
.+||||+||||+ ++..|+|||||++ + +...++|+++|+|.. +|+++++++||||++||+++|+|.+|+++
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 6778999999995 3 234578999999996 59999999999999999999999999999
Q ss_pred HHHHHhhcCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCCC
Q 015078 216 HDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQG 293 (413)
Q Consensus 216 f~~fL~~~~lv~~n~~vV~~-g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~~gI~~~g 293 (413)
|.+|+++. .+.+.|+ ++||+ .||..++++.|+++|. ..++|+..+++.+++. .+++|+.++++||++..
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 99999753 3456666 47995 8999999999988763 6899999999888763 57899999999999975
Q ss_pred CCCchHHHHHHHHHHHHHHHHhc
Q 015078 294 RAHCGLDDAKNTARLLALLMHRG 316 (413)
Q Consensus 294 ~~HrALdDA~aTA~Ll~~ll~~g 316 (413)
++|+|++||++|++||.+|+++.
T Consensus 144 ~aH~Al~Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 144 QAHRALDDVITLHRVFSALVGDL 166 (232)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999764
No 27
>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=1.3e-29 Score=233.08 Aligned_cols=161 Identities=17% Similarity=0.103 Sum_probs=131.8
Q ss_pred EEEEEEeeCCCCCCC-CCCCcEEEEcEEEEEcCC---C--------eEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhc
Q 015078 137 FVVIDFEATCDKDKN-PYPQEIIEFPSVIVSSVT---G--------QLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVD 204 (413)
Q Consensus 137 fVV~D~ETTGl~~~~-~~~deIIEIGAV~vd~~~---g--------~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~ 204 (413)
|||||+||||+ + +..++|||||||+++... + ++.++|+++|||.+ +|+++++.+||||++||.
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 578999999999997321 1 36789999999996 699999999999999999
Q ss_pred CCCCHHH-HHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHH
Q 015078 205 RGVTLSE-ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKE 282 (413)
Q Consensus 205 ~Ap~f~e-Vl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~ 282 (413)
++|++++ +.+.+.+|++... +..++|+||+ +||+ .||++++++.|+.+| ..+.++|+..+++.+.+ +|++
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 9998774 5555666665320 1124677787 8996 899999999998876 45678999999988775 8999
Q ss_pred HHHH-cCCCCCCCCCchHHHHHHHHHHHHH
Q 015078 283 AVEM-AGLAWQGRAHCGLDDAKNTARLLAL 311 (413)
Q Consensus 283 l~~~-~gI~~~g~~HrALdDA~aTA~Ll~~ 311 (413)
++++ ||++.. ++|+|++||.+|+++|.+
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 28
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.97 E-value=3.3e-29 Score=232.86 Aligned_cols=174 Identities=22% Similarity=0.225 Sum_probs=140.2
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEc-CCCe--EeeEEEEEEeCCCCCCCCcchhhhcCCChhh-hcCCCCHHH
Q 015078 136 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS-VTGQ--LEACFQTYVRPTCNQLLSDFCKDLTGIQQIQ-VDRGVTLSE 211 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~-~~g~--i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~ed-V~~Ap~f~e 211 (413)
.+||||+||||+ ++..++|||||||+|.. ++|. +.++|+++|+|....+|++++.++||||+++ ++++++..+
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 67789999999999962 2454 4689999999931125999999999999986 688898888
Q ss_pred HHHHHHHHHhhcCC---CCccEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc
Q 015078 212 ALLRHDKWLENKGI---KNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA 287 (413)
Q Consensus 212 Vl~~f~~fL~~~~l---v~~n~~vV~~g~fDir~fL~~~~~~~gi~-~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~ 287 (413)
++.+|.+++.+..- .+..+.|+|+++||+ .||++++++.|+. .|....+++|+..+.+.+++ ..+|++++++|
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 112466778889995 8999999999883 22112368999999998886 35899999999
Q ss_pred CCCCC-CCCCchHHHHHHHHHHHHHHHHh
Q 015078 288 GLAWQ-GRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 288 gI~~~-g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
||+.. .++|+|++||++||+||.+|+++
T Consensus 160 gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 160 GIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 99963 36899999999999999999864
No 29
>PRK07883 hypothetical protein; Validated
Probab=99.96 E-value=7.5e-29 Score=264.16 Aligned_cols=174 Identities=24% Similarity=0.223 Sum_probs=153.5
Q ss_pred CCCCCCCCCCcccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhh
Q 015078 124 AHPYDFQPQEFQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQV 203 (413)
Q Consensus 124 ~~p~~~~~q~~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV 203 (413)
++|+.+ ..|||||+||||+ ++..++|||||||+++ +++++++|+++|+|.. .|+++++.+||||++||
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 456653 7999999999998 6778999999999996 7888999999999985 69999999999999999
Q ss_pred cCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC---CCCCCH
Q 015078 204 DRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG---GVRCNL 280 (413)
Q Consensus 204 ~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~---~~~~~L 280 (413)
+++|++.+|+.+|.+|+++. +.|+||+.|| +.||+.+++++|+++| .+.++|+..+++.+++ ..+++|
T Consensus 77 ~~ap~~~evl~~f~~fl~~~------~lVaHNa~FD-~~fL~~~~~r~g~~~~--~~~~iDTl~lar~l~~~~~~~~~~L 147 (557)
T PRK07883 77 AGAPPIEEVLPAFLEFARGA------VLVAHNAPFD-IGFLRAAAARCGYPWP--GPPVLCTVRLARRVLPRDEAPNVRL 147 (557)
T ss_pred hCCCCHHHHHHHHHHHhcCC------EEEEeCcHHH-HHHHHHHHHHcCCCCC--CCCcEecHHHHHHhcccCCCCCCCH
Confidence 99999999999999999874 4566777999 4899999999999876 3578999999988875 357899
Q ss_pred HHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHhcccc
Q 015078 281 KEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHRGFKF 319 (413)
Q Consensus 281 ~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g~~~ 319 (413)
++++++||++.+ .+|+|++||++|++||.+++.+....
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 30
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.96 E-value=1.5e-30 Score=234.10 Aligned_cols=186 Identities=32% Similarity=0.498 Sum_probs=164.8
Q ss_pred ccEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 135 QYFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~-~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
..++|||||+|+.+|+ ++.+.+||||+|.+|+..+.+++|+|++||||..+|.|+.+|+.+|||||..|++||-|..|+
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 4789999999999875 578899999999999888889999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCCceeehHHHHHHhcCCCC-CCHHHHHHHcCCCC
Q 015078 214 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFNRWINLKVPFHEVFGGVR-CNLKEAVEMAGLAW 291 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~-~P~~~~~~iDl~~l~r~l~~~~~-~~L~~l~~~~gI~~ 291 (413)
++|..||..+.-. .+-++++||++||+ .|..++..+++. +| +..+++|++..|...++..+ .+|+.+++.+|+.+
T Consensus 84 E~f~r~L~~h~Pr-~~~~wa~wG~~Dm~-~l~q~~~~~~~~p~~-~kgp~vdl~~~yk~v~~~pr~tgln~ale~~G~sf 160 (210)
T COG5018 84 EDFIRKLNEHDPR-KNSTWATWGNMDMK-VLKQNCMFNHIPPFP-FKGPMVDLSLEYKNVFGDPRLTGLNKALEEYGDSF 160 (210)
T ss_pred HHHHHHHHhcCcc-cCCccccccchhHH-HHHHHHHhcCCCCcc-ccCccchHHHHHHHHhcCCccccHHHHHHHhcccc
Confidence 9999999886421 23368999999985 577888888876 33 56689999999999998654 79999999999999
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHhcccccccc
Q 015078 292 QGRAHCGLDDAKNTARLLALLMHRGFKFSITN 323 (413)
Q Consensus 292 ~g~~HrALdDA~aTA~Ll~~ll~~g~~~~i~e 323 (413)
.|++||||+||+++++|+..+......++.+.
T Consensus 161 ~G~~HraldDArn~~rl~klv~~~~~~~e~~~ 192 (210)
T COG5018 161 TGTHHRALDDARNAYRLFKLVEQDKQYLEKPK 192 (210)
T ss_pred CCchhhhHHHHHHHHHHHHHHcchhhhccCCC
Confidence 99999999999999999999998887776644
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=8.3e-29 Score=232.26 Aligned_cols=178 Identities=20% Similarity=0.188 Sum_probs=143.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEc-CCCeE--eeEEEEEEeCCCCCCCCcchhhhcCCChh-hhcCCCCHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS-VTGQL--EACFQTYVRPTCNQLLSDFCKDLTGIQQI-QVDRGVTLS 210 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~-~~g~i--~dsF~~~VkP~~~p~Ls~~~~~LTGIT~e-dV~~Ap~f~ 210 (413)
..+||||+||||+ ++..++|||||||+|.. .+|++ .++|+++|+|....+|++++.++||||++ |+++++++.
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 4799999999998 67789999999999852 24665 47899999984212699999999999976 699999999
Q ss_pred HHHHHHHHHHhhcC---CCCccEEEEEcCcchHHHHHHHHHHHcCCCC-CCCCCceeehHHHHHHhcCCCCCCHHHHHHH
Q 015078 211 EALLRHDKWLENKG---IKNTNFAVVTWSNWDCRVMLESECRFKKIWK-PPYFNRWINLKVPFHEVFGGVRCNLKEAVEM 286 (413)
Q Consensus 211 eVl~~f~~fL~~~~---lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~-P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~ 286 (413)
+++.+|.+|+.+.. +.+..++|+|+.+||+ .||+.++++.++.. |.....++|+..+++.+++ .++|++++++
T Consensus 85 ~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~-~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~--~~~L~~l~~~ 161 (200)
T TIGR01298 85 EALHEIFKVVRKAMKASGCQRAILVGHNANFDL-GFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG--QTVLAKACQA 161 (200)
T ss_pred HHHHHHHHHHHHHHHhcccCCCEEEEECchhhH-HHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC--cccHHHHHHH
Confidence 99999999885321 1123567778889996 89999999988642 2112468999999988776 3589999999
Q ss_pred cCCCCC-CCCCchHHHHHHHHHHHHHHHHhccc
Q 015078 287 AGLAWQ-GRAHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 287 ~gI~~~-g~~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
|||+.. .++|||++||++||+||.+|+.+..+
T Consensus 162 ~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~ 194 (200)
T TIGR01298 162 AGXDFDSTQAHSALYDTEKTAELFCEIVNRWKR 194 (200)
T ss_pred cCCCccccchhhhHHhHHHHHHHHHHHHHHHHH
Confidence 999863 26899999999999999999987643
No 32
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=2.6e-28 Score=270.13 Aligned_cols=165 Identities=22% Similarity=0.250 Sum_probs=146.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..|||||+||||+ ++ .++|||||||+++ +|+++++|+++|+|.. +|+++++.+||||++||++||+|++|++
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 5899999999998 44 4899999999995 7899999999999995 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQG 293 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g 293 (413)
+|.+|+++.. .|+||.+||+ .||++++.+.|+.++ ++++|+..+++.+++ ..+++|++++++||++..
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 9999998754 4566669995 899999988887653 568999999999887 467999999999999986
Q ss_pred CCCchHHHHHHHHHHHHHHHHhccc
Q 015078 294 RAHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 294 ~~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
++|+|++||++||+||.+|+++...
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=1.4e-27 Score=240.34 Aligned_cols=164 Identities=16% Similarity=0.159 Sum_probs=138.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..||||||||||+ ++..++|||||||+++ .+|++.++|+++|||.. + +.+ ..|||||++||++||+|.+|++
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 7888999999999996 47889999999999996 2 333 3799999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCC-------------------------CCCCCCCceeehHHHH
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKI-------------------------WKPPYFNRWINLKVPF 269 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi-------------------------~~P~~~~~~iDl~~l~ 269 (413)
+|.+||++.+ .|+|+..||+ .||..++++... ...+..+.++||..+.
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 5666779995 899999876411 0111346799999999
Q ss_pred HHhcC-CCCCCHHHHHHHcCCCC----------CCCCCchH--HHHHHHHHHHHHHHH
Q 015078 270 HEVFG-GVRCNLKEAVEMAGLAW----------QGRAHCGL--DDAKNTARLLALLMH 314 (413)
Q Consensus 270 r~l~~-~~~~~L~~l~~~~gI~~----------~g~~HrAL--dDA~aTA~Ll~~ll~ 314 (413)
+++++ .++++|++++++|||+. . .+|+|| +||+.+++||.++.+
T Consensus 191 Rrl~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~-~p~~~l~~~Da~ll~~l~~~~~~ 247 (377)
T PRK05601 191 RRQGVALDDIRIRGVAHTLGLDAPAAEASVERAQ-VPHRQLCREETLLVARLYFALRA 247 (377)
T ss_pred HHHcCCCCCCCHHHHHHHhCCCCCchhhhhhhhc-CChhhhhhHHHHHHHHHHHHhhc
Confidence 99986 57899999999999988 3 578998 699999999998743
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=7e-28 Score=222.50 Aligned_cols=162 Identities=18% Similarity=0.151 Sum_probs=129.6
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcC-CCCHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEALLRH 216 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~-Ap~f~eVl~~f 216 (413)
++||+||||+ ++..++|||||+|+++. ++.+.++|+++|+|.....+++.+..+||||++||.+ +|++.+++++|
T Consensus 1 ~~~D~ETTGl---~~~~d~Iieig~v~v~~-~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~ 76 (183)
T cd06138 1 LFYDYETFGL---NPSFDQILQFAAIRTDE-NFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKI 76 (183)
T ss_pred CEEEeecCCC---CCCCCceEEEEEEEECC-CCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHH
Confidence 5899999998 67789999999999973 4455699999999974224788999999999999999 99999999999
Q ss_pred HHHHhhcCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCCCC----CCceeehHHHHHHhc---C-----------CCC
Q 015078 217 DKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKPPY----FNRWINLKVPFHEVF---G-----------GVR 277 (413)
Q Consensus 217 ~~fL~~~~lv~~n~~vV~~-g~fDir~fL~~~~~~~gi~~P~~----~~~~iDl~~l~r~l~---~-----------~~~ 277 (413)
.+|+++. ..+.|+|+ ..||+ .||+.++++.++..+.. .+.++|+..+++..+ + .++
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 12345555 48995 89999999988743211 134578877666543 1 246
Q ss_pred CCHHHHHHHcCCCCCCCCCchHHHHHHHHHHH
Q 015078 278 CNLKEAVEMAGLAWQGRAHCGLDDAKNTARLL 309 (413)
Q Consensus 278 ~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll 309 (413)
++|++++++|||+.. ++|||++||++||+|+
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=2e-27 Score=266.47 Aligned_cols=167 Identities=23% Similarity=0.291 Sum_probs=148.3
Q ss_pred ccEEEEEEeeCCCCCCCCC-CCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPY-PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~-~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
..|||||+||||. ++. .++|||||||+++ +|+++++|+++|||.. +|+++++++||||++||++||+|.+|+
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 5799999999997 444 4899999999995 8899999999999986 699999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCC
Q 015078 214 LRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQ 292 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~ 292 (413)
.+|.+|+++.. .|+|+..|| +.||++++.+.|++.+ ..++||+..+.+.+++ ..+++|++++++||++..
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 99999998754 456666999 5899999999998643 5689999999999887 467899999999999985
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhccc
Q 015078 293 GRAHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 293 g~~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
++|+|++||++||+||.+|+++...
T Consensus 147 -~~H~Al~DA~ata~l~~~l~~~~~~ 171 (928)
T PRK08074 147 -QPHRADSDAEVTAELFLQLLNKLER 171 (928)
T ss_pred -CCCChHHHHHHHHHHHHHHHHHHHh
Confidence 8899999999999999999887543
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=4.8e-27 Score=261.47 Aligned_cols=165 Identities=24% Similarity=0.257 Sum_probs=147.2
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHH
Q 015078 136 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 215 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~ 215 (413)
.|||||+||||+ ++..++|||||+|+++ +|+++++|+++|+|.. +|+++++++||||++||++||+|.+|+.+
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 5678999999999995 7899999999999995 69999999999999999999999999999
Q ss_pred HHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 015078 216 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 294 (413)
Q Consensus 216 f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~ 294 (413)
|.+|+++. +.|+|+..||+ .||+.++++.|++. +.+.++|+..+.+.+++ ..+++|.+++++||++.. +
T Consensus 74 l~~~l~~~------~~VahN~~fD~-~fL~~~~~~~g~~~--~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~-~ 143 (850)
T TIGR01407 74 IYDLLEDG------IFVAHNVHFDL-NFLAKALKDCGYEP--LPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHE-N 143 (850)
T ss_pred HHHHhCCC------EEEEeCcHHHH-HHHHHHHHHcCCCC--CCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCC-C
Confidence 99999875 45566679995 89999999999864 34678999999998887 467899999999999986 7
Q ss_pred CCchHHHHHHHHHHHHHHHHhcc
Q 015078 295 AHCGLDDAKNTARLLALLMHRGF 317 (413)
Q Consensus 295 ~HrALdDA~aTA~Ll~~ll~~g~ 317 (413)
+|+|++||++||+||.+++++..
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=8e-27 Score=203.97 Aligned_cols=157 Identities=27% Similarity=0.308 Sum_probs=137.7
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 217 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~ 217 (413)
|+||+||||+ ++..++|||||+|+++. ++++.++|+.+|+|.. .++++++.+||||++++.+++++.+++.+|.
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 4688899999999996 5899999999999999999999999999999
Q ss_pred HHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHH-HHHcCCCCCCCC
Q 015078 218 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEA-VEMAGLAWQGRA 295 (413)
Q Consensus 218 ~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l-~~~~gI~~~g~~ 295 (413)
+|+++ .+++.|++.|| +.||++.+.+++. +.....|+|+..+++.+++. +.++|..+ ++.+|++.. ++
T Consensus 75 ~~l~~------~~~v~~n~~fD-~~~l~~~~~~~~~--~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~ 144 (159)
T cd06127 75 EFLGG------RVLVAHNASFD-LRFLNRELRRLGG--PPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE-GA 144 (159)
T ss_pred HHHCC------CEEEEeCcHhh-HHHHHHHHHHhCC--CCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC-CC
Confidence 99987 35677777999 4899999999883 33567899999999998874 46789988 899999874 78
Q ss_pred CchHHHHHHHHHHHH
Q 015078 296 HCGLDDAKNTARLLA 310 (413)
Q Consensus 296 HrALdDA~aTA~Ll~ 310 (413)
|+|++||++|++||.
T Consensus 145 H~Al~Da~~t~~l~~ 159 (159)
T cd06127 145 HRALADALATAELLL 159 (159)
T ss_pred CCcHHHHHHHHHHhC
Confidence 999999999999973
No 38
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=1.1e-26 Score=221.13 Aligned_cols=159 Identities=21% Similarity=0.201 Sum_probs=131.2
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHH
Q 015078 137 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 216 (413)
Q Consensus 137 fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f 216 (413)
++|||+||||+. .+|||||+|++. +|++.++|+++|+|.. +|+++++.+||||++||.++|++.+|+++|
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 789999999983 249999999984 7899999999999996 599999999999999999999999999985
Q ss_pred HHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC----
Q 015078 217 DKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ---- 292 (413)
Q Consensus 217 ~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~~---- 292 (413)
+++ .++|.|+..|| +.||.. ....|+||..++|++++..+++|..++++||++..
T Consensus 72 ---~~~------~~lVaHNa~FD-~~~L~~-----------~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~ 130 (219)
T PRK07983 72 ---YGS------EWYVAHNASFD-RRVLPE-----------MPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPG 130 (219)
T ss_pred ---cCC------CEEEEeCcHhh-HHHHhC-----------cCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCC
Confidence 444 35666777999 588841 23578999999999998656899999999998641
Q ss_pred CCCCchHHHHHHHHHHHHHHHHhcccccccccccc
Q 015078 293 GRAHCGLDDAKNTARLLALLMHRGFKFSITNSLMW 327 (413)
Q Consensus 293 g~~HrALdDA~aTA~Ll~~ll~~g~~~~i~e~l~~ 327 (413)
.++|||++||++||+||+++++... .++.+++.+
T Consensus 131 ~~aHrAl~Da~ata~ll~~l~~~~~-~~~~~l~~~ 164 (219)
T PRK07983 131 LHHHRALYDCYITAALLIDIMNTSG-WTAEEMADI 164 (219)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHcC-CCHHHHHHH
Confidence 3689999999999999999997532 234444444
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=215.82 Aligned_cols=146 Identities=20% Similarity=0.260 Sum_probs=122.3
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCH-------H
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL-------S 210 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f-------~ 210 (413)
||||+||||+ ++..++|||||||++ ++|++. |++||||.. +++++++++||||++||++||++ +
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 677899999999999 578875 999999985 69999999999999999999864 5
Q ss_pred HHHHHHHHHHhh-cCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC----CCCCHHHHHH
Q 015078 211 EALLRHDKWLEN-KGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG----VRCNLKEAVE 285 (413)
Q Consensus 211 eVl~~f~~fL~~-~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~----~~~~L~~l~~ 285 (413)
+|+++|++|+++ .+++ .|+..||+ .||+.. .++++|+..+++.+++. ++++|+++++
T Consensus 72 ~~~~~~~~~i~~~~vlV------gHn~~fD~-~fL~~~-----------~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~ 133 (161)
T cd06137 72 AARAALWKFIDPDTILV------GHSLQNDL-DALRMI-----------HTRVVDTAILTREAVKGPLAKRQWSLRTLCR 133 (161)
T ss_pred HHHHHHHHhcCCCcEEE------eccHHHHH-HHHhCc-----------CCCeeEehhhhhhccCCCcCCCCccHHHHHH
Confidence 899999999987 5444 44459996 898631 23689999999988764 4789999998
Q ss_pred H-cCCCCC--CCCCchHHHHHHHHHHHH
Q 015078 286 M-AGLAWQ--GRAHCGLDDAKNTARLLA 310 (413)
Q Consensus 286 ~-~gI~~~--g~~HrALdDA~aTA~Ll~ 310 (413)
+ ||++.. ..+|+|+.||++|++|++
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=2.1e-25 Score=213.35 Aligned_cols=165 Identities=25% Similarity=0.277 Sum_probs=145.9
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEee-EEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEA-CFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~d-sF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
..+||||+||||+ ++..++|||||+|.+. ++++.+ .|+++|+|.. .|++++.++||||.+||.++|.|.+++
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 4899999999998 6789999999999995 777764 4999999964 599999999999999999999999999
Q ss_pred HHHHHHHhh-cCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCC
Q 015078 214 LRHDKWLEN-KGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAW 291 (413)
Q Consensus 214 ~~f~~fL~~-~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~~gI~~ 291 (413)
++|.+|+++ .. .|+|+..||+ .||..++.+.+...+ ...++|+..+.+..++. ..++|+.+++++||+.
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 999999998 54 4566679995 999999999998865 56789999999999886 7889999999999994
Q ss_pred C-CCCCchHHHHHHHHHHHHHHHHh
Q 015078 292 Q-GRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 292 ~-g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
. ..+|+|+.||+++|.++..++..
T Consensus 157 ~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 157 NPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred CCcCCcchHHHHHHHHHHHHHHHhc
Confidence 3 25699999999999999999885
No 41
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=2.4e-25 Score=220.38 Aligned_cols=200 Identities=19% Similarity=0.137 Sum_probs=146.5
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcC-CC---eEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSV-TG---QLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 210 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~-~g---~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~ 210 (413)
..+||||+||||+ ++..++|||||+|+++.. +| ++.++|+++|+|.. +|+++++.|||||++||.+++...
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 34 45789999999995 599999999999999999998866
Q ss_pred HHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHh-cCCCCCCHHHHHHHcCC
Q 015078 211 EALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEV-FGGVRCNLKEAVEMAGL 289 (413)
Q Consensus 211 eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l-~~~~~~~L~~l~~~~gI 289 (413)
+++.+| ++.. .++|+||+.|| +.||++.+....- ..|.++....... .+..+++|++++++||
T Consensus 112 ~~l~~f---l~~~-----~vlVAHNA~FD-~~fL~~~~~~~~~------~~~~ct~~~i~~~~~~~~~~kL~~La~~~g- 175 (294)
T PRK09182 112 AAVDAL---IAPA-----DLIIAHNAGFD-RPFLERFSPVFAT------KPWACSVSEIDWSARGFEGTKLGYLAGQAG- 175 (294)
T ss_pred HHHHHH---hcCC-----CEEEEeCHHHH-HHHHHHHHHhccC------CcccccHHHHhhccccCCCCCHHHHHHHcC-
Confidence 655544 5442 45677888999 5999987654321 2344444333322 2346789999999999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHhccccccccccccccCCCCCcccCCCCCCCCCCCcccchhcccCCcc
Q 015078 290 AWQGRAHCGLDDAKNTARLLALLMHRGFKFSITNSLMWQTNDGSLTWNQFPERIFLPPHQLHKQMDLQNSIF 361 (413)
Q Consensus 290 ~~~g~~HrALdDA~aTA~Ll~~ll~~g~~~~i~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lP~~ 361 (413)
+.. .+|||++||++|++||.+++.........+.+....+|.-..+ -...|++.....++||--|-
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 444 6899999999999999998876654555665554332222221 01126777788888888875
No 42
>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=8e-26 Score=202.92 Aligned_cols=149 Identities=20% Similarity=0.235 Sum_probs=114.3
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 217 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~ 217 (413)
||||+||||+ ++. ++++||++|.+...+|.+. |++||+|.. .++++++.+||||++||++||+|.+|+++|.
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 443 3677776654322345543 999999985 5999999999999999999999999999999
Q ss_pred HHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHH-cCCCCCCC
Q 015078 218 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEM-AGLAWQGR 294 (413)
Q Consensus 218 ~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~--~~~~~L~~l~~~-~gI~~~g~ 294 (413)
+|+++.. .|.|+..||+ .||+ +..|. ..++|+..+...... .++++|++++++ +|++....
T Consensus 73 ~~l~~~v------lVgHn~~fD~-~~L~-------~~~~~--~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~ 136 (152)
T cd06144 73 ELLKGRI------LVGHALKNDL-KVLK-------LDHPK--KLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG 136 (152)
T ss_pred HHhCCCE------EEEcCcHHHH-HHhc-------CcCCC--ccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCC
Confidence 9998754 4556669996 7886 23332 357787554322222 357899999997 69987546
Q ss_pred CCchHHHHHHHHHHHH
Q 015078 295 AHCGLDDAKNTARLLA 310 (413)
Q Consensus 295 ~HrALdDA~aTA~Ll~ 310 (413)
+|||++||++|++||+
T Consensus 137 ~H~Al~DA~at~~l~~ 152 (152)
T cd06144 137 EHSSVEDARAAMRLYR 152 (152)
T ss_pred CcCcHHHHHHHHHHhC
Confidence 8999999999999984
No 43
>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=3.1e-25 Score=203.34 Aligned_cols=161 Identities=16% Similarity=0.173 Sum_probs=124.9
Q ss_pred EEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCC--CCCCcchhhh---cCCChhhhcCCCCHHH
Q 015078 137 FVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCN--QLLSDFCKDL---TGIQQIQVDRGVTLSE 211 (413)
Q Consensus 137 fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~--p~Ls~~~~~L---TGIT~edV~~Ap~f~e 211 (413)
+|+||+||||+ ++..++|||||||+++...+++.++|+.+|+|... +.+++++..+ ||||+++++++|++.+
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 67889999999999986667889999999999851 1234556666 5999999999999999
Q ss_pred HHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeeh---HHHHHHhcCCCCCCHHHHHHHc
Q 015078 212 ALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINL---KVPFHEVFGGVRCNLKEAVEMA 287 (413)
Q Consensus 212 Vl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl---~~l~r~l~~~~~~~L~~l~~~~ 287 (413)
|+.+|.+|+++..- .....+++++ +||+ .||+.++++.|.. +.++.+|+ ..+.+.+++.. . .+
T Consensus 78 vl~~~~~f~~~~~~-~~~~~lvgh~~~FD~-~fL~~~~~~~~~~---~~~~~~D~~~l~~l~~~l~p~~----~----~~ 144 (173)
T cd06135 78 AEAELLEFIKKYVP-KGKSPLAGNSVHQDR-RFLDKYMPELEEY---LHYRILDVSSIKELARRWYPEI----Y----RK 144 (173)
T ss_pred HHHHHHHHHHHhcC-CCCCceeecchhhCH-HHHHHHHHHHhcc---CCcchhhHHHHHHHHHHhCcHh----h----hc
Confidence 99999999986310 1122345544 9995 8999999988732 45667887 45666666521 1 15
Q ss_pred CCCCCCCCCchHHHHHHHHHHHHHHHH
Q 015078 288 GLAWQGRAHCGLDDAKNTARLLALLMH 314 (413)
Q Consensus 288 gI~~~g~~HrALdDA~aTA~Ll~~ll~ 314 (413)
+++. +..||||+||++|+.++.+.++
T Consensus 145 ~~~~-~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 145 APKK-KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred CCCC-CCCcchHHHHHHHHHHHHHHHH
Confidence 6765 4679999999999999998875
No 44
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.93 E-value=8.9e-26 Score=204.13 Aligned_cols=147 Identities=21% Similarity=0.253 Sum_probs=118.0
Q ss_pred EEEEEeeCCCCCCCCC--CCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPY--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 215 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~--~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~ 215 (413)
||||+||||+ ++. .++|++|++|.+ +|+++ |+++|||.. +++++++.+||||++||++||++++|+++
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 443 588999988876 46664 999999996 69999999999999999999999999999
Q ss_pred HHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHH--HHHh--cC-CCCCCHHHHHHHc---
Q 015078 216 HDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVP--FHEV--FG-GVRCNLKEAVEMA--- 287 (413)
Q Consensus 216 f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l--~r~l--~~-~~~~~L~~l~~~~--- 287 (413)
|.+|+++.++ |+|+..||+ .||+.. .| ...++|+..+ +++. ++ .++++|++++++|
T Consensus 71 l~~~l~~~vl------V~Hn~~~D~-~~l~~~-------~~--~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~ 134 (157)
T cd06149 71 ILKILKGKVV------VGHAIHNDF-KALKYF-------HP--KHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHR 134 (157)
T ss_pred HHHHcCCCEE------EEeCcHHHH-HHhccc-------CC--CcCEEECcccccchhhcCCcccCChhHHHHHHHHcCh
Confidence 9999998654 445559997 788632 22 2346787543 5443 45 3568999999999
Q ss_pred CCCCCCCCCchHHHHHHHHHHHH
Q 015078 288 GLAWQGRAHCGLDDAKNTARLLA 310 (413)
Q Consensus 288 gI~~~g~~HrALdDA~aTA~Ll~ 310 (413)
+++..++.|||+.||++|++||+
T Consensus 135 ~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 135 DIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred hhcCCCCCcCcHHHHHHHHHHhC
Confidence 67764467999999999999984
No 45
>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=3.3e-27 Score=206.63 Aligned_cols=162 Identities=27% Similarity=0.361 Sum_probs=124.6
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 217 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~ 217 (413)
||||+||||+ ++..++|||||+|+++.....+.+.|+++|+|...+.+++.++++||||+++|++++++.+++.+|.
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 5678999999999998655557899999999997445999999999999999999999999999999
Q ss_pred HHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHc-CCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCCC
Q 015078 218 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFK-KIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGRA 295 (413)
Q Consensus 218 ~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~-gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~~ 295 (413)
+|+.+. ...+.|+..||+ .++...+.+. +...| ....++|+..+.+..++ ...++|++++++||++..+.+
T Consensus 78 ~~~~~~-----~~~v~~n~~fd~-~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~ 150 (164)
T PF00929_consen 78 EFLKKN-----DILVGHNASFDI-GFLRREDKRFLGKPIP-KPNPFIDTLELARALFPNRKKYSLDDLAEYFGIPFDGTA 150 (164)
T ss_dssp HHHHHH-----TEEEETTCCHEE-ESSHHHHHHHHHHHHH-HHHHECEEEEEHHHHHHHHHHHSHHHHHHHTTSSSTSTT
T ss_pred hhhhcc-----cccccccccchh-hHHHHhhhhccccccc-ccchhhhhhHHHHHHhhccccCCHHHHHHHcCCCCCCCC
Confidence 999843 122333347886 6777776665 33222 11234454333333322 122689999999999998668
Q ss_pred CchHHHHHHHHHHH
Q 015078 296 HCGLDDAKNTARLL 309 (413)
Q Consensus 296 HrALdDA~aTA~Ll 309 (413)
|+|++||++|++||
T Consensus 151 H~Al~Da~~t~~l~ 164 (164)
T PF00929_consen 151 HDALDDARATAELF 164 (164)
T ss_dssp TSHHHHHHHHHHHH
T ss_pred cChHHHHHHHhCcC
Confidence 99999999999987
No 46
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.92 E-value=2.4e-25 Score=199.75 Aligned_cols=143 Identities=19% Similarity=0.223 Sum_probs=116.6
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCC-CHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV-TLSEALLRH 216 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap-~f~eVl~~f 216 (413)
|++|+||||.. .. ++|++|++|.+ +|++ .|++||||.. +++++++++||||++||++|| ++++|+++|
T Consensus 1 ~~iD~E~~g~~---~g-~ei~~i~~v~~---~~~~--~f~~lv~P~~--~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~ 69 (150)
T cd06145 1 FALDCEMCYTT---DG-LELTRVTVVDE---NGKV--VLDELVKPDG--EIVDYNTRFSGITEEMLENVTTTLEDVQKKL 69 (150)
T ss_pred CEEeeeeeeec---CC-CEEEEEEEEeC---CCCE--EEEEeECCCC--ccchhccCcCCCCHHHhccCCCCHHHHHHHH
Confidence 58999999984 23 99999999976 4444 4999999996 699999999999999999995 999999999
Q ss_pred HHHHh-hcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHc-CCCCC-
Q 015078 217 DKWLE-NKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMA-GLAWQ- 292 (413)
Q Consensus 217 ~~fL~-~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~-gI~~~- 292 (413)
.+|++ +.++ |.|+.+||+ .||+. ..++++|+..+++..++ .++++|++++++| ++...
T Consensus 70 ~~fl~~~~vl------VgHn~~fD~-~fL~~-----------~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~ 131 (150)
T cd06145 70 LSLISPDTIL------VGHSLENDL-KALKL-----------IHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQ 131 (150)
T ss_pred HHHhCCCCEE------EEcChHHHH-HHhhc-----------cCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeC
Confidence 99997 5444 444559996 79863 12458999999887765 4568999999887 54332
Q ss_pred -CCCCchHHHHHHHHHHH
Q 015078 293 -GRAHCGLDDAKNTARLL 309 (413)
Q Consensus 293 -g~~HrALdDA~aTA~Ll 309 (413)
+.+|||++||++|++||
T Consensus 132 ~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 132 GEGGHDSVEDARAALELV 149 (150)
T ss_pred CCCCCCcHHHHHHHHHHh
Confidence 36799999999999997
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=99.91 E-value=1.6e-23 Score=193.86 Aligned_cols=164 Identities=15% Similarity=0.126 Sum_probs=129.0
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCC--CCCCcchhhhc---CCChhhhcCCCCH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCN--QLLSDFCKDLT---GIQQIQVDRGVTL 209 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~--p~Ls~~~~~LT---GIT~edV~~Ap~f 209 (413)
+.||+||+||||+ +|..++|||||||+++.....+.+.|+.+|+|... ..++++++.+| |||+++++++|++
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 78899999999999974323345789999999851 12577888887 8999999999999
Q ss_pred HHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeeh--H-HHHHHhcCCCCCCHHHHHH
Q 015078 210 SEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINL--K-VPFHEVFGGVRCNLKEAVE 285 (413)
Q Consensus 210 ~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl--~-~l~r~l~~~~~~~L~~l~~ 285 (413)
.+|+.+|++|+++... .++..+|++. .|| +.||++.+.+.+.. +.++++|+ . .+.++++|. +
T Consensus 80 ~e~~~~~l~fl~~~~~-~~~~~l~g~~v~FD-~~FL~~~~~~~~~~---l~~~~~Dv~tl~~l~r~~~P~----~----- 145 (181)
T PRK05359 80 AEAEAQTLEFLKQWVP-AGKSPLCGNSIGQD-RRFLARYMPELEAY---FHYRNLDVSTLKELARRWKPE----I----- 145 (181)
T ss_pred HHHHHHHHHHHHHhcC-CCCCceeecchhhC-HHHHHHHHHHhccc---CCCcccchhHHHHHHHHhChh----h-----
Confidence 9999999999987644 3344456654 999 58999999877654 34677884 3 577777763 2
Q ss_pred HcCCCCCCCCCchHHHHHHHHHHHHHHHHhc
Q 015078 286 MAGLAWQGRAHCGLDDAKNTARLLALLMHRG 316 (413)
Q Consensus 286 ~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~g 316 (413)
+++++.. ..|||++||+++.+.+....+..
T Consensus 146 ~~~~~~~-~~HRal~D~~~s~~~~~~~~~~~ 175 (181)
T PRK05359 146 LNGFKKQ-GTHRALADIRESIAELKYYREHF 175 (181)
T ss_pred hhCCCCc-CCcccHHHHHHHHHHHHHHHHHh
Confidence 3588775 57999999999999998877643
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.90 E-value=7.9e-23 Score=213.75 Aligned_cols=172 Identities=16% Similarity=0.115 Sum_probs=130.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcC-CCCHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDR-GVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~-Ap~f~eVl 213 (413)
.+|||+|+||||+ +|..|+|||||||+++...+.+.+.|+.+|+|.....+++++..+||||++||.+ +.++.+++
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 7889999999999998433456688999999985223577899999999999965 66799999
Q ss_pred HHHHHHHhhcCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCC---C-CCCCceeehHHHHHHhc--------------C
Q 015078 214 LRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWK---P-PYFNRWINLKVPFHEVF--------------G 274 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~~-g~fDir~fL~~~~~~~gi~~---P-~~~~~~iDl~~l~r~l~--------------~ 274 (413)
++|.+|+... ..++|.|+ .+||+ .||+.++.+..+.. . ...+..+|+..+.+..+ +
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 13444444 47995 89999987654321 0 00122345554444332 1
Q ss_pred CCCCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 015078 275 GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 275 ~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
..+++|+++++++||+.. ++|+|++||++|++|+.+|.++
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 7899999999999999998865
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=9.2e-13 Score=95.48 Aligned_cols=44 Identities=34% Similarity=0.901 Sum_probs=40.5
Q ss_pred cceecCCCcCcceeccCCCCCCCceeecCCCcccCCCcccceeecCC
Q 015078 365 PSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 411 (413)
Q Consensus 365 ~~c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~~~ 411 (413)
|.|.||..+.+.|++|.|+|+||.||+|+++.. ..|+||+|.|+
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
>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=99.26 E-value=4.1e-10 Score=104.61 Aligned_cols=139 Identities=15% Similarity=0.002 Sum_probs=101.1
Q ss_pred EEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHH
Q 015078 138 VVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRH 216 (413)
Q Consensus 138 VV~D~ETTGl~~~-~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f 216 (413)
++||+||||..+. ++..++||+||++.. .+|... .+.....+.. +.+. ||+..+|...++..++|..|
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 467899999999887 345432 2333333321 1111 89999999999999999999
Q ss_pred HHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCC-CC-------------------CCceeehHHHHHHhcCC
Q 015078 217 DKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKP-PY-------------------FNRWINLKVPFHEVFGG 275 (413)
Q Consensus 217 ~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P-~~-------------------~~~~iDl~~l~r~l~~~ 275 (413)
.++++.... .+++.|++ +||+ .||...++.+|++.. .. -...+|+..+++..++.
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 34455556 8996 899999998888651 11 12368999999888887
Q ss_pred CCCCHHHHHHHcCCCC
Q 015078 276 VRCNLKEAVEMAGLAW 291 (413)
Q Consensus 276 ~~~~L~~l~~~~gI~~ 291 (413)
.+++|+++++.++...
T Consensus 147 ~sy~L~~v~~~~l~~~ 162 (199)
T cd05160 147 KSYTLDAVAEELLGEG 162 (199)
T ss_pred ccCCHHHHHHHHhCCC
Confidence 8899999999877543
No 51
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.23 E-value=1.1e-10 Score=112.84 Aligned_cols=157 Identities=19% Similarity=0.259 Sum_probs=112.1
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..+|++|.|..|..- +...+.+--++ +|| ..|.|+ |+.||||.. +++++-+..+||+.+.+.+|.+|+.|-.
T Consensus 105 ~r~vAmDCEMVG~Gp-~G~~s~lARvS--IVN-~~G~Vv--yDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~aQ~ 176 (280)
T KOG2249|consen 105 TRVVAMDCEMVGVGP-DGRESLLARVS--IVN-YHGHVV--YDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVAQK 176 (280)
T ss_pred ceEEEEeeeEeccCC-CccceeeeEEE--Eee-ccCcEe--eeeecCCCc--ccccceeeecccCHHHhccCccHHHHHH
Confidence 369999999999721 12234444443 334 467775 999999996 6999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehH--HHHHHhcC-CCCCCHHHHHH-HcCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLK--VPFHEVFG-GVRCNLKEAVE-MAGLA 290 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~--~l~r~l~~-~~~~~L~~l~~-~~gI~ 290 (413)
+++++|.+.+||||-. .-|+ .-|. +..|.- ..-||. ..+++++. ....+|..|.+ .+|++
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-------LEHPRS--MIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKD 240 (280)
T ss_pred HHHHHHhCCEEecccc------ccHH-HHHh-------hhCchh--hhcccccCchHHHHhhccCCccHHHHHHHHhchh
Confidence 9999999987777643 3454 2332 333321 123542 23344333 34568999885 57877
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHh
Q 015078 291 WQGRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 291 ~~g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
...-.|+.+.||.+|.+|+.++-.+
T Consensus 241 IQ~GeHsSvEDA~AtM~LY~~vk~q 265 (280)
T KOG2249|consen 241 IQVGEHSSVEDARATMELYKRVKVQ 265 (280)
T ss_pred hhccccCcHHHHHHHHHHHHHHHHH
Confidence 6434599999999999999987544
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=99.08 E-value=1.5e-09 Score=100.11 Aligned_cols=154 Identities=20% Similarity=0.245 Sum_probs=106.8
Q ss_pred ccEEEEEEeeCCCCCC-C-----CCCCcEEEEcEEEEEc-CCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCC
Q 015078 135 QYFVVIDFEATCDKDK-N-----PYPQEIIEFPSVIVSS-VTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGV 207 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~-~-----~~~deIIEIGAV~vd~-~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap 207 (413)
.+||-+|.|+|++... . ....++.-+.+|=.++ .+|+++ +..||+|.. ++.++.+..+|||.++++++.
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 5888899988876310 0 0123455555443110 256654 899999995 599999999999999999875
Q ss_pred ------CHHHHHHHHHHHHh-hcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCH
Q 015078 208 ------TLSEALLRHDKWLE-NKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNL 280 (413)
Q Consensus 208 ------~f~eVl~~f~~fL~-~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L 280 (413)
++++|..++.+++. +.+++||.. ..|+ ..| ++..|. ...+|+..+|+.- .....+|
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL------~nDL-~aL-------~l~hp~--~~viDTa~l~~~~-~~r~~sL 143 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGL------AKDF-RVI-------NIQVPK--EQVIDTVELFHLP-GQRKLSL 143 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccc------hhHH-HHh-------cCcCCC--cceEEcHHhccCC-CCCChhH
Confidence 68999999999885 444444433 5564 233 455442 3579998766431 1235689
Q ss_pred HHHHH-HcCCCCCCCCCchHHHHHHHHHHH
Q 015078 281 KEAVE-MAGLAWQGRAHCGLDDAKNTARLL 309 (413)
Q Consensus 281 ~~l~~-~~gI~~~g~~HrALdDA~aTA~Ll 309 (413)
..|++ ++|.......|+.+.||+++.+|+
T Consensus 144 k~La~~~L~~~IQ~~~HdSvEDArAam~Ly 173 (174)
T cd06143 144 RFLAWYLLGEKIQSETHDSIEDARTALKLY 173 (174)
T ss_pred HHHHHHHcCCcccCCCcCcHHHHHHHHHHh
Confidence 99886 578777655799999999999987
No 53
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=98.92 E-value=1.4e-08 Score=84.61 Aligned_cols=83 Identities=24% Similarity=0.235 Sum_probs=61.3
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 217 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~ 217 (413)
++||+||||+ ++..++|++|+....+ .+. .| +.. |.
T Consensus 1 ~~~DiEt~~~---~~~~~~i~~i~~~~~~--~~~---~~---~~~---------------------------------f~ 36 (96)
T cd06125 1 IAIDTEATGL---DGAVHEIIEIALADVN--PED---TA---VID---------------------------------LK 36 (96)
T ss_pred CEEEEECCCC---CCCCCcEEEEEEEEcc--CCC---EE---Eeh---------------------------------HH
Confidence 4799999998 5788999999887542 111 11 100 88
Q ss_pred HHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHH
Q 015078 218 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVP 268 (413)
Q Consensus 218 ~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l 268 (413)
+|+++... ...|.|+++||+ .||+++++++++..|....+++|++.+
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 345566679996 899999999999888667899999865
No 54
>PHA02570 dexA exonuclease; Provisional
Probab=98.89 E-value=1.2e-08 Score=96.75 Aligned_cols=162 Identities=15% Similarity=0.124 Sum_probs=105.9
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCC----------CCcchhhhcCCChhh-----
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQL----------LSDFCKDLTGIQQIQ----- 202 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~----------Ls~~~~~LTGIT~ed----- 202 (413)
++||+||.|. .....||+||||.+|...+ +..+|+.+|.....-+ ..+..+......|+.
T Consensus 4 lMIDlETmG~----~p~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~ 78 (220)
T PHA02570 4 FIIDFETFGN----TPDGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKN 78 (220)
T ss_pred EEEEeeccCC----CCCceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHh
Confidence 7899999984 4678999999999998666 6889998886422111 122223333344432
Q ss_pred hc---CCCCHHHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHc----C--CCCCCCCCceeehHHHHHHh
Q 015078 203 VD---RGVTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFK----K--IWKPPYFNRWINLKVPFHEV 272 (413)
Q Consensus 203 V~---~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~----g--i~~P~~~~~~iDl~~l~r~l 272 (413)
+. +..++.+++.+|.+||.....-.....+-++| +||+ .+|...+++. + ++.|..+..--|++.+....
T Consensus 79 L~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~-~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~~ 157 (220)
T PHA02570 79 LKPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDF-PILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEAT 157 (220)
T ss_pred ccCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCH-HHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhhh
Confidence 21 45789999999999999764222234455555 7995 8999999887 7 57776666667888766543
Q ss_pred -cCCC-------CCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 015078 273 -FGGV-------RCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 273 -~~~~-------~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
+.+. ...|+. + -+|+|+.||-.=|..+..-.+.
T Consensus 158 ~l~r~~~~cp~~~g~l~g--------f--v~H~sihDcakd~lml~y~~ry 198 (220)
T PHA02570 158 LLTRGMTTCPLPKGTLDG--------F--VAHDSIHDCAKDILMLIYAKRY 198 (220)
T ss_pred hccCCcccCCCcCccccc--------h--hhcccHHHHHHHHHHHHHHHHH
Confidence 2211 112211 2 5799999987776655544443
No 55
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=98.84 E-value=1.9e-08 Score=91.11 Aligned_cols=160 Identities=18% Similarity=0.182 Sum_probs=105.2
Q ss_pred cccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeE-eeEEEEEEeCCC--CCCCCcchhhhc---CCChhhhcCCC
Q 015078 134 FQYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQL-EACFQTYVRPTC--NQLLSDFCKDLT---GIQQIQVDRGV 207 (413)
Q Consensus 134 ~~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i-~dsF~~~VkP~~--~p~Ls~~~~~LT---GIT~edV~~Ap 207 (413)
++++|=||+|.||| ++..+.||||++++-|. +..+ .+.+...|.-.. -....+.+++.| |+++.-.+...
T Consensus 5 ~~nLiWIDlEMTGL---d~~~drIIEiA~iVTD~-~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~ 80 (184)
T COG1949 5 KNNLIWIDLEMTGL---DPERDRIIEIATIVTDA-NLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTV 80 (184)
T ss_pred CCceEEEeeeeccC---CcCcceEEEEEEEEecC-cccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhc
Confidence 46899999999998 78999999999999884 4443 444444444321 112456677765 57776667888
Q ss_pred CHHHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeeh---HHHHHHhcCCCCCCHHHH
Q 015078 208 TLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINL---KVPFHEVFGGVRCNLKEA 283 (413)
Q Consensus 208 ~f~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl---~~l~r~l~~~~~~~L~~l 283 (413)
+..+|-.+.++||+.-+-. +...++.++ ..| |.||.+..-+.--- +.++.+|+ +++.+++.|. +
T Consensus 81 t~~~aE~~~l~flkkwvp~-~~spicGNSI~qD-RrFl~r~MP~Le~y---fHYR~lDVSTlKELa~RW~P~----i--- 148 (184)
T COG1949 81 TEAEAEAQTLDFLKKWVPK-GVSPICGNSIAQD-RRFLFRYMPKLEAY---FHYRYLDVSTLKELARRWNPE----I--- 148 (184)
T ss_pred cHHHHHHHHHHHHHHhCCC-CCCCCccchhhHH-HHHHHHHhhhHHHH---hhhHhhhHHHHHHHHHhhCcH----h---
Confidence 9999999999999886443 223355553 579 89998765432111 23466775 4566666551 1
Q ss_pred HHHcCCCCCCCCCchHHHHHHHHHHHHHH
Q 015078 284 VEMAGLAWQGRAHCGLDDAKNTARLLALL 312 (413)
Q Consensus 284 ~~~~gI~~~g~~HrALdDA~aTA~Ll~~l 312 (413)
..| +..+..|+||+|.+-...=++.-
T Consensus 149 --~~~-~~K~~~H~Al~DI~ESI~EL~~Y 174 (184)
T COG1949 149 --LAG-FKKGGTHRALDDIRESIAELRYY 174 (184)
T ss_pred --hhc-cccccchhHHHHHHHHHHHHHHH
Confidence 123 33456799999987665544443
No 56
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.82 E-value=3.3e-08 Score=99.84 Aligned_cols=165 Identities=16% Similarity=0.176 Sum_probs=127.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCC-CcchhhhcCCChhhh-cCCCCHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLL-SDFCKDLTGIQQIQV-DRGVTLSEA 212 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~L-s~~~~~LTGIT~edV-~~Ap~f~eV 212 (413)
-+|.+.|.||.|. +|..|++-+|++|.-|..=+.|.+--..|++|.. .-| .+.+.-+||||.... +++.+..+.
T Consensus 9 ~tF~~yDYETfG~---~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsd-DyLP~P~a~LITGITPQ~~~~~G~~E~~F 84 (475)
T COG2925 9 PTFLFYDYETFGV---HPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPAD-DYLPQPGAVLITGITPQEAREKGINEAAF 84 (475)
T ss_pred CcEEEEehhhcCC---CcccccchhhheeeccccccccCCCeEEEecCcc-ccCCCCCceeeecCCHHHHHhcCCChHHH
Confidence 4899999999997 7899999999999998766677888999999985 233 467889999999877 478888888
Q ss_pred HHHHHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHHHcCCCCCCCCC------ceeehHHHHHHhcCC---------
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPPYFN------RWINLKVPFHEVFGG--------- 275 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~~~gi~~P~~~~------~~iDl~~l~r~l~~~--------- 275 (413)
..++..-+... +.+++.| -+|| ..+-++.|-|.-++ | +.. +-.|++.+.|..+-.
T Consensus 85 ~~~I~~~ls~P-----~Tcv~GYNniRFD-DEvtRy~fyRNF~D-P-Ya~sWqngNSRWDLLD~~RacyALRPeGI~Wp~ 156 (475)
T COG2925 85 AARIHAELTQP-----NTCVLGYNNIRFD-DEVTRYIFYRNFYD-P-YAWSWQNGNSRWDLLDVVRACYALRPEGINWPE 156 (475)
T ss_pred HHHHHHHhCCC-----Ceeeecccccccc-hHHHHHHHHHhcCc-h-hhhhhcCCCchhHHHHHHHHHHhcCcccCCCCc
Confidence 88887777653 5567775 3788 57777776665443 2 322 335777777766522
Q ss_pred -----CCCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHH
Q 015078 276 -----VRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALL 312 (413)
Q Consensus 276 -----~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~l 312 (413)
.+.+|+.+.+.-||+.. ++|+||.|++||..+...+
T Consensus 157 n~dG~pSFkLEhLt~ANgieH~-nAHdAmsDVyATIamAklv 197 (475)
T COG2925 157 NDDGLPSFKLEHLTKANGIEHS-NAHDAMSDVYATIAMAKLV 197 (475)
T ss_pred CCCCCcchhhHHHhhccccccc-hhhHHHHHHHHHHHHHHHH
Confidence 24589999999999984 8999999999997765543
No 57
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=98.71 E-value=7.9e-08 Score=87.98 Aligned_cols=163 Identities=17% Similarity=0.184 Sum_probs=113.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCC--CCCCCcchhhhcC---CChhhhcCCCCH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTC--NQLLSDFCKDLTG---IQQIQVDRGVTL 209 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~--~p~Ls~~~~~LTG---IT~edV~~Ap~f 209 (413)
.++|=+|+|.||| +-..+.||||+.++-|+.=..+.+.+...|+-.. -...++.|.+-|| +|..-+....++
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 6899999999998 5678999999999988654555677777777543 1236788888765 787788899999
Q ss_pred HHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeeh---HHHHHHhcCCCCCCHHHHHH
Q 015078 210 SEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINL---KVPFHEVFGGVRCNLKEAVE 285 (413)
Q Consensus 210 ~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl---~~l~r~l~~~~~~~L~~l~~ 285 (413)
.+|-.++++|+...+..+ +..++.++ .-| |.||.+.+-+.- .+ +..+.+|+ +.+.++++|.-.
T Consensus 103 ~~aEnevl~yikk~ip~~-~~~laGNSV~~D-rlFl~k~mPk~~-~~--lhyrivDVStIkeL~~Rw~P~~~-------- 169 (208)
T KOG3242|consen 103 ADAENEVLEYIKKHIPKG-KCPLAGNSVYMD-RLFLKKYMPKLI-KH--LHYRIVDVSTIKELARRWYPDIK-------- 169 (208)
T ss_pred HHHHHHHHHHHHHhCCCC-CCCccCcchhhH-HHHHHHHhHHHH-Hh--cceeeeeHHHHHHHHHHhCchhh--------
Confidence 999999999999875532 23344443 468 789988764321 11 23567886 567788877311
Q ss_pred HcCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 015078 286 MAGLAWQGRAHCGLDDAKNTARLLALLMH 314 (413)
Q Consensus 286 ~~gI~~~g~~HrALdDA~aTA~Ll~~ll~ 314 (413)
.+. |-....|||++|.+-...=|+.-.+
T Consensus 170 ~~a-PkK~~~HrAldDI~ESI~ELq~Yr~ 197 (208)
T KOG3242|consen 170 ARA-PKKKATHRALDDIRESIKELQYYRE 197 (208)
T ss_pred ccC-cccccccchHHHHHHHHHHHHHHHH
Confidence 111 2223469999998776555555443
No 58
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=98.53 E-value=4e-06 Score=78.33 Aligned_cols=129 Identities=16% Similarity=0.088 Sum_probs=88.3
Q ss_pred cEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 136 YFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~-~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..+.||+|||+..+. ++..++||.||.+.. ..+.+.. .++. +. ..+..-.+..+.|.
T Consensus 4 ~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~--~~~~~~~-----~~~~-----~~----------~~v~~~~~E~~lL~ 61 (195)
T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFADE--GGNKVIT-----WKKF-----DL----------PFVEVVKTEKEMIK 61 (195)
T ss_pred eEEEEEEEecCCCCCCCCCCCcEEEEEEecC--CCceEEE-----ecCC-----CC----------CeEEEeCCHHHHHH
Confidence 678999999965443 567899999998653 2233321 1121 10 13444567789999
Q ss_pred HHHHHHhhcCCCCccEEEEEc-C-cchHHHHHHHHHHHcCCCCCCC--------------------CCceeehHHHHHHh
Q 015078 215 RHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKPPY--------------------FNRWINLKVPFHEV 272 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~-g-~fDir~fL~~~~~~~gi~~P~~--------------------~~~~iDl~~l~r~l 272 (413)
+|.+++..... . ++++| + .||+ .||..-+.++|+.+|.- -...+|+...+++.
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 99999987421 2 34444 4 7996 89999999889876520 01367898888887
Q ss_pred cCCCCCCHHHHHH-HcCCCC
Q 015078 273 FGGVRCNLKEAVE-MAGLAW 291 (413)
Q Consensus 273 ~~~~~~~L~~l~~-~~gI~~ 291 (413)
+...+++|+++++ .+|.+.
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 59
>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=98.52 E-value=2.9e-06 Score=79.23 Aligned_cols=120 Identities=15% Similarity=0.121 Sum_probs=86.5
Q ss_pred cEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 136 YFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~-~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..+.||+||++..+. ++..+.||.||++..+ |.+ +.+. .+..+..+.|.
T Consensus 4 ~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~---g~~----~~~~-----------------------~~~~~E~~lL~ 53 (188)
T cd05781 4 KTLAFDIEVYSKYGTPNPRRDPIIVISLATSN---GDV----EFIL-----------------------AEGLDDRKIIR 53 (188)
T ss_pred eEEEEEEEecCCCCCCCCCCCCEEEEEEEeCC---CCE----EEEE-----------------------ecCCCHHHHHH
Confidence 679999999965443 5678999999987643 321 1111 12367889999
Q ss_pred HHHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHHHcCCCCCCCC-C-----------------ceeehHHHHHHhcC
Q 015078 215 RHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPPYF-N-----------------RWINLKVPFHEVFG 274 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~~~gi~~P~~~-~-----------------~~iDl~~l~r~l~~ 274 (413)
.|.+++....- -++++| ..||+ .||..-++++|+.++.-. . -.+|+....++...
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 245665 37997 899999999988654110 0 16888888888777
Q ss_pred CCCCCHHHHHHHcCCC
Q 015078 275 GVRCNLKEAVEMAGLA 290 (413)
Q Consensus 275 ~~~~~L~~l~~~~gI~ 290 (413)
.++++|+++++.+|+.
T Consensus 129 l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 129 VKVKTLENVAEYLGVM 144 (188)
T ss_pred CCCCCHHHHHHHHCCC
Confidence 7889999999999874
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=98.48 E-value=6.8e-07 Score=80.22 Aligned_cols=116 Identities=16% Similarity=0.116 Sum_probs=60.8
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 217 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~ 217 (413)
|+||+||||+ ++..+.|+-||++.++...... |..+.-.. +..++.+.++.
T Consensus 1 l~~DIET~Gl---~~~~~~i~liG~~~~~~~~~~~---~~~~~~~~-----------------------~~ee~~~~~~~ 51 (164)
T PF13482_consen 1 LFFDIETTGL---SPDNDTIYLIGVADFDDDEIIT---FIQWFAED-----------------------PDEEEIILEFF 51 (164)
T ss_dssp --EEEEESS----GG-G---EEEEEEE-ETTTTE----EEEE-GGG-----------------------HHHHHHHHH--
T ss_pred CcEEecCCCC---CCCCCCEEEEEEEEeCCCceEE---eeHhhccC-----------------------cHHHHHHHHHH
Confidence 5899999998 6667889999999887322221 32222111 12344555555
Q ss_pred HHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC
Q 015078 218 KWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ 292 (413)
Q Consensus 218 ~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~~ 292 (413)
+++.+. +.++..+| +||+ .||++.+.+++++. ...++|+...+++... .+++|.++.+.+|+...
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 33444454 8995 89999997777654 4578999887765443 56799999999998764
No 61
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.36 E-value=1.8e-05 Score=75.09 Aligned_cols=114 Identities=19% Similarity=0.227 Sum_probs=77.1
Q ss_pred CCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHHHHHhhcC
Q 015078 145 TCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKG 224 (413)
Q Consensus 145 TGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~~fL~~~~ 224 (413)
+|.....+..+.||.||++..+..++.+ . +. .. ...+..+.|.+|.+++...
T Consensus 41 ~~~~~l~~~~~~Iv~Is~~~~~~~~~~~-----~-~~-~~--------------------~~~~E~elL~~F~~~i~~~- 92 (208)
T cd05782 41 SGSDFLPLPFHKVVSISALYRDDDGGFL-----K-VR-TL--------------------DGADEKELLEDFFQLIEKK- 92 (208)
T ss_pred cCCCCCccccCceEEEEEEEEecCCCeE-----E-Ee-ec--------------------CCCCHHHHHHHHHHHHHHh-
Confidence 3333335568999999999875333321 1 11 10 0123378999999999974
Q ss_pred CCCccEEEEEc-C-cchHHHHHHHHHHHcCCCCCCCCC--------------ceeehHHHHHHhcCCCCCCHHHHHHHcC
Q 015078 225 IKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKPPYFN--------------RWINLKVPFHEVFGGVRCNLKEAVEMAG 288 (413)
Q Consensus 225 lv~~n~~vV~~-g-~fDir~fL~~~~~~~gi~~P~~~~--------------~~iDl~~l~r~l~~~~~~~L~~l~~~~g 288 (413)
+-++|+| | .||+ .||..-+..+|++.|..+. +.+|+..+++......+++|+++++.+|
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 1245665 4 7997 8999999999997774331 2688888776533346789999999999
Q ss_pred CCC
Q 015078 289 LAW 291 (413)
Q Consensus 289 I~~ 291 (413)
++-
T Consensus 168 ~~~ 170 (208)
T cd05782 168 IPG 170 (208)
T ss_pred CCC
Confidence 964
No 62
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.31 E-value=2.1e-06 Score=88.11 Aligned_cols=157 Identities=20% Similarity=0.276 Sum_probs=111.3
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhc-CCCCHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVD-RGVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~-~Ap~f~eVl 213 (413)
.+.+++|.|....+ ..-|+..+++|=+ ++++ -+..||+|.. +|-++.+..+|||.+|++ ...++++|-
T Consensus 216 ~~i~AlDCEm~~te----~g~el~RVt~VD~---~~~v--i~D~fVkP~~--~VvDy~T~~SGIT~~~~e~~t~tl~dvq 284 (380)
T KOG2248|consen 216 PNIFALDCEMVVTE----NGLELTRVTAVDR---DGKV--ILDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLEDVQ 284 (380)
T ss_pred CCeEEEEeeeeeec----cceeeEEeeeeec---cCcE--EeEEeecCCC--cccccccccccccHHHHhcCccCHHHHH
Confidence 58999999988753 2278888988855 4554 4889999995 599999999999999997 466799999
Q ss_pred HHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC--CCCCHHHHHH-HcCC
Q 015078 214 LRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG--VRCNLKEAVE-MAGL 289 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~--~~~~L~~l~~-~~gI 289 (413)
.+++.|+.. +.++|.++ .-|+ .-|+ +.. ..+||+..+|..-.+. .+.+|..+++ ++|.
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 34566654 5565 3332 223 3578987555433331 2235777775 3443
Q ss_pred CCC-C-CCCchHHHHHHHHHHHHHHHHhccccc
Q 015078 290 AWQ-G-RAHCGLDDAKNTARLLALLMHRGFKFS 320 (413)
Q Consensus 290 ~~~-g-~~HrALdDA~aTA~Ll~~ll~~g~~~~ 320 (413)
... + ..|+...||.++.+|+...+..+..++
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 63
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=98.15 E-value=4.7e-05 Score=69.44 Aligned_cols=145 Identities=19% Similarity=0.141 Sum_probs=96.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..+++||+||||+ ++..++|+.++... ..+. .|..-+++. .. .+++++++++.
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 55678888886542 2221 222111211 01 14567888999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc-CCC--
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA-GLA-- 290 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~-~~~L~~l~~~~-gI~-- 290 (413)
+|.+++++.. ...++|+..||+ .+|. ++|+.++ ..++|+..+...+.+.. +++|+++++.| |..
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 235677889995 6764 5677754 45789988877777654 67999998876 322
Q ss_pred --------------CCC-----CCCchHHHHHHHHHHHHHHHHhccc
Q 015078 291 --------------WQG-----RAHCGLDDAKNTARLLALLMHRGFK 318 (413)
Q Consensus 291 --------------~~g-----~~HrALdDA~aTA~Ll~~ll~~g~~ 318 (413)
+.. ..|.|..||.++.+|+..|.+...+
T Consensus 126 ~~~~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 126 SFEDLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred cHHHHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 000 1235888999999999988876543
No 64
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=98.12 E-value=2e-05 Score=74.69 Aligned_cols=172 Identities=19% Similarity=0.184 Sum_probs=112.9
Q ss_pred cEEEEEEeeCCCCC----C---C-----------CCCCcEEEEcEEEEEcCCCeEee----EEEEEEe---CCCCCCCCc
Q 015078 136 YFVVIDFEATCDKD----K---N-----------PYPQEIIEFPSVIVSSVTGQLEA----CFQTYVR---PTCNQLLSD 190 (413)
Q Consensus 136 ~fVV~D~ETTGl~~----~---~-----------~~~deIIEIGAV~vd~~~g~i~d----sF~~~Vk---P~~~p~Ls~ 190 (413)
+||++|.|.-|.-. . + -+.-.|||+|....| .+|++.+ +.+.-.+ +.. ..-++
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 67888888766511 0 1 123489999999998 5566644 4443333 221 13455
Q ss_pred chhhh---cCCChhhhc-CCCCHHHHHHHHHHHHhhcCCCC-ccEEEEE-cCcchHHHHHHHHHHHcCCCCC--------
Q 015078 191 FCKDL---TGIQQIQVD-RGVTLSEALLRHDKWLENKGIKN-TNFAVVT-WSNWDCRVMLESECRFKKIWKP-------- 256 (413)
Q Consensus 191 ~~~~L---TGIT~edV~-~Ap~f~eVl~~f~~fL~~~~lv~-~n~~vV~-~g~fDir~fL~~~~~~~gi~~P-------- 256 (413)
.++++ +||.-+-.+ .+.+.+ +|.+.+-..+++- .++.+|+ ++..|. .+|-+-+-...++--
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 66665 788877664 466655 4555555554443 4788888 478996 777666554333210
Q ss_pred -CCCCceeehHHHHHHhcCC-CCCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 015078 257 -PYFNRWINLKVPFHEVFGG-VRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMH 314 (413)
Q Consensus 257 -~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~ 314 (413)
.++..+.|++.+++..-+. ...+|..+++.++++..|..|.|-.|++.||..|.+|.+
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 1123456777776655442 245899999999999999999999999999999999864
No 65
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=98.09 E-value=0.00026 Score=67.13 Aligned_cols=145 Identities=14% Similarity=0.055 Sum_probs=86.0
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCC-cchhhhcCCChhhhcCCCCHHHH
Q 015078 136 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLS-DFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~--~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls-~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
..++||+||++..++ ++..|.||+|+.+.- .+|...- ....+.+..+. +. ..+..+-| .-.+..-.+..+.
T Consensus 3 rilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~--~~g~~~~-~~~~~~~~~~~-~~~~~~~~~~~--~~~v~~~~~E~~l 76 (204)
T cd05779 3 RVLAFDIETTKLPLKFPDAETDQIMMISYMID--GQGYLIV-NREIVSEDIED-FEYTPKPEYEG--PFKVFNEPDEKAL 76 (204)
T ss_pred eEEEEEEEecCCCCCCcCCCCCeEEEEEEEEe--cCCEEEe-ccccccccccc-ccccCCCCCCC--ceEEecCCCHHHH
Confidence 578999999875443 467899999997653 3443210 00011010000 00 00000111 0122335789999
Q ss_pred HHHHHHHHhhcCCCCccEEEEEc-C-cchHHHHHHHHHHHcCCCCCC-C---CC----------ceeehHHHHHHhc--C
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKPP-Y---FN----------RWINLKVPFHEVF--G 274 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~-g-~fDir~fL~~~~~~~gi~~P~-~---~~----------~~iDl~~l~r~l~--~ 274 (413)
|.+|.+++..... -++++| + +||+ .||..-++.+|+.+.. + .. -.+|+..++++.. .
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 135565 3 7997 8999989988876431 0 00 1478877777532 3
Q ss_pred CCCCCHHHHHH-HcCCCC
Q 015078 275 GVRCNLKEAVE-MAGLAW 291 (413)
Q Consensus 275 ~~~~~L~~l~~-~~gI~~ 291 (413)
.++++|+.+++ .+|..-
T Consensus 152 ~~sysLd~Va~~~Lg~~K 169 (204)
T cd05779 152 QGSQGLKAVTKAKLGYDP 169 (204)
T ss_pred CCCccHHHHHHHHhCCCc
Confidence 45789999999 488744
No 66
>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=97.95 E-value=0.00012 Score=71.66 Aligned_cols=172 Identities=22% Similarity=0.177 Sum_probs=94.7
Q ss_pred ccEEEEEEeeCCCCCCCC------------------CCCcEEEEcEEEEEcCCCeEeeEE-----EEEEeCCCCCCCCcc
Q 015078 135 QYFVVIDFEATCDKDKNP------------------YPQEIIEFPSVIVSSVTGQLEACF-----QTYVRPTCNQLLSDF 191 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~------------------~~deIIEIGAV~vd~~~g~i~dsF-----~~~VkP~~~p~Ls~~ 191 (413)
..||+||+|.||+....+ ..-.|||||...+...+++...++ +.++-|......+..
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 579999999999953222 346899999999932566654333 333233221111111
Q ss_pred hhh---hcCCChhhh-cCCCCHHHHHHH--HHHHHhhcCCC-----CccEEEEEcCcchHHHHHHHHHHHcCCCCCC---
Q 015078 192 CKD---LTGIQQIQV-DRGVTLSEALLR--HDKWLENKGIK-----NTNFAVVTWSNWDCRVMLESECRFKKIWKPP--- 257 (413)
Q Consensus 192 ~~~---LTGIT~edV-~~Ap~f~eVl~~--f~~fL~~~~lv-----~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~--- 257 (413)
+.+ -+|+.-+.+ .++.++...-++ ..+.++-+.+. .+..+|.|++-+|+ .||-..+-. ++|.
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 111 245554443 344444332221 11334333332 23567777888997 676655432 4442
Q ss_pred --------CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCC-----------------------CCC-CCchHHHHHHH
Q 015078 258 --------YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAW-----------------------QGR-AHCGLDDAKNT 305 (413)
Q Consensus 258 --------~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~-----------------------~g~-~HrALdDA~aT 305 (413)
+|...+||+-++.... ....+|+.+.+.+++.. .+. .|.|-.||+.|
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 1224678776664322 23458999999999764 344 89999999999
Q ss_pred HHHHHH
Q 015078 306 ARLLAL 311 (413)
Q Consensus 306 A~Ll~~ 311 (413)
+.+|.+
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 67
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=97.88 E-value=0.00036 Score=66.19 Aligned_cols=121 Identities=15% Similarity=0.055 Sum_probs=81.4
Q ss_pred cEEEEEEeeCCCCCC-----CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHH
Q 015078 136 YFVVIDFEATCDKDK-----NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 210 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~-----~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~ 210 (413)
..+.||+||+...+. ++..+.||.||...- ++. ... +. ....+..
T Consensus 10 kilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~---~~~-----~~~--------~~--------------~~~~~E~ 59 (207)
T cd05785 10 RRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDN---RGW-----EEV--------LH--------------AEDAAEK 59 (207)
T ss_pred eEEEEEEEecCCCCccCCCCCCCCCeEEEEecccC---CCc-----eee--------ec--------------cCCCCHH
Confidence 789999999876542 235689999986421 221 000 10 0157889
Q ss_pred HHHHHHHHHHhhcCCCCccEEEEEc-C-cchHHHHHHHHHHHcCCCCCC-------------C--------------C-C
Q 015078 211 EALLRHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKPP-------------Y--------------F-N 260 (413)
Q Consensus 211 eVl~~f~~fL~~~~lv~~n~~vV~~-g-~fDir~fL~~~~~~~gi~~P~-------------~--------------~-~ 260 (413)
+.|..|++++....- . ++++| + .||+ .+|...++++|+.++. . . .
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 999999999998421 2 34444 4 7997 8999999999887630 0 0 1
Q ss_pred ceeehHHHHHHh----cCCCCCCHHHHHHHcCCCC
Q 015078 261 RWINLKVPFHEV----FGGVRCNLKEAVEMAGLAW 291 (413)
Q Consensus 261 ~~iDl~~l~r~l----~~~~~~~L~~l~~~~gI~~ 291 (413)
..+|+..++++. +...+++|+++++.+|+.-
T Consensus 135 ~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~~ 169 (207)
T cd05785 135 HVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLAS 169 (207)
T ss_pred EEEEcHHHHHhhcccccCCCCCCHHHHHHHhcccC
Confidence 226888777752 3456789999999998744
No 68
>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=97.86 E-value=0.00047 Score=65.66 Aligned_cols=130 Identities=20% Similarity=0.211 Sum_probs=88.9
Q ss_pred CCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHHHHHhhcCCCCccEEE
Q 015078 153 YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNFAV 232 (413)
Q Consensus 153 ~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~~fL~~~~lv~~n~~v 232 (413)
.-.+||.|+++.++ ..+.+ .-.++-.+ .-+..+.+++|.+.++.. +..+
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 45899999999886 33333 11111111 123788999999999864 3345
Q ss_pred EEc-C-cchHHHHHHHHHHHcCCCCCCCCC---------------ceeehHHHHHHhcC-CCCCCHHHHHHHcCCCCCCC
Q 015078 233 VTW-S-NWDCRVMLESECRFKKIWKPPYFN---------------RWINLKVPFHEVFG-GVRCNLKEAVEMAGLAWQGR 294 (413)
Q Consensus 233 V~~-g-~fDir~fL~~~~~~~gi~~P~~~~---------------~~iDl~~l~r~l~~-~~~~~L~~l~~~~gI~~~g~ 294 (413)
|+| | .||+ .||..-.-.+|++.|.++. +.+||..++.. ++ ....+|+.+|..+|||-...
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 554 4 7997 8999999999999886442 24677776543 33 34679999999999985311
Q ss_pred C------------------CchHHHHHHHHHHHHHHHHh
Q 015078 295 A------------------HCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 295 ~------------------HrALdDA~aTA~Ll~~ll~~ 315 (413)
- .--..|+++|+.|+.++..-
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 11267999999999988653
No 69
>PRK05755 DNA polymerase I; Provisional
Probab=97.84 E-value=0.00017 Score=81.86 Aligned_cols=135 Identities=21% Similarity=0.181 Sum_probs=94.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..+++||+||||+ ++...+|+.|+.. . .++.. .+|.+. +|. .+++.
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 4789999999997 6778899998753 3 23421 233222 111 16888
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CCCC--
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GLAW-- 291 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~-gI~~-- 291 (413)
.|.+++++..+ ..|.|+..||+ .||. +.|+.++ ..++|++.....+.+...++|++++++| |+..
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 89999988532 24677789996 7876 3577654 4689998766666554348999999887 5541
Q ss_pred ----------------CCCCCchHHHHHHHHHHHHHHHHh
Q 015078 292 ----------------QGRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 292 ----------------~g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
+...|.|..|+..|.+|+..|.+.
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=97.74 E-value=1.3e-05 Score=61.98 Aligned_cols=52 Identities=10% Similarity=0.098 Sum_probs=46.5
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQ 103 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~ 103 (413)
+..++.+++++|++.|.++++||| |..++++++++...++.++++++|+|..
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
>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=97.65 E-value=0.0058 Score=58.61 Aligned_cols=137 Identities=15% Similarity=0.128 Sum_probs=84.8
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeEeeEEEEE-EeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 136 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEACFQTY-VRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~--~~~~deIIEIGAV~vd~~~g~i~dsF~~~-VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
..+.||+||+...+. +|..|+||.|+.+.-...+...... .-+ +++.. .++ ...|..-++..+.
T Consensus 8 ~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~-~~~~l~~~~--~~~----------~~~v~~~~~E~eL 74 (230)
T cd05777 8 RILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIR-NIFTLKTCA--PIV----------GAQVFSFETEEEL 74 (230)
T ss_pred eEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCcee-EEEEeCCCC--CCC----------CCEEEEECCHHHH
Confidence 689999999976542 4678999999988653111111111 112 22221 121 2334456789999
Q ss_pred HHHHHHHHhhcCCCCccEEEEEc-CcchHHHHHHHHHHHcCCCCC-CC--------------C-----------------
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTW-SNWDCRVMLESECRFKKIWKP-PY--------------F----------------- 259 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~-g~fDir~fL~~~~~~~gi~~P-~~--------------~----------------- 259 (413)
|..|.+++..... .+++-++ -.||+ .+|..-++..|+..- .+ +
T Consensus 75 L~~f~~~i~~~DP---Dii~GyN~~~FDl-~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~G 150 (230)
T cd05777 75 LLAWRDFVQEVDP---DIITGYNICNFDL-PYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEG 150 (230)
T ss_pred HHHHHHHHHhcCC---CEEEEecCCCCCH-HHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcC
Confidence 9999999987421 2333333 37996 788888887776521 00 0
Q ss_pred CceeehHHHHHHhcCCCCCCHHHHHH-HcCC
Q 015078 260 NRWINLKVPFHEVFGGVRCNLKEAVE-MAGL 289 (413)
Q Consensus 260 ~~~iDl~~l~r~l~~~~~~~L~~l~~-~~gI 289 (413)
.-.+|+...+++.+...+++|+++++ .+|.
T Consensus 151 R~~iD~~~~~~~~~kl~sy~L~~Va~~~Lg~ 181 (230)
T cd05777 151 RIQFDLLQVIQRDYKLRSYSLNSVSAHFLGE 181 (230)
T ss_pred EEeeeHHHHHHHhcCcccCcHHHHHHHHhCC
Confidence 12347777777777677899999987 4553
No 72
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=97.64 E-value=7.9e-05 Score=72.79 Aligned_cols=171 Identities=16% Similarity=0.135 Sum_probs=109.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEE-----EcC-------------CCeEeeEEEEEEeCCCCCCCCcchhhhc
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIV-----SSV-------------TGQLEACFQTYVRPTCNQLLSDFCKDLT 196 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~v-----d~~-------------~g~i~dsF~~~VkP~~~p~Ls~~~~~LT 196 (413)
.+|+++|+|+||+. ....+|-|+...-| +.+ .-++.+.-+-++-|.. ..++...++|
T Consensus 13 ~tf~fldleat~lp---~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~aeeit 87 (318)
T KOG4793|consen 13 RTFSFLDLEATGLP---GWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAEEIT 87 (318)
T ss_pred eEEEeeeeccccCC---cccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhhhhc
Confidence 69999999999984 34556777643322 211 0145566777777874 5778889999
Q ss_pred CCChhhh--cCCCCHHHHH-HHHHHHHhhcCCCCcc-EEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCceeehH-----
Q 015078 197 GIQQIQV--DRGVTLSEAL-LRHDKWLENKGIKNTN-FAVVTWS-NWDCRVMLESECRFKKIWKPPYFNRWINLK----- 266 (413)
Q Consensus 197 GIT~edV--~~Ap~f~eVl-~~f~~fL~~~~lv~~n-~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl~----- 266 (413)
|+++.-+ ..---|+..+ +-+..||+.-. .. ..|+|+| .+|+ .+|..+++..|+..|- +....|..
T Consensus 88 gls~~~~~l~rr~~~D~dla~LL~afls~lp---~p~CLVaHng~~~df-pil~qela~lg~~lpq-~lvcvdslpa~~a 162 (318)
T KOG4793|consen 88 GLSQPFLALQRRLAFDKDLAKLLTAFLSRLP---TPGCLVAHNGNEYDF-PILAQELAGLGYSLPQ-DLVCVDSLPALNA 162 (318)
T ss_pred ccccHHHHHHHHhhhhHHHHHHHHHHHhcCC---CCceEEeecCCcccc-HHHHHHHHhcCccchh-hhcCcchhHHHHH
Confidence 9999654 3444454443 34556666531 12 2455665 5786 7899999888887652 11112210
Q ss_pred ------------------------------------------------------HHH-------------HHhcC-----
Q 015078 267 ------------------------------------------------------VPF-------------HEVFG----- 274 (413)
Q Consensus 267 ------------------------------------------------------~l~-------------r~l~~----- 274 (413)
++. +.+|.
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 11111
Q ss_pred -------CCCCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHHHHHHh
Q 015078 275 -------GVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 275 -------~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
...++|+.++.++.+..++.+|||+.|...+.++++++-.+
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 11247889999999887788999999999999999987544
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=97.48 E-value=0.0056 Score=57.99 Aligned_cols=136 Identities=17% Similarity=0.075 Sum_probs=80.6
Q ss_pred cEEEEEEeeCCCC-CCCCC----CCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHH
Q 015078 136 YFVVIDFEATCDK-DKNPY----PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 210 (413)
Q Consensus 136 ~fVV~D~ETTGl~-~~~~~----~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~ 210 (413)
..+.||+||++.. +..|. .++||+|+.+ + .++. +.+ .++..... ...+... ....++..-.+..
T Consensus 6 rilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~--~-~~~~--~~v-~~~~~~~~-~~~~~~~----~~~~~v~~~~~E~ 74 (204)
T cd05783 6 KRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA--G-SDGL--KRV-LVLKREGV-EGLEGLL----PEGAEVEFFDSEK 74 (204)
T ss_pred eEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc--C-CCCC--cEE-EEEecCCc-ccccccC----CCCCeEEecCCHH
Confidence 7899999999642 22232 2789999875 2 1221 111 22221100 0100000 0112244457899
Q ss_pred HHHHHHHHHHhhcCCCCccEEEEEc-C-cchHHHHHHHHHHHcCCC---CCCC---------CCceeehHHHHHH-h---
Q 015078 211 EALLRHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFKKIW---KPPY---------FNRWINLKVPFHE-V--- 272 (413)
Q Consensus 211 eVl~~f~~fL~~~~lv~~n~~vV~~-g-~fDir~fL~~~~~~~gi~---~P~~---------~~~~iDl~~l~r~-l--- 272 (413)
+.|.+|.+++.+. . ++++| + +||+ .+|..-++++|+. .|.. ....+|+...++. .
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 3 7997 8999999999887 2211 1245788665543 1
Q ss_pred --c--CCCCCCHHHHHHHc-CC
Q 015078 273 --F--GGVRCNLKEAVEMA-GL 289 (413)
Q Consensus 273 --~--~~~~~~L~~l~~~~-gI 289 (413)
+ ...+++|+++++.+ |.
T Consensus 148 ~~~~~~~~~~~L~~Va~~~lg~ 169 (204)
T cd05783 148 YAFGNKYREYTLDAVAKALLGE 169 (204)
T ss_pred hhhccccccCcHHHHHHHhcCC
Confidence 2 23578999999866 54
No 74
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=97.41 E-value=0.00012 Score=78.45 Aligned_cols=41 Identities=34% Similarity=0.879 Sum_probs=36.8
Q ss_pred ccceecCCCcCcceeccCCCCCCCceeecCCCcccCCCcccceeec
Q 015078 364 HPSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWA 409 (413)
Q Consensus 364 ~~~c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~ 409 (413)
...|.||-++..++|+|.|||-||.||.|.. . ..|.||.|+
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 75
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=97.24 E-value=9.6e-05 Score=85.18 Aligned_cols=54 Identities=7% Similarity=0.027 Sum_probs=48.9
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
.|+..+.+||++|+++|++|||||| |++..+-+++|.+++++|+|.|.|+|.++
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 4667889999999999999999995 66668999999999999999999999874
No 76
>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=97.24 E-value=0.0035 Score=66.19 Aligned_cols=123 Identities=12% Similarity=0.164 Sum_probs=86.6
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
...+.|||||+ |+..-.-.+|++..+ ++...+.|+.|+-.. .....+++.
T Consensus 284 ~~~~ffDiEt~------P~~~~~yL~G~~~~~--~~~~~~~~~~fla~~----------------------~~~E~~~~~ 333 (457)
T TIGR03491 284 PGELIFDIESD------PDENLDYLHGFLVVD--KGQENEKYRPFLAED----------------------PNTEELAWQ 333 (457)
T ss_pred CccEEEEecCC------CCCCCceEEEEEEec--CCCCCcceeeeecCC----------------------chHHHHHHH
Confidence 46789999998 344566788887664 333223455554332 124567999
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCC---CCCceeehHHHHHHhc--CCCCCCHHHHHHHcCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP---YFNRWINLKVPFHEVF--GGVRCNLKEAVEMAGL 289 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~---~~~~~iDl~~l~r~l~--~~~~~~L~~l~~~~gI 289 (413)
+|.+|+.... +..|+||+.++ ...|++-+.+++..... +..+++|+....+..+ +..+++|+.++..+|.
T Consensus 334 ~f~~~l~~~~----~~~i~hY~~~e-~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~ 408 (457)
T TIGR03491 334 QFLQLLQSYP----DAPIYHYGETE-KDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGF 408 (457)
T ss_pred HHHHHHHHCC----CCeEEeeCHHH-HHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCc
Confidence 9999998742 45789999999 58899998888765311 2237899987766543 5668999999999998
Q ss_pred CCC
Q 015078 290 AWQ 292 (413)
Q Consensus 290 ~~~ 292 (413)
.+.
T Consensus 409 ~~~ 411 (457)
T TIGR03491 409 EWR 411 (457)
T ss_pred ccC
Confidence 775
No 77
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=97.23 E-value=0.00012 Score=83.66 Aligned_cols=54 Identities=11% Similarity=0.020 Sum_probs=49.0
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
.|+..+.++|++|+++|++|||||| |++..+-+++|.+++|+|+|.|.|+|.++
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 66778999999999999999999999874
No 78
>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=96.99 E-value=0.025 Score=53.19 Aligned_cols=120 Identities=12% Similarity=0.106 Sum_probs=77.1
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHH
Q 015078 136 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLR 215 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~ 215 (413)
..+.||+||++. .+|+.||.. +.++..++ .+=.+. ... | ..+.--++..+.|..
T Consensus 4 ~~~~fDIE~~~~-------~~i~~i~~~--~~~~~~i~----~~~~~~---~~~-------~---~~v~~~~~E~~lL~~ 57 (193)
T cd05784 4 KVVSLDIETSMD-------GELYSIGLY--GEGQERVL----MVGDPE---DDA-------P---DNIEWFADEKSLLLA 57 (193)
T ss_pred cEEEEEeecCCC-------CCEEEEEee--cCCCCEEE----EECCCC---CCC-------C---CEEEEECCHHHHHHH
Confidence 679999999974 289999863 33333332 111111 111 1 123445788999999
Q ss_pred HHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHHHcCCCCCCCC-----------------------CceeehHHHHH
Q 015078 216 HDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKPPYF-----------------------NRWINLKVPFH 270 (413)
Q Consensus 216 f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~~~gi~~P~~~-----------------------~~~iDl~~l~r 270 (413)
|.+++..... .+ +++| ..||+ .+|..-++++|++.+ +. .-.+|+..+.+
T Consensus 58 f~~~i~~~dP---Dv-i~g~N~~~FD~-~yl~~R~~~~~i~~~-~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k 131 (193)
T cd05784 58 LIAWFAQYDP---DI-IIGWNVINFDL-RLLQRRAEAHGLPLR-LGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALK 131 (193)
T ss_pred HHHHHHhhCC---CE-EEECCCcCcCH-HHHHHHHHHhCCCcc-cccCCCccccccCCcCCcceEEEeeEEEEEhHHHHH
Confidence 9999987521 23 3443 37997 788888888887642 11 01568777776
Q ss_pred H-hcCCCCCCHHHHHHHc
Q 015078 271 E-VFGGVRCNLKEAVEMA 287 (413)
Q Consensus 271 ~-l~~~~~~~L~~l~~~~ 287 (413)
+ .++..+++|+++++++
T Consensus 132 ~~~~kl~sy~L~~Va~~~ 149 (193)
T cd05784 132 TATYHFESFSLENVAQEL 149 (193)
T ss_pred HccCCCCcCCHHHHHHHH
Confidence 5 4677889999999854
No 79
>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=96.87 E-value=0.092 Score=54.17 Aligned_cols=162 Identities=17% Similarity=0.056 Sum_probs=98.8
Q ss_pred ccEEEEEEeeCCCCCCCC--C--CCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHH
Q 015078 135 QYFVVIDFEATCDKDKNP--Y--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 210 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~--~--~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~ 210 (413)
...++||+||+...+..| . .++||.|+.+.-+...............+.. .+. |+ .+..-.+..
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~--~~~-------~~---~~~~~~~E~ 70 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK--EID-------GV---EVYEFNNEK 70 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC--CCC-------CC---eEEecCCHH
Confidence 368999999997643112 2 6899999988876432222222233333332 122 22 233334888
Q ss_pred HHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCC----------C---------------------
Q 015078 211 EALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPP----------Y--------------------- 258 (413)
Q Consensus 211 eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~----------~--------------------- 258 (413)
+.|..|.+++..... .+++.+++ .||+ .+|...+...++.... .
T Consensus 71 ~lL~~f~~~i~~~dp---dii~g~N~~~FD~-~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 146 (471)
T smart00486 71 ELLKAFLEFIKKYDP---DIIYGHNISNFDL-PYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIK 146 (471)
T ss_pred HHHHHHHHHHHHhCC---CEEEeecCCCCCH-HHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEec
Confidence 999999999987532 34555554 6996 7888877765553210 0
Q ss_pred CCceeehHHHHHHhcCCCCCCHHHHHHHcCCC-CCCCC-------------------CchHHHHHHHHHHHHHH
Q 015078 259 FNRWINLKVPFHEVFGGVRCNLKEAVEMAGLA-WQGRA-------------------HCGLDDAKNTARLLALL 312 (413)
Q Consensus 259 ~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~-~~g~~-------------------HrALdDA~aTA~Ll~~l 312 (413)
..-.+|+...++..+...+++|+.+++++.-. ...-. .--+.||..+.+|+.++
T Consensus 147 g~~~~Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 147 GRLVIDLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred cEEEEEhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 01346888888888777788999988764431 11000 01156888888888875
No 80
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=96.83 E-value=0.0084 Score=58.31 Aligned_cols=118 Identities=16% Similarity=0.111 Sum_probs=72.1
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHH-HHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS-EAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~-eVl 213 (413)
+++++||+||||+ +...+.|+-.|...+ .... .+||-.. ++ ||.-+ -++
T Consensus 98 e~~~FFDiETTGL---~~ag~~I~~~g~a~~--~~~~------~~Vrq~~---lp----------------~p~~E~avl 147 (278)
T COG3359 98 EDVAFFDIETTGL---DRAGNTITLVGGARG--VDDT------MHVRQHF---LP----------------APEEEVAVL 147 (278)
T ss_pred cceEEEeeecccc---CCCCCeEEEEEEEEc--cCce------EEEEeec---CC----------------CcchhhHHH
Confidence 5899999999999 345566666666554 2333 2454442 22 22222 245
Q ss_pred HHHHHHHhhcCCCCccEEEEE-cC-cchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC--CCCCCHHHHHHHcCC
Q 015078 214 LRHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG--GVRCNLKEAVEMAGL 289 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~vV~-~g-~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~--~~~~~L~~l~~~~gI 289 (413)
+.|+....- + .+|+ +| +||+ .|+++ +.+..+++- +.+.-+||.-..|++-+ +.+.+|+++-+.+|+
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 556544411 2 4666 44 7995 99995 666655542 33456888766666654 246789998888988
Q ss_pred CCC
Q 015078 290 AWQ 292 (413)
Q Consensus 290 ~~~ 292 (413)
..+
T Consensus 218 ~R~ 220 (278)
T COG3359 218 RRE 220 (278)
T ss_pred ccc
Confidence 653
No 81
>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=96.75 E-value=0.068 Score=51.49 Aligned_cols=173 Identities=12% Similarity=0.009 Sum_probs=102.0
Q ss_pred cEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeEe---eEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHH
Q 015078 136 YFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLE---ACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLS 210 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~--~~~~deIIEIGAV~vd~~~g~i~---dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~ 210 (413)
+.+.||+|+.+-.+. +|..|.||.|+.++-+....... ...--++.+.... .+.. .....+....|.--++..
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 46789999999886532111111 1122334443210 1100 112244445667788999
Q ss_pred HHHHHHHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHHHcCCCCC--CC-----------------C----------
Q 015078 211 EALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKP--PY-----------------F---------- 259 (413)
Q Consensus 211 eVl~~f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~~~gi~~P--~~-----------------~---------- 259 (413)
+.|.+|.+++..... . +++.| -+||+ .+|..-++..++..- .+ +
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 999999999987522 2 23343 37996 777777766554320 00 0
Q ss_pred --CceeehHHHHHHhcCCCCCCHHHHHH-HcCCCCCCCCCchHHHHH------HHHHHHHHHHHh
Q 015078 260 --NRWINLKVPFHEVFGGVRCNLKEAVE-MAGLAWQGRAHCGLDDAK------NTARLLALLMHR 315 (413)
Q Consensus 260 --~~~iDl~~l~r~l~~~~~~~L~~l~~-~~gI~~~g~~HrALdDA~------aTA~Ll~~ll~~ 315 (413)
.-.+|+....+..+...+++|++++. .+|-....-+|..+.+.. ...+|+...+++
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 01247777777777778999999997 577644333566676653 345565555554
No 82
>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=96.74 E-value=0.00051 Score=61.26 Aligned_cols=52 Identities=12% Similarity=0.203 Sum_probs=46.6
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhh
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFES 102 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~ 102 (413)
-|..++.++|++|++.|.++||||| |....++|+.+...++.+++++.|+|.
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 83
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=96.73 E-value=0.026 Score=65.50 Aligned_cols=162 Identities=18% Similarity=0.169 Sum_probs=98.1
Q ss_pred cEEEEEEeeCCCCC-C--CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 136 YFVVIDFEATCDKD-K--NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 136 ~fVV~D~ETTGl~~-~--~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
..+.||+||++..+ + ++..|+||+|+.+... .|.-.+.+...|=.- . .|..+.| ..|..-++..+.
T Consensus 265 rilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~--~g~~~~~~~r~vftl-----~-~c~~i~g---~~V~~f~sE~eL 333 (1054)
T PTZ00166 265 RILSFDIECIKLKGLGFPEAENDPVIQISSVVTN--QGDEEEPLTKFIFTL-----K-ECASIAG---ANVLSFETEKEL 333 (1054)
T ss_pred EEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEee--CCCccCCcceEEEec-----C-ccccCCC---ceEEEeCCHHHH
Confidence 68999999997654 1 3567999999998653 333211121111111 0 1122222 345556789999
Q ss_pred HHHHHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHHHcCCCC-CCC-------------------C-----------
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWK-PPY-------------------F----------- 259 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~~~gi~~-P~~-------------------~----------- 259 (413)
|..|.+++....- .+ +++| ..||+ .+|..-++..|+.. +.+ +
T Consensus 334 L~~f~~~I~~~DP---DI-I~GYNi~~FDl-pYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~ 408 (1054)
T PTZ00166 334 LLAWAEFVIAVDP---DF-LTGYNIINFDL-PYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIE 408 (1054)
T ss_pred HHHHHHHHHhcCC---CE-EEecCCcCCcH-HHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEee
Confidence 9999999987421 23 3333 37996 78877777665541 100 0
Q ss_pred -CceeehHHHHHHhcCCCCCCHHHHHHH-cCCCCC------------CCCC-------chHHHHHHHHHHHHHHH
Q 015078 260 -NRWINLKVPFHEVFGGVRCNLKEAVEM-AGLAWQ------------GRAH-------CGLDDAKNTARLLALLM 313 (413)
Q Consensus 260 -~~~iDl~~l~r~l~~~~~~~L~~l~~~-~gI~~~------------g~~H-------rALdDA~aTA~Ll~~ll 313 (413)
.-.+|+..++++.+...+++|++++.+ +|.... +..+ -.+.||..+.+|+.+|.
T Consensus 409 GR~~iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 409 GRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred eEEEEEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 123577778877777788999999984 453221 1111 12678888888888763
No 84
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=96.70 E-value=0.0006 Score=77.74 Aligned_cols=54 Identities=6% Similarity=-0.002 Sum_probs=49.2
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
-|+.++.++|++|+++|.+|||||| |+++.+++++|.++++.++|.|.|+|.++
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 85
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=96.42 E-value=0.0013 Score=74.76 Aligned_cols=54 Identities=9% Similarity=0.110 Sum_probs=48.1
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
.|..++.++|++|++.|.+|||||| |++..+=+++|.+++++|+|.|.|+|.++
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 3567889999999999999999996 66667888999999999999999999874
No 86
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=96.41 E-value=0.0013 Score=74.69 Aligned_cols=53 Identities=4% Similarity=-0.172 Sum_probs=47.6
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
|..++.++|++|++.|.+|||||| |+.+.+.++++.+.++.+++.|.|+|.++
T Consensus 17 g~~~~~elv~~A~~~G~~aiAiTD--------h~~~~g~~~f~~~~~~~gik~I~G~E~~~ 69 (874)
T PRK09532 17 GASQLPALVDRAIELGMPAIALTD--------HGVMYGAIELLKVCRNKGIKPIIGNEMYV 69 (874)
T ss_pred ccCCHHHHHHHHHHCCCCEEEEec--------CCChhhHHHHHHHHHHcCCeEEEEEEEEe
Confidence 567889999999999999999995 66667889999999999999999999884
No 87
>PF03104 DNA_pol_B_exo1: DNA polymerase family B, exonuclease domain Several related DNA polymerases were too dissimilar to be included.; InterPro: IPR006133 DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases 2.7.7.7 from EC) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate []. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold [].; GO: 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1QHT_A 4AHC_A 3A2F_A 2JGU_A 4AIL_C 1NOY_A 1NOZ_B 3IAY_A 1WNS_A 3K5O_A ....
Probab=96.03 E-value=0.092 Score=51.82 Aligned_cols=130 Identities=15% Similarity=0.089 Sum_probs=80.0
Q ss_pred ccEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeE---eeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCH
Q 015078 135 QYFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQL---EACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTL 209 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~--~~~~deIIEIGAV~vd~~~g~i---~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f 209 (413)
-..+.||+||....+. ++..++|+.|+.+..+ .+.- .+.+.++..+.. ... ...|.--++.
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 3578999999988764 2211 122223322221 111 4455566899
Q ss_pred HHHHHHHHHHHhhcCCCCccEEEEEc-C-cchHHHHHHHHHHHcCCCCC----CCC------------------C-----
Q 015078 210 SEALLRHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFKKIWKP----PYF------------------N----- 260 (413)
Q Consensus 210 ~eVl~~f~~fL~~~~lv~~n~~vV~~-g-~fDir~fL~~~~~~~gi~~P----~~~------------------~----- 260 (413)
.+.|..|++++..... .+ +++| . .||+ .+|..-++..|+... ... .
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 9999999999987532 23 4444 3 6996 788888887754320 000 0
Q ss_pred -----ceeehHHHHHHhcCCCCCCHHHH
Q 015078 261 -----RWINLKVPFHEVFGGVRCNLKEA 283 (413)
Q Consensus 261 -----~~iDl~~l~r~l~~~~~~~L~~l 283 (413)
-.+|+..++++.+...+++|+++
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 24577788888887778888763
No 88
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=95.96 E-value=0.0028 Score=73.24 Aligned_cols=54 Identities=6% Similarity=-0.047 Sum_probs=48.3
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
.|..++.++|++|++.|++|||||| |++..+.++++.++++.|++.|.|+|.++
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 3677899999999999999999995 66667899999999999999999999873
No 89
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=95.96 E-value=0.0027 Score=73.94 Aligned_cols=54 Identities=6% Similarity=-0.156 Sum_probs=47.8
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
.|..++.++|++|++.|.+|||||| |++..+.+++|.+.++.++|+|.|+|.++
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 3567888999999999999999996 55667888999999999999999999884
No 90
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=95.83 E-value=0.0037 Score=72.29 Aligned_cols=54 Identities=9% Similarity=0.065 Sum_probs=47.7
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
.|..++.++|++|++.|.+|||||| |++..+=.++|.+++++|+|.|.|+|.+.
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 4668889999999999999999996 66667778899999999999999999873
No 91
>PRK05762 DNA polymerase II; Reviewed
Probab=95.75 E-value=0.27 Score=55.64 Aligned_cols=147 Identities=11% Similarity=0.078 Sum_probs=92.2
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
-..+.||+||++. .+|++|+..-. .+..+ ..|-+.. + . ..+.|..-++..+.|.
T Consensus 155 lrvlsfDIE~~~~-------~~i~sI~~~~~--~~~~v-----i~ig~~~-~-~----------~~~~v~~~~sE~~LL~ 208 (786)
T PRK05762 155 LKVVSLDIETSNK-------GELYSIGLEGC--GQRPV-----IMLGPPN-G-E----------ALDFLEYVADEKALLE 208 (786)
T ss_pred CeEEEEEEEEcCC-------CceEEeeecCC--CCCeE-----EEEECCC-C-C----------CcceEEEcCCHHHHHH
Confidence 3789999999852 37888886521 12222 1222221 1 1 0111555678999999
Q ss_pred HHHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHHHcCCCCC-------------CCCC----------ceeehHHHH
Q 015078 215 RHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRFKKIWKP-------------PYFN----------RWINLKVPF 269 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~~~gi~~P-------------~~~~----------~~iDl~~l~ 269 (413)
.|.+++..... .+ +++| .+||+ .+|..-++.+|+.+. .... -.+|+..+.
T Consensus 209 ~F~~~i~~~DP---DI-IvGyNi~~FDl-pyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~ 283 (786)
T PRK05762 209 KFNAWFAEHDP---DV-IIGWNVVQFDL-RLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDAL 283 (786)
T ss_pred HHHHHHHhcCC---CE-EEEeCCCCCcH-HHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHH
Confidence 99999988521 23 4443 37996 888888888888642 0110 256887777
Q ss_pred HHhc-CCCCCCHHHHHHHcCCCCCC--CCC-------------------chHHHHHHHHHHHHHH
Q 015078 270 HEVF-GGVRCNLKEAVEMAGLAWQG--RAH-------------------CGLDDAKNTARLLALL 312 (413)
Q Consensus 270 r~l~-~~~~~~L~~l~~~~gI~~~g--~~H-------------------rALdDA~aTA~Ll~~l 312 (413)
+... ...+++|+++++++..+... ..| -.+.||..|.+|+.++
T Consensus 284 k~~~~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 284 KSATWVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHhhccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 7655 56789999999876543211 110 1378999999998843
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=95.55 E-value=0.91 Score=40.23 Aligned_cols=91 Identities=20% Similarity=0.116 Sum_probs=55.8
Q ss_pred HHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHH-cC-
Q 015078 212 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEM-AG- 288 (413)
Q Consensus 212 Vl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~-~g- 288 (413)
++..+.+++++..+ ..+.|+..||+ .+|.+. .|+.. ..++|+ .+...+.+. .+++|+++++. +|
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 66667777776522 23455668996 566544 67654 357899 555555543 34899999865 46
Q ss_pred CCC--C---CCCC-----------chHHHHHHHHHHHHHHHHh
Q 015078 289 LAW--Q---GRAH-----------CGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 289 I~~--~---g~~H-----------rALdDA~aTA~Ll~~ll~~ 315 (413)
++. . +.-. -|-.||..|.+|+..|.++
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 1111 2566999999999888764
No 93
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=95.52 E-value=0.0051 Score=71.64 Aligned_cols=54 Identities=9% Similarity=-0.010 Sum_probs=47.8
Q ss_pred ccccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 43 TIVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 43 ~~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
-|..++.++|++|++.|.+|||||| |+...+..++|.++++.++++|.|+|.++
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 3567889999999999999999996 66667888999999999999999999874
No 94
>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=95.31 E-value=0.0071 Score=69.83 Aligned_cols=53 Identities=9% Similarity=0.006 Sum_probs=47.5
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
|..++.++|++|++.|.++||||| |+...+..+++.+.++.++++|.|+|.++
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 577889999999999999999996 66667888999999999999999999875
No 95
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=95.26 E-value=0.13 Score=49.06 Aligned_cols=157 Identities=14% Similarity=0.040 Sum_probs=92.7
Q ss_pred CCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCC------cchhhhcCCChhhhcCCC-CHHHHHHHHHHHHhhcCCC
Q 015078 154 PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLS------DFCKDLTGIQQIQVDRGV-TLSEALLRHDKWLENKGIK 226 (413)
Q Consensus 154 ~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls------~~~~~LTGIT~edV~~Ap-~f~eVl~~f~~fL~~~~lv 226 (413)
.--..|||++++.+++| |.+.||++|+|... ++- ..+.+-|+|..+-...+. ++.+++.++.+||+.....
T Consensus 7 ~y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~-p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~~ 84 (213)
T PF13017_consen 7 EYVPAEIAICKFSLKEG-IIDSFHTFINPGQI-PLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNKGG 84 (213)
T ss_pred cEEeEEEEEEEEecCCc-cchhhhcccCCCCC-CcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcCCC
Confidence 34568999999999998 78999999999952 122 233456778877666555 7999999999999986433
Q ss_pred CccEEEEEcC-cchH-HHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC----C----CCCCHHHHH-HHcC-------
Q 015078 227 NTNFAVVTWS-NWDC-RVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG----G----VRCNLKEAV-EMAG------- 288 (413)
Q Consensus 227 ~~n~~vV~~g-~fDi-r~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~----~----~~~~L~~l~-~~~g------- 288 (413)
+....|++.. .+.+ ...|+.-+...+.... ....++..++-.+.. . ...-+...+ ..+.
T Consensus 85 ~~~~~i~~~~~~~~~V~~cl~~La~~a~~~~~---~~v~~~~~lf~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 161 (213)
T PF13017_consen 85 EKMPPIFTKRDQIPRVQSCLKWLAKKAGEDND---FKVYDFEYLFFDLKNEKVDYRWDRQDFPSKTIADALFPKDFFEYS 161 (213)
T ss_pred CCcceEEEeHhHHHHHHHHHHHHHHhcCCCcc---eEeecHHHHHHHHHHHHhhcccccccCchHHHHHHHccchhhhcc
Confidence 3334455543 2221 2245555555554432 234455444433321 1 111111111 1111
Q ss_pred C--------CCCCCCCchHHHHHHHHHHHHHHHHh
Q 015078 289 L--------AWQGRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 289 I--------~~~g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
- ......+.|+..+.-+|..+...+..
T Consensus 162 ~~~~C~~He~~d~~~~Ca~s~v~r~ay~i~d~~c~ 196 (213)
T PF13017_consen 162 SNIRCDFHEEIDRSKYCALSTVKRWAYTISDYMCR 196 (213)
T ss_pred CCCceeecccCCCcccchhHHHHHHHHHHHHHHHH
Confidence 1 11123688999999999887776643
No 96
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=94.95 E-value=0.0096 Score=69.44 Aligned_cols=53 Identities=11% Similarity=0.008 Sum_probs=47.0
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhhcccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k~~~~~~~g~e~~~ 104 (413)
+..++.++|++|++.|.+|||||| |+.....++++.++++.++++|.|+|.++
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 567788999999999999999996 55556788999999999999999999874
No 97
>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=94.95 E-value=0.26 Score=47.47 Aligned_cols=149 Identities=13% Similarity=0.057 Sum_probs=90.8
Q ss_pred cEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEc---CC----CeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCC
Q 015078 136 YFVVIDFEATCDKDKNPYPQEIIEFPSVIVSS---VT----GQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVT 208 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~---~~----g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~ 208 (413)
+.+.|-+-|.-- ......||+.|+++.... .+ ......+.++++|......+..-...-.-....|.--++
T Consensus 4 ~v~sls~~T~~n--~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~ 81 (234)
T cd05776 4 TVMSLSIKTVLN--SKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFEN 81 (234)
T ss_pred EEEEEEeEEEec--CcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCC
Confidence 456667777631 112369999999987631 01 112345677888875311222222333333345677889
Q ss_pred HHHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCC------------CCCC-------------Cce
Q 015078 209 LSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWK------------PPYF-------------NRW 262 (413)
Q Consensus 209 f~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~------------P~~~-------------~~~ 262 (413)
..+.|..|++++....- .+++-|+. .||+ .+|-.-++..|++. |... .-.
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 99999999999987532 33333332 7996 77777777666542 1100 013
Q ss_pred eehHHHHHHhcCCCCCCHHHHHH-HcCCC
Q 015078 263 INLKVPFHEVFGGVRCNLKEAVE-MAGLA 290 (413)
Q Consensus 263 iDl~~l~r~l~~~~~~~L~~l~~-~~gI~ 290 (413)
+|+...++.+....+++|+++++ .+|..
T Consensus 158 ~D~~~~~k~~~~~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 158 CDTYLSAKELIRCKSYDLTELSQQVLGIE 186 (234)
T ss_pred hccHHHHHHHhCCCCCChHHHHHHHhCcC
Confidence 57777777777777899999998 67753
No 98
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=94.91 E-value=0.41 Score=56.51 Aligned_cols=161 Identities=18% Similarity=0.145 Sum_probs=99.5
Q ss_pred ccEEEEEEeeCCCCCCC--CCCCcEEEEcEEEEEcCCCeE----------eeEEEEEEeCCCCCCCCcchhhhcCCChhh
Q 015078 135 QYFVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQL----------EACFQTYVRPTCNQLLSDFCKDLTGIQQIQ 202 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~--~~~deIIEIGAV~vd~~~g~i----------~dsF~~~VkP~~~p~Ls~~~~~LTGIT~ed 202 (413)
-..++||+|||-+.-.. +..|+|.=|+. .+|+. |.+ ++.|+..=||+. .-+| -
T Consensus 246 p~VlAFDIETtKlPLKFPDae~DqIMMISY-MiDGq-GfLItNREiVs~DIedfEYTPKpE~---eG~F----------~ 310 (2173)
T KOG1798|consen 246 PRVLAFDIETTKLPLKFPDAESDQIMMISY-MIDGQ-GFLITNREIVSEDIEDFEYTPKPEY---EGPF----------C 310 (2173)
T ss_pred ceEEEEeeecccCCCCCCCcccceEEEEEE-EecCc-eEEEechhhhccchhhcccCCcccc---ccce----------E
Confidence 47889999999886433 46789988864 45643 332 233443333332 1112 1
Q ss_pred hcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEc-Cc-chHHHHHHHHHHHcCCCCCC-C-C---------CceeehHHHH
Q 015078 203 VDRGVTLSEALLRHDKWLENKGIKNTNFAVVTW-SN-WDCRVMLESECRFKKIWKPP-Y-F---------NRWINLKVPF 269 (413)
Q Consensus 203 V~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~-g~-fDir~fL~~~~~~~gi~~P~-~-~---------~~~iDl~~l~ 269 (413)
|-+-++....|++|.+-+.+. +.-++||+ |. || +.|+++-+..+|+.+-. + | -+++--...|
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 346788889999999988874 23467775 65 79 89999999999987521 1 0 0222223334
Q ss_pred HHh-----cCCCCCCHHHHHH-HcCCCC-------------CCCCCc---hHHHHHHHHHHHHHHHHh
Q 015078 270 HEV-----FGGVRCNLKEAVE-MAGLAW-------------QGRAHC---GLDDAKNTARLLALLMHR 315 (413)
Q Consensus 270 r~l-----~~~~~~~L~~l~~-~~gI~~-------------~g~~Hr---ALdDA~aTA~Ll~~ll~~ 315 (413)
+.. +|..+++|..+.+ ++|-.. +...|- ...||.||-.|+.+-...
T Consensus 386 rWVKRDSYLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP 453 (2173)
T KOG1798|consen 386 RWVKRDSYLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP 453 (2173)
T ss_pred hhhhhcccCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh
Confidence 433 3445678887764 455321 111233 489999999999886643
No 99
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=94.17 E-value=0.025 Score=57.97 Aligned_cols=56 Identities=5% Similarity=-0.046 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHHHHhc--cccccccccccccCCCCCcccCCCCCCCCCCCcccchhcccCCccc
Q 015078 300 DDAKNTARLLALLMHRG--FKFSITNSLMWQTNDGSLTWNQFPERIFLPPHQLHKQMDLQNSIFQ 362 (413)
Q Consensus 300 dDA~aTA~Ll~~ll~~g--~~~~i~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lP~~~ 362 (413)
++++.+..|..+|+++. ..|+..|.++.++ ++++| ++....++++++|+|++|||.
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 36666777888888764 4568899999888 99998 778899999999999999985
No 100
>PRK06361 hypothetical protein; Provisional
Probab=93.40 E-value=0.02 Score=53.76 Aligned_cols=53 Identities=4% Similarity=-0.157 Sum_probs=37.9
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcc--------hhhhcccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYP--------DSQKVHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~--------~~~k~~~~~~~g~e~~~ 104 (413)
+..++.++|++|.+.|.++|+||||+.. .+....+. ..++.+++++.|+|..+
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 33332221 12345899999999873
No 101
>PHA02528 43 DNA polymerase; Provisional
Probab=93.30 E-value=3.5 Score=47.39 Aligned_cols=166 Identities=14% Similarity=0.096 Sum_probs=90.4
Q ss_pred ccEEEEEEeeCCCCCC-CCC--CCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCC-CCCcchhhhcCCChhhhcCCCCHH
Q 015078 135 QYFVVIDFEATCDKDK-NPY--PQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQ-LLSDFCKDLTGIQQIQVDRGVTLS 210 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~-~~~--~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p-~Ls~~~~~LTGIT~edV~~Ap~f~ 210 (413)
-..+.||+||+...+. +|. .++||+||.. +..+.+ +..+.-+...+ ..........-.....+..-++..
T Consensus 106 lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~--~~~~~~----~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~ 179 (881)
T PHA02528 106 IRIANLDIEVTAEDGFPDPEEAKYEIDAITHY--DSIDDR----FYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTER 179 (881)
T ss_pred ccEEEEEEEECCCCCCCCcccCCCcEEEEEEe--cCCCCE----EEEEEecCcccccccCCcccccccCCeeEEEcCCHH
Confidence 3789999999864321 233 6699999872 322222 22222111000 000000000001111222357889
Q ss_pred HHHHHHHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHHH-cCCCC----CCC-----------C-----------Cc
Q 015078 211 EALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECRF-KKIWK----PPY-----------F-----------NR 261 (413)
Q Consensus 211 eVl~~f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~~-~gi~~----P~~-----------~-----------~~ 261 (413)
+.|..|.+|+....- -+++.| -.||+ .+|..-+++ .|+.+ +++ + .-
T Consensus 180 eLL~~F~~~i~~~DP----DII~GyNi~~FDl-pYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv 254 (881)
T PHA02528 180 EMLLEYINFWEENTP----VIFTGWNVELFDV-PYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGIS 254 (881)
T ss_pred HHHHHHHHHHHHhCC----cEEEecCCccCCH-HHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceE
Confidence 999999999977521 134444 37996 677777764 35331 100 0 01
Q ss_pred eeehHHHHHHh-c-CCCCCCHHHHHH-HcCCCCCCC----------------CCchHHHHHHHHHHHHH
Q 015078 262 WINLKVPFHEV-F-GGVRCNLKEAVE-MAGLAWQGR----------------AHCGLDDAKNTARLLAL 311 (413)
Q Consensus 262 ~iDl~~l~r~l-~-~~~~~~L~~l~~-~~gI~~~g~----------------~HrALdDA~aTA~Ll~~ 311 (413)
.+|+..+++.+ + ...+++|+++++ .+|...... .+-.+.||..+.+|+.+
T Consensus 255 ~lD~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 255 ILDYLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred EEeHHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 34666677764 2 356889999998 487643210 01237899999999877
No 102
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=93.19 E-value=0.1 Score=50.18 Aligned_cols=153 Identities=18% Similarity=0.200 Sum_probs=94.4
Q ss_pred CCcEEEEcEEEEEcCCCeE----eeEEEEEEeCCCCCCCCcchhhh---cCCChhhhc-CCCCHHHHHHHHHHHHhhcCC
Q 015078 154 PQEIIEFPSVIVSSVTGQL----EACFQTYVRPTCNQLLSDFCKDL---TGIQQIQVD-RGVTLSEALLRHDKWLENKGI 225 (413)
Q Consensus 154 ~deIIEIGAV~vd~~~g~i----~dsF~~~VkP~~~p~Ls~~~~~L---TGIT~edV~-~Ap~f~eVl~~f~~fL~~~~l 225 (413)
.-.||++|...-|..+++- .=.|+.-..|.. .-.+.++.+| .||.-+.-+ -+.. ..+|-+.|-+++|
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 3479999999888433322 335777777775 2356666665 355443322 1222 3467777777776
Q ss_pred C-CccEEEEEc-CcchHHHHHHHHHHHcCCCCCC-----------CCCceeehHHHHHHhcCCCCCCHHHHHHHcCCCCC
Q 015078 226 K-NTNFAVVTW-SNWDCRVMLESECRFKKIWKPP-----------YFNRWINLKVPFHEVFGGVRCNLKEAVEMAGLAWQ 292 (413)
Q Consensus 226 v-~~n~~vV~~-g~fDir~fL~~~~~~~gi~~P~-----------~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~gI~~~ 292 (413)
+ ...+.++++ +.+|. .+|-+.+.. .++|. ++..+.|++-+++..... +-.|.+...-++|...
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 5 345677774 67896 777665443 34441 111344555444433321 2257777778888888
Q ss_pred CCCCchHHHHHHHHHHHHHHHHh
Q 015078 293 GRAHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 293 g~~HrALdDA~aTA~Ll~~ll~~ 315 (413)
|..|.|-.||+.||+.|-..-..
T Consensus 230 g~QhQagsdaLlTa~~ff~~R~~ 252 (299)
T COG5228 230 GQQHQAGSDALLTADEFFLPRFS 252 (299)
T ss_pred chhhhccchhhhhhHHhcchhhh
Confidence 88999999999999988765443
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=92.27 E-value=7.4 Score=46.21 Aligned_cols=144 Identities=15% Similarity=0.104 Sum_probs=90.8
Q ss_pred cEEEEEEe--eCCCCCCCCCCCcEEEEcEEEEEcCC-----C--eEeeEEEEEEeCCCCCCCC-cchhhhcCCChhhhcC
Q 015078 136 YFVVIDFE--ATCDKDKNPYPQEIIEFPSVIVSSVT-----G--QLEACFQTYVRPTCNQLLS-DFCKDLTGIQQIQVDR 205 (413)
Q Consensus 136 ~fVV~D~E--TTGl~~~~~~~deIIEIGAV~vd~~~-----g--~i~dsF~~~VkP~~~p~Ls-~~~~~LTGIT~edV~~ 205 (413)
+++++||- +.-. +...++||.|+.+..+... . .....|...++|... .++ .+.....|+....|..
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 5321 3456899999888764200 1 122345566677321 122 2333566777778888
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCC----------CC---------CCCceeeh
Q 015078 206 GVTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWK----------PP---------YFNRWINL 265 (413)
Q Consensus 206 Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~----------P~---------~~~~~iDl 265 (413)
-.+..+.|..|++++....- ..++.++. +||+ .+|-.-+...+++. +. .-.-.+|+
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 89999999999999984321 34555553 7997 56655566666542 00 01135788
Q ss_pred HHHHHHhcCCCCCCHHHHHHHc
Q 015078 266 KVPFHEVFGGVRCNLKEAVEMA 287 (413)
Q Consensus 266 ~~l~r~l~~~~~~~L~~l~~~~ 287 (413)
...++..+..++++|+++++.+
T Consensus 657 ~~~~k~~~~~~sy~L~~v~~~~ 678 (1172)
T TIGR00592 657 EISAKELIRCKSYDLSELVQQI 678 (1172)
T ss_pred HHHHHHHhCcCCCCHHHHHHHH
Confidence 8888888877889999988743
No 104
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=91.49 E-value=4.8 Score=45.76 Aligned_cols=153 Identities=18% Similarity=0.108 Sum_probs=95.4
Q ss_pred ccEEEEEEeeCCCCCCCC--CCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 135 QYFVVIDFEATCDKDKNP--YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~--~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
-..++||+||+...+..+ ..+.|+.|+...-. .++.. ..+.. ....|. .|....+-.+.
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 478999999999865443 47888888766542 22222 11111 001111 16667788999
Q ss_pred HHHHHHHHhhcCCCCccEEEEE-cC-cchHHHHHHHHHHHcCCCCCC-------------C----CCceeehHHHHH-Hh
Q 015078 213 LLRHDKWLENKGIKNTNFAVVT-WS-NWDCRVMLESECRFKKIWKPP-------------Y----FNRWINLKVPFH-EV 272 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~-~g-~fDir~fL~~~~~~~gi~~P~-------------~----~~~~iDl~~l~r-~l 272 (413)
+..|.+++....- .+ +++ ++ +||+ .+|..-+...|++... + ...-+|+...++ +.
T Consensus 215 l~~~~~~i~~~dP---dV-Ivgyn~~~fd~-pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~ 289 (792)
T COG0417 215 LERFVELIREYDP---DV-IVGYNGDNFDW-PYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRP 289 (792)
T ss_pred HHHHHHHHHhcCC---CE-EEeccCCcCCh-HHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhh
Confidence 9999999987521 23 444 44 5995 8999999988887530 0 123468877777 46
Q ss_pred cCCCCCCHHHHHHHcCCCCC------CC---------------CCchHHHHHHHHHHHHH
Q 015078 273 FGGVRCNLKEAVEMAGLAWQ------GR---------------AHCGLDDAKNTARLLAL 311 (413)
Q Consensus 273 ~~~~~~~L~~l~~~~gI~~~------g~---------------~HrALdDA~aTA~Ll~~ 311 (413)
+....++|+..++.+...-. .. ....+.|+..+.+++.+
T Consensus 290 ~~~~~ysl~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~ 349 (792)
T COG0417 290 LNLKSYSLEAVSEALLGEGKREDIPYDSMEEIWPDWADSKLRLLLYNLSDADLVLRILLK 349 (792)
T ss_pred cccccccHHHHHHHhcccccccccCccchhhccccCccchhHHHHHHHHHHHHHHHHHHH
Confidence 66678899988765543211 00 12347788888877765
No 105
>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=91.12 E-value=3.6 Score=38.37 Aligned_cols=141 Identities=15% Similarity=0.025 Sum_probs=79.6
Q ss_pred ccEEEEEEeeCCCCCC-CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 135 QYFVVIDFEATCDKDK-NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~-~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
...|.||+|++..... ...+-.+|||+. . +. -.+|.+.. +.. .-.+.+
T Consensus 22 ~~vig~D~Ew~~~~~~~~~~~v~LiQiat-----~-~~-----~~lid~~~---~~~-----------------~~~~~~ 70 (193)
T cd06146 22 GRVVGIDSEWKPSFLGDSDPRVAILQLAT-----E-DE-----VFLLDLLA---LEN-----------------LESEDW 70 (193)
T ss_pred CCEEEEECccCCCccCCCCCCceEEEEec-----C-CC-----EEEEEchh---ccc-----------------cchHHH
Confidence 5889999999865321 124567888862 1 12 13444431 211 012233
Q ss_pred HH-HHHHHhhcCCCCccEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-----------CCCCCH
Q 015078 214 LR-HDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-----------GVRCNL 280 (413)
Q Consensus 214 ~~-f~~fL~~~~lv~~n~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-----------~~~~~L 280 (413)
.+ +.+++++. +++ |.|+...|+ .+|.+.+...+-. +.....++||..+++.+.. ..+.+|
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 33 44555653 333 445568896 5676543321100 0012468999887776542 235799
Q ss_pred HHHHHHc-CCCCC---------C------CCCchHHHHHHHHHHHHHHH
Q 015078 281 KEAVEMA-GLAWQ---------G------RAHCGLDDAKNTARLLALLM 313 (413)
Q Consensus 281 ~~l~~~~-gI~~~---------g------~~HrALdDA~aTA~Ll~~ll 313 (413)
.++++.+ |.+.. . +-+-|..||..+..|+.+|.
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 9999864 54321 1 12668999999999999885
No 106
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=90.42 E-value=4.4 Score=41.84 Aligned_cols=132 Identities=15% Similarity=0.161 Sum_probs=79.4
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
..+|+||.||.++ .++.+++.-| .+.+ .++ -.+|+|-. + +. +.++|
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 5666654433 2223 122 35777763 1 11 23333
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHH-HcCCCCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVE-MAGLAWQ 292 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~-~~~L~~l~~-~~gI~~~ 292 (413)
...+.+..++ -|.|.++||+ .+|...+ |+. | .+.+||+- ..++.|.. +++|.+|++ .+|+...
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---GLL-P---TPLFDTQI-AAKLAGFGTSHGLADLVEELLGVELD 127 (361)
T ss_pred --HHHhcCCcee----eeeccccccH-HHHHHhc---CCC-C---CchhHHHH-HHHHhCCcccccHHHHHHHHhCCccc
Confidence 3444444332 3678899998 4554433 442 2 23578864 44566643 889999996 5677653
Q ss_pred CCC---------------CchHHHHHHHHHHHHHHHHh
Q 015078 293 GRA---------------HCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 293 g~~---------------HrALdDA~aTA~Ll~~ll~~ 315 (413)
..+ --|..|+..+..|..+|.+.
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 211 23678999999988877654
No 107
>PHA03036 DNA polymerase; Provisional
Probab=90.02 E-value=12 Score=43.65 Aligned_cols=180 Identities=15% Similarity=0.100 Sum_probs=105.5
Q ss_pred cccEEEEEEeeCCCCCC--CCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCC---------Chhh
Q 015078 134 FQYFVVIDFEATCDKDK--NPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGI---------QQIQ 202 (413)
Q Consensus 134 ~~~fVV~D~ETTGl~~~--~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGI---------T~ed 202 (413)
...++.||+|+-. .+. ++..+.|+.|+...++. .|. +.--++++...-+.-...-..+-|. .-+.
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 4589999999985 332 35679999999877774 343 3345677764311011111112222 1112
Q ss_pred hcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEc-C-cchHHHHHHHHHHHc---CCCCCC--------------------
Q 015078 203 VDRGVTLSEALLRHDKWLENKGIKNTNFAVVTW-S-NWDCRVMLESECRFK---KIWKPP-------------------- 257 (413)
Q Consensus 203 V~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~-g-~fDir~fL~~~~~~~---gi~~P~-------------------- 257 (413)
+---++..+ +.+|.+++..... .+ |++| + +||++ .|..-++.. ++.++.
T Consensus 235 ~~~~~sE~~-ml~~~~~i~~~d~---D~-i~~yNg~nFD~~-Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~ 308 (1004)
T PHA03036 235 ELILCSEIV-LLRIAKKLLELEF---DY-VVTFNGHNFDLR-YISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHK 308 (1004)
T ss_pred eeecCCHHH-HHHHHHHHHhcCC---CE-EEeccCCCcchH-HHHHHHHHhccCceeeccCCCcccccceeecccccccc
Confidence 222355555 5577888876533 33 5564 4 79984 555444432 111100
Q ss_pred -----------CC----CceeehHHHHHHhcCCCCCCHHHHHHH-cCCC-----CCCCC-C---chHHHHHHHHHHHHHH
Q 015078 258 -----------YF----NRWINLKVPFHEVFGGVRCNLKEAVEM-AGLA-----WQGRA-H---CGLDDAKNTARLLALL 312 (413)
Q Consensus 258 -----------~~----~~~iDl~~l~r~l~~~~~~~L~~l~~~-~gI~-----~~g~~-H---rALdDA~aTA~Ll~~l 312 (413)
+. .-++|+....++-+...+++|+++.+. ||.. ...+. + .--.|+...+.||...
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 135688888888888889999999987 4320 00000 0 1135888999999999
Q ss_pred HHhcccccccc
Q 015078 313 MHRGFKFSITN 323 (413)
Q Consensus 313 l~~g~~~~i~e 323 (413)
|.-|.-.+|++
T Consensus 389 l~t~ny~~i~~ 399 (1004)
T PHA03036 389 LSTGNYVTIND 399 (1004)
T ss_pred hcccceeeecc
Confidence 99888777777
No 108
>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=88.94 E-value=3.9 Score=34.96 Aligned_cols=67 Identities=19% Similarity=0.119 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHcC
Q 015078 210 SEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMAG 288 (413)
Q Consensus 210 ~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~-~~~L~~l~~~~g 288 (413)
.++++.|.+|+++... ..++|+..+|+ .+|. ..++..+ ..++|+......+.+.. +++|++++++|.
T Consensus 40 ~~~~~~l~~~l~~~~~----~~v~~~~k~d~-~~L~----~~~~~~~---~~~~D~~~~ayll~~~~~~~~l~~l~~~~l 107 (155)
T cd00007 40 EEDLEALKELLEDEDI----TKVGHDAKFDL-VVLA----RDGIELP---GNIFDTMLAAYLLNPGEGSHSLDDLAKEYL 107 (155)
T ss_pred HHHHHHHHHHHcCCCC----cEEeccHHHHH-HHHH----HCCCCCC---CCcccHHHHHHHhCCCCCcCCHHHHHHHHc
Confidence 5677778888886421 23566678885 5664 4454443 35789987776666644 579999998873
No 109
>PRK09248 putative hydrolase; Validated
Probab=87.82 E-value=0.35 Score=46.65 Aligned_cols=60 Identities=5% Similarity=-0.001 Sum_probs=37.2
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcc-hhhhcccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYP-DSQKVHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~-~~~k~~~~~~~g~e~~~ 104 (413)
+..++.++|++|.++|.++|+||||....|.. .....+...-. ..++.+++++.|+|..+
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
>PRK05761 DNA polymerase I; Reviewed
Probab=86.83 E-value=5.8 Score=45.09 Aligned_cols=97 Identities=20% Similarity=0.084 Sum_probs=62.4
Q ss_pred CCHHHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCCCc------eeehHHHHHHh----c--
Q 015078 207 VTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYFNR------WINLKVPFHEV----F-- 273 (413)
Q Consensus 207 p~f~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~~~------~iDl~~l~r~l----~-- 273 (413)
++..+.|.+|.+|+.... ..|.-++ +||+ .+|..-++++|+....+... .+|+...++.. +
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 788999999999999863 2333344 7997 88988888889865422111 26664444311 1
Q ss_pred -C---CCCCCHHHHHH-HcCCCCCCC------------CCchHHHHHHHHHHH
Q 015078 274 -G---GVRCNLKEAVE-MAGLAWQGR------------AHCGLDDAKNTARLL 309 (413)
Q Consensus 274 -~---~~~~~L~~l~~-~~gI~~~g~------------~HrALdDA~aTA~Ll 309 (413)
+ .++++|+..++ .+|..-... ..-.+.||..|.+|+
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 677643210 122488999999884
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=86.48 E-value=17 Score=32.56 Aligned_cols=131 Identities=16% Similarity=0.040 Sum_probs=77.2
Q ss_pred ccEEEEEEeeCCCCC-CCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 135 QYFVVIDFEATCDKD-KNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~-~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
...|.||+|++.... +...+-.+|+|+ . .+ .-.+|++.. + ....
T Consensus 18 ~~~ig~D~E~~~~~~~~~~~~~~liQl~---~--~~------~~~l~~~~~---~---------------------~~~~ 62 (170)
T cd06141 18 EKVVGFDTEWRPSFRKGKRNKVALLQLA---T--ES------RCLLFQLAH---M---------------------DKLP 62 (170)
T ss_pred CCEEEEeCccCCccCCCCCCCceEEEEe---c--CC------cEEEEEhhh---h---------------------hccc
Confidence 588999999997621 012345677775 1 11 123444442 1 1111
Q ss_pred HHHHHHHhhcCCCCccEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC-CCCCHHHHHHHc-CCC
Q 015078 214 LRHDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG-VRCNLKEAVEMA-GLA 290 (413)
Q Consensus 214 ~~f~~fL~~~~lv~~n~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~-~~~~L~~l~~~~-gI~ 290 (413)
+.|.+++++. ++. +.|+...|+ .+|. +..|+.. ...+|+...+..+.+. ...+|.++++.+ |+.
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 445567785 4553 2456653 2458998777666554 346999999875 654
Q ss_pred CC-----------C------CCCchHHHHHHHHHHHHHHH
Q 015078 291 WQ-----------G------RAHCGLDDAKNTARLLALLM 313 (413)
Q Consensus 291 ~~-----------g------~~HrALdDA~aTA~Ll~~ll 313 (413)
.. . +-|-|..||..+.+|+.+|.
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 0 12568889999999988875
No 112
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=84.55 E-value=10 Score=40.95 Aligned_cols=140 Identities=12% Similarity=0.020 Sum_probs=76.5
Q ss_pred ccEEEEEEeeCCCCCCCC----CCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCC--CcchhhhcCCChhhhcCCCC
Q 015078 135 QYFVVIDFEATCDKDKNP----YPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLL--SDFCKDLTGIQQIQVDRGVT 208 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~----~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~L--s~~~~~LTGIT~edV~~Ap~ 208 (413)
-....||+|+|+.+ .| -..+|..|.-.-. .+ ..++|..+.-.....+. ........-+..-.+-.=++
T Consensus 106 i~~~~~DIEv~~~~--fp~~~~a~~~i~~i~~~d~--~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~s 179 (498)
T PHA02524 106 VVIDVVDIEVTAPE--FPEPKYAKYEIDMISHVRL--HN--GKKTYYIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFED 179 (498)
T ss_pred ceEEEEEEEecCCC--CCChhhcCCceEEEEeeec--cc--CCccEEEEeccccccCCCcccccccccccCCeEEEEeCC
Confidence 47888999999852 22 2346666654322 21 12334444211100001 11111111122334456788
Q ss_pred HHHHHHHHHHHHhhcCCCCccEEEEEc--CcchHHHHHHHHHH-HcCCCC----CCCC---------------------C
Q 015078 209 LSEALLRHDKWLENKGIKNTNFAVVTW--SNWDCRVMLESECR-FKKIWK----PPYF---------------------N 260 (413)
Q Consensus 209 f~eVl~~f~~fL~~~~lv~~n~~vV~~--g~fDir~fL~~~~~-~~gi~~----P~~~---------------------~ 260 (413)
..+.|.+|.+|+....- . ++.+| -+||+ .+|..-++ ..|+.. +.+. .
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 34444 37997 67766665 356531 1110 0
Q ss_pred ceeehHHHHHHh--cCCCCCCHHHHHH
Q 015078 261 RWINLKVPFHEV--FGGVRCNLKEAVE 285 (413)
Q Consensus 261 ~~iDl~~l~r~l--~~~~~~~L~~l~~ 285 (413)
-.+|+..++++. ....+++|+++++
T Consensus 255 v~iDl~~l~kk~s~~~l~sYsL~~Vs~ 281 (498)
T PHA02524 255 ALMDYMDVFKKFSFTPMPDYKLGNVGY 281 (498)
T ss_pred EEeEHHHHHHHhhhccCCCCCHHHHHH
Confidence 135777788775 4567899999876
No 113
>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=84.17 E-value=35 Score=35.19 Aligned_cols=129 Identities=17% Similarity=0.195 Sum_probs=73.1
Q ss_pred ccEEEEEEeeCCCCCCCCCC--CcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYP--QEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~--deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
..+|.||+|++... .+. --+|+|+. .+. ..+|.|-. +..
T Consensus 18 ~~~ia~DtE~~~~~---~y~~~l~LiQia~------~~~-----~~liD~~~---~~~---------------------- 58 (367)
T TIGR01388 18 FPFVALDTEFVRER---TFWPQLGLIQVAD------GEQ-----LALIDPLV---IID---------------------- 58 (367)
T ss_pred CCEEEEeccccCCC---CCCCcceEEEEee------CCe-----EEEEeCCC---ccc----------------------
Confidence 47999999998762 222 34555541 111 24666642 110
Q ss_pred HHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcC-CCCCCHHHHHHHc-CCC
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFG-GVRCNLKEAVEMA-GLA 290 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~-~~~~~L~~l~~~~-gI~ 290 (413)
+..|.+++++..+ ..|.|+...|+ .+|. +.+...| ...+||.-.. .+.+ ..+.+|.++++.| |+.
T Consensus 59 ~~~L~~lL~d~~i----~KV~h~~k~Dl-~~L~----~~~~~~~---~~~fDtqlAa-~lL~~~~~~~l~~Lv~~~Lg~~ 125 (367)
T TIGR01388 59 WSPLKELLRDESV----VKVLHAASEDL-EVFL----NLFGELP---QPLFDTQIAA-AFCGFGMSMGYAKLVQEVLGVE 125 (367)
T ss_pred HHHHHHHHCCCCc----eEEEeecHHHH-HHHH----HHhCCCC---CCcccHHHHH-HHhCCCCCccHHHHHHHHcCCC
Confidence 2334456665321 23567778886 5554 3333343 3468987544 4444 3356899998765 665
Q ss_pred CCCCC------C---------chHHHHHHHHHHHHHHHHh
Q 015078 291 WQGRA------H---------CGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 291 ~~g~~------H---------rALdDA~aTA~Ll~~ll~~ 315 (413)
....+ . -|..||..+..|+..|.++
T Consensus 126 l~K~~~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~ 165 (367)
T TIGR01388 126 LDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMER 165 (367)
T ss_pred CCcccccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 42110 1 3778888888888777654
No 114
>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=83.98 E-value=18 Score=32.39 Aligned_cols=131 Identities=15% Similarity=-0.009 Sum_probs=74.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
...|.||+|+..... ...+-.+|||+. .++.+ .+|++.. +.. ..+
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 112345666642 11222 3444442 211 123
Q ss_pred HHHHHHhhcCCCCccEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CCCCC
Q 015078 215 RHDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GLAWQ 292 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~-gI~~~ 292 (413)
.+.+++++. ++. +.|+...|+ ..|. +..|+.+. ..+|+...+..+-+..+.+|.+++++| |+...
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---RDFGEKLQ----RLFDTTIAANLKGLPERWSLASLVEHFLGKTLD 124 (161)
T ss_pred HHHHHhCCC-----CEEEEEeccHHHH-HHHH---HHcCCCcc----cHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCC
Confidence 344556653 233 445567785 4443 23566532 347987765543333356899999875 76431
Q ss_pred ---------C------CCCchHHHHHHHHHHHHHHH
Q 015078 293 ---------G------RAHCGLDDAKNTARLLALLM 313 (413)
Q Consensus 293 ---------g------~~HrALdDA~aTA~Ll~~ll 313 (413)
. +-|-|..||..+.+|+.+|.
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 1 23668899999999998874
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=79.35 E-value=2 Score=30.10 Aligned_cols=29 Identities=31% Similarity=0.638 Sum_probs=22.1
Q ss_pred ceeccCCCCCCCceeecCCCcccCCCcccceeecCC
Q 015078 376 GMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 411 (413)
Q Consensus 376 ~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~~~ 411 (413)
.+|.|-|..- .||||.|+ +.|.|-+|..+
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
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=78.08 E-value=1.1 Score=50.78 Aligned_cols=110 Identities=23% Similarity=0.292 Sum_probs=70.5
Q ss_pred CCCcchhhhcCCChhhhcCC------CCHHHHHHHHHHHHhhcCCCCccEEEEEcC-cchHHHHHHHHHHHcCCCCCCCC
Q 015078 187 LLSDFCKDLTGIQQIQVDRG------VTLSEALLRHDKWLENKGIKNTNFAVVTWS-NWDCRVMLESECRFKKIWKPPYF 259 (413)
Q Consensus 187 ~Ls~~~~~LTGIT~edV~~A------p~f~eVl~~f~~fL~~~~lv~~n~~vV~~g-~fDir~fL~~~~~~~gi~~P~~~ 259 (413)
++.++-++..||..-||+-- -++..++.++. +|-+.+ +++|.+| +-|. +-.+|..| -
T Consensus 972 ~VvDYLTqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~-~Li~~G-----viFVGHGL~nDF--------rvINi~Vp--~ 1035 (1118)
T KOG1275|consen 972 KVVDYLTQYSGIKPGDLDPTTSEKRLTTLKVLYLKLR-LLIQRG-----VIFVGHGLQNDF--------RVINIHVP--E 1035 (1118)
T ss_pred HHHHHHHHhcCCCccccCCccCcceehhHHHHHHHHH-HHHHcC-----cEEEcccccccc--------eEEEEecC--h
Confidence 46677888999999999632 23455555543 443332 3566665 3343 33455555 2
Q ss_pred CceeehHHHHHHhcCCC-CCCHHHHHH-HcCCCCCCCCCchHHHHHHHHHHHHHHHH
Q 015078 260 NRWINLKVPFHEVFGGV-RCNLKEAVE-MAGLAWQGRAHCGLDDAKNTARLLALLMH 314 (413)
Q Consensus 260 ~~~iDl~~l~r~l~~~~-~~~L~~l~~-~~gI~~~g~~HrALdDA~aTA~Ll~~ll~ 314 (413)
.+.+|+..+|+ .|.+ -.+|..|+. .+|.......|+.+.||+.+.+|+.+-++
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 45778766553 2322 237888885 46766655689999999999999987664
No 117
>COG0613 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]
Probab=77.31 E-value=1.5 Score=43.10 Aligned_cols=52 Identities=4% Similarity=-0.048 Sum_probs=41.9
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhc-chhhhcccccccchhhc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFY-PDSQKVHHCQMNSFESQ 103 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~-~~~~k~~~~~~~g~e~~ 103 (413)
++-++.++|++|++-|-..+|||| |-.+..-+++- .+....++..+.|+|-.
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 55666788888888654
No 118
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=74.55 E-value=37 Score=29.41 Aligned_cols=90 Identities=20% Similarity=0.175 Sum_probs=53.8
Q ss_pred HHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCC-CCHHHHHHHc-CCC
Q 015078 213 LLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVR-CNLKEAVEMA-GLA 290 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~-~~L~~l~~~~-gI~ 290 (413)
+..+.+|+++... ..++|+..+|+ .+|. +.|+.++ + ++|+.-.+..+.+... ++|.++++.| |+.
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 4556667765421 24566778885 5554 4687754 2 3898766655566443 6999998775 554
Q ss_pred CCC---C--------CC----chHHHHHHHHHHHHHHHHh
Q 015078 291 WQG---R--------AH----CGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 291 ~~g---~--------~H----rALdDA~aTA~Ll~~ll~~ 315 (413)
.+. . .. .|..||.++.+|+..|.++
T Consensus 131 ~~~~~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~ 170 (172)
T smart00474 131 LDKEEQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKE 170 (172)
T ss_pred CCcccCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 211 0 01 2566677777777766543
No 119
>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=72.81 E-value=49 Score=30.76 Aligned_cols=78 Identities=12% Similarity=-0.078 Sum_probs=46.8
Q ss_pred EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCC--------CCCCHHHHHHHc-CCCC-----------
Q 015078 232 VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGG--------VRCNLKEAVEMA-GLAW----------- 291 (413)
Q Consensus 232 vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~--------~~~~L~~l~~~~-gI~~----------- 291 (413)
+.|+...|+ .+|. +..|+... .++|+...+..+.+. ...+|.++++.| |++.
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 566677885 4542 35576532 347886543332211 124788887764 5532
Q ss_pred ------CCC------CCchHHHHHHHHHHHHHHHHhcc
Q 015078 292 ------QGR------AHCGLDDAKNTARLLALLMHRGF 317 (413)
Q Consensus 292 ------~g~------~HrALdDA~aTA~Ll~~ll~~g~ 317 (413)
..+ -+-|..||..+..|+..|++...
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 111 14578999999999999887654
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=58.37 E-value=6.7 Score=38.05 Aligned_cols=60 Identities=10% Similarity=0.110 Sum_probs=38.6
Q ss_pred ccCCchhhhhhhhcCCceeeecccCCCC-CCCCCC------cCCchhhcch----hhh--cccccccchhhcc
Q 015078 45 VHPGGDAGESIHQLSSEFVEYSNEFYNN-PTYQHD------FGSWSTFYPD----SQK--VHHCQMNSFESQF 104 (413)
Q Consensus 45 ~~~~~~~i~~~~~~g~~aiait~~~~~~-~~~h~~------~q~~p~~~~~----~~k--~~~~~~~g~e~~~ 104 (413)
..+..++|++|.+-|-+.|+||||+... +..... ..++|.+... .+| .++++..|+|..+
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 111110 1234443321 122 3689999999875
No 121
>PRK07945 hypothetical protein; Provisional
Probab=57.37 E-value=7.5 Score=39.62 Aligned_cols=61 Identities=7% Similarity=-0.019 Sum_probs=38.6
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCC-cCCchhhcch----hhh-cccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHD-FGSWSTFYPD----SQK-VHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~-~q~~p~~~~~----~~k-~~~~~~~g~e~~~ 104 (413)
+..++.++|++|.+-|.+.|+||||+-.-+...+. .+.++..+.. .++ .+++++.|+|..+
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 56778899999999999999999876542111111 1112222211 122 3588999999874
No 122
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.15 E-value=33 Score=39.74 Aligned_cols=96 Identities=14% Similarity=0.015 Sum_probs=60.6
Q ss_pred CHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc
Q 015078 208 TLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA 287 (413)
Q Consensus 208 ~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~ 287 (413)
+...++..|..|+++..+ ..+.|+..||+ .+|. ++|+.++ ..+.|+.-...-+-+...++|++++++|
T Consensus 362 ~~~~~~~~l~~~l~~~~~----~~v~~n~K~d~-~~l~----~~gi~~~---~~~~Dt~la~yll~~~~~~~l~~la~~y 429 (887)
T TIGR00593 362 LTILTDDKFARWLLNEQI----KKIGHDAKFLM-HLLK----REGIELG---GVIFDTMLAAYLLDPAQVSTLDTLARRY 429 (887)
T ss_pred hhHHHHHHHHHHHhCCCC----cEEEeeHHHHH-HHHH----hCCCCCC---CcchhHHHHHHHcCCCCCCCHHHHHHHH
Confidence 355677788888987532 24677788995 6664 6788764 2467887554444444456999998776
Q ss_pred -CCCC---C---CC------------CCchHHHHHHHHHHHHHHHHh
Q 015078 288 -GLAW---Q---GR------------AHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 288 -gI~~---~---g~------------~HrALdDA~aTA~Ll~~ll~~ 315 (413)
+... . +. ...|..||..|.+|+..|...
T Consensus 430 l~~~~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 430 LVEELILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred cCcccccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3110 0 10 013667888888888776554
No 123
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=55.83 E-value=5.5 Score=44.84 Aligned_cols=160 Identities=20% Similarity=0.160 Sum_probs=89.7
Q ss_pred cEEEEEEeeCCCCCCC--CCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHH
Q 015078 136 YFVVIDFEATCDKDKN--PYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEAL 213 (413)
Q Consensus 136 ~fVV~D~ETTGl~~~~--~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl 213 (413)
..+-||+|+.|-.+.. +..|.||+|+-++. .-|+- +-||+-.. .|.+ .++|.-.+|-.-...+++|
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 4567999999986644 46789999987654 22321 11222221 1222 3567777777777777777
Q ss_pred HHHHHHHhh---cCCCCccEEEEEcCcchHHHHHHHHHHHcCCC-CCCCCC-----c-----------------------
Q 015078 214 LRHDKWLEN---KGIKNTNFAVVTWSNWDCRVMLESECRFKKIW-KPPYFN-----R----------------------- 261 (413)
Q Consensus 214 ~~f~~fL~~---~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~-~P~~~~-----~----------------------- 261 (413)
+.-.+|+.+ .++.|.|+. .||+ .+|-.-++-.||+ ||.+-. .
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 776666655 344455542 7896 5444444444443 342111 1
Q ss_pred ---eeehHHHHHHhcCCCCCCHHHHHHHc-CCCCCCCCCchH-------------------HHHHHHHHHHHHHH
Q 015078 262 ---WINLKVPFHEVFGGVRCNLKEAVEMA-GLAWQGRAHCGL-------------------DDAKNTARLLALLM 313 (413)
Q Consensus 262 ---~iDl~~l~r~l~~~~~~~L~~l~~~~-gI~~~g~~HrAL-------------------dDA~aTA~Ll~~ll 313 (413)
-+|+.....+-|...+|+|+...-+| |-.-++-||+-+ -||+.=-+|+.+|+
T Consensus 417 GRlqfDllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siItdLQng~~~TRRRlA~YCLkDAYLPlRLlekLM 491 (1066)
T KOG0969|consen 417 GRLQFDLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIITDLQNGNEQTRRRLAVYCLKDAYLPLRLLEKLM 491 (1066)
T ss_pred ceeeehHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchhhhhcCcHHHHHHHHHHHhhhhcchHHHHHHHH
Confidence 12333444455556678888877654 333333455543 56666666766654
No 124
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=55.08 E-value=1.1e+02 Score=33.87 Aligned_cols=131 Identities=21% Similarity=0.264 Sum_probs=73.2
Q ss_pred EEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHHHHH
Q 015078 138 VVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALLRHD 217 (413)
Q Consensus 138 VV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~ 217 (413)
+.+|+||+|+ ++....++-++...- . +. .|| |..+ + +..-+++..+.
T Consensus 25 ~a~~~et~~l---~~~~~~lvg~s~~~~---~----~~--~yi-~~~~-----------~---------~~~~~~~~~l~ 71 (593)
T COG0749 25 IAFDTETDGL---DPHGADLVGLSVASE---E----EA--AYI-PLLH-----------G---------PEQLNVLAALK 71 (593)
T ss_pred ceeecccccc---CcccCCeeEEEeecc---c----cc--eeE-eecc-----------c---------hhhhhhHHHHH
Confidence 9999999998 556667776643321 1 11 121 2211 0 11112888999
Q ss_pred HHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhc--CCCCCCHHHHHHHc-CCCCC--
Q 015078 218 KWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVF--GGVRCNLKEAVEMA-GLAWQ-- 292 (413)
Q Consensus 218 ~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~--~~~~~~L~~l~~~~-gI~~~-- 292 (413)
.|+.+... -.+.++..+|+ .+| .++|+. + ....|+.- +.-+. +...+.|++++++| +....
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 99988641 12333447884 444 467754 2 23457753 33333 23467899988877 32211
Q ss_pred ------CC-------------CCchHHHHHHHHHHHHHHHHh
Q 015078 293 ------GR-------------AHCGLDDAKNTARLLALLMHR 315 (413)
Q Consensus 293 ------g~-------------~HrALdDA~aTA~Ll~~ll~~ 315 (413)
+. .-.+-.||.+|.+|...|..+
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 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=54.52 E-value=4.4 Score=40.29 Aligned_cols=42 Identities=24% Similarity=0.688 Sum_probs=22.4
Q ss_pred cc-ccccceecCCCcCcceeccCCCCCCCceeecC----CCcccCCCcccc
Q 015078 360 IF-QYHPSCFCGVKSSKGMVRKPGPKQGSVFFGCG----NWTVTRGARCHF 405 (413)
Q Consensus 360 ~~-~~~~~c~cg~~~~~~~~~~~gp~qg~~f~~c~----~~~~~~~~~c~~ 405 (413)
|+ +++|+ ||-....++++..++ +|+.|.-|+ -|...| .+|+|
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
>PRK08392 hypothetical protein; Provisional
Probab=54.36 E-value=6.8 Score=37.05 Aligned_cols=56 Identities=7% Similarity=0.028 Sum_probs=37.9
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhc----chhhhcccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFY----PDSQKVHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~----~~~~k~~~~~~~g~e~~~ 104 (413)
+..++.++|+.|.+-|-+.|+||||.... ....++... ...++.+++++.|+|..+
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 011333322 223445788899999764
No 127
>PHA02563 DNA polymerase; Provisional
Probab=54.32 E-value=1.6e+02 Score=32.98 Aligned_cols=39 Identities=13% Similarity=0.130 Sum_probs=26.6
Q ss_pred HHHHHHHHhhcCCCCcc-EEEEEcCcchHHHHHHHHHHHcC
Q 015078 213 LLRHDKWLENKGIKNTN-FAVVTWSNWDCRVMLESECRFKK 252 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n-~~vV~~g~fDir~fL~~~~~~~g 252 (413)
+++|++|+....-..++ .+.+|++.|| ..||-+.+.+++
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 44888888842111122 4678889999 489999888765
No 128
>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=53.38 E-value=1.6e+02 Score=26.00 Aligned_cols=92 Identities=16% Similarity=0.102 Sum_probs=52.1
Q ss_pred HHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHc-CCCCCCCCCceeehHHHHHHhcCCCCCCHHHHHHHc-CC
Q 015078 212 ALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFK-KIWKPPYFNRWINLKVPFHEVFGGVRCNLKEAVEMA-GL 289 (413)
Q Consensus 212 Vl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~-gi~~P~~~~~~iDl~~l~r~l~~~~~~~L~~l~~~~-gI 289 (413)
+...|.+++++.. -..++|+...|+ ..|. ++ |+. + +..+|+.-....+-+..+++|+++++.| |+
T Consensus 52 ~~~~l~~ll~~~~----i~kv~~d~K~~~-~~L~----~~~gi~-~---~~~~D~~laayLl~p~~~~~l~~l~~~~l~~ 118 (178)
T cd06142 52 DLSPLKELLADPN----IVKVFHAAREDL-ELLK----RDFGIL-P---QNLFDTQIAARLLGLGDSVGLAALVEELLGV 118 (178)
T ss_pred cHHHHHHHHcCCC----ceEEEeccHHHH-HHHH----HHcCCC-C---CCcccHHHHHHHhCCCccccHHHHHHHHhCC
Confidence 3444566676542 123556667774 4443 44 766 2 2457987544444344446999998864 65
Q ss_pred CCC-----CC---C-------CchHHHHHHHHHHHHHHHHhc
Q 015078 290 AWQ-----GR---A-------HCGLDDAKNTARLLALLMHRG 316 (413)
Q Consensus 290 ~~~-----g~---~-------HrALdDA~aTA~Ll~~ll~~g 316 (413)
... +. . +.|..||.++.+|+..|.++.
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 0 125667888888887776553
No 129
>PRK00912 ribonuclease P protein component 3; Provisional
Probab=52.03 E-value=8.9 Score=36.76 Aligned_cols=50 Identities=12% Similarity=-0.011 Sum_probs=33.7
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcchhhh-cccccccchhhc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYPDSQK-VHHCQMNSFESQ 103 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~~~~k-~~~~~~~g~e~~ 103 (413)
+-.++.+++++|.+.|-+.|+|||| ... +|......+. .+++++.|+|-.
T Consensus 14 ~~~~~~e~i~~A~~~Gl~~i~itdH--------~~~--~~~~~~~~~~~~~i~Il~GiEi~ 64 (237)
T PRK00912 14 GYDTVLRLISEASHLGYSGIALSNH--------SDK--YPESKPELEDLLGFEIFRGVEIV 64 (237)
T ss_pred CcchHHHHHHHHHHCCCCEEEEecC--------ccc--ccchhHHHHHhcCCcEEeeEEEe
Confidence 3457889999999999999999964 332 2221110111 278888899864
No 130
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=44.36 E-value=16 Score=42.12 Aligned_cols=37 Identities=16% Similarity=0.512 Sum_probs=23.9
Q ss_pred cceecCCCcCcceeccCCCCCCCceeecCCCcccCCCcccceeecCC
Q 015078 365 PSCFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWAFT 411 (413)
Q Consensus 365 ~~c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~~~ 411 (413)
|-|-||- .++.+-|. -|+.||+|+++ +.|.|..|.-+
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
>COG1387 HIS2 Histidinol phosphatase and related hydrolases of the PHP family [Amino acid transport and metabolism / General function prediction only]
Probab=43.24 E-value=16 Score=35.26 Aligned_cols=60 Identities=10% Similarity=-0.027 Sum_probs=35.8
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCCcCCchhhcc----hhhhcccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHDFGSWSTFYP----DSQKVHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~~q~~p~~~~----~~~k~~~~~~~g~e~~~ 104 (413)
+..++.+++++|.+-|.+.++||||+-..+. .....-++.... ..++..++++-|+|..+
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 4456778899999999999999964443211 000000222211 12334477888888874
No 132
>PRK07328 histidinol-phosphatase; Provisional
Probab=43.05 E-value=14 Score=36.11 Aligned_cols=60 Identities=3% Similarity=0.026 Sum_probs=37.7
Q ss_pred ccCCchhhhhhhhcCCceeeecccCCCCCCC----CCC----cCCchhhcch----hhh-cccccccchhhcc
Q 015078 45 VHPGGDAGESIHQLSSEFVEYSNEFYNNPTY----QHD----FGSWSTFYPD----SQK-VHHCQMNSFESQF 104 (413)
Q Consensus 45 ~~~~~~~i~~~~~~g~~aiait~~~~~~~~~----h~~----~q~~p~~~~~----~~k-~~~~~~~g~e~~~ 104 (413)
..++.++|++|.+-|-+.|+||||+-.-..+ +.. ...++++... .+| .+++++.|+|..+
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 4467899999999999999999876541000 000 0123333321 122 3688999999875
No 133
>PRK10829 ribonuclease D; Provisional
Probab=41.09 E-value=2.2e+02 Score=29.69 Aligned_cols=129 Identities=16% Similarity=0.176 Sum_probs=79.5
Q ss_pred ccEEEEEEeeCCCCCCCCCC--CcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYP--QEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEA 212 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~--deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eV 212 (413)
...|+||+|+... ..+. --+|+|+ + ... -.+|.|-. +.+
T Consensus 22 ~~~lalDtEf~~~---~ty~~~l~LiQl~----~--~~~-----~~LiD~l~---~~d---------------------- 62 (373)
T PRK10829 22 FPAIALDTEFVRT---RTYYPQLGLIQLY----D--GEQ-----LSLIDPLG---ITD---------------------- 62 (373)
T ss_pred CCeEEEecccccC---ccCCCceeEEEEe----c--CCc-----eEEEecCC---ccc----------------------
Confidence 5789999999875 3332 4455554 2 111 25676652 221
Q ss_pred HHHHHHHHhhcCCCCccEE-EEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHH-HcCC
Q 015078 213 LLRHDKWLENKGIKNTNFA-VVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVE-MAGL 289 (413)
Q Consensus 213 l~~f~~fL~~~~lv~~n~~-vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~-~~~L~~l~~-~~gI 289 (413)
+..|.+.+.+. +++ |.|.+++|+ .+|.. ..|+. | .+++||...+ .+.|.. +.+|..+++ ++|+
T Consensus 63 ~~~L~~ll~~~-----~ivKV~H~~~~Dl-~~l~~---~~g~~-p---~~~fDTqiaa-~~lg~~~~~gl~~Lv~~~lgv 128 (373)
T PRK10829 63 WSPFKALLRDP-----QVTKFLHAGSEDL-EVFLN---AFGEL-P---QPLIDTQILA-AFCGRPLSCGFASMVEEYTGV 128 (373)
T ss_pred hHHHHHHHcCC-----CeEEEEeChHhHH-HHHHH---HcCCC-c---CCeeeHHHHH-HHcCCCccccHHHHHHHHhCC
Confidence 13345556664 333 567789997 56643 45653 2 3578996544 556644 679999886 5777
Q ss_pred CCCC---------------CCCchHHHHHHHHHHHHHHHHhc
Q 015078 290 AWQG---------------RAHCGLDDAKNTARLLALLMHRG 316 (413)
Q Consensus 290 ~~~g---------------~~HrALdDA~aTA~Ll~~ll~~g 316 (413)
.... +-+-|..|+..+..|+.+|.++.
T Consensus 129 ~ldK~~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L 170 (373)
T PRK10829 129 TLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAET 170 (373)
T ss_pred ccCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5421 12457899999999988877653
No 134
>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=40.10 E-value=19 Score=40.14 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=24.9
Q ss_pred eecCCCcCcceeccCCCCCCCceeecCCCcccCC--CcccceeecC
Q 015078 367 CFCGVKSSKGMVRKPGPKQGSVFFGCGNWTVTRG--ARCHFFEWAF 410 (413)
Q Consensus 367 c~cg~~~~~~~~~~~gp~qg~~f~~c~~~~~~~~--~~c~~f~w~~ 410 (413)
|-||- .+++ +=|.+ || |.+|+|++.-++ ++|.|=+|..
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 135
>PRK05588 histidinol-phosphatase; Provisional
Probab=39.02 E-value=24 Score=34.03 Aligned_cols=59 Identities=7% Similarity=-0.032 Sum_probs=37.5
Q ss_pred ccCCchhhhhhhhcCCceeeecccCCCCCCCCC-CcCCchhhcchhhhc-ccccccchhhcc
Q 015078 45 VHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQH-DFGSWSTFYPDSQKV-HHCQMNSFESQF 104 (413)
Q Consensus 45 ~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~-~~q~~p~~~~~~~k~-~~~~~~g~e~~~ 104 (413)
..+..++|++|.+-|-+.+ ||||+-.-..++. .....+.+....++. ++++..|+|..+
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 112444444433443 478888998864
No 136
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=37.09 E-value=66 Score=28.42 Aligned_cols=57 Identities=18% Similarity=0.147 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCC-------CCCceeehHHHHHH
Q 015078 206 GVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPP-------YFNRWINLKVPFHE 271 (413)
Q Consensus 206 Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~-------~~~~~iDl~~l~r~ 271 (413)
..+-.+.++.+++.++... ..+||.+.+|+ +..|+.-++. +|. +..+.+||..+|+.
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 23566667799 5777665543 221 12345677766665
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=37.01 E-value=2.5e+02 Score=24.90 Aligned_cols=108 Identities=17% Similarity=0.087 Sum_probs=60.7
Q ss_pred ccEEEEEEeeCCCCCCCCCCCcEEEEcEEEEEcCCCeEeeEEEEEEeCCCCCCCCcchhhhcCCChhhhcCCCCHHHHHH
Q 015078 135 QYFVVIDFEATCDKDKNPYPQEIIEFPSVIVSSVTGQLEACFQTYVRPTCNQLLSDFCKDLTGIQQIQVDRGVTLSEALL 214 (413)
Q Consensus 135 ~~fVV~D~ETTGl~~~~~~~deIIEIGAV~vd~~~g~i~dsF~~~VkP~~~p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~ 214 (413)
.+.+.+|+|++|. ++...+|+-|+.. . . ++ ..||.+.. . + ++..
T Consensus 3 ~~~~~~~~~~~~~---~~~~~~l~~i~l~--~-~-~~-----~~~i~~~~--~----------~------------~~~~ 46 (178)
T cd06140 3 ADEVALYVELLGE---NYHTADIIGLALA--N-G-GG-----AYYIPLEL--A----------L------------LDLA 46 (178)
T ss_pred CCceEEEEEEcCC---CcceeeEEEEEEE--e-C-Cc-----EEEEeccc--h----------H------------HHHH
Confidence 4678999999996 4555666544322 2 1 11 23454331 1 0 1455
Q ss_pred HHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeehHHHHHHhcCCC-CCCHHHHHHHc-CCC
Q 015078 215 RHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINLKVPFHEVFGGV-RCNLKEAVEMA-GLA 290 (413)
Q Consensus 215 ~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl~~l~r~l~~~~-~~~L~~l~~~~-gI~ 290 (413)
.|.+++++... ..++|+..+|+ .+| .+.|+.++ ..+.|+.-..--+-+.. +++|++++++| ++.
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 23455566664 444 46788765 34578875444444443 37999998765 443
No 138
>PRK07726 DNA topoisomerase III; Provisional
Probab=30.61 E-value=30 Score=38.63 Aligned_cols=17 Identities=12% Similarity=0.161 Sum_probs=12.2
Q ss_pred ceeecCCCcccCCCcccceeecC
Q 015078 388 VFFGCGNWTVTRGARCHFFEWAF 410 (413)
Q Consensus 388 ~f~~c~~~~~~~~~~c~~f~w~~ 410 (413)
.||||.||+ |.|+.|..
T Consensus 629 ~f~~Cs~~~------~~~~~~~~ 645 (658)
T PRK07726 629 KMLVCQDRE------CGKRKNVS 645 (658)
T ss_pred eeEecCCCc------cccccccc
Confidence 499999952 66668743
No 139
>PRK08609 hypothetical protein; Provisional
Probab=29.66 E-value=36 Score=37.32 Aligned_cols=61 Identities=7% Similarity=-0.138 Sum_probs=38.0
Q ss_pred cccCCchhhhhhhhcCCceeeecccCCCCCCCCCC-cCCchhhcc---hh-hh-cccccccchhhcc
Q 015078 44 IVHPGGDAGESIHQLSSEFVEYSNEFYNNPTYQHD-FGSWSTFYP---DS-QK-VHHCQMNSFESQF 104 (413)
Q Consensus 44 ~~~~~~~~i~~~~~~g~~aiait~~~~~~~~~h~~-~q~~p~~~~---~~-~k-~~~~~~~g~e~~~ 104 (413)
+..+..++++.|.+-|-+.|+||||.-..+..++. ...++..+. .. ++ .++++..|+|..+
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 11 11 3688899999885
No 140
>PRK06599 DNA topoisomerase I; Validated
Probab=27.34 E-value=39 Score=37.80 Aligned_cols=26 Identities=31% Similarity=0.806 Sum_probs=18.3
Q ss_pred eeccCCCCCCCceeecCCCcccCCCcccceeec
Q 015078 377 MVRKPGPKQGSVFFGCGNWTVTRGARCHFFEWA 409 (413)
Q Consensus 377 ~~~~~gp~qg~~f~~c~~~~~~~~~~c~~f~w~ 409 (413)
++.+-|.. |+ ||+|.|| ..|.|..|.
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
>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=24.21 E-value=3.1e+02 Score=24.91 Aligned_cols=101 Identities=15% Similarity=0.059 Sum_probs=63.6
Q ss_pred CCCCcchhhhcCCChhhhcCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCCCCceeeh
Q 015078 186 QLLSDFCKDLTGIQQIQVDRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPYFNRWINL 265 (413)
Q Consensus 186 p~Ls~~~~~LTGIT~edV~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~~~~~iDl 265 (413)
|.|++.+.+- -| +-.+++|.-|-..++.|.+|+....-+.| ++..+ - ..||..-....+| |.
T Consensus 41 pvLp~dil~e-aV-PGnIR~AeHFv~flkR~veylk~rlrv~~---v~~e~--P-~sFL~~~~~~~~i----------d~ 102 (146)
T PF06777_consen 41 PVLPDDILKE-AV-PGNIRRAEHFVAFLKRFVEYLKTRLRVQH---VISES--P-LSFLQHLKDETFI----------DR 102 (146)
T ss_pred CCCchhhhhh-cC-CchHHhHHHHHHHHHHHHHHHHHHhhhcc---eeecC--H-HHHHHHHHHHhCC----------Cc
Confidence 3456554432 22 55678899999999999999998642221 22223 2 3688766555444 33
Q ss_pred HHHHHHhcCCCCCCHHHHHHHcCCCCCCCCCchHHHHHHHHHHHH
Q 015078 266 KVPFHEVFGGVRCNLKEAVEMAGLAWQGRAHCGLDDAKNTARLLA 310 (413)
Q Consensus 266 ~~l~r~l~~~~~~~L~~l~~~~gI~~~g~~HrALdDA~aTA~Ll~ 310 (413)
+. .+.+. -||..++.-++|... ..-++|.++-.-|-|+-
T Consensus 103 k~-LrFc~----eRL~sLl~TLei~d~-~df~~L~~Va~FaTLv~ 141 (146)
T PF06777_consen 103 KP-LRFCS----ERLSSLLRTLEITDI-DDFSALQLVADFATLVS 141 (146)
T ss_pred HH-HHHHH----HHHHHHHHHHCCCcH-hhhhHHHHHHHHHHHHH
Confidence 22 23333 279999999999764 34678888777776653
No 142
>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=22.29 E-value=57 Score=33.08 Aligned_cols=40 Identities=30% Similarity=0.809 Sum_probs=31.8
Q ss_pred cccceecCCCcCcceeccCCCCCCCceeecC----CCcccCCCcccc
Q 015078 363 YHPSCFCGVKSSKGMVRKPGPKQGSVFFGCG----NWTVTRGARCHF 405 (413)
Q Consensus 363 ~~~~c~cg~~~~~~~~~~~gp~qg~~f~~c~----~~~~~~~~~c~~ 405 (413)
++|+ ||-....++|+.-|+.+|..|.-|+ .|...| .+|+|
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 143
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=21.08 E-value=2e+02 Score=27.73 Aligned_cols=83 Identities=18% Similarity=0.133 Sum_probs=39.9
Q ss_pred cCCCCHHHHHHHHHHHHhhcCCCCccEEEEEcCcchHHHHHHHHHHHcCCCCCCC-CCceeehHHHHHHhcC-CCCCCHH
Q 015078 204 DRGVTLSEALLRHDKWLENKGIKNTNFAVVTWSNWDCRVMLESECRFKKIWKPPY-FNRWINLKVPFHEVFG-GVRCNLK 281 (413)
Q Consensus 204 ~~Ap~f~eVl~~f~~fL~~~~lv~~n~~vV~~g~fDir~fL~~~~~~~gi~~P~~-~~~~iDl~~l~r~l~~-~~~~~L~ 281 (413)
.+..+|.+.|.++++-.+-. .+.++.-+.+-+...|+..+...|++.-.+ ...|+.+...+..+++ .++.+++
T Consensus 74 ~~~~s~~~~L~~~~~~~~~~-----~~~~~~P~d~~l~~~l~~~~~~~~i~~~~~~~~~Fl~s~~~f~~~~~~~k~~~Me 148 (224)
T PF04244_consen 74 ENTQSFEDALARALKQHGID-----RLHVMEPGDYRLEQRLESLAQQLGIPLEVLEDPHFLTSREEFAEWFEGRKRLRME 148 (224)
T ss_dssp T--SSHHHHHHHHHHHH---------EEEE--S-HHHHHHHHH----SSS-EEEE--TTSSS-HHHHHHHHTT-SS--HH
T ss_pred cccccHHHHHHHHHHHcCCC-----EEEEECCCCHHHHHHHHhhhcccCCceEEeCCCCccCCHHHHHHHHccCCceeHH
Confidence 34457888887776655432 233333355444455666666677764222 2357777888888776 4566776
Q ss_pred ----HHHHHcCCCC
Q 015078 282 ----EAVEMAGLAW 291 (413)
Q Consensus 282 ----~l~~~~gI~~ 291 (413)
.+++++||=.
T Consensus 149 ~FYR~mRkr~~ILm 162 (224)
T PF04244_consen 149 YFYREMRKRFGILM 162 (224)
T ss_dssp HHHHHHHHHHTTTE
T ss_pred HHHHHHHHHcCccc
Confidence 3667777643
No 144
>TIGR01685 MDP-1 magnesium-dependent phosphatase-1. This model represents two closely related clades of sequences from eukaryotes and archaea. The mouse enzyme has been characterized as a phosphatase and has been positively identified as a member of the haloacid dehalogenase (HAD) superfamily by site-directed mutagenesis of the active site residues.
Probab=20.80 E-value=3.3e+02 Score=25.09 Aligned_cols=12 Identities=25% Similarity=0.321 Sum_probs=10.3
Q ss_pred cEEEEEEeeCCC
Q 015078 136 YFVVIDFEATCD 147 (413)
Q Consensus 136 ~fVV~D~ETTGl 147 (413)
.+||||++.|-.
T Consensus 3 ~~~~~~~~~~~~ 14 (174)
T TIGR01685 3 RVIVFDLDGTLW 14 (174)
T ss_pred cEEEEeCCCCCc
Confidence 689999999965
Done!