Query 023906
Match_columns 275
No_of_seqs 269 out of 1451
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 07:31:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023906.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023906hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2249 3'-5' exonuclease [Rep 100.0 9.1E-39 2E-43 278.7 17.5 166 77-242 102-271 (280)
2 cd06144 REX4_like DEDDh 3'-5' 100.0 4.5E-35 9.7E-40 242.9 17.0 149 83-231 1-152 (152)
3 cd06149 ISG20 DEDDh 3'-5' exon 100.0 6.2E-34 1.3E-38 237.4 16.9 149 83-231 1-157 (157)
4 cd06145 REX1_like DEDDh 3'-5' 100.0 1.3E-33 2.8E-38 233.8 15.9 145 83-231 1-150 (150)
5 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 8.7E-34 1.9E-38 237.4 12.5 145 83-231 1-161 (161)
6 PRK08517 DNA polymerase III su 100.0 5.9E-31 1.3E-35 235.5 21.1 175 76-255 64-252 (257)
7 TIGR01406 dnaQ_proteo DNA poly 100.0 1.8E-31 3.8E-36 234.9 16.8 160 81-241 1-176 (225)
8 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 1.5E-31 3.3E-36 224.2 14.7 148 83-231 1-174 (174)
9 PRK05711 DNA polymerase III su 100.0 5E-31 1.1E-35 233.7 17.9 156 80-236 4-175 (240)
10 PRK07247 DNA polymerase III su 100.0 9.3E-31 2E-35 225.4 18.4 153 79-236 4-168 (195)
11 cd06130 DNA_pol_III_epsilon_li 100.0 9.8E-31 2.1E-35 216.2 16.8 145 82-231 1-155 (156)
12 PRK07740 hypothetical protein; 100.0 1.9E-30 4.1E-35 230.9 19.7 159 76-238 55-227 (244)
13 PRK09146 DNA polymerase III su 100.0 2.2E-30 4.7E-35 229.7 19.6 159 75-237 42-227 (239)
14 PRK06310 DNA polymerase III su 100.0 2.2E-30 4.7E-35 231.3 19.5 168 78-250 5-186 (250)
15 cd06131 DNA_pol_III_epsilon_Ec 100.0 7E-31 1.5E-35 220.1 14.5 149 82-233 1-166 (167)
16 PRK06195 DNA polymerase III su 100.0 3.2E-30 6.9E-35 236.9 18.9 153 81-238 2-165 (309)
17 PRK06063 DNA polymerase III su 100.0 5.6E-30 1.2E-34 235.4 20.1 158 77-239 12-181 (313)
18 PRK07942 DNA polymerase III su 100.0 2.5E-30 5.4E-35 228.6 16.6 159 77-238 3-181 (232)
19 PRK06807 DNA polymerase III su 100.0 5.5E-30 1.2E-34 235.2 18.4 154 79-237 7-172 (313)
20 TIGR00573 dnaq exonuclease, DN 100.0 5.8E-30 1.3E-34 224.1 17.0 164 77-241 4-181 (217)
21 PRK07983 exodeoxyribonuclease 100.0 6.5E-30 1.4E-34 223.9 17.0 162 82-252 2-169 (219)
22 PRK09145 DNA polymerase III su 100.0 1.3E-29 2.8E-34 219.4 17.4 153 79-235 28-199 (202)
23 PRK07748 sporulation inhibitor 100.0 4.5E-30 9.8E-35 223.2 14.5 155 79-236 3-179 (207)
24 PRK06309 DNA polymerase III su 100.0 2.5E-29 5.4E-34 222.2 19.2 154 80-238 2-167 (232)
25 smart00479 EXOIII exonuclease 100.0 2.4E-29 5.3E-34 209.7 15.4 157 81-238 1-168 (169)
26 PRK06722 exonuclease; Provisio 100.0 2.1E-29 4.5E-34 227.2 15.7 157 78-235 3-179 (281)
27 PRK05168 ribonuclease T; Provi 100.0 1.1E-28 2.3E-33 215.3 17.1 166 70-238 7-202 (211)
28 cd06134 RNaseT DEDDh 3'-5' exo 100.0 8.8E-29 1.9E-33 212.3 15.9 154 81-237 6-189 (189)
29 TIGR01298 RNaseT ribonuclease 100.0 1.8E-28 4E-33 212.1 16.8 161 76-239 4-194 (200)
30 PRK07246 bifunctional ATP-depe 100.0 4.3E-28 9.3E-33 247.4 20.4 159 77-239 4-172 (820)
31 PRK07883 hypothetical protein; 100.0 5.8E-28 1.3E-32 237.1 20.0 160 76-239 11-184 (557)
32 COG2176 PolC DNA polymerase II 100.0 4.2E-29 9E-34 251.4 11.3 164 71-238 412-587 (1444)
33 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 2.7E-28 5.8E-33 207.2 13.0 146 82-232 1-176 (177)
34 PRK08074 bifunctional ATP-depe 100.0 2.5E-27 5.4E-32 245.0 20.2 156 79-238 2-170 (928)
35 cd06133 ERI-1_3'hExo_like DEDD 99.9 2.6E-27 5.7E-32 199.2 14.8 151 82-233 1-175 (176)
36 TIGR01405 polC_Gram_pos DNA po 99.9 3.9E-27 8.4E-32 246.0 18.8 162 74-239 183-357 (1213)
37 PRK05601 DNA polymerase III su 99.9 4.5E-27 9.7E-32 216.9 16.8 153 76-233 42-245 (377)
38 TIGR01407 dinG_rel DnaQ family 99.9 6.3E-27 1.4E-31 240.5 18.8 155 81-239 1-167 (850)
39 PRK09182 DNA polymerase III su 99.9 3E-26 6.4E-31 208.7 16.3 172 76-253 33-218 (294)
40 cd06127 DEDDh DEDDh 3'-5' exon 99.9 2.9E-26 6.4E-31 187.4 14.6 147 83-231 1-159 (159)
41 cd06138 ExoI_N N-terminal DEDD 99.9 8.8E-27 1.9E-31 198.8 11.5 145 83-230 1-182 (183)
42 PF00929 RNase_T: Exonuclease; 99.9 7.7E-28 1.7E-32 197.2 1.2 147 83-230 1-164 (164)
43 COG0847 DnaQ DNA polymerase II 99.9 2.3E-25 4.9E-30 197.6 16.3 154 80-236 13-181 (243)
44 PTZ00315 2'-phosphotransferase 99.9 4.8E-25 1E-29 213.7 19.0 156 79-235 55-253 (582)
45 PRK11779 sbcB exonuclease I; P 99.9 1E-23 2.2E-28 202.6 17.0 167 78-247 4-208 (476)
46 PRK00448 polC DNA polymerase I 99.9 1.2E-23 2.6E-28 222.5 15.8 159 76-238 415-585 (1437)
47 PRK05359 oligoribonuclease; Pr 99.9 1.8E-23 3.8E-28 178.3 13.7 147 79-237 2-175 (181)
48 KOG2248 3'-5' exonuclease [Rep 99.9 3E-23 6.5E-28 193.4 15.5 154 78-235 214-373 (380)
49 cd06135 Orn DEDDh 3'-5' exonuc 99.9 7.8E-24 1.7E-28 179.2 10.3 145 82-236 1-171 (173)
50 KOG0542 Predicted exonuclease 99.7 1.3E-17 2.9E-22 145.2 8.2 157 79-236 55-241 (280)
51 KOG3242 Oligoribonuclease (3'- 99.6 1.8E-15 3.8E-20 125.1 8.8 154 76-237 22-199 (208)
52 COG5018 KapD Inhibitor of the 99.6 2E-16 4.3E-21 130.3 3.2 155 80-236 4-184 (210)
53 KOG1275 PAB-dependent poly(A) 99.6 1.9E-15 4.2E-20 149.9 7.7 177 79-256 909-1116(1118)
54 COG1949 Orn Oligoribonuclease 99.6 1.2E-14 2.7E-19 119.1 8.7 151 78-237 4-178 (184)
55 COG2925 SbcB Exonuclease I [DN 99.5 6.4E-13 1.4E-17 122.0 12.1 173 78-253 7-217 (475)
56 cd05160 DEDDy_DNA_polB_exo DED 99.1 8E-10 1.7E-14 95.0 13.2 123 82-212 1-163 (199)
57 cd06139 DNA_polA_I_Ecoli_like_ 98.9 8.2E-08 1.8E-12 81.4 14.8 141 79-239 4-172 (193)
58 PF01612 DNA_pol_A_exo1: 3'-5' 98.8 1.3E-07 2.8E-12 78.7 12.1 133 80-236 20-174 (176)
59 cd06125 DnaQ_like_exo DnaQ-lik 98.7 1.3E-07 2.8E-12 72.3 9.1 37 152-188 35-83 (96)
60 PF04857 CAF1: CAF1 family rib 98.5 7E-07 1.5E-11 80.4 11.0 149 80-232 22-262 (262)
61 PRK05755 DNA polymerase I; Pro 98.5 6.1E-07 1.3E-11 93.4 11.9 132 79-238 314-470 (880)
62 PF13482 RNase_H_2: RNase_H su 98.4 1.3E-06 2.7E-11 72.6 7.6 124 83-233 1-133 (164)
63 COG0349 Rnd Ribonuclease D [Tr 98.3 6.3E-06 1.4E-10 76.7 11.1 132 80-238 17-167 (361)
64 cd06146 mut-7_like_exo DEDDy 3 98.2 1.8E-05 3.8E-10 68.1 11.9 87 148-234 70-192 (193)
65 cd05781 DNA_polB_B3_exo DEDDy 98.2 1.9E-05 4.1E-10 67.7 11.5 105 80-211 3-144 (188)
66 cd05780 DNA_polB_Kod1_like_exo 98.2 3.2E-05 6.9E-10 66.6 12.6 116 80-213 3-157 (195)
67 cd06129 RNaseD_like DEDDy 3'-5 98.2 4E-05 8.6E-10 63.8 12.2 129 79-234 12-160 (161)
68 PF10108 DNA_pol_B_exo2: Predi 98.1 0.00017 3.7E-09 62.7 15.0 90 144-234 36-170 (209)
69 PRK10829 ribonuclease D; Provi 98.0 9.4E-05 2E-09 69.9 13.0 132 79-238 21-171 (373)
70 KOG4793 Three prime repair exo 97.9 1.5E-05 3.2E-10 70.9 5.7 169 76-245 9-299 (318)
71 cd00007 35EXOc 3'-5' exonuclea 97.9 0.00036 7.8E-09 56.2 13.6 67 146-212 40-111 (155)
72 cd06141 WRN_exo DEDDy 3'-5' ex 97.9 0.00015 3.2E-09 60.6 11.4 85 150-234 63-169 (170)
73 TIGR01388 rnd ribonuclease D. 97.9 0.00031 6.6E-09 66.4 13.9 132 79-238 17-167 (367)
74 cd05785 DNA_polB_like2_exo Unc 97.7 0.0016 3.5E-08 56.7 14.3 33 142-174 55-91 (207)
75 cd05779 DNA_polB_epsilon_exo D 97.7 0.00093 2E-08 58.1 12.5 71 142-212 70-169 (204)
76 cd06148 Egl_like_exo DEDDy 3'- 97.6 0.0012 2.6E-08 56.9 12.5 137 77-239 7-179 (197)
77 cd05784 DNA_polB_II_exo DEDDy 97.6 0.0015 3.3E-08 56.2 12.6 117 80-213 3-155 (193)
78 KOG0304 mRNA deadenylase subun 97.6 0.00024 5.1E-09 61.6 6.9 154 81-236 25-238 (239)
79 cd05782 DNA_polB_like1_exo Unc 97.5 0.00065 1.4E-08 59.2 9.4 68 144-212 77-170 (208)
80 cd05777 DNA_polB_delta_exo DED 97.5 0.011 2.4E-07 52.1 17.1 86 79-174 6-104 (230)
81 COG3359 Predicted exonuclease 97.5 0.001 2.2E-08 58.8 10.2 129 79-233 97-238 (278)
82 cd05778 DNA_polB_zeta_exo inac 97.4 0.0048 1E-07 54.6 14.0 143 81-224 5-204 (231)
83 cd05783 DNA_polB_B1_exo DEDDy 97.3 0.014 3E-07 50.7 14.7 73 141-213 69-172 (204)
84 smart00474 35EXOc 3'-5' exonuc 97.2 0.016 3.4E-07 47.4 14.0 62 149-212 64-131 (172)
85 PTZ00166 DNA polymerase delta 97.2 0.0082 1.8E-07 64.0 14.8 148 78-233 262-482 (1054)
86 PHA02570 dexA exonuclease; Pro 97.0 0.0022 4.7E-08 56.0 7.2 91 83-174 4-124 (220)
87 cd06142 RNaseD_exo DEDDy 3'-5' 97.0 0.032 7E-07 46.3 13.6 90 149-238 53-161 (178)
88 PRK05762 DNA polymerase II; Re 96.9 0.015 3.3E-07 60.3 13.4 139 78-233 153-348 (786)
89 smart00486 POLBc DNA polymeras 96.8 0.063 1.4E-06 51.3 16.4 84 80-174 3-102 (471)
90 PHA02528 43 DNA polymerase; Pr 96.8 0.029 6.3E-07 58.7 14.3 153 76-232 102-323 (881)
91 cd06140 DNA_polA_I_Bacillus_li 96.6 0.1 2.2E-06 43.5 14.3 105 80-212 3-113 (178)
92 PF03104 DNA_pol_B_exo1: DNA p 96.6 0.013 2.8E-07 53.6 9.3 87 78-174 155-255 (325)
93 cd05776 DNA_polB_alpha_exo ina 96.4 0.03 6.5E-07 49.6 9.7 75 139-213 76-188 (234)
94 KOG1798 DNA polymerase epsilon 96.3 0.042 9E-07 59.1 11.8 164 79-245 245-462 (2173)
95 COG0749 PolA DNA polymerase I 96.1 0.037 8.1E-07 55.1 9.8 90 148-237 66-180 (593)
96 PHA02524 43A DNA polymerase su 95.8 0.17 3.6E-06 49.7 12.6 95 76-173 102-212 (498)
97 cd06147 Rrp6p_like_exo DEDDy 3 95.5 0.24 5.1E-06 42.1 11.4 60 151-211 68-131 (192)
98 COG0417 PolB DNA polymerase el 95.4 0.29 6.3E-06 50.9 13.5 74 139-212 205-309 (792)
99 KOG0969 DNA polymerase delta, 94.6 0.0081 1.7E-07 60.7 -0.5 135 78-222 272-460 (1066)
100 TIGR00593 pola DNA polymerase 94.2 0.17 3.7E-06 53.2 8.1 93 145-238 363-478 (887)
101 TIGR00592 pol2 DNA polymerase 93.8 2.2 4.7E-05 46.5 15.8 83 130-212 569-683 (1172)
102 TIGR03491 RecB family nuclease 93.3 1.6 3.4E-05 42.5 12.6 126 80-234 284-428 (457)
103 KOG3657 Mitochondrial DNA poly 93.2 0.21 4.6E-06 51.2 6.5 32 157-188 240-275 (1075)
104 COG5228 POP2 mRNA deadenylase 93.0 0.26 5.7E-06 43.1 5.9 148 80-234 42-250 (299)
105 PF00843 Arena_nucleocap: Aren 92.4 0.15 3.3E-06 48.7 4.0 142 77-226 369-527 (533)
106 cd09018 DEDDy_polA_RNaseD_like 91.4 1.2 2.6E-05 35.5 7.8 59 152-211 45-109 (150)
107 PRK05761 DNA polymerase I; Rev 90.0 3.1 6.7E-05 43.4 11.2 88 143-230 208-334 (787)
108 PHA02563 DNA polymerase; Provi 81.2 4.9 0.00011 40.8 7.1 68 76-174 8-82 (630)
109 PHA03036 DNA polymerase; Provi 78.8 19 0.00041 38.6 10.6 101 72-174 152-273 (1004)
110 PRK14975 bifunctional 3'-5' ex 68.2 14 0.00031 36.8 6.6 58 182-239 72-146 (553)
111 cd06128 DNA_polA_exo DEDDy 3'- 63.9 19 0.00041 28.8 5.5 59 152-211 45-109 (151)
112 KOG0970 DNA polymerase alpha, 59.3 31 0.00067 37.3 7.1 154 78-233 527-751 (1429)
113 PF13017 Maelstrom: piRNA path 58.3 11 0.00024 32.8 3.3 62 96-157 9-79 (213)
114 PF11074 DUF2779: Domain of un 56.1 41 0.00089 27.0 6.0 33 142-174 54-88 (130)
115 KOG0968 DNA polymerase zeta, c 40.8 84 0.0018 34.3 6.8 94 68-173 671-769 (1488)
116 TIGR00592 pol2 DNA polymerase 22.5 65 0.0014 35.4 2.6 33 142-174 267-303 (1172)
No 1
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=9.1e-39 Score=278.75 Aligned_cols=166 Identities=52% Similarity=0.868 Sum_probs=156.9
Q ss_pred CCCCcEEEEEEeecCCCC-CCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHH
Q 023906 77 FSLTDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (275)
Q Consensus 77 ~~~~~~vviD~EtTGl~~-~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (275)
.+.+++|+|||||+|.++ |+...+|+|+|+|..|.++||.||+|..+|++|+|.++||+++++.+|.+|+.|+.++.+|
T Consensus 102 ~~~~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~kl 181 (280)
T KOG2249|consen 102 GSLTRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKL 181 (280)
T ss_pred cccceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHH
Confidence 345579999999999995 6889999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCEEEEEcchhhHHHhcccCCCCceeehhccchhhc---CCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHH
Q 023906 156 IEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLK---NGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMK 232 (275)
Q Consensus 156 l~~~ilVgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~~---~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~ 232 (275)
|.|+|||||.+++||.+|.+.||+..++||+.+.+++. ....+||+.|+.++||+++|.+.|++.+||+|||+||.+
T Consensus 182 L~gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsSvEDA~AtM~LY~~ 261 (280)
T KOG2249|consen 182 LKGRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVGEHSSVEDARATMELYKR 261 (280)
T ss_pred HhCCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhccccCcHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999987663 467899999999999999999999999999999999999
Q ss_pred hHHHHHHHHH
Q 023906 233 NRKQWEKSVK 242 (275)
Q Consensus 233 l~~~~e~~l~ 242 (275)
...+||+...
T Consensus 262 vk~qwe~~~~ 271 (280)
T KOG2249|consen 262 VKVQWEKIEA 271 (280)
T ss_pred HHHHHHHHhh
Confidence 9999998665
No 2
>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=100.00 E-value=4.5e-35 Score=242.94 Aligned_cols=149 Identities=59% Similarity=0.959 Sum_probs=135.4
Q ss_pred EEEEEeecCCCCC-CeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCCCEE
Q 023906 83 VAMDCEMVGISQG-NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRIL 161 (275)
Q Consensus 83 vviD~EtTGl~~~-~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~~il 161 (275)
|+|||||||+++. ++++|++|.+++.+|.++|++||+|..+++++++.+||||++||+++|+|.+++.+|.+|++++++
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~~l~~~vl 80 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCCCHHHHHHHHHHHhCCCEE
Confidence 6899999999965 689999999999889999999999999999999999999999999999999999999999999999
Q ss_pred EEEcchhhHHHhcccCCCCceeehhccchhhcC--CCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHH
Q 023906 162 VGHALHNDLKALLLTHSKKDLRDTSEYQPFLKN--GRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYM 231 (275)
Q Consensus 162 VgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~~~--~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~ 231 (275)
||||+.||+.||+..+++..++||..+..+... ..+++|+.||..+||+++..++|+|++||++|++||+
T Consensus 81 VgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred EEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence 999999999999999888889999887655432 4789999996556899986568999999999999984
No 3
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=100.00 E-value=6.2e-34 Score=237.44 Aligned_cols=149 Identities=44% Similarity=0.709 Sum_probs=130.5
Q ss_pred EEEEEeecCCCCC-CeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCCCEE
Q 023906 83 VAMDCEMVGISQG-NKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRIL 161 (275)
Q Consensus 83 vviD~EtTGl~~~-~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~~il 161 (275)
|+|||||||++++ ++.+|++|.+++.+|.++|++||+|..+++++++.+||||+++|++||+|++++.+|.+|+++++|
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~~l~~~vl 80 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCCCHHHHHHHHHHHcCCCEE
Confidence 6899999999954 678999999998889999999999999999999999999999999999999999999999999999
Q ss_pred EEEcchhhHHHhcccCCCCceeehhccch---h--hcCCCCccHHHHHHHHcCCcCC--CCCCChHHHHHHHHHHHH
Q 023906 162 VGHALHNDLKALLLTHSKKDLRDTSEYQP---F--LKNGRSKALRHLAAEILAVEIQ--NGEHCPIDDARAAMLLYM 231 (275)
Q Consensus 162 VgHn~~fDl~~L~~~~~~~~~iDt~~l~~---~--~~~~~~~sL~~l~~~~lgi~~~--~~~H~Al~DA~ata~L~~ 231 (275)
||||+.||++||++.++...++||..+.. . ++...+++|+.||..++|..++ ..+|+|++||++|++||+
T Consensus 81 V~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred EEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 99999999999999988878899986532 2 3455779999996655544443 347999999999999984
No 4
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=100.00 E-value=1.3e-33 Score=233.80 Aligned_cols=145 Identities=41% Similarity=0.618 Sum_probs=127.7
Q ss_pred EEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCC-CHHHHHHHHHHHhC-CCE
Q 023906 83 VAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAK-DFPTVQKKVAELIE-GRI 160 (275)
Q Consensus 83 vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~-~~~ev~~~l~~~l~-~~i 160 (275)
|+|||||||++.+ .+|++|.+++.+|+++|++||+|..+++++++++||||++||.++| +|++++.+|.+|++ +.+
T Consensus 1 ~~iD~E~~g~~~g--~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~~~~v 78 (150)
T cd06145 1 FALDCEMCYTTDG--LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTI 78 (150)
T ss_pred CEEeeeeeeecCC--CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhCCCCE
Confidence 5899999999865 6777777778889999999999999999999999999999999995 99999999999997 899
Q ss_pred EEEEcchhhHHHhcccCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCC--CCCCChHHHHHHHHHHHH
Q 023906 161 LVGHALHNDLKALLLTHSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQ--NGEHCPIDDARAAMLLYM 231 (275)
Q Consensus 161 lVgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~--~~~H~Al~DA~ata~L~~ 231 (275)
|||||+.||+.||+..+++ ++||+.+++.+ +...+++|+.||..++|+.++ .++|+|++||++|++||.
T Consensus 79 lVgHn~~fD~~fL~~~~~~--~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 79 LVGHSLENDLKALKLIHPR--VIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred EEEcChHHHHHHhhccCCC--EEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 9999999999999987654 89999887654 445578999997677787664 368999999999999983
No 5
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=100.00 E-value=8.7e-34 Score=237.37 Aligned_cols=145 Identities=37% Similarity=0.606 Sum_probs=127.8
Q ss_pred EEEEEeecCCCC--CCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCC-------HHHHHHHHH
Q 023906 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKD-------FPTVQKKVA 153 (275)
Q Consensus 83 vviD~EtTGl~~--~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~-------~~ev~~~l~ 153 (275)
|+|||||||+++ ++|++||+|.+.+ |+++|++||+|..+++++++.+||||++||.++|+ |++++.+|.
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~--g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~ 78 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLT--GEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALW 78 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCC--CeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHH
Confidence 689999999984 5899999999855 88889999999999999999999999999998875 459999999
Q ss_pred HHhCC-CEEEEEcchhhHHHhcccCCCCceeehhccchhhcC-C---CCccHHHHHHHHcCCcCCC--CCCChHHHHHHH
Q 023906 154 ELIEG-RILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLKN-G---RSKALRHLAAEILAVEIQN--GEHCPIDDARAA 226 (275)
Q Consensus 154 ~~l~~-~ilVgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~~~-~---~~~sL~~l~~~~lgi~~~~--~~H~Al~DA~at 226 (275)
+|+++ .+|||||+.||+.||+..++. ++||+.+++.+.. . .+++|..||..+||++++. ++|+|++||++|
T Consensus 79 ~~i~~~~vlVgHn~~fD~~fL~~~~~~--~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at 156 (161)
T cd06137 79 KFIDPDTILVGHSLQNDLDALRMIHTR--VVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAA 156 (161)
T ss_pred HhcCCCcEEEeccHHHHHHHHhCcCCC--eeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHH
Confidence 99997 999999999999999987554 8999999876633 3 5799999977779998853 589999999999
Q ss_pred HHHHH
Q 023906 227 MLLYM 231 (275)
Q Consensus 227 a~L~~ 231 (275)
++||+
T Consensus 157 ~~l~~ 161 (161)
T cd06137 157 REVVL 161 (161)
T ss_pred HHHhC
Confidence 99984
No 6
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=5.9e-31 Score=235.51 Aligned_cols=175 Identities=21% Similarity=0.257 Sum_probs=146.2
Q ss_pred CCCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHH
Q 023906 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~ 151 (275)
......||+||+||||+++ ++|+|||+|.+.+ |.++ |++||+|. +++++++++||||++++.++|++.+|+.+
T Consensus 64 ~~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~--g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap~~~evl~~ 140 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKN--GEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEE 140 (257)
T ss_pred CCCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCCCHHHHHHH
Confidence 3456789999999999984 4899999999975 6665 88999996 78999999999999999999999999999
Q ss_pred HHHHhCCCEEEEEcchhhHHHhcc-------cCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCCCChHHHHH
Q 023906 152 VAELIEGRILVGHALHNDLKALLL-------THSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGEHCPIDDAR 224 (275)
Q Consensus 152 l~~~l~~~ilVgHn~~fDl~~L~~-------~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ 224 (275)
|.+|+++.++||||+.||+.||+. .......+||..+++.+....+++|..| +++||++.. .+|+|++||.
T Consensus 141 f~~fl~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L-~~~lgi~~~-~~HrAl~DA~ 218 (257)
T PRK08517 141 FRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFL-KELLGIEIE-VHHRAYADAL 218 (257)
T ss_pred HHHHHCCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHH-HHHcCcCCC-CCCChHHHHH
Confidence 999999999999999999999962 2222457899888765544567899999 789999987 6999999999
Q ss_pred HHHHHHHHhHHHHHH---HHHHHHHHHHHhhhcC
Q 023906 225 AAMLLYMKNRKQWEK---SVKDQTRLEQKQKNRK 255 (275)
Q Consensus 225 ata~L~~~l~~~~e~---~l~~~~~~~~k~~~~~ 255 (275)
+|++||..+..++.. .+.+++.+.+..++.+
T Consensus 219 ata~ll~~ll~~~~~~~~t~~~L~~~~k~~~~~~ 252 (257)
T PRK08517 219 AAYEIFKICLLNLPSYIKTTEDLIDFSKTAKTLK 252 (257)
T ss_pred HHHHHHHHHHHHhHHhhcCHHHHHHHhhhccccc
Confidence 999999999887754 4456666666444433
No 7
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.98 E-value=1.8e-31 Score=234.88 Aligned_cols=160 Identities=20% Similarity=0.215 Sum_probs=135.7
Q ss_pred cEEEEEEeecCCCC---CCeeEEEEEEEEeCCCc-EEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHh
Q 023906 81 DVVAMDCEMVGISQ---GNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (275)
Q Consensus 81 ~~vviD~EtTGl~~---~~iieIaav~v~d~~g~-~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (275)
++|+||+||||+++ ++|||||+|.+.+.... ..|+.||+|..++++.+++|||||+++|.++|+|.+++.+|.+|+
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~fi 80 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHHh
Confidence 58999999999994 48999999998863211 139999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEcchhhHHHhccc-------CC----CCceeehhccchhhcCCCCccHHHHHHHHcCCcCCC-CCCChHHHHH
Q 023906 157 EGRILVGHALHNDLKALLLT-------HS----KKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQN-GEHCPIDDAR 224 (275)
Q Consensus 157 ~~~ilVgHn~~fDl~~L~~~-------~~----~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~-~~H~Al~DA~ 224 (275)
++.++||||+.||+.||+.. .+ ...++||..+++.+....+++|+.| +++||++..+ ..|+|+.||+
T Consensus 81 ~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L-~~~~gi~~~~r~~H~Al~DA~ 159 (225)
T TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDAL-CKRFKVDNSHRTLHGALLDAH 159 (225)
T ss_pred CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHH-HHhcCCCCCCCCCcCHHHHHH
Confidence 99999999999999999721 11 1578999988776544567899999 7999999764 3699999999
Q ss_pred HHHHHHHHhHHHHHHHH
Q 023906 225 AAMLLYMKNRKQWEKSV 241 (275)
Q Consensus 225 ata~L~~~l~~~~e~~l 241 (275)
+|++||..+...+...+
T Consensus 160 ~~a~v~~~l~~~~~~~~ 176 (225)
T TIGR01406 160 LLAEVYLALTGGQESLL 176 (225)
T ss_pred HHHHHHHHHHcCCcchh
Confidence 99999999987665543
No 8
>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=99.97 E-value=1.5e-31 Score=224.20 Aligned_cols=148 Identities=37% Similarity=0.550 Sum_probs=133.0
Q ss_pred EEEEEeecCCCC--------CCe-------eEEEEEEEEe----CCCcEEEEEEecCCccccccceeecCCCHHHHcCCC
Q 023906 83 VAMDCEMVGISQ--------GNK-------SALGRVSLVN----KWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAK 143 (275)
Q Consensus 83 vviD~EtTGl~~--------~~i-------ieIaav~v~d----~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~ 143 (275)
|++|||++|+++ |.- .++|+|+++| ..|+++||.||+|..+|.+|+|+++|||+++|.++.
T Consensus 1 ~a~d~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~vllD~~VkP~~~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 1 VAIDAEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred CceeeeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCEEEeeeECCCCCccCcCccccccCHHHcCccc
Confidence 467888877774 332 4899999999 689999999999999999999999999999998764
Q ss_pred ------CHHHHHHHHHHHhC-CCEEEEEcchhhHHHhcccCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCC
Q 023906 144 ------DFPTVQKKVAELIE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGE 216 (275)
Q Consensus 144 ------~~~ev~~~l~~~l~-~~ilVgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~ 216 (275)
++++++.++..++. +++||||.+.+|+.+|++.||+..++||+.+++. +..+.+||+.|+.++||.++|.+.
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~-~~~r~~sLk~La~~~L~~~IQ~~~ 159 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHL-PGQRKLSLRFLAWYLLGEKIQSET 159 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccC-CCCCChhHHHHHHHHcCCcccCCC
Confidence 69999999999996 9999999999999999999998899999988765 344578999999999999999889
Q ss_pred CChHHHHHHHHHHHH
Q 023906 217 HCPIDDARAAMLLYM 231 (275)
Q Consensus 217 H~Al~DA~ata~L~~ 231 (275)
|++++||+|||+||+
T Consensus 160 HdSvEDArAam~Ly~ 174 (174)
T cd06143 160 HDSIEDARTALKLYR 174 (174)
T ss_pred cCcHHHHHHHHHHhC
Confidence 999999999999984
No 9
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=5e-31 Score=233.70 Aligned_cols=156 Identities=19% Similarity=0.234 Sum_probs=133.3
Q ss_pred CcEEEEEEeecCCCC---CCeeEEEEEEEEeCCCc-EEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHH
Q 023906 80 TDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (275)
Q Consensus 80 ~~~vviD~EtTGl~~---~~iieIaav~v~d~~g~-~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (275)
.++|+||+||||+++ ++|||||+|.+.+.... ..|+.||+|..+|++.+++|||||+++|.++|+|.+++.+|.+|
T Consensus 4 ~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f~~f 83 (240)
T PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83 (240)
T ss_pred CeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHHHHH
Confidence 579999999999994 48999999999863211 13899999999999999999999999999999999999999999
Q ss_pred hCCCEEEEEcchhhHHHhccc-------CC----CCceeehhccchhhcCCCCccHHHHHHHHcCCcCCC-CCCChHHHH
Q 023906 156 IEGRILVGHALHNDLKALLLT-------HS----KKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQN-GEHCPIDDA 223 (275)
Q Consensus 156 l~~~ilVgHn~~fDl~~L~~~-------~~----~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~-~~H~Al~DA 223 (275)
+++.+|||||+.||+.||+.. .+ ...++||..+++.+....+++|+.| |++||++... ..|+|+.||
T Consensus 84 i~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL-~~~~gi~~~~r~~H~AL~DA 162 (240)
T PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDAL-CKRYGIDNSHRTLHGALLDA 162 (240)
T ss_pred hCCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHH-HHHCCCCCCCCCCCCHHHHH
Confidence 999999999999999999722 23 1458999988876644567899999 6899998753 369999999
Q ss_pred HHHHHHHHHhHHH
Q 023906 224 RAAMLLYMKNRKQ 236 (275)
Q Consensus 224 ~ata~L~~~l~~~ 236 (275)
++|++||..+...
T Consensus 163 ~~~A~v~~~l~~~ 175 (240)
T PRK05711 163 EILAEVYLAMTGG 175 (240)
T ss_pred HHHHHHHHHHHCc
Confidence 9999999998754
No 10
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=9.3e-31 Score=225.38 Aligned_cols=153 Identities=19% Similarity=0.234 Sum_probs=129.0
Q ss_pred CCcEEEEEEeecCCC-CCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHH
Q 023906 79 LTDVVAMDCEMVGIS-QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (275)
Q Consensus 79 ~~~~vviD~EtTGl~-~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (275)
+.+||+|||||||++ .++|||||+|.+.+ |.++ |++||+|..+++++++.+||||++||+++|+|.+++.+|.+|
T Consensus 4 ~~~~vvlD~EtTGl~~~~eIIeIgaV~v~~--g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~~f 81 (195)
T PRK07247 4 LETYIAFDLEFNTVNGVSHIIQVSAVKYDD--HKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEF 81 (195)
T ss_pred CCeEEEEEeeCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHHHH
Confidence 568999999999998 56899999999986 5544 999999999999999999999999999999999999999999
Q ss_pred hCCCEEEEEcch-hhHHHhccc---CCCCceeehhccc--hh---hcCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHH
Q 023906 156 IEGRILVGHALH-NDLKALLLT---HSKKDLRDTSEYQ--PF---LKNGRSKALRHLAAEILAVEIQNGEHCPIDDARAA 226 (275)
Q Consensus 156 l~~~ilVgHn~~-fDl~~L~~~---~~~~~~iDt~~l~--~~---~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at 226 (275)
+++.++||||+. ||+.||... .+....+|+.... +. +++..+++|.+| +++||++. .+|+|++||++|
T Consensus 82 ~~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~L-a~~~gi~~--~~HrAl~DA~~t 158 (195)
T PRK07247 82 VGELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTV-ADFLGIKG--RGHNSLEDARMT 158 (195)
T ss_pred HCCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHH-HHhcCCCC--CCcCCHHHHHHH
Confidence 999999999996 899999732 2222346664322 11 234567999999 68999985 479999999999
Q ss_pred HHHHHHhHHH
Q 023906 227 MLLYMKNRKQ 236 (275)
Q Consensus 227 a~L~~~l~~~ 236 (275)
+.||.++++.
T Consensus 159 a~v~~~ll~~ 168 (195)
T PRK07247 159 ARVYESFLES 168 (195)
T ss_pred HHHHHHHHhh
Confidence 9999998654
No 11
>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=9.8e-31 Score=216.17 Aligned_cols=145 Identities=26% Similarity=0.416 Sum_probs=130.1
Q ss_pred EEEEEEeecCCCCCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCCC
Q 023906 82 VVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGR 159 (275)
Q Consensus 82 ~vviD~EtTGl~~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~~ 159 (275)
||+|||||||..+++|++||+|.+.+ |+++ |+.||+|..+++++++++||||++++.++++|.+++.+|.+|+++.
T Consensus 1 ~v~~D~Ettg~~~~~ii~ig~v~~~~--~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~~~l~~~ 78 (156)
T cd06130 1 FVAIDFETANADRASACSIGLVKVRD--GQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78 (156)
T ss_pred CEEEEEeCCCCCCCceEEEEEEEEEC--CEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCCCHHHHHHHHHHHhCCC
Confidence 68999999998888999999999875 5554 8899999999999999999999999999999999999999999999
Q ss_pred EEEEEcchhhHHHhc-------ccCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHH
Q 023906 160 ILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYM 231 (275)
Q Consensus 160 ilVgHn~~fDl~~L~-------~~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~ 231 (275)
++||||+.||+.+|+ +..+...++|+..+.+.+ +...+++|..+ +++||++.+ +|+|++||++|++||.
T Consensus 79 ~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l-~~~~g~~~~--~H~Al~Da~~ta~l~~ 155 (156)
T cd06130 79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTV-AEHLGIELN--HHDALEDARACAEILL 155 (156)
T ss_pred EEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHH-HHHcCCCcc--CcCchHHHHHHHHHHh
Confidence 999999999999995 345567799998877654 44578899999 689999987 8999999999999985
No 12
>PRK07740 hypothetical protein; Provisional
Probab=99.97 E-value=1.9e-30 Score=230.93 Aligned_cols=159 Identities=19% Similarity=0.249 Sum_probs=137.2
Q ss_pred CCCCCcEEEEEEeecCCCC---CCeeEEEEEEEEeCCCcE-E--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHH
Q 023906 76 DFSLTDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGNL-I--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~---~~iieIaav~v~d~~g~~-i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~ 149 (275)
.+...++|+|||||||+++ ++|+|||+|.+.+ +.+ . |+.+|+|..+++++++++||||+++|+++|+|.+++
T Consensus 55 ~~~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~--~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl 132 (244)
T PRK07740 55 PLTDLPFVVFDLETTGFSPQQGDEILSIGAVKTKG--GEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVL 132 (244)
T ss_pred CccCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHH
Confidence 4445689999999999984 5899999999875 444 2 888999999999999999999999999999999999
Q ss_pred HHHHHHhCCCEEEEEcchhhHHHhccc------CC-CCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHH
Q 023906 150 KKVAELIEGRILVGHALHNDLKALLLT------HS-KKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPID 221 (275)
Q Consensus 150 ~~l~~~l~~~ilVgHn~~fDl~~L~~~------~~-~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~ 221 (275)
.+|.+|++++++||||+.||+.||... .+ ...++||..+++.+ +....++|+++ +.+||++.. ++|+|++
T Consensus 133 ~~f~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l-~~~~gi~~~-~~H~Al~ 210 (244)
T PRK07740 133 HRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDA-LAYYGIPIP-RRHHALG 210 (244)
T ss_pred HHHHHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHH-HHHCCcCCC-CCCCcHH
Confidence 999999999999999999999999621 11 24689999887755 44568899999 689999998 5899999
Q ss_pred HHHHHHHHHHHhHHHHH
Q 023906 222 DARAAMLLYMKNRKQWE 238 (275)
Q Consensus 222 DA~ata~L~~~l~~~~e 238 (275)
||++|++||.++..+.+
T Consensus 211 Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 211 DALMTAKLWAILLVEAQ 227 (244)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999987754
No 13
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.2e-30 Score=229.75 Aligned_cols=159 Identities=19% Similarity=0.211 Sum_probs=135.8
Q ss_pred CCCCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcE----EEEEEecCCccccccceeecCCCHHHHcCCCCHHHH
Q 023906 75 DDFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNL----IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (275)
Q Consensus 75 ~~~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~----i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev 148 (275)
.......||+||+||||+++ ++|+|||+|.+.+ +.+ .|+++|+|..+|++.++.|||||+++|.++|+|.++
T Consensus 42 ~~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~--~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~ev 119 (239)
T PRK09146 42 TPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTL--QRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERI 119 (239)
T ss_pred CCcccCCEEEEEeECCCCCCCCCcEEEEEEEEEEC--CeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHH
Confidence 35556789999999999994 6999999999875 433 388999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEEcchhhHHHhccc-------CCCCceeehhccchhh-cC-------------CCCccHHHHHHHH
Q 023906 149 QKKVAELIEGRILVGHALHNDLKALLLT-------HSKKDLRDTSEYQPFL-KN-------------GRSKALRHLAAEI 207 (275)
Q Consensus 149 ~~~l~~~l~~~ilVgHn~~fDl~~L~~~-------~~~~~~iDt~~l~~~~-~~-------------~~~~sL~~l~~~~ 207 (275)
+.+|.+|+++.++||||+.||+.||+.. .....++||+.+++.+ +. ..+++|.++ +.+
T Consensus 120 l~~l~~~~~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l-~~~ 198 (239)
T PRK09146 120 LDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADS-RLR 198 (239)
T ss_pred HHHHHHHhCCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHH-HHH
Confidence 9999999999999999999999999632 1234689999887543 11 156789999 689
Q ss_pred cCCcCCCCCCChHHHHHHHHHHHHHhHHHH
Q 023906 208 LAVEIQNGEHCPIDDARAAMLLYMKNRKQW 237 (275)
Q Consensus 208 lgi~~~~~~H~Al~DA~ata~L~~~l~~~~ 237 (275)
||++.. ++|+|++||.+|++||..+...+
T Consensus 199 ~gl~~~-~~H~Al~DA~ata~l~~~~~~~~ 227 (239)
T PRK09146 199 YGLPAY-SPHHALTDAIATAELLQAQIAHH 227 (239)
T ss_pred cCCCCC-CCCCcHHHHHHHHHHHHHHHHHH
Confidence 999976 68999999999999999987665
No 14
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.2e-30 Score=231.34 Aligned_cols=168 Identities=19% Similarity=0.290 Sum_probs=142.8
Q ss_pred CCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHH
Q 023906 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~ 153 (275)
...+||+|||||||+++ ++|+|||+|.+.. +.++ |+.+|+|..+|++.++.+||||+++|+++|+|.+++.+|.
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~--~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~~ 82 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDRIIEFAAIRFTF--DEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIK 82 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCeEEEEEEEEEEC--CeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHHH
Confidence 34689999999999984 6899999998864 3333 8899999999999999999999999999999999999999
Q ss_pred HHhCC-CEEEEEcchhhHHHhcccC---------CCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCCCChHHHH
Q 023906 154 ELIEG-RILVGHALHNDLKALLLTH---------SKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGEHCPIDDA 223 (275)
Q Consensus 154 ~~l~~-~ilVgHn~~fDl~~L~~~~---------~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA 223 (275)
+|+++ .++||||+.||+.||...+ ....++||..+++.++...+++|..| +++||++.. ++|+|++||
T Consensus 83 ~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l-~~~~g~~~~-~aH~Al~Da 160 (250)
T PRK06310 83 GFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEAL-AVHFNVPYD-GNHRAMKDV 160 (250)
T ss_pred HHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHH-HHHCCCCCC-CCcChHHHH
Confidence 99985 9999999999999997321 12568999988887766667899999 689999987 699999999
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 023906 224 RAAMLLYMKNRKQWEKSVKDQTRLEQK 250 (275)
Q Consensus 224 ~ata~L~~~l~~~~e~~l~~~~~~~~k 250 (275)
.+|++||..+...+. .+.+.+....+
T Consensus 161 ~at~~vl~~l~~~~~-~~~~l~~~~~~ 186 (250)
T PRK06310 161 EINIKVFKHLCKRFR-TLEQLKQILSK 186 (250)
T ss_pred HHHHHHHHHHHHhcc-cHHHHHHHhhc
Confidence 999999999988774 34555555543
No 15
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.97 E-value=7e-31 Score=220.06 Aligned_cols=149 Identities=19% Similarity=0.274 Sum_probs=128.3
Q ss_pred EEEEEEeecCCCC---CCeeEEEEEEEEeCCCcE---EEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHH
Q 023906 82 VVAMDCEMVGISQ---GNKSALGRVSLVNKWGNL---IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (275)
Q Consensus 82 ~vviD~EtTGl~~---~~iieIaav~v~d~~g~~---i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (275)
+|+||+||||+++ ++|+|||+|.+.+ +.+ .|+.+|+|..++++.++++||||++++.++++|.+++.+|.+|
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~--~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~ 78 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELIN--RRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDF 78 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEEC--CcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHH
Confidence 5899999999986 4899999998865 332 3889999999999999999999999999999999999999999
Q ss_pred hCCCEEEEEcchhhHHHhcccC----------CCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCC-CCCChHHHHH
Q 023906 156 IEGRILVGHALHNDLKALLLTH----------SKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQN-GEHCPIDDAR 224 (275)
Q Consensus 156 l~~~ilVgHn~~fDl~~L~~~~----------~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~-~~H~Al~DA~ 224 (275)
+++.++||||+.||+.||+..+ ....++||..+.+.+.....++|.++ +++||++.++ ++|+|++||+
T Consensus 79 l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l-~~~~~i~~~~~~~H~Al~Da~ 157 (167)
T cd06131 79 IRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDAL-CKRFGIDNSHRTLHGALLDAE 157 (167)
T ss_pred HCCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHH-HHHCCCCCCCCCCCChHHHHH
Confidence 9999999999999999996221 22468999887765544467899999 7999999863 4799999999
Q ss_pred HHHHHHHHh
Q 023906 225 AAMLLYMKN 233 (275)
Q Consensus 225 ata~L~~~l 233 (275)
+|++||.++
T Consensus 158 ~~a~l~~~l 166 (167)
T cd06131 158 LLAEVYLEL 166 (167)
T ss_pred HHHHHHHHh
Confidence 999999875
No 16
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.2e-30 Score=236.88 Aligned_cols=153 Identities=20% Similarity=0.337 Sum_probs=135.5
Q ss_pred cEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEE--EEEEecCCc-cccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC
Q 023906 81 DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLE-RVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (275)
Q Consensus 81 ~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i--~~~~V~P~~-~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (275)
+||+||+||||...++|||||+|.+.+ |.++ |++||+|.. .++++++.|||||+++|+++|+|.+++.+|.+|++
T Consensus 2 ~~vviD~ETTg~~~d~IieIgav~v~~--g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~~fl~ 79 (309)
T PRK06195 2 NFVAIDFETANEKRNSPCSIGIVVVKD--GEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFN 79 (309)
T ss_pred cEEEEEEeCCCCCCCceEEEEEEEEEC--CEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHHHHhC
Confidence 699999999998888999999999976 6665 899999985 67888999999999999999999999999999999
Q ss_pred CCEEEEEcchhhHHHhc-------ccCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHH
Q 023906 158 GRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLL 229 (275)
Q Consensus 158 ~~ilVgHn~~fDl~~L~-------~~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L 229 (275)
+.++||||+.||+.||+ ...+...++||..+++.+ +...+++|..| +.+||++. .+|+|++||++|++|
T Consensus 80 ~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L-~~~~gi~~--~~H~Al~DA~ata~l 156 (309)
T PRK06195 80 NNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTV-NNFLGYEF--KHHDALADAMACSNI 156 (309)
T ss_pred CCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHH-HHHcCCCC--cccCCHHHHHHHHHH
Confidence 99999999999999996 334556789999887654 56678999999 79999985 489999999999999
Q ss_pred HHHhHHHHH
Q 023906 230 YMKNRKQWE 238 (275)
Q Consensus 230 ~~~l~~~~e 238 (275)
|..+..+..
T Consensus 157 ~~~l~~~~~ 165 (309)
T PRK06195 157 LLNISKELN 165 (309)
T ss_pred HHHHHHHhc
Confidence 999987654
No 17
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=5.6e-30 Score=235.38 Aligned_cols=158 Identities=23% Similarity=0.202 Sum_probs=136.0
Q ss_pred CCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHH
Q 023906 77 FSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKV 152 (275)
Q Consensus 77 ~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l 152 (275)
..+..||+||+||||+++ ++|||||+|.+. .+|.++ |.+||+|.. ++.++.|||||+++|.++|+|.+++.+|
T Consensus 12 ~~~~~fvvlD~ETTGl~p~~d~IIeIgav~v~-~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap~f~ev~~~l 88 (313)
T PRK06063 12 HYPRGWAVVDVETSGFRPGQARIISLAVLGLD-ADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQFADIAGEV 88 (313)
T ss_pred CCCCCEEEEEEECCCCCCCCCEEEEEEEEEEE-CCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCCCHHHHHHHH
Confidence 346789999999999995 489999988885 346665 889999974 4678999999999999999999999999
Q ss_pred HHHhCCCEEEEEcchhhHHHhcc-------cCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHH
Q 023906 153 AELIEGRILVGHALHNDLKALLL-------THSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDAR 224 (275)
Q Consensus 153 ~~~l~~~ilVgHn~~fDl~~L~~-------~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ 224 (275)
.+|++++++||||+.||+.||.. ..+...++||+.+++.+ +...+++|.+| +++||++.. ++|+|++||+
T Consensus 89 ~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l-~~~~gi~~~-~~H~Al~DA~ 166 (313)
T PRK06063 89 AELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETL-AAHWGVPQQ-RPHDALDDAR 166 (313)
T ss_pred HHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHH-HHHcCCCCC-CCCCcHHHHH
Confidence 99999999999999999999972 23445689999888765 45678899999 689999976 6999999999
Q ss_pred HHHHHHHHhHHHHHH
Q 023906 225 AAMLLYMKNRKQWEK 239 (275)
Q Consensus 225 ata~L~~~l~~~~e~ 239 (275)
+|++||..++.....
T Consensus 167 ata~l~~~ll~~~~~ 181 (313)
T PRK06063 167 VLAGILRPSLERARE 181 (313)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999877654
No 18
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=2.5e-30 Score=228.62 Aligned_cols=159 Identities=17% Similarity=0.178 Sum_probs=132.4
Q ss_pred CCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcC-CCCHHHHHHH
Q 023906 77 FSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRK-AKDFPTVQKK 151 (275)
Q Consensus 77 ~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~-a~~~~ev~~~ 151 (275)
....+||+||+||||+++ ++|+|||+|.+. .+|.++ |++||+|..+|+++++.|||||++++.+ ++++.+++.+
T Consensus 3 ~~~~~~vv~D~ETTGl~p~~d~Iieig~v~v~-~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e 81 (232)
T PRK07942 3 WHPGPLAAFDLETTGVDPETARIVTAALVVVD-ADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAE 81 (232)
T ss_pred cccCcEEEEEeccCCCCCCCCeeEEEEEEEEe-CCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHH
Confidence 345789999999999984 689999988875 346555 8899999999999999999999999975 7888889988
Q ss_pred HHHHh-----CCCEEEEEcchhhHHHhcccC--------CCCceeehhccchhhcC--CCCccHHHHHHHHcCCcCCCCC
Q 023906 152 VAELI-----EGRILVGHALHNDLKALLLTH--------SKKDLRDTSEYQPFLKN--GRSKALRHLAAEILAVEIQNGE 216 (275)
Q Consensus 152 l~~~l-----~~~ilVgHn~~fDl~~L~~~~--------~~~~~iDt~~l~~~~~~--~~~~sL~~l~~~~lgi~~~~~~ 216 (275)
|..++ ++.+|||||+.||+.||...+ ....++|+..+.+.+.. ..+++|.+| +++||++.. ++
T Consensus 82 ~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l-~~~~gi~~~-~a 159 (232)
T PRK07942 82 IADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTAL-CEHYGVRLD-NA 159 (232)
T ss_pred HHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHH-HHHcCCCCC-CC
Confidence 88776 588999999999999996221 12457899877654422 346899999 699999987 69
Q ss_pred CChHHHHHHHHHHHHHhHHHHH
Q 023906 217 HCPIDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 217 H~Al~DA~ata~L~~~l~~~~e 238 (275)
|+|++||++|++||..+...+.
T Consensus 160 H~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 160 HEATADALAAARVAWALARRFP 181 (232)
T ss_pred CChHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999988776
No 19
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=5.5e-30 Score=235.15 Aligned_cols=154 Identities=21% Similarity=0.302 Sum_probs=137.2
Q ss_pred CCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHH
Q 023906 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (275)
+.+||+||+||||+++ ++|+|||+|.+.+ |.++ |+.+|+|..+++++++.+||||+++|.++++|.+|+.+|.+
T Consensus 7 ~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~--g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f~~ 84 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYRN--HELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLA 84 (313)
T ss_pred CCCEEEEEEECCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHHHH
Confidence 5789999999999984 6999999999975 6665 89999999999999999999999999999999999999999
Q ss_pred HhCCCEEEEEcchhhHHHhc-------ccCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHH
Q 023906 155 LIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARAA 226 (275)
Q Consensus 155 ~l~~~ilVgHn~~fDl~~L~-------~~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at 226 (275)
|+++.++||||+.||+.||. +..+...++||..+++.+ +....++|.+| +++||++. .+|+|++||++|
T Consensus 85 fl~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L-~~~lgi~~--~~H~Al~DA~~t 161 (313)
T PRK06807 85 FLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETL-KRMLGIRL--SSHNAFDDCITC 161 (313)
T ss_pred HHcCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHH-HHHcCCCC--CCcChHHHHHHH
Confidence 99999999999999999996 335566789998877644 45667899999 69999998 589999999999
Q ss_pred HHHHHHhHHHH
Q 023906 227 MLLYMKNRKQW 237 (275)
Q Consensus 227 a~L~~~l~~~~ 237 (275)
++||.++....
T Consensus 162 a~l~~~l~~~~ 172 (313)
T PRK06807 162 AAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHhh
Confidence 99999997764
No 20
>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=5.8e-30 Score=224.08 Aligned_cols=164 Identities=21% Similarity=0.295 Sum_probs=136.0
Q ss_pred CCCCcEEEEEEeecCCCCC-CeeEEEEEEEEeCCCc-EEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHH
Q 023906 77 FSLTDVVAMDCEMVGISQG-NKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (275)
Q Consensus 77 ~~~~~~vviD~EtTGl~~~-~iieIaav~v~d~~g~-~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (275)
.....||+||+||||++++ .|+|||+|.+.+.... ..|++||+|..++++.++.+||||+++|.++|+|.+++.+|.+
T Consensus 4 l~~~~fvv~D~ETTGl~~~~~IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~~~~ 83 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83 (217)
T ss_pred EEecCEEEEEecCCCCCCCCCEEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHHHHH
Confidence 4457899999999999842 4999999998764211 1389999999999999999999999999999999999999999
Q ss_pred HhCCCEEEEEcchhhHHHhcccC--------CCCceeehhccchhh-c--CCCCccHHHHHHHHcCCcCCC-CCCChHHH
Q 023906 155 LIEGRILVGHALHNDLKALLLTH--------SKKDLRDTSEYQPFL-K--NGRSKALRHLAAEILAVEIQN-GEHCPIDD 222 (275)
Q Consensus 155 ~l~~~ilVgHn~~fDl~~L~~~~--------~~~~~iDt~~l~~~~-~--~~~~~sL~~l~~~~lgi~~~~-~~H~Al~D 222 (275)
|+++.++||||+.||+.||+..+ +...++|+..+.+.+ + ...+++|..+ +++||++... .+|+|++|
T Consensus 84 ~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l-~~~~gl~~~~~~~H~Al~D 162 (217)
T TIGR00573 84 YIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDAL-CKRYEITNSHRALHGALAD 162 (217)
T ss_pred HhCCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHH-HHHcCCCCCCcccCCHHHH
Confidence 99999999999999999997221 234578887665433 2 2346799999 6999998652 48999999
Q ss_pred HHHHHHHHHHhHHHHHHHH
Q 023906 223 ARAAMLLYMKNRKQWEKSV 241 (275)
Q Consensus 223 A~ata~L~~~l~~~~e~~l 241 (275)
|++|++||..+..++.+..
T Consensus 163 A~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 163 AFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred HHHHHHHHHHHHhcchhhc
Confidence 9999999999998876654
No 21
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.97 E-value=6.5e-30 Score=223.86 Aligned_cols=162 Identities=15% Similarity=0.148 Sum_probs=133.8
Q ss_pred EEEEEEeecCCCCCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCCC
Q 023906 82 VVAMDCEMVGISQGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGR 159 (275)
Q Consensus 82 ~vviD~EtTGl~~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~~ 159 (275)
++|||+||||++ +.|||||+|.|.+ |.++ |++||+|..+|++++++|||||++||.++|+|.+++.. |+++.
T Consensus 2 ~~vlD~ETTGl~-~~IieIg~v~v~~--~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~---~~~~~ 75 (219)
T PRK07983 2 LRVIDTETCGLQ-GGIVEIASVDVID--GKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPH---YYGSE 75 (219)
T ss_pred eEEEEEECCCCC-CCCEEEEEEEEEC--CEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHH---HcCCC
Confidence 799999999997 4599999999986 6665 99999999999999999999999999999999999886 57899
Q ss_pred EEEEEcchhhHHHhcccCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCC----CCCCChHHHHHHHHHHHHHhHH
Q 023906 160 ILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQ----NGEHCPIDDARAAMLLYMKNRK 235 (275)
Q Consensus 160 ilVgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~----~~~H~Al~DA~ata~L~~~l~~ 235 (275)
+|||||+.||++||... ...++||..+++.+.+...++|..| +++||++.. ..+|||++||++|+.||.++.+
T Consensus 76 ~lVaHNa~FD~~~L~~~--~~~~idTl~lar~l~p~~~~~l~~L-~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 76 WYVAHNASFDRRVLPEM--PGEWICTMKLARRLWPGIKYSNMAL-YKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred EEEEeCcHhhHHHHhCc--CCCcEeHHHHHHHHccCCCCCHHHH-HHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 99999999999999743 2358999999875533334899989 689998742 3589999999999999999986
Q ss_pred HHHHHHHHHHHHHHHhh
Q 023906 236 QWEKSVKDQTRLEQKQK 252 (275)
Q Consensus 236 ~~e~~l~~~~~~~~k~~ 252 (275)
...-...+++.+.++.+
T Consensus 153 ~~~~~~~~l~~~~~~~~ 169 (219)
T PRK07983 153 TSGWTAEEMADITGRPS 169 (219)
T ss_pred HcCCCHHHHHHHhcCCc
Confidence 54434455555554443
No 22
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=1.3e-29 Score=219.44 Aligned_cols=153 Identities=22% Similarity=0.308 Sum_probs=129.0
Q ss_pred CCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE----EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHH
Q 023906 79 LTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI----YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKV 152 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i----~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l 152 (275)
..+||+||+||||+++ ++|+|||+|.+.+ +.++ |+.||+|...++++++.+||||++++++++++.+++.+|
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~--~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~~ 105 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRG--NRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQL 105 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEEC--CEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHHH
Confidence 3689999999999984 6999999998865 3332 889999999999999999999999999999999999999
Q ss_pred HHHhCCCEEEEEcchhhHHHhccc------C-CCCceeehhccchh-----hc-CCCCccHHHHHHHHcCCcCCCCCCCh
Q 023906 153 AELIEGRILVGHALHNDLKALLLT------H-SKKDLRDTSEYQPF-----LK-NGRSKALRHLAAEILAVEIQNGEHCP 219 (275)
Q Consensus 153 ~~~l~~~ilVgHn~~fDl~~L~~~------~-~~~~~iDt~~l~~~-----~~-~~~~~sL~~l~~~~lgi~~~~~~H~A 219 (275)
.+|+++.++||||+.||+.||... . ....++|++.++.. ++ ...+++|+++ +++||++.. ++|+|
T Consensus 106 ~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l-~~~~gi~~~-~~H~A 183 (202)
T PRK09145 106 LAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAI-LKHLDLPVL-GRHDA 183 (202)
T ss_pred HHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHH-HHHcCCCCC-CCCCc
Confidence 999999999999999999999622 1 12357888765421 12 2346899999 699999987 68999
Q ss_pred HHHHHHHHHHHHHhHH
Q 023906 220 IDDARAAMLLYMKNRK 235 (275)
Q Consensus 220 l~DA~ata~L~~~l~~ 235 (275)
++||++|++||.++.+
T Consensus 184 l~DA~ata~l~~~l~~ 199 (202)
T PRK09145 184 LNDAIMAALIFLRLRK 199 (202)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999998865
No 23
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.97 E-value=4.5e-30 Score=223.24 Aligned_cols=155 Identities=20% Similarity=0.228 Sum_probs=128.7
Q ss_pred CCcEEEEEEeecCCCC--------CCeeEEEEEEEEeCCCcEE--EEEEecCCc--cccccceeecCCCHHHHcCCCCHH
Q 023906 79 LTDVVAMDCEMVGISQ--------GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFP 146 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~--------~~iieIaav~v~d~~g~~i--~~~~V~P~~--~i~~~~~~ihGIt~e~l~~a~~~~ 146 (275)
..+||+||+||||++. ++|||||+|.+.+ |.++ |++||+|.. +++++++++||||+++|.++|+|.
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~--~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ 80 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVG--CEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFE 80 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEec--CcChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHH
Confidence 4579999999999752 4899999999976 4544 999999987 689999999999999999999999
Q ss_pred HHHHHHHHHhCC-CEEEEEcchhhHHHhc-------ccCCC-Cceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCC
Q 023906 147 TVQKKVAELIEG-RILVGHALHNDLKALL-------LTHSK-KDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGE 216 (275)
Q Consensus 147 ev~~~l~~~l~~-~ilVgHn~~fDl~~L~-------~~~~~-~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~ 216 (275)
+++.+|.+|+++ ..+|+||+.||+.||. +..|. ..++|+..+++.+ +....++|.++ +++||++..+.+
T Consensus 81 evl~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~-~~~~gi~~~~~~ 159 (207)
T PRK07748 81 ELVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKA-IEEYGKEGTGKH 159 (207)
T ss_pred HHHHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHH-HHHcCCCCCCCC
Confidence 999999999998 4566677899999996 22332 3567777655433 44566899998 799999987568
Q ss_pred CChHHHHHHHHHHHHHhHHH
Q 023906 217 HCPIDDARAAMLLYMKNRKQ 236 (275)
Q Consensus 217 H~Al~DA~ata~L~~~l~~~ 236 (275)
|+|++||++|++||.++..+
T Consensus 160 H~Al~DA~~ta~l~~~l~~~ 179 (207)
T PRK07748 160 HCALDDAMTTYNIFKLVEKD 179 (207)
T ss_pred cChHHHHHHHHHHHHHHHhC
Confidence 99999999999999998766
No 24
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.5e-29 Score=222.22 Aligned_cols=154 Identities=18% Similarity=0.208 Sum_probs=132.3
Q ss_pred CcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC
Q 023906 80 TDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (275)
Q Consensus 80 ~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (275)
.++|+||+||||+++ ++|+|||++ +......|+.+|+|..+|++.+++|||||+++|+++|+|.+++.+|.+|++
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v---~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p~f~ev~~~~~~fi~ 78 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAY---NGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG 78 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEE---cCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHHHHc
Confidence 469999999999983 689999975 322344599999999999999999999999999999999999999999998
Q ss_pred -CCEEEEEcc-hhhHHHhcc-------cCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHH
Q 023906 158 -GRILVGHAL-HNDLKALLL-------THSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAM 227 (275)
Q Consensus 158 -~~ilVgHn~-~fDl~~L~~-------~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata 227 (275)
+.++||||+ .||+.||.. ..+...++||..+++.+ +....++|..+ +.+||++.. ++|+|++||.+|+
T Consensus 79 ~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l-~~~~~~~~~-~aH~Al~Da~~t~ 156 (232)
T PRK06309 79 TDNILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYL-RQVYGFEEN-QAHRALDDVITLH 156 (232)
T ss_pred CCCEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHH-HHHcCCCCC-CCCCcHHHHHHHH
Confidence 479999995 899999962 23445789999887655 44567899999 689999876 6999999999999
Q ss_pred HHHHHhHHHHH
Q 023906 228 LLYMKNRKQWE 238 (275)
Q Consensus 228 ~L~~~l~~~~e 238 (275)
+||.++.+++.
T Consensus 157 ~vl~~l~~~~~ 167 (232)
T PRK06309 157 RVFSALVGDLS 167 (232)
T ss_pred HHHHHHHHHHH
Confidence 99999988764
No 25
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.96 E-value=2.4e-29 Score=209.67 Aligned_cols=157 Identities=31% Similarity=0.484 Sum_probs=133.8
Q ss_pred cEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCC
Q 023906 81 DVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (275)
Q Consensus 81 ~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~ 158 (275)
.||+||+||||+++ ++|+|||+|.+.++.-...|+.||+|..+++++++.+||||++++.++++|.+++.+|.+|+++
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~~l~~ 80 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLKG 80 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHHhcC
Confidence 38999999999984 4899999888865321223999999988999999999999999999999999999999999999
Q ss_pred CEEEEEcc-hhhHHHhcccC-------CC-CceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHH
Q 023906 159 RILVGHAL-HNDLKALLLTH-------SK-KDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLL 229 (275)
Q Consensus 159 ~ilVgHn~-~fDl~~L~~~~-------~~-~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L 229 (275)
.++|+||. .||+.+|+..+ |. ..++|+..+++.+.+...++|.++ +++||++..+.+|+|++||++|++|
T Consensus 81 ~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l-~~~~~~~~~~~~H~A~~Da~~t~~l 159 (169)
T smart00479 81 KILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKL-AERLGLEVIGRAHRALDDARATAKL 159 (169)
T ss_pred CEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHH-HHHCCCCCCCCCcCcHHHHHHHHHH
Confidence 99999999 99999997322 21 347999888765544448999999 6999999885459999999999999
Q ss_pred HHHhHHHHH
Q 023906 230 YMKNRKQWE 238 (275)
Q Consensus 230 ~~~l~~~~e 238 (275)
|.++.+.|.
T Consensus 160 ~~~~~~~~~ 168 (169)
T smart00479 160 FKKLVERLL 168 (169)
T ss_pred HHHHHHHhh
Confidence 999988874
No 26
>PRK06722 exonuclease; Provisional
Probab=99.96 E-value=2.1e-29 Score=227.19 Aligned_cols=157 Identities=18% Similarity=0.251 Sum_probs=130.0
Q ss_pred CCCcEEEEEEeecCCC-----CCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHH
Q 023906 78 SLTDVVAMDCEMVGIS-----QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~-----~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~ 150 (275)
+...|||||+||||.. +++|||||+|.|.++.+.++ |++||+|..+++++++.+||||++||.+||+|.+|+.
T Consensus 3 ~~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl~ 82 (281)
T PRK06722 3 NATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIE 82 (281)
T ss_pred CCCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHHH
Confidence 3578999999999643 26899999999987555666 9999999999999999999999999999999999999
Q ss_pred HHHHHhCCCEEEEEcchhhHHHhccc-------CCC---Cceeehhccch-hhcC--CCCccHHHHHHHHcCCcCCCCCC
Q 023906 151 KVAELIEGRILVGHALHNDLKALLLT-------HSK---KDLRDTSEYQP-FLKN--GRSKALRHLAAEILAVEIQNGEH 217 (275)
Q Consensus 151 ~l~~~l~~~ilVgHn~~fDl~~L~~~-------~~~---~~~iDt~~l~~-~~~~--~~~~sL~~l~~~~lgi~~~~~~H 217 (275)
+|.+|+++.++|+||+.||++||... .|. ..++|+..++. .++. ...++|..+ +++||++..+.+|
T Consensus 83 ef~~fig~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l-~~~lgL~~~g~~H 161 (281)
T PRK06722 83 KFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSA-VEQLGLIWEGKQH 161 (281)
T ss_pred HHHHHHCCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHH-HHHCCCCCCCCCc
Confidence 99999998888888899999999732 222 12466665432 2222 245789999 7999999876789
Q ss_pred ChHHHHHHHHHHHHHhHH
Q 023906 218 CPIDDARAAMLLYMKNRK 235 (275)
Q Consensus 218 ~Al~DA~ata~L~~~l~~ 235 (275)
+|++||.+|+.||.++..
T Consensus 162 rAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 162 RALADAENTANILLKAYS 179 (281)
T ss_pred CcHHHHHHHHHHHHHHhc
Confidence 999999999999999873
No 27
>PRK05168 ribonuclease T; Provisional
Probab=99.96 E-value=1.1e-28 Score=215.26 Aligned_cols=166 Identities=22% Similarity=0.303 Sum_probs=134.7
Q ss_pred CCCCCCCCCCCcEEEEEEeecCCC--CCCeeEEEEEEEEeC-CCcE----EEEEEecC--CccccccceeecCCCHHH-H
Q 023906 70 LTPINDDFSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNK-WGNL----IYDEFVRP--LERVVDFRTRISGIRPRD-L 139 (275)
Q Consensus 70 ~~p~~~~~~~~~~vviD~EtTGl~--~~~iieIaav~v~d~-~g~~----i~~~~V~P--~~~i~~~~~~ihGIt~e~-l 139 (275)
+.|....+....+|+||+||||++ .++|||||+|.+... +|.+ .|++||+| ..++++++++|||||+++ +
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~ 86 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPL 86 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhh
Confidence 344445566778999999999998 459999999999732 3543 39999999 458999999999999986 7
Q ss_pred cCCCCHHHHHHHHHHHhC---------CCEEEEEcchhhHHHhccc----------CCCCceeehhccchhhcCCCCccH
Q 023906 140 RKAKDFPTVQKKVAELIE---------GRILVGHALHNDLKALLLT----------HSKKDLRDTSEYQPFLKNGRSKAL 200 (275)
Q Consensus 140 ~~a~~~~ev~~~l~~~l~---------~~ilVgHn~~fDl~~L~~~----------~~~~~~iDt~~l~~~~~~~~~~sL 200 (275)
++++++.+++.++.+|+. +.++||||+.||+.||... ++...++||..+++.+.+ ..+|
T Consensus 87 ~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~--~~~L 164 (211)
T PRK05168 87 RGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG--QTVL 164 (211)
T ss_pred hcCCChHHHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC--CCCH
Confidence 899999999988888764 7899999999999999622 223358999988875532 3579
Q ss_pred HHHHHHHcCCcCCC-CCCChHHHHHHHHHHHHHhHHHHH
Q 023906 201 RHLAAEILAVEIQN-GEHCPIDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 201 ~~l~~~~lgi~~~~-~~H~Al~DA~ata~L~~~l~~~~e 238 (275)
..+ ++++|++... .+|+|++||.+|++||.++..++.
T Consensus 165 ~~l-~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~ 202 (211)
T PRK05168 165 AKA-CQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWK 202 (211)
T ss_pred HHH-HHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 998 6899999752 589999999999999999988864
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=99.96 E-value=8.8e-29 Score=212.29 Aligned_cols=154 Identities=23% Similarity=0.277 Sum_probs=123.3
Q ss_pred cEEEEEEeecCCC--CCCeeEEEEEEEEeC-CCcE----EEEEEecC--CccccccceeecCCCHHH-HcCCCCHHHHHH
Q 023906 81 DVVAMDCEMVGIS--QGNKSALGRVSLVNK-WGNL----IYDEFVRP--LERVVDFRTRISGIRPRD-LRKAKDFPTVQK 150 (275)
Q Consensus 81 ~~vviD~EtTGl~--~~~iieIaav~v~d~-~g~~----i~~~~V~P--~~~i~~~~~~ihGIt~e~-l~~a~~~~ev~~ 150 (275)
.+|+||+||||++ .++|||||+|.|.+. +|.+ .|+++|+| ..+|++.+++|||||+++ +.+++...+++.
T Consensus 6 ~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~~~~~ 85 (189)
T cd06134 6 LPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEKEALK 85 (189)
T ss_pred eeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchHHHHH
Confidence 4799999999998 458999999999853 4543 39999999 468999999999999987 567776666666
Q ss_pred HHHHHh---------CCCEEEEEcchhhHHHhccc----------CCCCceeehhccchhhcCCCCccHHHHHHHHcCCc
Q 023906 151 KVAELI---------EGRILVGHALHNDLKALLLT----------HSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVE 211 (275)
Q Consensus 151 ~l~~~l---------~~~ilVgHn~~fDl~~L~~~----------~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~ 211 (275)
+|..++ ++.++||||+.||+.||+.. ++...++||..+.+.+.+ .++|..+ +++||++
T Consensus 86 ~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~--~~~L~~l-~~~~gi~ 162 (189)
T cd06134 86 EIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG--QTVLAKA-CQAAGIE 162 (189)
T ss_pred HHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC--CCcHHHH-HHHCCCC
Confidence 655554 26899999999999999721 122357999998876533 4579998 6899998
Q ss_pred CC-CCCCChHHHHHHHHHHHHHhHHHH
Q 023906 212 IQ-NGEHCPIDDARAAMLLYMKNRKQW 237 (275)
Q Consensus 212 ~~-~~~H~Al~DA~ata~L~~~l~~~~ 237 (275)
+. .++|+|++||++|++||.++.++|
T Consensus 163 ~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 163 FDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred CCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 64 358999999999999999999887
No 29
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.96 E-value=1.8e-28 Score=212.11 Aligned_cols=161 Identities=19% Similarity=0.228 Sum_probs=131.4
Q ss_pred CCCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeC-CCcEE----EEEEecCC--ccccccceeecCCCHH-HHcCCCCH
Q 023906 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNK-WGNLI----YDEFVRPL--ERVVDFRTRISGIRPR-DLRKAKDF 145 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~-~g~~i----~~~~V~P~--~~i~~~~~~ihGIt~e-~l~~a~~~ 145 (275)
++....+||||+||||+++ ++|+|||+|.|... .|.+. |+++|+|. .+|++.+++|||||++ ++.+++++
T Consensus 4 ~~~~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~~~ 83 (200)
T TIGR01298 4 RFRGYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAVSE 83 (200)
T ss_pred hhcCCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCcch
Confidence 4456679999999999994 58999999999743 45543 88999984 5899999999999976 68999999
Q ss_pred HHHHHHHHHHh---------CCCEEEEEcchhhHHHhccc----------CCCCceeehhccchhhcCCCCccHHHHHHH
Q 023906 146 PTVQKKVAELI---------EGRILVGHALHNDLKALLLT----------HSKKDLRDTSEYQPFLKNGRSKALRHLAAE 206 (275)
Q Consensus 146 ~ev~~~l~~~l---------~~~ilVgHn~~fDl~~L~~~----------~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~ 206 (275)
.+++.++..++ ++.++||||+.||+.||+.. ++...++||..+++.+. ..++|..+ ++
T Consensus 84 ~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~--~~~~L~~l-~~ 160 (200)
T TIGR01298 84 YEALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAY--GQTVLAKA-CQ 160 (200)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHc--CcccHHHH-HH
Confidence 88888888776 67899999999999999722 12235899998887553 23579999 68
Q ss_pred HcCCcCC-CCCCChHHHHHHHHHHHHHhHHHHHH
Q 023906 207 ILAVEIQ-NGEHCPIDDARAAMLLYMKNRKQWEK 239 (275)
Q Consensus 207 ~lgi~~~-~~~H~Al~DA~ata~L~~~l~~~~e~ 239 (275)
+||++.. ..+|+|++||.+|++||..+..++.+
T Consensus 161 ~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~ 194 (200)
T TIGR01298 161 AAGXDFDSTQAHSALYDTEKTAELFCEIVNRWKR 194 (200)
T ss_pred HcCCCccccchhhhHHhHHHHHHHHHHHHHHHHH
Confidence 9999864 25899999999999999999888753
No 30
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=4.3e-28 Score=247.36 Aligned_cols=159 Identities=27% Similarity=0.388 Sum_probs=138.8
Q ss_pred CCCCcEEEEEEeecCCC-CCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHH
Q 023906 77 FSLTDVVAMDCEMVGIS-QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (275)
Q Consensus 77 ~~~~~~vviD~EtTGl~-~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~ 153 (275)
.+..+|||||+||||++ .++|||||+|.+.+ |.++ |.++|+|..+|+++++.+||||++||.++|+|++|+.+|.
T Consensus 4 ~~~~~~vvvD~ETTGl~~~d~IIeIgaV~v~~--g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~~~ 81 (820)
T PRK07246 4 KKLRKYAVVDLEATGAGPNASIIQVGIVIIEG--GEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIY 81 (820)
T ss_pred ccCCCEEEEEEecCCcCCCCeEEEEEEEEEEC--CEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHHHHHH
Confidence 34678999999999998 56999999999876 6665 8999999999999999999999999999999999999999
Q ss_pred HHhCCCEEEEEcchhhHHHhccc-----C-CCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHH
Q 023906 154 ELIEGRILVGHALHNDLKALLLT-----H-SKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARAA 226 (275)
Q Consensus 154 ~~l~~~ilVgHn~~fDl~~L~~~-----~-~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at 226 (275)
+|+++.++||||+.||+.||... + ....++||..+++.+ +...+++|.+| +++||++.. ++|+|++||++|
T Consensus 82 ~~l~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L-~~~lgl~~~-~~H~Al~DA~at 159 (820)
T PRK07246 82 DLIEDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHL-SRELNIDLA-DAHTAIADARAT 159 (820)
T ss_pred HHhCCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHH-HHHcCCCCC-CCCCHHHHHHHH
Confidence 99999999999999999999621 1 124578999887654 55678999999 689999987 689999999999
Q ss_pred HHHHHHhHHHHHH
Q 023906 227 MLLYMKNRKQWEK 239 (275)
Q Consensus 227 a~L~~~l~~~~e~ 239 (275)
++||..+..+...
T Consensus 160 a~L~~~l~~~l~~ 172 (820)
T PRK07246 160 AELFLKLLQKIES 172 (820)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999876543
No 31
>PRK07883 hypothetical protein; Validated
Probab=99.96 E-value=5.8e-28 Score=237.15 Aligned_cols=160 Identities=21% Similarity=0.254 Sum_probs=140.7
Q ss_pred CCCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHH
Q 023906 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~ 151 (275)
......||+||+||||+++ ++|+|||+|.+.+ |.++ |+.+|+|..+++++++.+||||+++|.++++|.+++.+
T Consensus 11 ~~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~--g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~ 88 (557)
T PRK07883 11 PLRDVTFVVVDLETTGGSPAGDAITEIGAVKVRG--GEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA 88 (557)
T ss_pred CCcCCCEEEEEEecCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 3445789999999999985 5999999999975 6666 99999999999999999999999999999999999999
Q ss_pred HHHHhCCCEEEEEcchhhHHHhc-------ccCCCCceeehhccchhh-c--CCCCccHHHHHHHHcCCcCCCCCCChHH
Q 023906 152 VAELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFL-K--NGRSKALRHLAAEILAVEIQNGEHCPID 221 (275)
Q Consensus 152 l~~~l~~~ilVgHn~~fDl~~L~-------~~~~~~~~iDt~~l~~~~-~--~~~~~sL~~l~~~~lgi~~~~~~H~Al~ 221 (275)
|.+|+++.++||||+.||+.||. +.++...++||..+++.+ + ...+++|.++ +++||++.. ++|+|++
T Consensus 89 f~~fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L-~~~~gi~~~-~~H~Al~ 166 (557)
T PRK07883 89 FLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTL-ARLFGATTT-PTHRALD 166 (557)
T ss_pred HHHHhcCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHH-HHHCCcccC-CCCCHHH
Confidence 99999999999999999999996 344555689999887544 3 4578899999 689999987 6899999
Q ss_pred HHHHHHHHHHHhHHHHHH
Q 023906 222 DARAAMLLYMKNRKQWEK 239 (275)
Q Consensus 222 DA~ata~L~~~l~~~~e~ 239 (275)
||.+|++||.++..++..
T Consensus 167 DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 167 DARATVDVLHGLIERLGN 184 (557)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 999999999999888754
No 32
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.96 E-value=4.2e-29 Score=251.38 Aligned_cols=164 Identities=26% Similarity=0.322 Sum_probs=147.5
Q ss_pred CCCCCCCCCCcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHH
Q 023906 71 TPINDDFSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (275)
Q Consensus 71 ~p~~~~~~~~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ 146 (275)
.|.........|||||+||||++ .++|||||++.+.+ |++| |+.|++|..+++...+++||||++||.++++..
T Consensus 412 N~~d~~l~datyVVfDiETTGLs~~~d~iIE~aAvKikn--g~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~ 489 (1444)
T COG2176 412 NPDDQKLDDATYVVFDIETTGLSPVYDEIIEIAAVKIKN--GRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIE 489 (1444)
T ss_pred CccccccccccEEEEEeecCCcCcccchhhhheeeeeeC--CcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHH
Confidence 34455667788999999999999 46999999999988 8888 999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCCEEEEEcchhhHHHhccc-------CCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCC
Q 023906 147 TVQKKVAELIEGRILVGHALHNDLKALLLT-------HSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHC 218 (275)
Q Consensus 147 ev~~~l~~~l~~~ilVgHn~~fDl~~L~~~-------~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~ 218 (275)
+|+.+|.+|++++++||||++||++||+.. .-.+.+|||+.+++.+ |..++++|..+ |+.||+.++ .+||
T Consensus 490 ~vL~kf~~~~~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l-~kk~~v~le-~hHR 567 (1444)
T COG2176 490 EVLEKFREFIGDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTL-CKKLGVELE-RHHR 567 (1444)
T ss_pred HHHHHHHHHhcCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHH-HHHhCccHH-Hhhh
Confidence 999999999999999999999999999722 2235689999999887 67899999999 799999997 6999
Q ss_pred hHHHHHHHHHHHHHhHHHHH
Q 023906 219 PIDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 219 Al~DA~ata~L~~~l~~~~e 238 (275)
|.+||.||+.||..+++...
T Consensus 568 A~yDaeat~~vf~~f~~~~k 587 (1444)
T COG2176 568 ADYDAEATAKVFFVFLKDLK 587 (1444)
T ss_pred hhhhHHHHHHHHHHHHHHHH
Confidence 99999999999999877654
No 33
>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=99.96 E-value=2.7e-28 Score=207.22 Aligned_cols=146 Identities=16% Similarity=0.152 Sum_probs=117.8
Q ss_pred EEEEEEeecCCC---CCCeeEEEEEEEEeCC---C--------cEE--EEEEecCCccccccceeecCCCHHHHcCCCCH
Q 023906 82 VVAMDCEMVGIS---QGNKSALGRVSLVNKW---G--------NLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDF 145 (275)
Q Consensus 82 ~vviD~EtTGl~---~~~iieIaav~v~d~~---g--------~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~ 145 (275)
||+||+||||++ .++|+|||+|.|.++. + +++ |+++|+|..+|++.++.|||||++++.++++|
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~~~ 80 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCCCc
Confidence 689999999997 3599999999987531 1 123 88999999999999999999999999999988
Q ss_pred HH-HHHHHHHHhC----CCEEEEEcc-hhhHHHhcc-------cCC-CCceeehhccchhhcCCCCccHHHHHHHHcCCc
Q 023906 146 PT-VQKKVAELIE----GRILVGHAL-HNDLKALLL-------THS-KKDLRDTSEYQPFLKNGRSKALRHLAAEILAVE 211 (275)
Q Consensus 146 ~e-v~~~l~~~l~----~~ilVgHn~-~fDl~~L~~-------~~~-~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~ 211 (275)
.+ +++.+.+|++ +.+|||||+ .||++||+. ..+ ...++||+.+++.+.. +|.+|+..+||++
T Consensus 81 ~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~----~L~~l~~~~~~~~ 156 (177)
T cd06136 81 DSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ----SLGSLYKRLFGQE 156 (177)
T ss_pred cHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh----hHHHHHHHHhCCC
Confidence 64 5666666663 458999998 899999962 222 2346798877765532 8999965579999
Q ss_pred CCCCCCChHHHHHHHHHHHHH
Q 023906 212 IQNGEHCPIDDARAAMLLYMK 232 (275)
Q Consensus 212 ~~~~~H~Al~DA~ata~L~~~ 232 (275)
.. ++|+|++||.+|+++|.+
T Consensus 157 ~~-~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 157 PK-NSHTAEGDVLALLKCALH 176 (177)
T ss_pred cc-cccchHHHHHHHHHHHhh
Confidence 87 699999999999999874
No 34
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2.5e-27 Score=244.99 Aligned_cols=156 Identities=28% Similarity=0.386 Sum_probs=138.2
Q ss_pred CCcEEEEEEeecCCCC---CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHH
Q 023906 79 LTDVVAMDCEMVGISQ---GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~---~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~ 153 (275)
..+|||||+||||+++ ++|||||+|.+.+ |+++ |++||+|..+|+++++.+||||+++|.++|+|.+++.+|.
T Consensus 2 ~~~~vvvD~ETTG~~p~~~d~IIeigav~v~~--~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~ 79 (928)
T PRK08074 2 SKRFVVVDLETTGNSPKKGDKIIQIAAVVVED--GEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIV 79 (928)
T ss_pred CCCEEEEEEeCCCCCCCCCCcEEEEEEEEEEC--CEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHH
Confidence 5789999999999873 4899999999975 6666 9999999999999999999999999999999999999999
Q ss_pred HHhCCCEEEEEcchhhHHHhcc-------cCCCCceeehhccchh-hcCCCCccHHHHHHHHcCCcCCCCCCChHHHHHH
Q 023906 154 ELIEGRILVGHALHNDLKALLL-------THSKKDLRDTSEYQPF-LKNGRSKALRHLAAEILAVEIQNGEHCPIDDARA 225 (275)
Q Consensus 154 ~~l~~~ilVgHn~~fDl~~L~~-------~~~~~~~iDt~~l~~~-~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~a 225 (275)
.|++++++||||+.||+.||+. ..+...++||..+.+. ++...+++|.+| +++||++.. ++|+|++||++
T Consensus 80 ~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l-~~~l~i~~~-~~H~Al~DA~a 157 (928)
T PRK08074 80 ELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDL-SEELGLEHD-QPHRADSDAEV 157 (928)
T ss_pred HHhCCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHH-HHhCCCCCC-CCCChHHHHHH
Confidence 9999999999999999999972 2234568999988765 466778999999 699999987 79999999999
Q ss_pred HHHHHHHhHHHHH
Q 023906 226 AMLLYMKNRKQWE 238 (275)
Q Consensus 226 ta~L~~~l~~~~e 238 (275)
|+.||.++..++.
T Consensus 158 ta~l~~~l~~~~~ 170 (928)
T PRK08074 158 TAELFLQLLNKLE 170 (928)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999977654
No 35
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.95 E-value=2.6e-27 Score=199.20 Aligned_cols=151 Identities=23% Similarity=0.290 Sum_probs=127.4
Q ss_pred EEEEEEeecCCCC-------CCeeEEEEEEEEeCCCcEE--EEEEecCCc--cccccceeecCCCHHHHcCCCCHHHHHH
Q 023906 82 VVAMDCEMVGISQ-------GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQK 150 (275)
Q Consensus 82 ~vviD~EtTGl~~-------~~iieIaav~v~d~~g~~i--~~~~V~P~~--~i~~~~~~ihGIt~e~l~~a~~~~ev~~ 150 (275)
||+||+||||+++ ++|+|||+|.+....+.++ |++||+|.. .++++++++||||++++.++++|.+|+.
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 6899999999984 6899999888865433243 999999998 8999999999999999999999999999
Q ss_pred HHHHHhCCC--EEEEEcchhhHHHhcc----------cCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCC
Q 023906 151 KVAELIEGR--ILVGHALHNDLKALLL----------THSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEH 217 (275)
Q Consensus 151 ~l~~~l~~~--ilVgHn~~fDl~~L~~----------~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H 217 (275)
+|.+|+++. .+++|+..||+.+|.. ......++|+..+++.. +....++|.++ +.+||++..+..|
T Consensus 81 ~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l-~~~~gi~~~~~~H 159 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKA-LEYLGLEFEGRHH 159 (176)
T ss_pred HHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHH-HHHCCCCCCCCCc
Confidence 999999986 6666677999887641 22335689998887655 34468999999 6999999986699
Q ss_pred ChHHHHHHHHHHHHHh
Q 023906 218 CPIDDARAAMLLYMKN 233 (275)
Q Consensus 218 ~Al~DA~ata~L~~~l 233 (275)
+|++||++|++||.++
T Consensus 160 ~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 160 RGLDDARNIARILKRL 175 (176)
T ss_pred CcHHHHHHHHHHHHHh
Confidence 9999999999999876
No 36
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.95 E-value=3.9e-27 Score=246.04 Aligned_cols=162 Identities=25% Similarity=0.358 Sum_probs=142.8
Q ss_pred CCCC-CCCcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHH
Q 023906 74 NDDF-SLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (275)
Q Consensus 74 ~~~~-~~~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev 148 (275)
+.+. ...+||+||+||||++ .++|+|||+|.+.+ |.++ |+.||+|..+++++++++||||+++|++++++.++
T Consensus 183 ~~~l~~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~--g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~ev 260 (1213)
T TIGR01405 183 DQKLLDDATYVVFDIETTGLSPQYDEIIEFGAVKVKN--GRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEV 260 (1213)
T ss_pred ccccccCCcEEEEEeEecCCCCCCCeEEEEEEEEEEC--CeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHH
Confidence 3344 5678999999999998 46999999999986 6666 99999999999999999999999999999999999
Q ss_pred HHHHHHHhCCCEEEEEcchhhHHHhccc-------CCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChH
Q 023906 149 QKKVAELIEGRILVGHALHNDLKALLLT-------HSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPI 220 (275)
Q Consensus 149 ~~~l~~~l~~~ilVgHn~~fDl~~L~~~-------~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al 220 (275)
+.+|.+|+++++|||||+.||+.||+.. .....++||+.+++.+ +..+.++|..| +++||++.. ++|+|+
T Consensus 261 l~~f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~L-ak~lgi~~~-~~HrAl 338 (1213)
T TIGR01405 261 LEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNI-CKKLGVDLD-DHHRAD 338 (1213)
T ss_pred HHHHHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHH-HHHcCCCCC-CCcCHH
Confidence 9999999999999999999999999722 1234689999888765 56788999999 688999998 599999
Q ss_pred HHHHHHHHHHHHhHHHHHH
Q 023906 221 DDARAAMLLYMKNRKQWEK 239 (275)
Q Consensus 221 ~DA~ata~L~~~l~~~~e~ 239 (275)
+||.+|++||..+.+++++
T Consensus 339 ~DA~aTa~I~~~ll~~l~~ 357 (1213)
T TIGR01405 339 YDAEATAKVFKVMVEQLKE 357 (1213)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999887764
No 37
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=4.5e-27 Score=216.94 Aligned_cols=153 Identities=18% Similarity=0.246 Sum_probs=128.9
Q ss_pred CCCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHH
Q 023906 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~ 151 (275)
......||+||+||||+++ ++|||||+|.+.. +|.++ |++||+|...+.+ ..|||||+++|.++|+|.+++.+
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~-~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTA-DGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEc-CCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCCCHHHHHHH
Confidence 4455789999999999994 5899999999972 25554 9999999875444 47999999999999999999999
Q ss_pred HHHHhCCCEEEEEcchhhHHHhcccC----------------------------------CCCceeehhccchhh-cCCC
Q 023906 152 VAELIEGRILVGHALHNDLKALLLTH----------------------------------SKKDLRDTSEYQPFL-KNGR 196 (275)
Q Consensus 152 l~~~l~~~ilVgHn~~fDl~~L~~~~----------------------------------~~~~~iDt~~l~~~~-~~~~ 196 (275)
|.+|+++++|||||+.||++||...+ ....++||+.+.+.+ +...
T Consensus 119 l~~fL~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~ 198 (377)
T PRK05601 119 LDRLIDGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALD 198 (377)
T ss_pred HHHHhCCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCC
Confidence 99999999999999999999986321 113589999988765 5678
Q ss_pred CccHHHHHHHHcCCcC----------CCCCCChH--HHHHHHHHHHHHh
Q 023906 197 SKALRHLAAEILAVEI----------QNGEHCPI--DDARAAMLLYMKN 233 (275)
Q Consensus 197 ~~sL~~l~~~~lgi~~----------~~~~H~Al--~DA~ata~L~~~l 233 (275)
+++|..| +++||++. + ..|+|| +||+.++.||..+
T Consensus 199 ~~rL~~L-a~~lGi~~p~~~A~~~Ra~-~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 199 DIRIRGV-AHTLGLDAPAAEASVERAQ-VPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred CCCHHHH-HHHhCCCCCchhhhhhhhc-CChhhhhhHHHHHHHHHHHHh
Confidence 8999999 68999998 3 368888 6999999999876
No 38
>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=6.3e-27 Score=240.49 Aligned_cols=155 Identities=26% Similarity=0.347 Sum_probs=136.8
Q ss_pred cEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHh
Q 023906 81 DVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (275)
Q Consensus 81 ~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (275)
+||+||+||||++ .++|||||+|.+.+ |+++ |+++|+|..+|+++++++||||++++.++|+|.+++.+|.+|+
T Consensus 1 ~~vvvD~ETTG~~~~~~~IIeig~v~v~~--~~i~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~~l 78 (850)
T TIGR01407 1 RYAVVDLETTGTQLSFDKIIQIGIVVVED--GEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLL 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEEC--CEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHHHh
Confidence 4899999999998 46999999999865 6666 9999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEcchhhHHHhcc-------cCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHH
Q 023906 157 EGRILVGHALHNDLKALLL-------THSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAML 228 (275)
Q Consensus 157 ~~~ilVgHn~~fDl~~L~~-------~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~ 228 (275)
++.++||||+.||+.||.. ......++||..+.+.+ +...+++|.+| +++||++.. ++|+|++||.+|++
T Consensus 79 ~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l-~~~~gi~~~-~~H~Al~DA~ata~ 156 (850)
T TIGR01407 79 EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSEL-SEALGLTHE-NPHRADSDAQATAE 156 (850)
T ss_pred CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHH-HHHCCCCCC-CCCChHHHHHHHHH
Confidence 9999999999999999972 22234689999887655 55678999999 689999987 69999999999999
Q ss_pred HHHHhHHHHHH
Q 023906 229 LYMKNRKQWEK 239 (275)
Q Consensus 229 L~~~l~~~~e~ 239 (275)
||.++..++..
T Consensus 157 l~~~l~~~~~~ 167 (850)
T TIGR01407 157 LLLLLFEKMEK 167 (850)
T ss_pred HHHHHHHHHHh
Confidence 99999776543
No 39
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=3e-26 Score=208.72 Aligned_cols=172 Identities=16% Similarity=0.179 Sum_probs=130.3
Q ss_pred CCCCCcEEEEEEeecCCCC--CCeeEEEEEEEEe-CCCcE---E--EEEEecCCccccccceeecCCCHHHHcCCCCHHH
Q 023906 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVN-KWGNL---I--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPT 147 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~--~~iieIaav~v~d-~~g~~---i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~e 147 (275)
......+|+||+||||+++ ++|||||+|.+.. .+|.+ + |+.|++|..+|++.++.|||||++|+.+++...+
T Consensus 33 ~~~~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~~ 112 (294)
T PRK09182 33 GEFVRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPA 112 (294)
T ss_pred CCCCCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcHH
Confidence 4456789999999999994 6999999999973 23543 2 8899999999999999999999999999886543
Q ss_pred HHHHHHHHhC-CCEEEEEcchhhHHHhccc---CCCCceeehhccchh-hcCCCCccHHHHHHHHcCCcCCCCCCChHHH
Q 023906 148 VQKKVAELIE-GRILVGHALHNDLKALLLT---HSKKDLRDTSEYQPF-LKNGRSKALRHLAAEILAVEIQNGEHCPIDD 222 (275)
Q Consensus 148 v~~~l~~~l~-~~ilVgHn~~fDl~~L~~~---~~~~~~iDt~~l~~~-~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~D 222 (275)
.|..|++ +.+|||||+.||+.||... ++...+.|++..... .+...+++|..| +.+||. .. ++|+|++|
T Consensus 113 ---~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~L-a~~~g~-~~-~aHrAl~D 186 (294)
T PRK09182 113 ---AVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYL-AGQAGF-FH-EGHRAVDD 186 (294)
T ss_pred ---HHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHH-HHHcCC-CC-CCcChHHH
Confidence 4667776 4699999999999999733 333446677643322 234578999999 689993 33 68999999
Q ss_pred HHHHHHHHHHhHHHHH-HHHHHHHHHHHHhhh
Q 023906 223 ARAAMLLYMKNRKQWE-KSVKDQTRLEQKQKN 253 (275)
Q Consensus 223 A~ata~L~~~l~~~~e-~~l~~~~~~~~k~~~ 253 (275)
|.+|++||..++.... ..+.+++....+.+.
T Consensus 187 a~Ata~ll~~~l~~~~~~~l~~Ll~~~~~~~~ 218 (294)
T PRK09182 187 CQALLELLARPLPETGQPPLAELLEASRRSRV 218 (294)
T ss_pred HHHHHHHHHHHHhhcCCcCHHHHHHHhccCee
Confidence 9999999998765433 345566665544444
No 40
>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=99.94 E-value=2.9e-26 Score=187.42 Aligned_cols=147 Identities=27% Similarity=0.341 Sum_probs=126.6
Q ss_pred EEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCC
Q 023906 83 VAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (275)
Q Consensus 83 vviD~EtTGl~--~~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~ 158 (275)
|+|||||||++ .++|+|||+|.+.+. ++++ |+.||+|...+.++++.+|||+++++.+++++.+++.+|.+|+++
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~-~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~~l~~ 79 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGG-IEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECC-cChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCCCHHHHHHHHHHHHCC
Confidence 68999999999 469999998888643 4444 999999999999999999999999999999999999999999999
Q ss_pred CEEEEEcchhhHHHhccc-------CCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHH
Q 023906 159 RILVGHALHNDLKALLLT-------HSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLY 230 (275)
Q Consensus 159 ~ilVgHn~~fDl~~L~~~-------~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~ 230 (275)
.++||||+.||+.+|+.. .....++|++.+++.+ +....++|..+.+.++|++.. .+|+|++||++|++||
T Consensus 80 ~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE-GAHRALADALATAELL 158 (159)
T ss_pred CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC-CCCCcHHHHHHHHHHh
Confidence 999999999999999732 3456799999877544 556677888875678998876 6999999999999998
Q ss_pred H
Q 023906 231 M 231 (275)
Q Consensus 231 ~ 231 (275)
.
T Consensus 159 ~ 159 (159)
T cd06127 159 L 159 (159)
T ss_pred C
Confidence 3
No 41
>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=99.94 E-value=8.8e-27 Score=198.83 Aligned_cols=145 Identities=20% Similarity=0.182 Sum_probs=116.5
Q ss_pred EEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE--EEEEecCCc--cccccceeecCCCHHHHcC-CCCHHHHHHHHHHH
Q 023906 83 VAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRK-AKDFPTVQKKVAEL 155 (275)
Q Consensus 83 vviD~EtTGl~--~~~iieIaav~v~d~~g~~i--~~~~V~P~~--~i~~~~~~ihGIt~e~l~~-a~~~~ev~~~l~~~ 155 (275)
++||+||||++ .++|||||+|.+.+ ++.++ |+.+|+|.. .+++.+..+||||+++|.+ ++++.+++.+|..|
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~-~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~~~ 79 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDE-NFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRL 79 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECC-CCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHHHH
Confidence 58999999998 45899999988753 33444 889999875 5677899999999999999 89999999999999
Q ss_pred hC--CCEEEEEc-chhhHHHhcccCC-------------CCceeehhccchhh----c----------CCCCccHHHHHH
Q 023906 156 IE--GRILVGHA-LHNDLKALLLTHS-------------KKDLRDTSEYQPFL----K----------NGRSKALRHLAA 205 (275)
Q Consensus 156 l~--~~ilVgHn-~~fDl~~L~~~~~-------------~~~~iDt~~l~~~~----~----------~~~~~sL~~l~~ 205 (275)
++ +.++|||| +.||+.||+..+. ....+||..+.+.+ + +..+++|+++ +
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l-~ 158 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDL-A 158 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHH-H
Confidence 95 67999997 7999999972211 12346777554432 1 2356889999 6
Q ss_pred HHcCCcCCCCCCChHHHHHHHHHHH
Q 023906 206 EILAVEIQNGEHCPIDDARAAMLLY 230 (275)
Q Consensus 206 ~~lgi~~~~~~H~Al~DA~ata~L~ 230 (275)
++||++.. ++|+|++||++|++|+
T Consensus 159 ~~~gi~~~-~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 159 QANGIEHS-NAHDALSDVEATIALA 182 (183)
T ss_pred HHCCCCcc-ccccHHHHHHHHHHHh
Confidence 89999986 6999999999999986
No 42
>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=7.7e-28 Score=197.21 Aligned_cols=147 Identities=27% Similarity=0.416 Sum_probs=124.6
Q ss_pred EEEEEeecCCCC--CCeeEEEEEEEEeCCC--cEEEEEEecCCcc--ccccceeecCCCHHHHcCCCCHHHHHHHHHHHh
Q 023906 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWG--NLIYDEFVRPLER--VVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (275)
Q Consensus 83 vviD~EtTGl~~--~~iieIaav~v~d~~g--~~i~~~~V~P~~~--i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (275)
|+|||||||+++ ++|+|||+|.+.+... ...|++||+|... ++++++.+||||.++|.+++++.+++.+|.+|+
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~~~ 80 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEEFL 80 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhhhh
Confidence 799999999995 6999999999987553 3449999999997 999999999999999999999999999999999
Q ss_pred C-CCEEEEEcchhhHHHhc--------ccCC-CCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHHHH
Q 023906 157 E-GRILVGHALHNDLKALL--------LTHS-KKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDARA 225 (275)
Q Consensus 157 ~-~~ilVgHn~~fDl~~L~--------~~~~-~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~a 225 (275)
. +.++||||+.||..++. ..+| ...++|+..+.+.. +....++|+.+ ++.||++..+.+|+|++||++
T Consensus 81 ~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l-~~~~~~~~~~~~H~Al~Da~~ 159 (164)
T PF00929_consen 81 KKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDL-AEYFGIPFDGTAHDALDDARA 159 (164)
T ss_dssp HHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHH-HHHTTSSSTSTTTSHHHHHHH
T ss_pred hcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHH-HHHcCCCCCCCCcChHHHHHH
Confidence 8 89999999999987764 2233 23578888776543 33334899999 799999998557999999999
Q ss_pred HHHHH
Q 023906 226 AMLLY 230 (275)
Q Consensus 226 ta~L~ 230 (275)
|++||
T Consensus 160 t~~l~ 164 (164)
T PF00929_consen 160 TAELF 164 (164)
T ss_dssp HHHHH
T ss_pred HhCcC
Confidence 99997
No 43
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.93 E-value=2.3e-25 Score=197.59 Aligned_cols=154 Identities=25% Similarity=0.315 Sum_probs=134.1
Q ss_pred CcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE---EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHH
Q 023906 80 TDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (275)
Q Consensus 80 ~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i---~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (275)
.++|+||+||||++ .++|||||+|.+.+ +.++ |+.||+|..+++++...+||||.+++.++|.|.++..++.+
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~--~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~~ 90 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLED--GRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFLD 90 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEEC--CeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHHH
Confidence 68999999999998 56999999999998 5444 88999998899999999999999999999999999999999
Q ss_pred HhCC-CEEEEEcchhhHHHhc-------ccCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCC-CCCCChHHHHH
Q 023906 155 LIEG-RILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQ-NGEHCPIDDAR 224 (275)
Q Consensus 155 ~l~~-~ilVgHn~~fDl~~L~-------~~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~-~~~H~Al~DA~ 224 (275)
|+++ .++||||+.||+.||. ...+...++||..+.+.. ++...++|+.| +.++|++.. ...|+|+.||.
T Consensus 91 ~i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l-~~~~gi~~~~~~~H~Al~Da~ 169 (243)
T COG0847 91 FIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDAL-AERLGIDRNPFHPHRALFDAL 169 (243)
T ss_pred HHCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHH-HHHcCCCcCCcCCcchHHHHH
Confidence 9998 9999999999999996 223334577998887655 44488999999 689999943 14799999999
Q ss_pred HHHHHHHHhHHH
Q 023906 225 AAMLLYMKNRKQ 236 (275)
Q Consensus 225 ata~L~~~l~~~ 236 (275)
+++.+|..+...
T Consensus 170 ~~a~~~~~~~~~ 181 (243)
T COG0847 170 ALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHhc
Confidence 999999998774
No 44
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.93 E-value=4.8e-25 Score=213.68 Aligned_cols=156 Identities=17% Similarity=0.225 Sum_probs=128.1
Q ss_pred CCcEEEEEEeecCCCC-----CCeeEEEEEEEEeCCCcEE--EEEEecCCc--cccccceeecCCCHHHHcCCCCHHHHH
Q 023906 79 LTDVVAMDCEMVGISQ-----GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~-----~~iieIaav~v~d~~g~~i--~~~~V~P~~--~i~~~~~~ihGIt~e~l~~a~~~~ev~ 149 (275)
...|||||+||||+++ ++|||||+|.|...+|+++ |++||+|.. +++++++++||||++||++||+|.+|+
T Consensus 55 ~d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl 134 (582)
T PTZ00315 55 FDAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVY 134 (582)
T ss_pred CCeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHH
Confidence 5789999999999872 5899999999854457776 999999987 799999999999999999999999999
Q ss_pred HHHHHHhCCC----------EEEEEcchhhHH-Hhc--------ccCC--CCceeehh-ccchhh-c-----------CC
Q 023906 150 KKVAELIEGR----------ILVGHALHNDLK-ALL--------LTHS--KKDLRDTS-EYQPFL-K-----------NG 195 (275)
Q Consensus 150 ~~l~~~l~~~----------ilVgHn~~fDl~-~L~--------~~~~--~~~~iDt~-~l~~~~-~-----------~~ 195 (275)
.+|.+|+++. ++|+||+.||+. ||. ...| ...++|.. .+...+ + ..
T Consensus 135 ~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~~ 214 (582)
T PTZ00315 135 CEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPPL 214 (582)
T ss_pred HHHHHHHhccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCcccccccccccccc
Confidence 9999999643 699999999995 773 1222 23466653 233332 2 23
Q ss_pred CCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHHhHH
Q 023906 196 RSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRK 235 (275)
Q Consensus 196 ~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~l~~ 235 (275)
..++|.++ ++.+|+++.+.+|+|++||++|++||.++..
T Consensus 215 ~~~~L~~a-l~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~ 253 (582)
T PTZ00315 215 GPSDMPDM-LQMLGLPLQGRHHSGIDDCRNIAAVLCELLR 253 (582)
T ss_pred CCcCHHHH-HHHCCCCCCCCCcCcHHHHHHHHHHHHHHHH
Confidence 56899999 6999999997899999999999999999864
No 45
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.91 E-value=1e-23 Score=202.65 Aligned_cols=167 Identities=16% Similarity=0.136 Sum_probs=128.4
Q ss_pred CCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE---EEEEecCCc--cccccceeecCCCHHHHcC-CCCHHHHH
Q 023906 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI---YDEFVRPLE--RVVDFRTRISGIRPRDLRK-AKDFPTVQ 149 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i---~~~~V~P~~--~i~~~~~~ihGIt~e~l~~-a~~~~ev~ 149 (275)
+..+|||+|+||||+++ ++|+|||+|.+.+ ++.++ |..||+|.. .+++.++.|||||++++.+ +.+..+++
T Consensus 4 ~~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~-~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~ 82 (476)
T PRK11779 4 MQPTFLWHDYETFGANPALDRPAQFAGIRTDA-DLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFA 82 (476)
T ss_pred CCCcEEEEEEECCCCCCCCCeeEEEEEEEEeC-CCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHH
Confidence 45679999999999994 6999999998864 23333 889999986 3456799999999999955 56899999
Q ss_pred HHHHHHhC--CCEEEEEc-chhhHHHhcccCC----------------CCceeehhccchhh-------c----CCCCcc
Q 023906 150 KKVAELIE--GRILVGHA-LHNDLKALLLTHS----------------KKDLRDTSEYQPFL-------K----NGRSKA 199 (275)
Q Consensus 150 ~~l~~~l~--~~ilVgHn-~~fDl~~L~~~~~----------------~~~~iDt~~l~~~~-------~----~~~~~s 199 (275)
.+|.+|+. +.++|||| ++||..||+..+. +.+++|++.+...+ + +..+++
T Consensus 83 ~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~r 162 (476)
T PRK11779 83 ARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFK 162 (476)
T ss_pred HHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCc
Confidence 99999995 89999997 7999999873221 12344554433221 1 236789
Q ss_pred HHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 023906 200 LRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQTRL 247 (275)
Q Consensus 200 L~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~l~~~~e~~l~~~~~~ 247 (275)
|+.| +..+|++.. ++|+|++||++|++|++.+.....+.....+..
T Consensus 163 Le~L-~~~~gI~~~-~AHdALsDa~aT~~la~~l~~~qP~l~~~~~~~ 208 (476)
T PRK11779 163 LEHL-TKANGIEHE-NAHDAMSDVYATIAMAKLIKQKQPKLFDYLFQL 208 (476)
T ss_pred HHHH-HHHcCCCCC-CCCCcHHHHHHHHHHHHHHHHhChHHHHHHHHh
Confidence 9999 689999987 699999999999999999987744444444444
No 46
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.91 E-value=1.2e-23 Score=222.45 Aligned_cols=159 Identities=29% Similarity=0.401 Sum_probs=139.9
Q ss_pred CCCCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHH
Q 023906 76 DFSLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKK 151 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~ 151 (275)
.+...++|++|+||||+++ ++|+|||+|.+.+ |.++ |+.||+|..+++++++++||||++++.+++++.+++..
T Consensus 415 ~L~~~~~VVfDLETTGL~~~~deIIEIgAV~V~~--G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~ 492 (1437)
T PRK00448 415 DLKDATYVVFDVETTGLSAVYDEIIEIGAVKIKN--GEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPK 492 (1437)
T ss_pred hhccCcEEEEEhhhcCCCCchhhhheeeeEEEeC--CeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHH
Confidence 4445689999999999984 5899999999875 6666 99999999999999999999999999999999999999
Q ss_pred HHHHhCCCEEEEEcchhhHHHhc-------ccCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCCCCChHHHH
Q 023906 152 VAELIEGRILVGHALHNDLKALL-------LTHSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNGEHCPIDDA 223 (275)
Q Consensus 152 l~~~l~~~ilVgHn~~fDl~~L~-------~~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA 223 (275)
|.+|++|.++||||+.||+.||+ +..+...++||+.+++.+ +....++|..| +++||+... ++|||++||
T Consensus 493 f~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~L-Ak~lGL~~~-~~HrAl~DA 570 (1437)
T PRK00448 493 FKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTL-AKKFGVELE-HHHRADYDA 570 (1437)
T ss_pred HHHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHH-HHHcCCCCC-CCcChHHHH
Confidence 99999999999999999999985 323445689998887655 45678999999 689999998 589999999
Q ss_pred HHHHHHHHHhHHHHH
Q 023906 224 RAAMLLYMKNRKQWE 238 (275)
Q Consensus 224 ~ata~L~~~l~~~~e 238 (275)
.+|++||.++.++.+
T Consensus 571 ~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 571 EATAYLLIKFLKDLK 585 (1437)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999987765
No 47
>PRK05359 oligoribonuclease; Provisional
Probab=99.90 E-value=1.8e-23 Score=178.32 Aligned_cols=147 Identities=16% Similarity=0.191 Sum_probs=113.8
Q ss_pred CCcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE---EEEEecCCcc----ccccceeec---CCCHHHHcCCCCHH
Q 023906 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLER----VVDFRTRIS---GIRPRDLRKAKDFP 146 (275)
Q Consensus 79 ~~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i---~~~~V~P~~~----i~~~~~~ih---GIt~e~l~~a~~~~ 146 (275)
..+|||||+||||++ .++|+|||+|.+ +..+.++ |..+|+|... ++++++.+| |||++++++++++.
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieIgaV~~-~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~ 80 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEIATIVT-DADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEA 80 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEEEEEEE-cCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHH
Confidence 467999999999999 469999999966 4334444 8889999864 467788887 89999999999999
Q ss_pred HHHHHHHHHhC------CCEEEEEcchhhHHHhcccC------CCCceeehhcc---chhhcCCCCccHHHHHHHHcCCc
Q 023906 147 TVQKKVAELIE------GRILVGHALHNDLKALLLTH------SKKDLRDTSEY---QPFLKNGRSKALRHLAAEILAVE 211 (275)
Q Consensus 147 ev~~~l~~~l~------~~ilVgHn~~fDl~~L~~~~------~~~~~iDt~~l---~~~~~~~~~~sL~~l~~~~lgi~ 211 (275)
+++.+|.+|++ +.+|||||+.||+.||...+ ..++++|++.+ ++.+. +.+ +++++
T Consensus 81 e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~----P~~------~~~~~ 150 (181)
T PRK05359 81 EAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWK----PEI------LNGFK 150 (181)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhC----hhh------hhCCC
Confidence 99999999994 58899999999999997332 22456675433 33221 111 34666
Q ss_pred CCCCCCChHHHHHHHHHHHHHhHHHH
Q 023906 212 IQNGEHCPIDDARAAMLLYMKNRKQW 237 (275)
Q Consensus 212 ~~~~~H~Al~DA~ata~L~~~l~~~~ 237 (275)
.. +.|||++||+++..+|+.+++.+
T Consensus 151 ~~-~~HRal~D~~~s~~~~~~~~~~~ 175 (181)
T PRK05359 151 KQ-GTHRALADIRESIAELKYYREHF 175 (181)
T ss_pred Cc-CCcccHHHHHHHHHHHHHHHHHh
Confidence 66 58999999999999999887653
No 48
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.90 E-value=3e-23 Score=193.36 Aligned_cols=154 Identities=41% Similarity=0.560 Sum_probs=139.6
Q ss_pred CCCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCC-CCHHHHHHHHHHHh
Q 023906 78 SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKA-KDFPTVQKKVAELI 156 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a-~~~~ev~~~l~~~l 156 (275)
...+++++||||.....| .|+++|.+||.+++++||.||+|..+|.+|.|.++|||++++.++ .++++++.+|..|+
T Consensus 214 ~~~~i~AlDCEm~~te~g--~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~~ 291 (380)
T KOG2248|consen 214 KSPNIFALDCEMVVTENG--LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLELI 291 (380)
T ss_pred CCCCeEEEEeeeeeeccc--eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHhhc
Confidence 346899999999999877 699999999999999999999999999999999999999999855 69999999999999
Q ss_pred C-CCEEEEEcchhhHHHhcccCCCCceeehhccchhhcC--CCCccHHHHHHHHcCCcCC--CCCCChHHHHHHHHHHHH
Q 023906 157 E-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLKN--GRSKALRHLAAEILAVEIQ--NGEHCPIDDARAAMLLYM 231 (275)
Q Consensus 157 ~-~~ilVgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~~~--~~~~sL~~l~~~~lgi~~~--~~~H~Al~DA~ata~L~~ 231 (275)
. ++|||||.+..||..|++.|+. ++||+.++.+-.+ ....+|+.|+..++|..++ .+.|++.+||.+|++|+.
T Consensus 292 ~~~TILVGHSLenDL~aLKl~H~~--ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~ 369 (380)
T KOG2248|consen 292 SKNTILVGHSLENDLKALKLDHPS--VIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHDSVEDALACMKLVK 369 (380)
T ss_pred CcCcEEEeechhhHHHHHhhhCCc--eeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHH
Confidence 7 9999999999999999999998 9999988766544 3567899999999999998 347999999999999998
Q ss_pred HhHH
Q 023906 232 KNRK 235 (275)
Q Consensus 232 ~l~~ 235 (275)
....
T Consensus 370 ~k~~ 373 (380)
T KOG2248|consen 370 LKIK 373 (380)
T ss_pred HHHh
Confidence 6644
No 49
>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=99.90 E-value=7.8e-24 Score=179.18 Aligned_cols=145 Identities=18% Similarity=0.230 Sum_probs=108.6
Q ss_pred EEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE--EEEEecCCcccc----ccceee---cCCCHHHHcCCCCHHHHHH
Q 023906 82 VVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI--YDEFVRPLERVV----DFRTRI---SGIRPRDLRKAKDFPTVQK 150 (275)
Q Consensus 82 ~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i--~~~~V~P~~~i~----~~~~~i---hGIt~e~l~~a~~~~ev~~ 150 (275)
+|+||+||||+++ ++|+|||+|.+.+..+.+. |+.+|+|...++ +++..+ |||+++++.++|++.+++.
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~ 80 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEA 80 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHH
Confidence 5899999999994 6899999997754333333 999999987554 455566 5999999999999999999
Q ss_pred HHHHHhCC------CEEEEEcchhhHHHhcccCC------CCceeehhc---cchhhcCCCCccHHHHHHHHcCCcCCCC
Q 023906 151 KVAELIEG------RILVGHALHNDLKALLLTHS------KKDLRDTSE---YQPFLKNGRSKALRHLAAEILAVEIQNG 215 (275)
Q Consensus 151 ~l~~~l~~------~ilVgHn~~fDl~~L~~~~~------~~~~iDt~~---l~~~~~~~~~~sL~~l~~~~lgi~~~~~ 215 (275)
+|.+|+++ .++||||+.||+.||+..+. .++.+|+.. +.+.+.. .+. .+++... .
T Consensus 81 ~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p----~~~-----~~~~~~~-~ 150 (173)
T cd06135 81 ELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYP----EIY-----RKAPKKK-G 150 (173)
T ss_pred HHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCc----Hhh-----hcCCCCC-C
Confidence 99999974 69999999999999973321 233567643 2332211 111 1455544 5
Q ss_pred CCChHHHHHHHHHHHHHhHHH
Q 023906 216 EHCPIDDARAAMLLYMKNRKQ 236 (275)
Q Consensus 216 ~H~Al~DA~ata~L~~~l~~~ 236 (275)
.|||++||++|+.+|.++++-
T Consensus 151 ~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 151 THRALDDIRESIAELKYYREN 171 (173)
T ss_pred CcchHHHHHHHHHHHHHHHHH
Confidence 899999999999999988653
No 50
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.72 E-value=1.3e-17 Score=145.16 Aligned_cols=157 Identities=20% Similarity=0.291 Sum_probs=122.7
Q ss_pred CCcEEEEEEeecCCC--C----CCeeEEEEEEEEeCCCcEE---EEEEecCCc--cccccceeecCCCHHHHcCCCCHHH
Q 023906 79 LTDVVAMDCEMVGIS--Q----GNKSALGRVSLVNKWGNLI---YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPT 147 (275)
Q Consensus 79 ~~~~vviD~EtTGl~--~----~~iieIaav~v~d~~g~~i---~~~~V~P~~--~i~~~~~~ihGIt~e~l~~a~~~~e 147 (275)
-.-+++||+|+|+.. . .+|||+.+|.+.+.+..++ |+.||+|.. .++++|+.+|||.+++|+.||+|.+
T Consensus 55 fdYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~ 134 (280)
T KOG0542|consen 55 FDYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQ 134 (280)
T ss_pred cceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHH
Confidence 355899999999987 1 3899999997876554444 999999997 7899999999999999999999999
Q ss_pred HHHHHHHHhC--------CCEEEEEcchhhHHHh-c-------ccCCC--Cceeehhccchh-hcCCCCccHHHHHHHHc
Q 023906 148 VQKKVAELIE--------GRILVGHALHNDLKAL-L-------LTHSK--KDLRDTSEYQPF-LKNGRSKALRHLAAEIL 208 (275)
Q Consensus 148 v~~~l~~~l~--------~~ilVgHn~~fDl~~L-~-------~~~~~--~~~iDt~~l~~~-~~~~~~~sL~~l~~~~l 208 (275)
|+.+|..|+. +..-..-...-|+... . +..|. .++||....+.. +.....-.+..+ .+++
T Consensus 135 vl~~f~~Wlr~~~~~~k~~~~Afvtdg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~m-Le~~ 213 (280)
T KOG0542|consen 135 VLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGM-LEHY 213 (280)
T ss_pred HHHHHHHHHHHhhcccccCceEEEeCchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHH-HHHh
Confidence 9999999993 2333333336666443 2 44443 367888766543 333356678887 7999
Q ss_pred CCcCCCCCCChHHHHHHHHHHHHHhHHH
Q 023906 209 AVEIQNGEHCPIDDARAAMLLYMKNRKQ 236 (275)
Q Consensus 209 gi~~~~~~H~Al~DA~ata~L~~~l~~~ 236 (275)
|++++|.+|++++||+.++.|..++...
T Consensus 214 gL~f~Gr~HsGiDDa~Nia~I~~kM~~d 241 (280)
T KOG0542|consen 214 GLQFEGRAHSGIDDARNIARIAQKMIRD 241 (280)
T ss_pred CCcccCCcccCchhHHHHHHHHHHHHhC
Confidence 9999999999999999999999998764
No 51
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.62 E-value=1.8e-15 Score=125.14 Aligned_cols=154 Identities=18% Similarity=0.212 Sum_probs=114.9
Q ss_pred CCCCCcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE---EEEEecCCc----cccccceeec---CCCHHHHcCCC
Q 023906 76 DFSLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLE----RVVDFRTRIS---GIRPRDLRKAK 143 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i---~~~~V~P~~----~i~~~~~~ih---GIt~e~l~~a~ 143 (275)
+...+++|+|||||||++ .++|+||| +.|.|++.+++ ++..|+-+. .+.++|.+-| |+|..-+....
T Consensus 22 ~~l~q~lVWiD~EMTGLdvekd~i~Eia-cIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~ 100 (208)
T KOG3242|consen 22 DKLKQPLVWIDCEMTGLDVEKDRIIEIA-CIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKI 100 (208)
T ss_pred ccccCceEEEeeeccccccccceeEEEE-EEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhc
Confidence 445688999999999999 67999999 77889888877 777787554 5667776654 68899999999
Q ss_pred CHHHHHHHHHHHh------CCCEEEEEcchhhHHHhccc------CCCCceeehhccchhhcCCCCccHHHHHHHHcCCc
Q 023906 144 DFPTVQKKVAELI------EGRILVGHALHNDLKALLLT------HSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVE 211 (275)
Q Consensus 144 ~~~ev~~~l~~~l------~~~ilVgHn~~fDl~~L~~~------~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~ 211 (275)
+++++..++.+|+ +.++|.|..+..|..||... |-.++++|.+.+.....++.+ .+. .+.-.
T Consensus 101 tl~~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVStIkeL~~Rw~P-~~~-----~~aPk 174 (208)
T KOG3242|consen 101 TLADAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVSTIKELARRWYP-DIK-----ARAPK 174 (208)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHHHHHHHHHHhCc-hhh-----ccCcc
Confidence 9999999999999 36788999999999999844 445678888875433222111 000 00001
Q ss_pred CCCCCCChHHHHHHHHHHHHHhHHHH
Q 023906 212 IQNGEHCPIDDARAAMLLYMKNRKQW 237 (275)
Q Consensus 212 ~~~~~H~Al~DA~ata~L~~~l~~~~ 237 (275)
....|||++|.+..+.-++.++.-|
T Consensus 175 -K~~~HrAldDI~ESI~ELq~Yr~ni 199 (208)
T KOG3242|consen 175 -KKATHRALDDIRESIKELQYYRENI 199 (208)
T ss_pred -cccccchHHHHHHHHHHHHHHHHHh
Confidence 1146999999999998888877654
No 52
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.62 E-value=2e-16 Score=130.28 Aligned_cols=155 Identities=16% Similarity=0.173 Sum_probs=119.3
Q ss_pred CcEEEEEEeecCCCC------CCeeEEEEEEEEeCCCcEE--EEEEecCCc--cccccceeecCCCHHHHcCCCCHHHHH
Q 023906 80 TDVVAMDCEMVGISQ------GNKSALGRVSLVNKWGNLI--YDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (275)
Q Consensus 80 ~~~vviD~EtTGl~~------~~iieIaav~v~d~~g~~i--~~~~V~P~~--~i~~~~~~ihGIt~e~l~~a~~~~ev~ 149 (275)
..+++||+|.|...- .+|+||++..|..-+-.++ |.+||+|.. .++.+|..++||++..|++||-|..|+
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 458999999998861 2789998655533334555 999999997 788999999999999999999999999
Q ss_pred HHHHHHhC------CCEEEEEcchhhHHHhccc-----CC----CCceeehhccchhh-cCCCCccHHHHHHHHcCCcCC
Q 023906 150 KKVAELIE------GRILVGHALHNDLKALLLT-----HS----KKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQ 213 (275)
Q Consensus 150 ~~l~~~l~------~~ilVgHn~~fDl~~L~~~-----~~----~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~ 213 (275)
++|..|+. +..++.+. .+|++.|... .+ ...++|....+.-. ...+...|..+ .+.+|..++
T Consensus 84 E~f~r~L~~h~Pr~~~~wa~wG-~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~a-le~~G~sf~ 161 (210)
T COG5018 84 EDFIRKLNEHDPRKNSTWATWG-NMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKA-LEEYGDSFT 161 (210)
T ss_pred HHHHHHHHhcCcccCCcccccc-chhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHH-HHHhccccC
Confidence 99999993 23344444 8999988611 11 23567876655433 33344678876 799999999
Q ss_pred CCCCChHHHHHHHHHHHHHhHHH
Q 023906 214 NGEHCPIDDARAAMLLYMKNRKQ 236 (275)
Q Consensus 214 ~~~H~Al~DA~ata~L~~~l~~~ 236 (275)
|.+|+||+||+.+++|+..+...
T Consensus 162 G~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 162 GTHHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred CchhhhHHHHHHHHHHHHHHcch
Confidence 99999999999999999987654
No 53
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.59 E-value=1.9e-15 Score=149.90 Aligned_cols=177 Identities=31% Similarity=0.467 Sum_probs=147.7
Q ss_pred CCcEEEEEEeecCCCCC---------------CeeEEEEEEEEeCCC----cEEEEEEecCCccccccceeecCCCHHHH
Q 023906 79 LTDVVAMDCEMVGISQG---------------NKSALGRVSLVNKWG----NLIYDEFVRPLERVVDFRTRISGIRPRDL 139 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~~---------------~iieIaav~v~d~~g----~~i~~~~V~P~~~i~~~~~~ihGIt~e~l 139 (275)
+..+|+||-|.+-+..+ ...++|+|++++++| -...|-||--.+.|.||-|+++||-+.||
T Consensus 909 ~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~PGDL 988 (1118)
T KOG1275|consen 909 SGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKPGDL 988 (1118)
T ss_pred CCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCcccc
Confidence 56899999999998621 124899999999773 33488999999999999999999999999
Q ss_pred cCC------CCHHHHHHHHHHHhC-CCEEEEEcchhhHHHhcccCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcC
Q 023906 140 RKA------KDFPTVQKKVAELIE-GRILVGHALHNDLKALLLTHSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEI 212 (275)
Q Consensus 140 ~~a------~~~~ev~~~l~~~l~-~~ilVgHn~~fDl~~L~~~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~ 212 (275)
.-. .++.-+..++.=++. |.++|||.+..|++++++..|..+++||..++.. +..+..||..||.++||..+
T Consensus 989 Dp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL~nDFrvINi~Vp~~QiiDTv~lf~~-~s~R~LSLrfLa~~lLg~~I 1067 (1118)
T KOG1275|consen 989 DPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGLQNDFRVINIHVPEEQIIDTVTLFRL-GSQRMLSLRFLAWELLGETI 1067 (1118)
T ss_pred CCccCcceehhHHHHHHHHHHHHHcCcEEEcccccccceEEEEecChhhheeeeEEEec-ccccEEEHHHHHHHHhcchh
Confidence 532 367888888888887 9999999999999999999999999999988754 34677899999999999999
Q ss_pred CCCCCChHHHHHHHHHHHHHhHH-----HHHHHHHHHHHHHHHhhhcCC
Q 023906 213 QNGEHCPIDDARAAMLLYMKNRK-----QWEKSVKDQTRLEQKQKNRKP 256 (275)
Q Consensus 213 ~~~~H~Al~DA~ata~L~~~l~~-----~~e~~l~~~~~~~~k~~~~~~ 256 (275)
|.++|++++||+.++.||+++.+ .+++.++..+...+...++.|
T Consensus 1068 Q~~~HDSIeDA~taLkLYk~Yl~lkeq~~~~~~l~niye~gr~~q~k~P 1116 (1118)
T KOG1275|consen 1068 QMEAHDSIEDARTALKLYKKYLKLKEQGKLESELRNIYECGRPNQFKVP 1116 (1118)
T ss_pred hccccccHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhhcCccccCCCC
Confidence 98999999999999999998853 566677777766655555543
No 54
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.56 E-value=1.2e-14 Score=119.10 Aligned_cols=151 Identities=13% Similarity=0.231 Sum_probs=110.4
Q ss_pred CCCcEEEEEEeecCCCC--CCeeEEEEEEEEeCCCcEE---EEEEecCCc----cccccceeec---CCCHHHHcCCCCH
Q 023906 78 SLTDVVAMDCEMVGISQ--GNKSALGRVSLVNKWGNLI---YDEFVRPLE----RVVDFRTRIS---GIRPRDLRKAKDF 145 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~~--~~iieIaav~v~d~~g~~i---~~~~V~P~~----~i~~~~~~ih---GIt~e~l~~a~~~ 145 (275)
...++|+|||||||+++ ++||||| ..|.|.+.+++ +..-|.-.. .+.+++++.| |++..-.+...+.
T Consensus 4 ~~~nLiWIDlEMTGLd~~~drIIEiA-~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~ 82 (184)
T COG1949 4 NKNNLIWIDLEMTGLDPERDRIIEIA-TIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTE 82 (184)
T ss_pred cCCceEEEeeeeccCCcCcceEEEEE-EEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccH
Confidence 45789999999999994 5899999 56678888887 444454332 6677888775 6788877888899
Q ss_pred HHHHHHHHHHh------CCCEEEEEcchhhHHHhcccCCC------CceeehhccchhhcCCCCccHHHHHHHHcCCcCC
Q 023906 146 PTVQKKVAELI------EGRILVGHALHNDLKALLLTHSK------KDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQ 213 (275)
Q Consensus 146 ~ev~~~l~~~l------~~~ilVgHn~~fDl~~L~~~~~~------~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~ 213 (275)
.++..++.+|+ +..++.|..+.-|.+||...+|. ++++|.+.+.....++.+. + +.|.. .
T Consensus 83 ~~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVSTlKELa~RW~P~----i---~~~~~-K 154 (184)
T COG1949 83 AEAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVSTLKELARRWNPE----I---LAGFK-K 154 (184)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHHHHHHHHHhhCcH----h---hhccc-c
Confidence 99999988888 35799999999999999866664 3455665543322222210 1 12322 2
Q ss_pred CCCCChHHHHHHHHHHHHHhHHHH
Q 023906 214 NGEHCPIDDARAAMLLYMKNRKQW 237 (275)
Q Consensus 214 ~~~H~Al~DA~ata~L~~~l~~~~ 237 (275)
++.|+||+|.+-.+.-++.+++.|
T Consensus 155 ~~~H~Al~DI~ESI~EL~~YR~~f 178 (184)
T COG1949 155 GGTHRALDDIRESIAELRYYREHF 178 (184)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHh
Confidence 368999999999999999888765
No 55
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.46 E-value=6.4e-13 Score=122.04 Aligned_cols=173 Identities=17% Similarity=0.155 Sum_probs=131.6
Q ss_pred CCCcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEE---EEEEecCCccc-c-ccceeecCCCHHHH-cCCCCHHHHH
Q 023906 78 SLTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLI---YDEFVRPLERV-V-DFRTRISGIRPRDL-RKAKDFPTVQ 149 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i---~~~~V~P~~~i-~-~~~~~ihGIt~e~l-~~a~~~~ev~ 149 (275)
....|.+.|.||.|.+ .+++.++|.|.- |.+-++| ...|++|.+.. + +.+.-|||||++.. +.+.+..+..
T Consensus 7 ~~~tF~~yDYETfG~~Pa~DRPaQFAgiRT-D~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~ 85 (475)
T COG2925 7 KQPTFLFYDYETFGVHPALDRPAQFAGIRT-DIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFA 85 (475)
T ss_pred CCCcEEEEehhhcCCCcccccchhhheeec-cccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHH
Confidence 3457999999999999 468889997776 5556666 77899999743 3 46889999999987 5778888888
Q ss_pred HHHHHHhC--CCEEEEEcc-hhhHHHhccc----------------CCCCceeehhccchhh-c----------CCCCcc
Q 023906 150 KKVAELIE--GRILVGHAL-HNDLKALLLT----------------HSKKDLRDTSEYQPFL-K----------NGRSKA 199 (275)
Q Consensus 150 ~~l~~~l~--~~ilVgHn~-~fDl~~L~~~----------------~~~~~~iDt~~l~~~~-~----------~~~~~s 199 (275)
..|..-+. ++++||||- +||-.+-+.. ..+++++|.+...-.+ | +..+.+
T Consensus 86 ~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFk 165 (475)
T COG2925 86 ARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFK 165 (475)
T ss_pred HHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchh
Confidence 88877663 899999995 9998877622 2234556665433222 2 234678
Q ss_pred HHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhh
Q 023906 200 LRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQTRLEQKQKN 253 (275)
Q Consensus 200 L~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~l~~~~e~~l~~~~~~~~k~~~ 253 (275)
|+.| ...-|++.. ++|+|++|++||+.+.+.++..-.+.....+..+.|.+-
T Consensus 166 LEhL-t~ANgieH~-nAHdAmsDVyATIamAklvk~~QPrLfdy~f~~R~K~~~ 217 (475)
T COG2925 166 LEHL-TKANGIEHS-NAHDAMSDVYATIAMAKLVKTAQPRLFDYLFQLRKKHKL 217 (475)
T ss_pred hHHH-hhccccccc-hhhHHHHHHHHHHHHHHHHHhhCcHHHHHHHHhccHHHH
Confidence 9999 688899877 799999999999999999988877777777776665543
No 56
>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=99.14 E-value=8e-10 Score=95.04 Aligned_cols=123 Identities=17% Similarity=0.124 Sum_probs=87.7
Q ss_pred EEEEEEeecCC----C--CCCeeEEEEEEEEeCCCcEE-EEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHH
Q 023906 82 VVAMDCEMVGI----S--QGNKSALGRVSLVNKWGNLI-YDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (275)
Q Consensus 82 ~vviD~EtTGl----~--~~~iieIaav~v~d~~g~~i-~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (275)
+++||+||||. + .++|++||.+...+ |... +.....+.....+ ||+..++...++..+++..|.+
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~--g~~~~~~~~~~~~~~~~~------~i~~~~v~~~~~E~~lL~~f~~ 72 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFD--GVKVVFLLKTSTVGDDIE------FIDGIEVEYFADEKELLKRFFD 72 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeC--CceeeEEEeecccCCcCC------CCCCceEEEeCCHHHHHHHHHH
Confidence 47899999998 4 46899999766544 5443 3322333221111 8888889999999999999999
Q ss_pred HhCC---CEEEEEcc-hhhHHHhc-------ccCC----------------------CCceeehhccchhhcCCCCccHH
Q 023906 155 LIEG---RILVGHAL-HNDLKALL-------LTHS----------------------KKDLRDTSEYQPFLKNGRSKALR 201 (275)
Q Consensus 155 ~l~~---~ilVgHn~-~fDl~~L~-------~~~~----------------------~~~~iDt~~l~~~~~~~~~~sL~ 201 (275)
++.. .++||||+ .||+.+|. +... ...++|+..+.+......+++|+
T Consensus 73 ~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l~sy~L~ 152 (199)
T cd05160 73 IIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLD 152 (199)
T ss_pred HHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCcccCCHH
Confidence 9975 59999999 99999985 2220 12357887666554447889999
Q ss_pred HHHHHHcCCcC
Q 023906 202 HLAAEILAVEI 212 (275)
Q Consensus 202 ~l~~~~lgi~~ 212 (275)
.+|..++|...
T Consensus 153 ~v~~~~l~~~k 163 (199)
T cd05160 153 AVAEELLGEGK 163 (199)
T ss_pred HHHHHHhCCCC
Confidence 99777777643
No 57
>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=98.88 E-value=8.2e-08 Score=81.37 Aligned_cols=141 Identities=21% Similarity=0.185 Sum_probs=93.7
Q ss_pred CCcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHh
Q 023906 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (275)
Q Consensus 79 ~~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (275)
...++++|+|++|++ .++++.++ +....+..+| .-+.+. . + .+++++.+++..|..++
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~---~~~~~~~~~~-~~~~~~-~-------~--------~~~~~~~~~~~~l~~~l 63 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGIS---FAVEPGEAYY-IPLGHD-Y-------G--------GEQLPREEVLAALKPLL 63 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEE---EEcCCCCEEE-EecCCC-c-------c--------ccCCCHHHHHHHHHHHH
Confidence 356899999999998 35655555 3333343322 101110 0 0 14567888999999999
Q ss_pred CCC--EEEEEcchhhHHHhcccC--CCCceeehhccchhhcCCC-CccHHHHHHHHcCCcCC----------------C-
Q 023906 157 EGR--ILVGHALHNDLKALLLTH--SKKDLRDTSEYQPFLKNGR-SKALRHLAAEILAVEIQ----------------N- 214 (275)
Q Consensus 157 ~~~--ilVgHn~~fDl~~L~~~~--~~~~~iDt~~l~~~~~~~~-~~sL~~l~~~~lgi~~~----------------~- 214 (275)
.+. .+|+||+.||+.+|.... ....++||..++..+.+.. ..+|+.++..++|.... .
T Consensus 64 ~~~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~ 143 (193)
T cd06139 64 EDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQV 143 (193)
T ss_pred hCCCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCcccc
Confidence 754 799999999999996221 1234689988877664433 57999998777765410 0
Q ss_pred ----CCCChHHHHHHHHHHHHHhHHHHHH
Q 023906 215 ----GEHCPIDDARAAMLLYMKNRKQWEK 239 (275)
Q Consensus 215 ----~~H~Al~DA~ata~L~~~l~~~~e~ 239 (275)
..|.|..||.++..|+..+....+.
T Consensus 144 ~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 144 PLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 1235788899999999988777644
No 58
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=98.76 E-value=1.3e-07 Score=78.67 Aligned_cols=133 Identities=26% Similarity=0.346 Sum_probs=86.0
Q ss_pred CcEEEEEEeecCCCC-CCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC-
Q 023906 80 TDVVAMDCEMVGISQ-GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE- 157 (275)
Q Consensus 80 ~~~vviD~EtTGl~~-~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~- 157 (275)
.++|+||+||+|+.. ..-..++.+.+.+. ... .++.|...-... +...|.+++.
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~--~~~--~i~~~~~~~~~~--------------------~~~~l~~ll~~ 75 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNPKIALIQLATG--EGC--YIIDPIDLGDNW--------------------ILDALKELLED 75 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSEEEEEEEEEES--CEE--EEECGTTSTTTT--------------------HHHHHHHHHTT
T ss_pred CCeEEEEEEECCCCccccCCeEEEEEEecC--CCc--eeeeeccccccc--------------------hHHHHHHHHhC
Confidence 459999999999984 23355666777663 222 122222110000 6777888887
Q ss_pred -CCEEEEEcchhhHHHhcc--cCCCCceeehhccchhhcCCCCccHHHHHHHHcC-CcCCC----C--C-CC--------
Q 023906 158 -GRILVGHALHNDLKALLL--THSKKDLRDTSEYQPFLKNGRSKALRHLAAEILA-VEIQN----G--E-HC-------- 218 (275)
Q Consensus 158 -~~ilVgHn~~fDl~~L~~--~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lg-i~~~~----~--~-H~-------- 218 (275)
+.+.||||+.||+.+|.. .....++.||......+.....++|++|+.+++| .+... . . -+
T Consensus 76 ~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~ 155 (176)
T PF01612_consen 76 PNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQIE 155 (176)
T ss_dssp TTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHHH
T ss_pred CCccEEEEEEechHHHHHHHhccccCCccchhhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHHH
Confidence 568999999999999973 3444568999554445544444999999999999 33311 1 1 12
Q ss_pred -hHHHHHHHHHHHHHhHHH
Q 023906 219 -PIDDARAAMLLYMKNRKQ 236 (275)
Q Consensus 219 -Al~DA~ata~L~~~l~~~ 236 (275)
|-.||..+.+||..+..+
T Consensus 156 YAa~D~~~~~~l~~~l~~~ 174 (176)
T PF01612_consen 156 YAAQDAVVTFRLYEKLKPQ 174 (176)
T ss_dssp HHHHHHHTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 455888888888887665
No 59
>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=98.69 E-value=1.3e-07 Score=72.33 Aligned_cols=37 Identities=27% Similarity=0.257 Sum_probs=26.1
Q ss_pred HHHHhCC---CEEEEEcchhhHHHhcccC---------CCCceeehhcc
Q 023906 152 VAELIEG---RILVGHALHNDLKALLLTH---------SKKDLRDTSEY 188 (275)
Q Consensus 152 l~~~l~~---~ilVgHn~~fDl~~L~~~~---------~~~~~iDt~~l 188 (275)
|.+|+++ .++||||+.||+.||.... ....++||..+
T Consensus 35 f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 35 LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 6677753 6899999999999986222 12356777654
No 60
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=98.54 E-value=7e-07 Score=80.43 Aligned_cols=149 Identities=23% Similarity=0.308 Sum_probs=89.0
Q ss_pred CcEEEEEEeecCCCC--C---------------------CeeEEEEEEEEeCCCcEE-------EEEEecCCcc-cc-cc
Q 023906 80 TDVVAMDCEMVGISQ--G---------------------NKSALGRVSLVNKWGNLI-------YDEFVRPLER-VV-DF 127 (275)
Q Consensus 80 ~~~vviD~EtTGl~~--~---------------------~iieIaav~v~d~~g~~i-------~~~~V~P~~~-i~-~~ 127 (275)
..||+||+|+||+.. . .++++|...+.+.++..- |+-++-|... .. ..
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 459999999999971 1 389999554425555543 2222233321 11 01
Q ss_pred ce---eecCCCHHHH-cCCCCHHHHHH-----HHHHH---h----C-CCEEEEEcchhhHHHhc----------------
Q 023906 128 RT---RISGIRPRDL-RKAKDFPTVQK-----KVAEL---I----E-GRILVGHALHNDLKALL---------------- 174 (275)
Q Consensus 128 ~~---~ihGIt~e~l-~~a~~~~ev~~-----~l~~~---l----~-~~ilVgHn~~fDl~~L~---------------- 174 (275)
+. .-||+.-..+ .++.++....+ ++..+ + + ..+|||||.-+|+.+|-
T Consensus 102 sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~ 181 (262)
T PF04857_consen 102 SLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKE 181 (262)
T ss_dssp HHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHH
T ss_pred hHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHH
Confidence 11 1267776554 56666544442 22111 1 2 48999999999998863
Q ss_pred ---ccCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcC-----------------------CCC-CCChHHHHHHHH
Q 023906 175 ---LTHSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEI-----------------------QNG-EHCPIDDARAAM 227 (275)
Q Consensus 175 ---~~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~-----------------------~~~-~H~Al~DA~ata 227 (275)
..+|. ++||..+..... ....+|..+ .+.++... .+. .|.|-.||.+|+
T Consensus 182 ~~~~~FP~--i~DtK~la~~~~-~~~~~L~~l-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg 257 (262)
T PF04857_consen 182 LLRELFPR--IYDTKYLAEECP-GKSTSLQEL-AEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTG 257 (262)
T ss_dssp HHHHHSSS--EEEHHHHHTSTT-TS-SSHHHH-HHHTTSTT----EEE-TTS-------------SS-TTSHHHHHHHHH
T ss_pred HHHHHCcc--cccHHHHHHhcc-ccccCHHHH-HHHhCCCccccccccccccccccccccccccCCCCCCCcchHHHHHH
Confidence 22455 899988776543 456789999 68888765 333 899999999999
Q ss_pred HHHHH
Q 023906 228 LLYMK 232 (275)
Q Consensus 228 ~L~~~ 232 (275)
.+|.+
T Consensus 258 ~~F~~ 262 (262)
T PF04857_consen 258 CVFIK 262 (262)
T ss_dssp HHHHH
T ss_pred HHHcC
Confidence 99864
No 61
>PRK05755 DNA polymerase I; Provisional
Probab=98.54 E-value=6.1e-07 Score=93.44 Aligned_cols=132 Identities=22% Similarity=0.253 Sum_probs=90.6
Q ss_pred CCcEEEEEEeecCCC--CCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHh
Q 023906 79 LTDVVAMDCEMVGIS--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELI 156 (275)
Q Consensus 79 ~~~~vviD~EtTGl~--~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l 156 (275)
...+++||+||+|++ .++++.|+ +.+ .+|... || |. +++. .+++..|.+|+
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~i~~i~-ls~--~~g~~~---~i-p~----------~~i~----------~~~l~~l~~~L 366 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAELVGLS-FAV--EPGEAA---YI-PL----------DQLD----------REVLAALKPLL 366 (880)
T ss_pred ccCeEEEEeccCCCCcccccEEEEE-EEe--CCCcEE---EE-ec----------cccc----------HHHHHHHHHHH
Confidence 357999999999998 34665555 333 335332 22 21 1121 16778888999
Q ss_pred CC--CEEEEEcchhhHHHhcc---cCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCC-----------------
Q 023906 157 EG--RILVGHALHNDLKALLL---THSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQN----------------- 214 (275)
Q Consensus 157 ~~--~ilVgHn~~fDl~~L~~---~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~----------------- 214 (275)
++ .++|+||+.||+.+|.. ..+ ..++||+.....+.....++|++++..++|++...
T Consensus 367 ~d~~v~kV~HNakfDl~~L~~~gi~~~-~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple 445 (880)
T PRK05755 367 EDPAIKKVGQNLKYDLHVLARYGIELR-GIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLE 445 (880)
T ss_pred hCCCCcEEEeccHhHHHHHHhCCCCcC-CCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccccCHH
Confidence 75 34899999999999962 222 35899988776664333489999987777776310
Q ss_pred -CCCChHHHHHHHHHHHHHhHHHHH
Q 023906 215 -GEHCPIDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 215 -~~H~Al~DA~ata~L~~~l~~~~e 238 (275)
..|.|..|+..+..||..+.....
T Consensus 446 ~~~~YAa~Dv~~~~~L~~~L~~~L~ 470 (880)
T PRK05755 446 EAAEYAAEDADVTLRLHEVLKPKLL 470 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 137799999999999999876643
No 62
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=98.37 E-value=1.3e-06 Score=72.61 Aligned_cols=124 Identities=14% Similarity=0.069 Sum_probs=55.9
Q ss_pred EEEEEeecCCCC--CCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCCCE
Q 023906 83 VAMDCEMVGISQ--GNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRI 160 (275)
Q Consensus 83 vviD~EtTGl~~--~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~~i 160 (275)
++||+||||+++ +.+.-||.+.+ +.+....|..+...... ....+.+.+..+.+...
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~-~~~~~~~~~~~~~~~~~--------------------ee~~~~~~~~~l~~~~~ 59 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADF-DDDEIITFIQWFAEDPD--------------------EEEIILEFFELLDEADN 59 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE--ETTTTE-EEEE-GGGHH--------------------HHHHHHH--HHHHTT--
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEe-CCCceEEeeHhhccCcH--------------------HHHHHHHHHHHHhcCCe
Confidence 589999999985 57777885544 43333324444432110 01222222322335789
Q ss_pred EEEEcc-hhhHHHhcc-----cCC-CCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHHh
Q 023906 161 LVGHAL-HNDLKALLL-----THS-KKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKN 233 (275)
Q Consensus 161 lVgHn~-~fDl~~L~~-----~~~-~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~l 233 (275)
+|+||. .||+.+|+. ..+ ....+|+........ ..+++|+.+ +..+|+.... --.+-..+..+|..+
T Consensus 60 iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~-~~~~~Lk~v-e~~lg~~~~~----~~~~G~~~~~~~~~~ 133 (164)
T PF13482_consen 60 IVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHF-LESYSLKNV-EKFLGIERRD----DDISGSESVKLYKEY 133 (164)
T ss_dssp EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TT-SCCTT--SH-HH---------------HHHHHHHHHH--
T ss_pred EEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhcc-CCCCCHHHH-hhhccccccc----CCCCHHHHHHHHHHH
Confidence 999996 999999972 222 456788876554322 267799999 6789987641 113334455556554
No 63
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=98.30 E-value=6.3e-06 Score=76.71 Aligned_cols=132 Identities=23% Similarity=0.281 Sum_probs=92.6
Q ss_pred CcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC--
Q 023906 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE-- 157 (275)
Q Consensus 80 ~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~-- 157 (275)
..+|+||+|+.|..+-+ -.++.|.|.++++ . .+|+|..++ .+.++| ..++.
T Consensus 17 ~~~iAiDTEf~r~~t~~-p~LcLIQi~~~e~-~---~lIdpl~~~---------------~d~~~l-------~~Ll~d~ 69 (361)
T COG0349 17 SKAIAIDTEFMRLRTYY-PRLCLIQISDGEG-A---SLIDPLAGI---------------LDLPPL-------VALLADP 69 (361)
T ss_pred CCceEEecccccccccC-CceEEEEEecCCC-c---eEecccccc---------------cccchH-------HHHhcCC
Confidence 56999999999998432 3688888888666 2 456664321 122333 33332
Q ss_pred CCEEEEEcchhhHHHhccc--CCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCC------CC---------hH
Q 023906 158 GRILVGHALHNDLKALLLT--HSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGE------HC---------PI 220 (275)
Q Consensus 158 ~~ilVgHn~~fDl~~L~~~--~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~------H~---------Al 220 (275)
+-+=|-|+++||+.+|... .-...++||....++++...+++|++|+.+++|++++.++ ++ |.
T Consensus 70 ~v~KIfHaa~~DL~~l~~~~g~~p~plfdTqiAa~l~g~~~~~gl~~Lv~~ll~v~ldK~~q~SDW~~RPLs~~Ql~YAa 149 (361)
T COG0349 70 NVVKIFHAARFDLEVLLNLFGLLPTPLFDTQIAAKLAGFGTSHGLADLVEELLGVELDKSEQRSDWLARPLSEAQLEYAA 149 (361)
T ss_pred ceeeeeccccccHHHHHHhcCCCCCchhHHHHHHHHhCCcccccHHHHHHHHhCCcccccccccccccCCCCHHHHHHHH
Confidence 3345889999999999733 2234589999888888666699999999999999987532 33 46
Q ss_pred HHHHHHHHHHHHhHHHHH
Q 023906 221 DDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 221 ~DA~ata~L~~~l~~~~e 238 (275)
.|+.....||.++....+
T Consensus 150 ~DV~yL~~l~~~L~~~L~ 167 (361)
T COG0349 150 ADVEYLLPLYDKLTEELA 167 (361)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 788888888888865443
No 64
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=98.24 E-value=1.8e-05 Score=68.14 Aligned_cols=87 Identities=21% Similarity=0.268 Sum_probs=63.6
Q ss_pred HHHHHHHHhCC--CEEEEEcchhhHHHhcccCC--------CCceeehhccchhhcC-----------CCCccHHHHHHH
Q 023906 148 VQKKVAELIEG--RILVGHALHNDLKALLLTHS--------KKDLRDTSEYQPFLKN-----------GRSKALRHLAAE 206 (275)
Q Consensus 148 v~~~l~~~l~~--~ilVgHn~~fDl~~L~~~~~--------~~~~iDt~~l~~~~~~-----------~~~~sL~~l~~~ 206 (275)
+...|..++.+ -+-|||++.+|+.+|...++ ..+++|+..++..+.. ....||..+|..
T Consensus 70 ~~~~L~~ll~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~~~ 149 (193)
T cd06146 70 WDRLLKRLFEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLVQE 149 (193)
T ss_pred HHHHHHHHhCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHHHH
Confidence 33446777764 45699999999999974432 2469999877654321 356899999999
Q ss_pred HcCCcCCCC---------------CCChHHHHHHHHHHHHHhH
Q 023906 207 ILAVEIQNG---------------EHCPIDDARAAMLLYMKNR 234 (275)
Q Consensus 207 ~lgi~~~~~---------------~H~Al~DA~ata~L~~~l~ 234 (275)
++|...... -+-|..||.++..||.++.
T Consensus 150 ~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 150 VLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 999876532 1557889999999998875
No 65
>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=98.21 E-value=1.9e-05 Score=67.73 Aligned_cols=105 Identities=17% Similarity=0.223 Sum_probs=67.7
Q ss_pred CcEEEEEEeec---CCC---CCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHH
Q 023906 80 TDVVAMDCEMV---GIS---QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (275)
Q Consensus 80 ~~~vviD~EtT---Gl~---~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~ 153 (275)
-+.++||+||+ |+. .+.|+.||.+. .+|.+.+-. ....+..+++..|.
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~---~~g~~~~~~-----------------------~~~~~E~~lL~~F~ 56 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLAT---SNGDVEFIL-----------------------AEGLDDRKIIREFV 56 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEe---CCCCEEEEE-----------------------ecCCCHHHHHHHHH
Confidence 46899999999 432 24677777432 234432100 12457888999999
Q ss_pred HHhC---CCEEEEEcc-hhhHHHhc-------ccCC--C------------------CceeehhccchhhcCCCCccHHH
Q 023906 154 ELIE---GRILVGHAL-HNDLKALL-------LTHS--K------------------KDLRDTSEYQPFLKNGRSKALRH 202 (275)
Q Consensus 154 ~~l~---~~ilVgHn~-~fDl~~L~-------~~~~--~------------------~~~iDt~~l~~~~~~~~~~sL~~ 202 (275)
+++. -.+|+|||. .||+.+|. +..+ + ...+|...+.+......+++|++
T Consensus 57 ~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~ 136 (188)
T cd05781 57 KYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLEN 136 (188)
T ss_pred HHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHH
Confidence 9985 468999998 89999984 1111 0 01455554444333467899999
Q ss_pred HHHHHcCCc
Q 023906 203 LAAEILAVE 211 (275)
Q Consensus 203 l~~~~lgi~ 211 (275)
+| ++||..
T Consensus 137 Va-~~Lg~~ 144 (188)
T cd05781 137 VA-EYLGVM 144 (188)
T ss_pred HH-HHHCCC
Confidence 95 679874
No 66
>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=98.19 E-value=3.2e-05 Score=66.57 Aligned_cols=116 Identities=13% Similarity=0.117 Sum_probs=74.2
Q ss_pred CcEEEEEEeec---CC-C--CCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHH
Q 023906 80 TDVVAMDCEMV---GI-S--QGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVA 153 (275)
Q Consensus 80 ~~~vviD~EtT---Gl-~--~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~ 153 (275)
-++++||+||+ |. + .+.|+.||.+. ..+..++.. ++.. ...+....+..+++..|.
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~---~~~~~~~~~--~~~~-------------~~~v~~~~~E~~lL~~F~ 64 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFAD---EGGNKVITW--KKFD-------------LPFVEVVKTEKEMIKRFI 64 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEec---CCCceEEEe--cCCC-------------CCeEEEeCCHHHHHHHHH
Confidence 36899999998 43 2 35788888432 224333211 1111 012333456788999999
Q ss_pred HHhC---CCEEEEEcc-hhhHHHhc-------ccCC----------------------CCceeehhccchhhcCCCCccH
Q 023906 154 ELIE---GRILVGHAL-HNDLKALL-------LTHS----------------------KKDLRDTSEYQPFLKNGRSKAL 200 (275)
Q Consensus 154 ~~l~---~~ilVgHn~-~fDl~~L~-------~~~~----------------------~~~~iDt~~l~~~~~~~~~~sL 200 (275)
+++. -.++||||. .||+.+|. +..+ ....+|+..+.+......+++|
T Consensus 65 ~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~sy~L 144 (195)
T cd05780 65 EIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTL 144 (195)
T ss_pred HHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCCcCcH
Confidence 9886 479999998 89999984 2211 1125566555544445678999
Q ss_pred HHHHHHHcCCcCC
Q 023906 201 RHLAAEILAVEIQ 213 (275)
Q Consensus 201 ~~l~~~~lgi~~~ 213 (275)
+.++.++||.+..
T Consensus 145 ~~v~~~~Lg~~k~ 157 (195)
T cd05780 145 ERVYEELFGIEKE 157 (195)
T ss_pred HHHHHHHhCCCCC
Confidence 9998889998754
No 67
>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=98.16 E-value=4e-05 Score=63.84 Aligned_cols=129 Identities=19% Similarity=0.179 Sum_probs=82.9
Q ss_pred CCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcE-EEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC
Q 023906 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNL-IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~-i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (275)
...+|+||+|......-. -.++.+.+....+.+ +++..-.+ . ....|.+++.
T Consensus 12 ~~~~ig~D~E~~~~~~~~-~~~~liQl~~~~~~~~l~d~~~~~---------------~-----------~~~~L~~lL~ 64 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYY-GEVALIQLCVSEEKCYLFDPLSLS---------------V-----------DWQGLKMLLE 64 (161)
T ss_pred CCCEEEEECCccCCCCCC-CceEEEEEEECCCCEEEEecccCc---------------c-----------CHHHHHHHhC
Confidence 567999999999876210 124444444431222 23321100 0 1233556676
Q ss_pred CC--EEEEEcchhhHHHhcc--cCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCC---------------CCC
Q 023906 158 GR--ILVGHALHNDLKALLL--THSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNG---------------EHC 218 (275)
Q Consensus 158 ~~--ilVgHn~~fDl~~L~~--~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~---------------~H~ 218 (275)
+. +.|||++..|+..|.. ......++|+...+..+......+|..++..++|+..+.. -|-
T Consensus 65 d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~qi~Y 144 (161)
T cd06129 65 NPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLY 144 (161)
T ss_pred CCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHHHHH
Confidence 43 5699999999999853 3333456899887776644456799999888889876431 256
Q ss_pred hHHHHHHHHHHHHHhH
Q 023906 219 PIDDARAAMLLYMKNR 234 (275)
Q Consensus 219 Al~DA~ata~L~~~l~ 234 (275)
|..||.++..||.++.
T Consensus 145 Aa~Da~~l~~l~~~l~ 160 (161)
T cd06129 145 AAADVYALLIIYTKLR 160 (161)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7889999999998774
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=98.09 E-value=0.00017 Score=62.72 Aligned_cols=90 Identities=20% Similarity=0.242 Sum_probs=65.7
Q ss_pred CHHHHHHHHHHHhC--CCEEEEEcc-hhhHHHhc-------ccCCC-----------------CceeehhccchhhcCCC
Q 023906 144 DFPTVQKKVAELIE--GRILVGHAL-HNDLKALL-------LTHSK-----------------KDLRDTSEYQPFLKNGR 196 (275)
Q Consensus 144 ~~~ev~~~l~~~l~--~~ilVgHn~-~fDl~~L~-------~~~~~-----------------~~~iDt~~l~~~~~~~~ 196 (275)
+..+++..|.++++ ...||+||. .||+.+|. +..|. .+-+|++.+........
T Consensus 36 ~E~~lL~~F~~~~~~~~p~LVs~NG~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~~~g~~~ 115 (209)
T PF10108_consen 36 DEKELLQDFFDLVEKYNPQLVSFNGRGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLSFYGAKA 115 (209)
T ss_pred CHHHHHHHHHHHHHhCCCeEEecCCccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHhccCccc
Confidence 37888999999996 557999997 99999985 22221 12467776655555566
Q ss_pred CccHHHHHHHHcCCcCCCCC------------------CChHHHHHHHHHHHHHhH
Q 023906 197 SKALRHLAAEILAVEIQNGE------------------HCPIDDARAAMLLYMKNR 234 (275)
Q Consensus 197 ~~sL~~l~~~~lgi~~~~~~------------------H~Al~DA~ata~L~~~l~ 234 (275)
..||+.+ |..+|++-..+- .=-..|+.+|+.||+++.
T Consensus 116 ~~sLd~l-a~~lgiPgK~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~ 170 (209)
T PF10108_consen 116 RTSLDEL-AALLGIPGKDDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFE 170 (209)
T ss_pred cCCHHHH-HHHcCCCCCCCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8899999 799999864221 122569999999999984
No 69
>PRK10829 ribonuclease D; Provisional
Probab=98.02 E-value=9.4e-05 Score=69.93 Aligned_cols=132 Identities=21% Similarity=0.231 Sum_probs=89.6
Q ss_pred CCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhCC
Q 023906 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEG 158 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~~ 158 (275)
...+|+||+|+.+... .--.++.|.|.++.+ + .+|.|.. |+ + +..|.+++.+
T Consensus 21 ~~~~lalDtEf~~~~t-y~~~l~LiQl~~~~~--~--~LiD~l~-----------~~--d----------~~~L~~ll~~ 72 (373)
T PRK10829 21 AFPAIALDTEFVRTRT-YYPQLGLIQLYDGEQ--L--SLIDPLG-----------IT--D----------WSPFKALLRD 72 (373)
T ss_pred cCCeEEEecccccCcc-CCCceeEEEEecCCc--e--EEEecCC-----------cc--c----------hHHHHHHHcC
Confidence 4678999999998762 112466666655332 2 2444421 11 0 2346666753
Q ss_pred -C-EEEEEcchhhHHHhc--ccCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCC---------------CCh
Q 023906 159 -R-ILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGE---------------HCP 219 (275)
Q Consensus 159 -~-ilVgHn~~fDl~~L~--~~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~---------------H~A 219 (275)
. +-|+|++.+|+.+|. +.+....++||...+.++....+.+|..|+.+++|+..+... +=|
T Consensus 73 ~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~YA 152 (373)
T PRK10829 73 PQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYA 152 (373)
T ss_pred CCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHHH
Confidence 3 348999999999984 334445799998888777555578999999999999876421 446
Q ss_pred HHHHHHHHHHHHHhHHHHH
Q 023906 220 IDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 220 l~DA~ata~L~~~l~~~~e 238 (275)
..|+..+..||..+..+.+
T Consensus 153 a~Dv~~L~~l~~~L~~~L~ 171 (373)
T PRK10829 153 AADVFYLLPIAAKLMAETE 171 (373)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7899999999998866444
No 70
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=97.94 E-value=1.5e-05 Score=70.94 Aligned_cols=169 Identities=15% Similarity=0.118 Sum_probs=102.6
Q ss_pred CCCCCcEEEEEEeecCCC--CCCeeEEEEEEE-----E------eCCCc------EE---EEEEecCCccccccceeecC
Q 023906 76 DFSLTDVVAMDCEMVGIS--QGNKSALGRVSL-----V------NKWGN------LI---YDEFVRPLERVVDFRTRISG 133 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~--~~~iieIaav~v-----~------d~~g~------~i---~~~~V~P~~~i~~~~~~ihG 133 (275)
-.++..|+++|.|+||+. ..+|.|+....| . |.++. .+ ...++.|.....+.+.+|+|
T Consensus 9 ~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeeitg 88 (318)
T KOG4793|consen 9 VPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEITG 88 (318)
T ss_pred CCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhhcc
Confidence 334678999999999996 224444433222 1 11111 12 33457788788888999999
Q ss_pred CCHHHHc--CCCCHH-HHHHHHHHHhC----CCEEEEEcc-hhhHHHhc-------ccC---------------------
Q 023906 134 IRPRDLR--KAKDFP-TVQKKVAELIE----GRILVGHAL-HNDLKALL-------LTH--------------------- 177 (275)
Q Consensus 134 It~e~l~--~a~~~~-ev~~~l~~~l~----~~ilVgHn~-~fDl~~L~-------~~~--------------------- 177 (275)
+++.-+. +..-|+ ++.+-|..|+. --.||+||. .||+.+|. +..
T Consensus 89 ls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a~s 168 (318)
T KOG4793|consen 89 LSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRANS 168 (318)
T ss_pred cccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhhcC
Confidence 9996653 223343 33344456663 357999997 88887763 000
Q ss_pred ----CC------------------------------------------------------Cceeehhccch-----hhc-
Q 023906 178 ----SK------------------------------------------------------KDLRDTSEYQP-----FLK- 193 (275)
Q Consensus 178 ----~~------------------------------------------------------~~~iDt~~l~~-----~~~- 193 (275)
+. +..++.+...+ ..|
T Consensus 169 ~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~ 248 (318)
T KOG4793|consen 169 MVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPT 248 (318)
T ss_pred cccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCC
Confidence 00 00011110000 001
Q ss_pred CCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 023906 194 NGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQWEKSVKDQT 245 (275)
Q Consensus 194 ~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~l~~~~e~~l~~~~ 245 (275)
....++|+.| +.++......++|+|+.|+..+-++++++...+-..+.++.
T Consensus 249 p~~vs~le~L-at~~~~~p~l~ahra~~Dv~~~~k~~q~~~idlla~l~~la 299 (318)
T KOG4793|consen 249 PKLVSSLEAL-ATYYSLTPELDAHRALSDVLLLSKVFQKLTIDLLASLSDLA 299 (318)
T ss_pred CccchhHHHH-HHHhhcCcccchhhhccccchhhhHHHHhhhhhhhhhhhhh
Confidence 1224578888 57888888888999999999999999999777665555443
No 71
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=97.94 E-value=0.00036 Score=56.19 Aligned_cols=67 Identities=30% Similarity=0.318 Sum_probs=48.8
Q ss_pred HHHHHHHHHHhCC--CEEEEEcchhhHHHhcccC--CCCceeehhccchhhcCCC-CccHHHHHHHHcCCcC
Q 023906 146 PTVQKKVAELIEG--RILVGHALHNDLKALLLTH--SKKDLRDTSEYQPFLKNGR-SKALRHLAAEILAVEI 212 (275)
Q Consensus 146 ~ev~~~l~~~l~~--~ilVgHn~~fDl~~L~~~~--~~~~~iDt~~l~~~~~~~~-~~sL~~l~~~~lgi~~ 212 (275)
..+...|.+|+.+ ..+||||+.||+.+|.... ....++||+.+...+.... .++|+.++.++++...
T Consensus 40 ~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~ 111 (155)
T cd00007 40 EEDLEALKELLEDEDITKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIEL 111 (155)
T ss_pred HHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCC
Confidence 5567778888874 4599999999999996221 1234789988777664433 5799999888877763
No 72
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=97.93 E-value=0.00015 Score=60.55 Aligned_cols=85 Identities=21% Similarity=0.268 Sum_probs=61.7
Q ss_pred HHHHHHhC--CCEEEEEcchhhHHHhc--ccCCCCceeehhccchhhcCC-CCccHHHHHHHHcCCcCC--CC-------
Q 023906 150 KKVAELIE--GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLKNG-RSKALRHLAAEILAVEIQ--NG------- 215 (275)
Q Consensus 150 ~~l~~~l~--~~ilVgHn~~fDl~~L~--~~~~~~~~iDt~~l~~~~~~~-~~~sL~~l~~~~lgi~~~--~~------- 215 (275)
..|.+++. +...|||++.+|+.+|. +......++|+..++..+... ...+|..++..++|.... ..
T Consensus 63 ~~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~ 142 (170)
T cd06141 63 PSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWE 142 (170)
T ss_pred HHHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCC
Confidence 34666775 34679999999999985 232233578999877766543 346999998888898776 21
Q ss_pred --------CCChHHHHHHHHHHHHHhH
Q 023906 216 --------EHCPIDDARAAMLLYMKNR 234 (275)
Q Consensus 216 --------~H~Al~DA~ata~L~~~l~ 234 (275)
-|-|..||..+..||..+.
T Consensus 143 ~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 143 ARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 1557889999999998764
No 73
>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=97.88 E-value=0.00031 Score=66.40 Aligned_cols=132 Identities=27% Similarity=0.314 Sum_probs=84.2
Q ss_pred CCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC-
Q 023906 79 LTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE- 157 (275)
Q Consensus 79 ~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~- 157 (275)
...+|+||+|+++...- --.++.|.|.. +..+ .+|.|... .+ +..|.+++.
T Consensus 17 ~~~~ia~DtE~~~~~~y-~~~l~LiQia~--~~~~--~liD~~~~-------------~~----------~~~L~~lL~d 68 (367)
T TIGR01388 17 TFPFVALDTEFVRERTF-WPQLGLIQVAD--GEQL--ALIDPLVI-------------ID----------WSPLKELLRD 68 (367)
T ss_pred cCCEEEEeccccCCCCC-CCcceEEEEee--CCeE--EEEeCCCc-------------cc----------HHHHHHHHCC
Confidence 45799999999887521 11345555544 3332 24444210 00 233556665
Q ss_pred -CCEEEEEcchhhHHHhccc--CCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCC------CC---------h
Q 023906 158 -GRILVGHALHNDLKALLLT--HSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGE------HC---------P 219 (275)
Q Consensus 158 -~~ilVgHn~~fDl~~L~~~--~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~------H~---------A 219 (275)
+.+.|+|++.+|+.+|... .....++||...+..+......+|..++..++|+.+..+. .+ |
T Consensus 69 ~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~YA 148 (367)
T TIGR01388 69 ESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYA 148 (367)
T ss_pred CCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHHH
Confidence 3457999999999998622 1223578998877666554457999998899998765321 22 6
Q ss_pred HHHHHHHHHHHHHhHHHHH
Q 023906 220 IDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 220 l~DA~ata~L~~~l~~~~e 238 (275)
..||.++..||..+..+.+
T Consensus 149 a~Dv~~L~~L~~~L~~~L~ 167 (367)
T TIGR01388 149 AADVTYLLPLYAKLMERLE 167 (367)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7788888888888865543
No 74
>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=97.69 E-value=0.0016 Score=56.71 Aligned_cols=33 Identities=18% Similarity=0.298 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHhCC---CEEEEEcc-hhhHHHhc
Q 023906 142 AKDFPTVQKKVAELIEG---RILVGHAL-HNDLKALL 174 (275)
Q Consensus 142 a~~~~ev~~~l~~~l~~---~ilVgHn~-~fDl~~L~ 174 (275)
..+..+++..|.+++.. .+|||||+ .||+.+|.
T Consensus 55 ~~~E~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~ 91 (207)
T cd05785 55 DAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLR 91 (207)
T ss_pred CCCHHHHHHHHHHHHHHhCCCEEeccCCcccCHHHHH
Confidence 57789999999999963 79999999 99999984
No 75
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=97.68 E-value=0.00093 Score=58.09 Aligned_cols=71 Identities=15% Similarity=0.040 Sum_probs=47.5
Q ss_pred CCCHHHHHHHHHHHhCC---CEEEEEcc-hhhHHHhc-------ccCC----C------------Cceeehhccchh--h
Q 023906 142 AKDFPTVQKKVAELIEG---RILVGHAL-HNDLKALL-------LTHS----K------------KDLRDTSEYQPF--L 192 (275)
Q Consensus 142 a~~~~ev~~~l~~~l~~---~ilVgHn~-~fDl~~L~-------~~~~----~------------~~~iDt~~l~~~--~ 192 (275)
..+..+++..|.+++.. .+++|||. .||+.+|. +... + .-.+|...+.+. .
T Consensus 70 ~~~E~~lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~ 149 (204)
T cd05779 70 EPDEKALLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSY 149 (204)
T ss_pred CCCHHHHHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhc
Confidence 46788999999999963 59999998 99999984 1111 0 013444433321 1
Q ss_pred cCCCCccHHHHHHHHcCCcC
Q 023906 193 KNGRSKALRHLAAEILAVEI 212 (275)
Q Consensus 193 ~~~~~~sL~~l~~~~lgi~~ 212 (275)
....+++|+.+|..+||..-
T Consensus 150 l~~~sysLd~Va~~~Lg~~K 169 (204)
T cd05779 150 LPQGSQGLKAVTKAKLGYDP 169 (204)
T ss_pred CCCCCccHHHHHHHHhCCCc
Confidence 12358899999777899754
No 76
>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=97.63 E-value=0.0012 Score=56.90 Aligned_cols=137 Identities=19% Similarity=0.235 Sum_probs=83.4
Q ss_pred CCCCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcE-EEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHH
Q 023906 77 FSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNL-IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (275)
Q Consensus 77 ~~~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~-i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (275)
....++|+||+|+++.+... .++.|.|....+.+ +||.+--+. ......|.++
T Consensus 7 l~~~~~i~~D~E~~~~~~~~--~~~LiQia~~~~~v~l~D~~~~~~------------------------~~~~~~L~~i 60 (197)
T cd06148 7 LKKQKVIGLDCEGVNLGRKG--KLCLVQIATRTGQIYLFDILKLGS------------------------IVFINGLKDI 60 (197)
T ss_pred hhhCCEEEEEcccccCCCCC--CEEEEEEeeCCCcEEEEEhhhccc------------------------hhHHHHHHHH
Confidence 34477999999999887322 34444443331222 243321110 0112445566
Q ss_pred hC--CCEEEEEcchhhHHHhc--ccCCCCceeehhccchhhcC--------CCCccHHHHHHHHcCCcCC----------
Q 023906 156 IE--GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLKN--------GRSKALRHLAAEILAVEIQ---------- 213 (275)
Q Consensus 156 l~--~~ilVgHn~~fDl~~L~--~~~~~~~~iDt~~l~~~~~~--------~~~~sL~~l~~~~lgi~~~---------- 213 (275)
+. +.+.|+|++.+|+.+|. +...-..++||......+.. ....+|..++..++|++..
T Consensus 61 Le~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~~~ 140 (197)
T cd06148 61 LESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKLMR 140 (197)
T ss_pred hcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHHHh
Confidence 65 34569999999999983 33322357899866544421 1235899998888888752
Q ss_pred ----CCC---------CChHHHHHHHHHHHHHhHHHHHH
Q 023906 214 ----NGE---------HCPIDDARAAMLLYMKNRKQWEK 239 (275)
Q Consensus 214 ----~~~---------H~Al~DA~ata~L~~~l~~~~e~ 239 (275)
... +=|..||..+..||..+......
T Consensus 141 ~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~ 179 (197)
T cd06148 141 EDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALIS 179 (197)
T ss_pred cCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhh
Confidence 111 34677999999999988777654
No 77
>cd05784 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged
Probab=97.59 E-value=0.0015 Score=56.23 Aligned_cols=117 Identities=16% Similarity=0.104 Sum_probs=69.6
Q ss_pred CcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC--
Q 023906 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE-- 157 (275)
Q Consensus 80 ~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~-- 157 (275)
=++++||+||+|.+ .|..||. .+...+.++- +=.+. ... | ..+.-.++..+++..|.+++.
T Consensus 3 l~~~~fDIE~~~~~--~i~~i~~---~~~~~~~i~~-~~~~~-~~~-------~---~~v~~~~~E~~lL~~f~~~i~~~ 65 (193)
T cd05784 3 LKVVSLDIETSMDG--ELYSIGL---YGEGQERVLM-VGDPE-DDA-------P---DNIEWFADEKSLLLALIAWFAQY 65 (193)
T ss_pred ccEEEEEeecCCCC--CEEEEEe---ecCCCCEEEE-ECCCC-CCC-------C---CEEEEECCHHHHHHHHHHHHHhh
Confidence 36899999999864 6666653 2332233221 11111 110 1 112233577888999998885
Q ss_pred -CCEEEEEcc-hhhHHHhc-------ccCC------------------------CCceeehhccchh-hcCCCCccHHHH
Q 023906 158 -GRILVGHAL-HNDLKALL-------LTHS------------------------KKDLRDTSEYQPF-LKNGRSKALRHL 203 (275)
Q Consensus 158 -~~ilVgHn~-~fDl~~L~-------~~~~------------------------~~~~iDt~~l~~~-~~~~~~~sL~~l 203 (275)
-.+|+|||+ .||+.+|. +.+. ..-++|+..+.+. .....+++|+++
T Consensus 66 dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~~kl~sy~L~~V 145 (193)
T cd05784 66 DPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENV 145 (193)
T ss_pred CCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHccCCCCcCCHHHH
Confidence 369999998 99999984 2210 0114455433322 234679999999
Q ss_pred HHHHcCCcCC
Q 023906 204 AAEILAVEIQ 213 (275)
Q Consensus 204 ~~~~lgi~~~ 213 (275)
|..+||..-.
T Consensus 146 a~~~Lg~~K~ 155 (193)
T cd05784 146 AQELLGEGKL 155 (193)
T ss_pred HHHHhCCCcc
Confidence 8889986543
No 78
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=97.55 E-value=0.00024 Score=61.57 Aligned_cols=154 Identities=19% Similarity=0.205 Sum_probs=98.7
Q ss_pred cEEEEEEeecCCC--C--------C-------------CeeEEEEEEEEeCCCcE------EEEE--E-ecCCc-ccccc
Q 023906 81 DVVAMDCEMVGIS--Q--------G-------------NKSALGRVSLVNKWGNL------IYDE--F-VRPLE-RVVDF 127 (275)
Q Consensus 81 ~~vviD~EtTGl~--~--------~-------------~iieIaav~v~d~~g~~------i~~~--~-V~P~~-~i~~~ 127 (275)
++|++|+|.-|.- + + .+|++| +.+.|.+|+. ++.- - ..+.. ...+.
T Consensus 25 ~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlG-lTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~a~~ 103 (239)
T KOG0304|consen 25 PYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLG-LTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMYAQD 103 (239)
T ss_pred CeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhhee-eeeeccCCCCCCCCCceeEEecccCCchhhccchh
Confidence 5899999988863 1 0 488999 8888876654 2211 1 22222 22222
Q ss_pred ce---eecCCCHHHH-cCCCCHHHHHHHHHH---Hh-CCCEEEEEcchhhHHHhc-----ccCCC-------------Cc
Q 023906 128 RT---RISGIRPRDL-RKAKDFPTVQKKVAE---LI-EGRILVGHALHNDLKALL-----LTHSK-------------KD 181 (275)
Q Consensus 128 ~~---~ihGIt~e~l-~~a~~~~ev~~~l~~---~l-~~~ilVgHn~~fDl~~L~-----~~~~~-------------~~ 181 (275)
.. .-+||.-+.. +.+....+..+.+.. .+ ++-.+|..+..+|+++|- -..|. ..
T Consensus 104 SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~ 183 (239)
T KOG0304|consen 104 SIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPF 183 (239)
T ss_pred hHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcch
Confidence 22 2378877665 345555443333322 11 356789999999999873 11221 12
Q ss_pred eeehhccchhhcC-CCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHHhHHH
Q 023906 182 LRDTSEYQPFLKN-GRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNRKQ 236 (275)
Q Consensus 182 ~iDt~~l~~~~~~-~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~l~~~ 236 (275)
+.|+..+...+.+ .-..+|..+ ++.||+.-.+.+|.|-+|+..|+..|.++++.
T Consensus 184 vYDiK~l~~~c~~~~l~~GL~~l-A~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~~ 238 (239)
T KOG0304|consen 184 VYDVKYLMKFCEGLSLKGGLQRL-ADLLGLKRVGIAHQAGSDSLLTARVFFKLKEL 238 (239)
T ss_pred hhhHHHHHHhhhhhhhhcCHHHH-HHHhCCCeeecccccCcHHHHHHHHHHHHHhc
Confidence 5566655555533 245689999 69999999888999999999999999998753
No 79
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=97.52 E-value=0.00065 Score=59.17 Aligned_cols=68 Identities=22% Similarity=0.187 Sum_probs=47.8
Q ss_pred CHHHHHHHHHHHhC--CCEEEEEcc-hhhHHHhc-------ccCCCC----------------ceeehhccchhhcCCCC
Q 023906 144 DFPTVQKKVAELIE--GRILVGHAL-HNDLKALL-------LTHSKK----------------DLRDTSEYQPFLKNGRS 197 (275)
Q Consensus 144 ~~~ev~~~l~~~l~--~~ilVgHn~-~fDl~~L~-------~~~~~~----------------~~iDt~~l~~~~~~~~~ 197 (275)
+-.+++..|.+++. ..+|||||. .||+.+|. +..|.. +.+|+..+........+
T Consensus 77 ~E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~~~~~~~ 156 (208)
T cd05782 77 DEKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARAR 156 (208)
T ss_pred CHHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhccCccCC
Confidence 34778888888886 568999998 99999985 222210 15666655444333578
Q ss_pred ccHHHHHHHHcCCcC
Q 023906 198 KALRHLAAEILAVEI 212 (275)
Q Consensus 198 ~sL~~l~~~~lgi~~ 212 (275)
++|+.+ ++++|++.
T Consensus 157 ~~L~~v-a~~lG~~~ 170 (208)
T cd05782 157 ASLDLL-AKLLGIPG 170 (208)
T ss_pred CCHHHH-HHHhCCCC
Confidence 899999 58999854
No 80
>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=97.50 E-value=0.011 Score=52.09 Aligned_cols=86 Identities=16% Similarity=0.224 Sum_probs=51.0
Q ss_pred CCcEEEEEEeecCCC---C----CCeeEEEEEEEEeCCCcEEEEE-E-ecCCccccccceeecCCCHHHHcCCCCHHHHH
Q 023906 79 LTDVVAMDCEMVGIS---Q----GNKSALGRVSLVNKWGNLIYDE-F-VRPLERVVDFRTRISGIRPRDLRKAKDFPTVQ 149 (275)
Q Consensus 79 ~~~~vviD~EtTGl~---~----~~iieIaav~v~d~~g~~i~~~-~-V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~ 149 (275)
+-+.++||+||.... | +.|+.|+.+.-.++....+... + +.+..+++ | ..+....+..+++
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~-------~---~~v~~~~~E~eLL 75 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV-------G---AQVFSFETEEELL 75 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC-------C---CEEEEECCHHHHH
Confidence 456899999998542 2 3666666332222211121111 1 22222221 1 1223346788999
Q ss_pred HHHHHHhC---CCEEEEEcc-hhhHHHhc
Q 023906 150 KKVAELIE---GRILVGHAL-HNDLKALL 174 (275)
Q Consensus 150 ~~l~~~l~---~~ilVgHn~-~fDl~~L~ 174 (275)
..|.+++. -.+++|||+ .||+.+|.
T Consensus 76 ~~f~~~i~~~DPDii~GyN~~~FDl~yL~ 104 (230)
T cd05777 76 LAWRDFVQEVDPDIITGYNICNFDLPYLL 104 (230)
T ss_pred HHHHHHHHhcCCCEEEEecCCCCCHHHHH
Confidence 99998885 479999998 89999973
No 81
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=97.50 E-value=0.001 Score=58.78 Aligned_cols=129 Identities=18% Similarity=0.114 Sum_probs=71.2
Q ss_pred CCcEEEEEEeecCCC-CCC-eeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCC-HHHHHHHHHHH
Q 023906 79 LTDVVAMDCEMVGIS-QGN-KSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKD-FPTVQKKVAEL 155 (275)
Q Consensus 79 ~~~~vviD~EtTGl~-~~~-iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~-~~ev~~~l~~~ 155 (275)
..++++||+||||++ .+. |.-+|...+.+ +......+.-| +|. -..+.+.|...
T Consensus 97 ~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~--~~~~Vrq~~lp---------------------~p~~E~avle~fl~~ 153 (278)
T COG3359 97 AEDVAFFDIETTGLDRAGNTITLVGGARGVD--DTMHVRQHFLP---------------------APEEEVAVLENFLHD 153 (278)
T ss_pred ccceEEEeeeccccCCCCCeEEEEEEEEccC--ceEEEEeecCC---------------------CcchhhHHHHHHhcC
Confidence 567999999999999 343 33334333322 33322222222 111 12344445554
Q ss_pred hCCCEEEEEcc-hhhHHHhc---cc-C---CCCceeehhccchhhc--CCCCccHHHHHHHHcCCcCCCCCCChHHHHHH
Q 023906 156 IEGRILVGHAL-HNDLKALL---LT-H---SKKDLRDTSEYQPFLK--NGRSKALRHLAAEILAVEIQNGEHCPIDDARA 225 (275)
Q Consensus 156 l~~~ilVgHn~-~fDl~~L~---~~-~---~~~~~iDt~~l~~~~~--~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~a 225 (275)
..-..||.+|. .||+.|++ .. + +...-+|...-.+.+. .....+|+.+ .+.+|+.-.. --.-.|+..
T Consensus 154 ~~~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~V-Er~LGi~R~e--dtdG~~~p~ 230 (278)
T COG3359 154 PDFNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTV-ERILGIRREE--DTDGYDGPE 230 (278)
T ss_pred CCcceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhH-HHHhCccccc--cCCCcchHH
Confidence 55669999997 99999998 11 1 1122345544333331 1356689988 6788877542 222245555
Q ss_pred HHHHHHHh
Q 023906 226 AMLLYMKN 233 (275)
Q Consensus 226 ta~L~~~l 233 (275)
...+|++.
T Consensus 231 lyr~~~~~ 238 (278)
T COG3359 231 LYRLYRRY 238 (278)
T ss_pred HHHHHHHc
Confidence 56666554
No 82
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=97.43 E-value=0.0048 Score=54.56 Aligned_cols=143 Identities=11% Similarity=0.077 Sum_probs=79.8
Q ss_pred cEEEEEEeecCCC---C----CCeeEEEEEEEEeCCCcEEE------EEEecCCccccccceeecCCCHHHHcCCCCHHH
Q 023906 81 DVVAMDCEMVGIS---Q----GNKSALGRVSLVNKWGNLIY------DEFVRPLERVVDFRTRISGIRPRDLRKAKDFPT 147 (275)
Q Consensus 81 ~~vviD~EtTGl~---~----~~iieIaav~v~d~~g~~i~------~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~e 147 (275)
.++.||+|+.+.+ | |.|+.|+-+ +.+....... ..++.+...-........++....+.--.+..+
T Consensus 5 ~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~~ 83 (231)
T cd05778 5 TILSLEVHVNTRGDLLPDPEFDPISAIFYC-IDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVESELE 83 (231)
T ss_pred EEEEEEEEECCCCCCCcCCCCCCeeEEEEE-EecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeCCHHH
Confidence 4789999998654 2 367777733 4332211111 122333221000001111232333445567888
Q ss_pred HHHHHHHHh---CCCEEEEEcc-hhhHHHhc-------cc-----CCC---------------C-------------cee
Q 023906 148 VQKKVAELI---EGRILVGHAL-HNDLKALL-------LT-----HSK---------------K-------------DLR 183 (275)
Q Consensus 148 v~~~l~~~l---~~~ilVgHn~-~fDl~~L~-------~~-----~~~---------------~-------------~~i 183 (275)
++..|.+++ +-.+|+|||+ .||+.+|- .. +.+ + -++
T Consensus 84 LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi~l 163 (231)
T cd05778 84 LFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHIL 163 (231)
T ss_pred HHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEEEe
Confidence 888888887 4689999999 99999873 10 101 0 012
Q ss_pred ehhccchhhcCCCCccHHHHHHHHcCCcCCCCCCChHHHHH
Q 023906 184 DTSEYQPFLKNGRSKALRHLAAEILAVEIQNGEHCPIDDAR 224 (275)
Q Consensus 184 Dt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ 224 (275)
|...+.+.-....+|+|++++..+||.....-.|..+.+..
T Consensus 164 D~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~ 204 (231)
T cd05778 164 NVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWY 204 (231)
T ss_pred EhHHHHHHHcCcccCCHHHHHHHHhCCCCCCCCHHHHHHHH
Confidence 33222222235678999999889999876643455566653
No 83
>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=97.27 E-value=0.014 Score=50.67 Aligned_cols=73 Identities=15% Similarity=0.057 Sum_probs=48.3
Q ss_pred CCCCHHHHHHHHHHHhC-CCEEEEEcc-hhhHHHhc-----ccCC----------------CCceeehhccchh--h---
Q 023906 141 KAKDFPTVQKKVAELIE-GRILVGHAL-HNDLKALL-----LTHS----------------KKDLRDTSEYQPF--L--- 192 (275)
Q Consensus 141 ~a~~~~ev~~~l~~~l~-~~ilVgHn~-~fDl~~L~-----~~~~----------------~~~~iDt~~l~~~--~--- 192 (275)
.-.+..+++..|.+++. ..++||||. .||+.+|. +..+ ....+|....... +
T Consensus 69 ~~~~E~~lL~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~ 148 (204)
T cd05783 69 FFDSEKELIREAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVY 148 (204)
T ss_pred ecCCHHHHHHHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhh
Confidence 34678999999999986 569999998 99999984 1111 1123455332211 0
Q ss_pred ---cCCCCccHHHHHHHHcCCcCC
Q 023906 193 ---KNGRSKALRHLAAEILAVEIQ 213 (275)
Q Consensus 193 ---~~~~~~sL~~l~~~~lgi~~~ 213 (275)
....+++|+.+|..++|..-.
T Consensus 149 ~~~~~~~~~~L~~Va~~~lg~~K~ 172 (204)
T cd05783 149 AFGNKYREYTLDAVAKALLGEGKV 172 (204)
T ss_pred hhccccccCcHHHHHHHhcCCCcc
Confidence 123689999997777787543
No 84
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=97.22 E-value=0.016 Score=47.39 Aligned_cols=62 Identities=27% Similarity=0.312 Sum_probs=44.1
Q ss_pred HHHHHHHhC--CCEEEEEcchhhHHHhc---ccCCCCceeehhccchhh-cCCCCccHHHHHHHHcCCcC
Q 023906 149 QKKVAELIE--GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEI 212 (275)
Q Consensus 149 ~~~l~~~l~--~~ilVgHn~~fDl~~L~---~~~~~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~ 212 (275)
...|.+|+. +...||||+.+|+.+|. +..+ .++|++..+..+ +.....+|+.++..++|...
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~--~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~ 131 (172)
T smart00474 64 LEILKDLLEDETITKVGHNAKFDLHVLARFGIELE--NIFDTMLAAYLLLGGPSKHGLATLLKEYLGVEL 131 (172)
T ss_pred HHHHHHHhcCCCceEEEechHHHHHHHHHCCCccc--chhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCC
Confidence 445667775 45689999999999995 3333 358998766655 33443699999888888774
No 85
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.19 E-value=0.0082 Score=63.95 Aligned_cols=148 Identities=16% Similarity=0.096 Sum_probs=85.9
Q ss_pred CCCcEEEEEEeecCCC--------CCCeeEEEEEEEEeCCCc-EEEEEEecCCccccccceeecCCCHHHHcCCCCHHHH
Q 023906 78 SLTDVVAMDCEMVGIS--------QGNKSALGRVSLVNKWGN-LIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTV 148 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~--------~~~iieIaav~v~d~~g~-~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev 148 (275)
.+-++++||+||++.. .+.|++|+.+....+... .+...++-+.. +..+.| ..+..-.+..++
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~-----c~~i~g---~~V~~f~sE~eL 333 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE-----CASIAG---ANVLSFETEKEL 333 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc-----cccCCC---ceEEEeCCHHHH
Confidence 4567999999998642 257888886544332111 11111111111 112222 123334677888
Q ss_pred HHHHHHHhC---CCEEEEEcc-hhhHHHhc-------cc----CCC------------------------------Ccee
Q 023906 149 QKKVAELIE---GRILVGHAL-HNDLKALL-------LT----HSK------------------------------KDLR 183 (275)
Q Consensus 149 ~~~l~~~l~---~~ilVgHn~-~fDl~~L~-------~~----~~~------------------------------~~~i 183 (275)
+..|.+|+. -.+|+|||+ .||+.+|. +. +.+ .-++
T Consensus 334 L~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~i 413 (1054)
T PTZ00166 334 LLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQF 413 (1054)
T ss_pred HHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEEEE
Confidence 888888884 689999998 89999873 11 000 0123
Q ss_pred ehhccchhhcCCCCccHHHHHHHHcCCcCCCCCC-------------------ChHHHHHHHHHHHHHh
Q 023906 184 DTSEYQPFLKNGRSKALRHLAAEILAVEIQNGEH-------------------CPIDDARAAMLLYMKN 233 (275)
Q Consensus 184 Dt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~H-------------------~Al~DA~ata~L~~~l 233 (275)
|+..+.+......+++|++++..+||.....-.| =.+.||..+++|+.++
T Consensus 414 Dl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl 482 (1054)
T PTZ00166 414 DVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKL 482 (1054)
T ss_pred EHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333332223467899999988899966432111 1256777777777765
No 86
>PHA02570 dexA exonuclease; Provisional
Probab=97.04 E-value=0.0022 Score=56.00 Aligned_cols=91 Identities=18% Similarity=0.192 Sum_probs=56.3
Q ss_pred EEEEEeecCCCCC-CeeEEEEEEEEeCCCcEE--EEEEecCCccccc-cceeec-CC------------CHH---HHc--
Q 023906 83 VAMDCEMVGISQG-NKSALGRVSLVNKWGNLI--YDEFVRPLERVVD-FRTRIS-GI------------RPR---DLR-- 140 (275)
Q Consensus 83 vviD~EtTGl~~~-~iieIaav~v~d~~g~~i--~~~~V~P~~~i~~-~~~~ih-GI------------t~e---~l~-- 140 (275)
+.||+||.|..++ -|++||+|-+...-| .. |+.+|.....+.- ...+.. +. ++| .|.
T Consensus 4 lMIDlETmG~~p~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s 82 (220)
T PHA02570 4 FIIDFETFGNTPDGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPS 82 (220)
T ss_pred EEEEeeccCCCCCceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCC
Confidence 6899999999955 899999888754223 22 5544542211110 011111 11 111 111
Q ss_pred -CCCCHHHHHHHHHHHhC--C-----CEEEEEcchhhHHHhc
Q 023906 141 -KAKDFPTVQKKVAELIE--G-----RILVGHALHNDLKALL 174 (275)
Q Consensus 141 -~a~~~~ev~~~l~~~l~--~-----~ilVgHn~~fDl~~L~ 174 (275)
+..++.+++.+|.+|+. + ..+.|....||+.+|.
T Consensus 83 ~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 83 DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred CccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHH
Confidence 23679999999999995 2 3577888999999995
No 87
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=96.96 E-value=0.032 Score=46.27 Aligned_cols=90 Identities=30% Similarity=0.333 Sum_probs=59.4
Q ss_pred HHHHHHHhC--CCEEEEEcchhhHHHhcc--cCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCCC------C--
Q 023906 149 QKKVAELIE--GRILVGHALHNDLKALLL--THSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNG------E-- 216 (275)
Q Consensus 149 ~~~l~~~l~--~~ilVgHn~~fDl~~L~~--~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~------~-- 216 (275)
...|..++. +...||||+.+|+.+|.. ......+.|+......+......+|+.++..++|...... .
T Consensus 53 ~~~l~~ll~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~ 132 (178)
T cd06142 53 LSPLKELLADPNIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKR 132 (178)
T ss_pred HHHHHHHHcCCCceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCC
Confidence 344666775 457899999999999852 2223346899876666644444699999888888763211 0
Q ss_pred -------CChHHHHHHHHHHHHHhHHHHH
Q 023906 217 -------HCPIDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 217 -------H~Al~DA~ata~L~~~l~~~~e 238 (275)
+-+..||.++..|+..+.++.+
T Consensus 133 ~l~~~~~~yaa~~a~~l~~L~~~l~~~L~ 161 (178)
T cd06142 133 PLTDEQLEYAALDVRYLLPLYEKLKEELE 161 (178)
T ss_pred CCCHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 0255667777778777766554
No 88
>PRK05762 DNA polymerase II; Reviewed
Probab=96.92 E-value=0.015 Score=60.27 Aligned_cols=139 Identities=14% Similarity=0.094 Sum_probs=82.8
Q ss_pred CCCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC
Q 023906 78 SLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (275)
..-++++||+||++- +.|..|+.. +.....++- +.+..... .+.+...++-.+++..|.+++.
T Consensus 153 p~lrvlsfDIE~~~~--~~i~sI~~~---~~~~~~vi~--ig~~~~~~----------~~~v~~~~sE~~LL~~F~~~i~ 215 (786)
T PRK05762 153 PPLKVVSLDIETSNK--GELYSIGLE---GCGQRPVIM--LGPPNGEA----------LDFLEYVADEKALLEKFNAWFA 215 (786)
T ss_pred CCCeEEEEEEEEcCC--CceEEeeec---CCCCCeEEE--EECCCCCC----------cceEEEcCCHHHHHHHHHHHHH
Confidence 556899999999874 355555532 211222211 22211110 0114445788899999999985
Q ss_pred ---CCEEEEEcc-hhhHHHhc-------ccC--------------CC-----------Cceeehhccchhh-cCCCCccH
Q 023906 158 ---GRILVGHAL-HNDLKALL-------LTH--------------SK-----------KDLRDTSEYQPFL-KNGRSKAL 200 (275)
Q Consensus 158 ---~~ilVgHn~-~fDl~~L~-------~~~--------------~~-----------~~~iDt~~l~~~~-~~~~~~sL 200 (275)
-.+++|||+ .||+.+|. +.+ +. .-.+|+..+.+.. ....+++|
T Consensus 216 ~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~~~l~sysL 295 (786)
T PRK05762 216 EHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSATWVFDSFSL 295 (786)
T ss_pred hcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhhccCCCCCH
Confidence 479999998 89999984 111 00 0134444333322 24578999
Q ss_pred HHHHHHHcCCcCCC-CCC-------------------ChHHHHHHHHHHHHHh
Q 023906 201 RHLAAEILAVEIQN-GEH-------------------CPIDDARAAMLLYMKN 233 (275)
Q Consensus 201 ~~l~~~~lgi~~~~-~~H-------------------~Al~DA~ata~L~~~l 233 (275)
+.+|..++|..... ..| =.+.||..|..|+.++
T Consensus 296 ~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~kl 348 (786)
T PRK05762 296 EYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEKT 348 (786)
T ss_pred HHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 99988888865321 111 1367899999998854
No 89
>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=96.85 E-value=0.063 Score=51.34 Aligned_cols=84 Identities=14% Similarity=0.135 Sum_probs=48.7
Q ss_pred CcEEEEEEeecCCC---------CCCeeEEEEEEEEeCCCcEE--EEE-EecCCccccccceeecCCCHHHHcCCCCHHH
Q 023906 80 TDVVAMDCEMVGIS---------QGNKSALGRVSLVNKWGNLI--YDE-FVRPLERVVDFRTRISGIRPRDLRKAKDFPT 147 (275)
Q Consensus 80 ~~~vviD~EtTGl~---------~~~iieIaav~v~d~~g~~i--~~~-~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~e 147 (275)
..+++||+||+... .+.|+.|+.+.- +...... ... ...+...+. |+. +..-....+
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~-------~~~---~~~~~~E~~ 71 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVIN-DGDKKGPEERICFTLGTCKEID-------GVE---VYEFNNEKE 71 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEE-ECCCCCCceeEEEEecCcCCCC-------CCe---EEecCCHHH
Confidence 56899999998764 235556663332 2222111 111 123332222 211 222236778
Q ss_pred HHHHHHHHhC---CCEEEEEcc-hhhHHHhc
Q 023906 148 VQKKVAELIE---GRILVGHAL-HNDLKALL 174 (275)
Q Consensus 148 v~~~l~~~l~---~~ilVgHn~-~fDl~~L~ 174 (275)
++..|.+++. ..+++|||. .||+.+|.
T Consensus 72 lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~ 102 (471)
T smart00486 72 LLKAFLEFIKKYDPDIIYGHNISNFDLPYII 102 (471)
T ss_pred HHHHHHHHHHHhCCCEEEeecCCCCCHHHHH
Confidence 8888888874 469999999 69999874
No 90
>PHA02528 43 DNA polymerase; Provisional
Probab=96.78 E-value=0.029 Score=58.68 Aligned_cols=153 Identities=14% Similarity=0.003 Sum_probs=83.9
Q ss_pred CCCCCcEEEEEEeecCCC--C------CCeeEEEEEEEEeCCCcEEEEEEec---CCccccccceeecCCCHHHHcCCCC
Q 023906 76 DFSLTDVVAMDCEMVGIS--Q------GNKSALGRVSLVNKWGNLIYDEFVR---PLERVVDFRTRISGIRPRDLRKAKD 144 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~--~------~~iieIaav~v~d~~g~~i~~~~V~---P~~~i~~~~~~ihGIt~e~l~~a~~ 144 (275)
+.+.-++++||+||+.-+ | +.|+.|| +.+..+..++-..+. |.....+... -.-.....+....+
T Consensus 102 ~~p~lrv~s~DIE~~~~~gfP~p~~~~d~IisIs---l~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~~~~v~~~~~~s 177 (881)
T PHA02528 102 DRSKIRIANLDIEVTAEDGFPDPEEAKYEIDAIT---HYDSIDDRFYVFDLGSVEEWDAKGDEVP-QEILDKVVYMPFDT 177 (881)
T ss_pred CCCCccEEEEEEEECCCCCCCCcccCCCcEEEEE---EecCCCCEEEEEEecCcccccccCCccc-ccccCCeeEEEcCC
Confidence 434678999999997622 1 2455555 455545542222221 1000000000 00001111222467
Q ss_pred HHHHHHHHHHHhC---CCEEEEEcc-hhhHHHhc-----c-c--C----CCCc------------------------eee
Q 023906 145 FPTVQKKVAELIE---GRILVGHAL-HNDLKALL-----L-T--H----SKKD------------------------LRD 184 (275)
Q Consensus 145 ~~ev~~~l~~~l~---~~ilVgHn~-~fDl~~L~-----~-~--~----~~~~------------------------~iD 184 (275)
-.+++..|.+|+. -.+|+|||+ .||+.+|. + . . .... ++|
T Consensus 178 E~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD 257 (881)
T PHA02528 178 EREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILD 257 (881)
T ss_pred HHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEe
Confidence 8999999999984 579999998 99999873 0 1 0 0000 112
Q ss_pred hhccchhh--cCCCCccHHHHHHHHcCCcCCCC----------------CCChHHHHHHHHHHHHH
Q 023906 185 TSEYQPFL--KNGRSKALRHLAAEILAVEIQNG----------------EHCPIDDARAAMLLYMK 232 (275)
Q Consensus 185 t~~l~~~~--~~~~~~sL~~l~~~~lgi~~~~~----------------~H~Al~DA~ata~L~~~ 232 (275)
...+.+.+ ....+++|++++..+||..-..- .+=.+.||..+.+|+.+
T Consensus 258 ~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 258 YLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 22222211 23568999999877899765421 12236688888888877
No 91
>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=96.64 E-value=0.1 Score=43.51 Aligned_cols=105 Identities=23% Similarity=0.196 Sum_probs=65.6
Q ss_pred CcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC--
Q 023906 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE-- 157 (275)
Q Consensus 80 ~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~-- 157 (275)
.+.++||+|++|.++.. -.+..+.+... +... ||.+... + .+...|.+++.
T Consensus 3 ~~~~~~~~~~~~~~~~~-~~l~~i~l~~~-~~~~---~i~~~~~----------~------------~~~~~l~~~l~~~ 55 (178)
T cd06140 3 ADEVALYVELLGENYHT-ADIIGLALANG-GGAY---YIPLELA----------L------------LDLAALKEWLEDE 55 (178)
T ss_pred CCceEEEEEEcCCCcce-eeEEEEEEEeC-CcEE---EEeccch----------H------------HHHHHHHHHHhCC
Confidence 46789999999988422 12333555442 2222 2322110 0 14455667776
Q ss_pred CCEEEEEcchhhHHHhc---ccCCCCceeehhccchhhcCC-CCccHHHHHHHHcCCcC
Q 023906 158 GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLKNG-RSKALRHLAAEILAVEI 212 (275)
Q Consensus 158 ~~ilVgHn~~fDl~~L~---~~~~~~~~iDt~~l~~~~~~~-~~~sL~~l~~~~lgi~~ 212 (275)
+...|+||+.+|+.+|. +..+. .+.||+...-.+... .+++|+.++.+++|.+.
T Consensus 56 ~~~ki~~d~K~~~~~l~~~gi~~~~-~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 56 KIPKVGHDAKRAYVALKRHGIELAG-VAFDTMLAAYLLDPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred CCceeccchhHHHHHHHHCCCcCCC-cchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCC
Confidence 35689999999999985 33332 357998776666443 34799999888888763
No 92
>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=96.62 E-value=0.013 Score=53.61 Aligned_cols=87 Identities=13% Similarity=0.081 Sum_probs=52.3
Q ss_pred CCCcEEEEEEeecCCCC-------CCeeEEEEEEEEe---CCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHH
Q 023906 78 SLTDVVAMDCEMVGISQ-------GNKSALGRVSLVN---KWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPT 147 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~~-------~~iieIaav~v~d---~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~e 147 (275)
.+-++++||+||...+. +.|+.|+.+.-.. ......+-.+. +...+.. ...+.-..+..+
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~-~~~~~~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLG-SCDSIED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECS-CSCCTTC---------TTEEEEESSHHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEec-CCCCCCC---------CcEEEEECCHHH
Confidence 56789999999998761 2566666322211 11222222222 2222111 222333467788
Q ss_pred HHHHHHHHh---CCCEEEEEcc-hhhHHHhc
Q 023906 148 VQKKVAELI---EGRILVGHAL-HNDLKALL 174 (275)
Q Consensus 148 v~~~l~~~l---~~~ilVgHn~-~fDl~~L~ 174 (275)
++..|.+++ +-.+++|||+ .||+.+|.
T Consensus 225 lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 225 LLEAFLDIIQEYDPDIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHHHHS-SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHHhcCCcEEEEecccCCCHHHHH
Confidence 888888887 4689999999 89999984
No 93
>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=96.36 E-value=0.03 Score=49.57 Aligned_cols=75 Identities=28% Similarity=0.300 Sum_probs=51.8
Q ss_pred HcCCCCHHHHHHHHHHHhC---CCEEEEEcc-hhhHHHhc-------cc------------CCC---------------C
Q 023906 139 LRKAKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL-------LT------------HSK---------------K 180 (275)
Q Consensus 139 l~~a~~~~ev~~~l~~~l~---~~ilVgHn~-~fDl~~L~-------~~------------~~~---------------~ 180 (275)
+.-..+..+++..|..++. -.++||||+ .||+.+|- +. .|. .
T Consensus 76 v~~~~~E~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GR 155 (234)
T cd05776 76 VRIFENERALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGR 155 (234)
T ss_pred EEEeCCHHHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCc
Confidence 3345678888999988884 689999999 99999983 11 010 1
Q ss_pred ceeehhccchhhcCCCCccHHHHHHHHcCCcCC
Q 023906 181 DLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQ 213 (275)
Q Consensus 181 ~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~ 213 (275)
-++|+....+.+....+|+|.++|..+||....
T Consensus 156 l~~D~~~~~k~~~~~~sY~L~~va~~~Lg~~k~ 188 (234)
T cd05776 156 LLCDTYLSAKELIRCKSYDLTELSQQVLGIERQ 188 (234)
T ss_pred hhhccHHHHHHHhCCCCCChHHHHHHHhCcCcc
Confidence 134554444433347899999998889998543
No 94
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=96.33 E-value=0.042 Score=59.15 Aligned_cols=164 Identities=19% Similarity=0.193 Sum_probs=96.2
Q ss_pred CCcEEEEEEeecCCC---CC-CeeEEEEEEE-EeCCCcEEEEEEecCCccccccc----eeecCCCHHHHcCCCCHHHHH
Q 023906 79 LTDVVAMDCEMVGIS---QG-NKSALGRVSL-VNKWGNLIYDEFVRPLERVVDFR----TRISGIRPRDLRKAKDFPTVQ 149 (275)
Q Consensus 79 ~~~~vviD~EtTGl~---~~-~iieIaav~v-~d~~g~~i~~~~V~P~~~i~~~~----~~ihGIt~e~l~~a~~~~ev~ 149 (275)
.-.+++||+|||-+. |+ +-.+|-.|+. +|+.|..|.+.=|-- ..|.++- -++-| +=.+-+.+....++
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs-~DIedfEYTPKpE~eG--~F~v~Ne~dEv~Ll 321 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVS-EDIEDFEYTPKPEYEG--PFCVFNEPDEVGLL 321 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhc-cchhhcccCCcccccc--ceEEecCCcHHHHH
Confidence 457999999999997 44 3345555554 577777664432210 0111110 00001 00123456667778
Q ss_pred HHHHHHh---CCCEEEEEcc-hhhHHHhc-------------ccCCC-------Cceeehhccchhhc-----CCCCccH
Q 023906 150 KKVAELI---EGRILVGHAL-HNDLKALL-------------LTHSK-------KDLRDTSEYQPFLK-----NGRSKAL 200 (275)
Q Consensus 150 ~~l~~~l---~~~ilVgHn~-~fDl~~L~-------------~~~~~-------~~~iDt~~l~~~~~-----~~~~~sL 200 (275)
.++.+.+ +-.++|.+|. =||+.|+. +.+.+ ..+..-+..+++.. +..+.+|
T Consensus 322 ~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSqgL 401 (2173)
T KOG1798|consen 322 QRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQGL 401 (2173)
T ss_pred HHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCcccch
Confidence 8877766 3689999998 67999985 11111 01222222333321 2457899
Q ss_pred HHHHHHHcCCcCCC-------------C---CCChHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 023906 201 RHLAAEILAVEIQN-------------G---EHCPIDDARAAMLLYMKNRKQWEKSVKDQT 245 (275)
Q Consensus 201 ~~l~~~~lgi~~~~-------------~---~H~Al~DA~ata~L~~~l~~~~e~~l~~~~ 245 (275)
+.+....||.+... . +--+.+||-||.-||.++...|--.+-..+
T Consensus 402 KAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhPFIFsLctII 462 (2173)
T KOG1798|consen 402 KAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHPFIFSLCTII 462 (2173)
T ss_pred hHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhhHHhhhhhcc
Confidence 99888889976532 1 344689999999999999776654444333
No 95
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=96.11 E-value=0.037 Score=55.05 Aligned_cols=90 Identities=24% Similarity=0.172 Sum_probs=62.9
Q ss_pred HHHHHHHHhC--CCEEEEEcchhhHHHhcccCC-CCceeehhccchhh-cCCCCccHHHHHHHHcCCcCCCC--------
Q 023906 148 VQKKVAELIE--GRILVGHALHNDLKALLLTHS-KKDLRDTSEYQPFL-KNGRSKALRHLAAEILAVEIQNG-------- 215 (275)
Q Consensus 148 v~~~l~~~l~--~~ilVgHn~~fDl~~L~~~~~-~~~~iDt~~l~~~~-~~~~~~sL~~l~~~~lgi~~~~~-------- 215 (275)
+...+..|+. +...||||+.||+.+|...-. .....||+...-.+ ++...+.+++|+..+++......
T Consensus 66 ~~~~l~~~l~~~~~~kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~ 145 (593)
T COG0749 66 VLAALKPLLEDEGIKKVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGK 145 (593)
T ss_pred hHHHHHHHhhCcccchhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhcccc
Confidence 7788889997 456999999999999963222 23467888655444 45557899999777777665421
Q ss_pred -------------CCChHHHHHHHHHHHHHhHHHH
Q 023906 216 -------------EHCPIDDARAAMLLYMKNRKQW 237 (275)
Q Consensus 216 -------------~H~Al~DA~ata~L~~~l~~~~ 237 (275)
.-.+-.||.++.+|+..+..+.
T Consensus 146 ~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l 180 (593)
T COG0749 146 KQLTFADVKLEKATEYAAEDADATLRLESILEPEL 180 (593)
T ss_pred ccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 1234568888888888876543
No 96
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=95.80 E-value=0.17 Score=49.72 Aligned_cols=95 Identities=14% Similarity=0.079 Sum_probs=55.4
Q ss_pred CCCCCcEEEEEEeecCCC-CC---CeeEEEEEEEEeCC--C--cEEEEEE--ecCCccccccceee-cC-CCHHHHcCCC
Q 023906 76 DFSLTDVVAMDCEMVGIS-QG---NKSALGRVSLVNKW--G--NLIYDEF--VRPLERVVDFRTRI-SG-IRPRDLRKAK 143 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~-~~---~iieIaav~v~d~~--g--~~i~~~~--V~P~~~i~~~~~~i-hG-It~e~l~~a~ 143 (275)
+...-++..||+|.|+.. |+ ...+|-++...|.. . -.+|+.+ +.+-. +....+ -+ +..-.+-..+
T Consensus 102 d~~~i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~v~v~~f~ 178 (498)
T PHA02524 102 DRDDVVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLVKDVGHWD---PKKSVLEKYILDNVVYMPFE 178 (498)
T ss_pred chhhceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEeccccccCCC---cccccccccccCCeEEEEeC
Confidence 445567999999998865 43 23456666665532 1 1223332 11111 000000 00 1111123346
Q ss_pred CHHHHHHHHHHHhC---CCEEEEEcc-hhhHHHh
Q 023906 144 DFPTVQKKVAELIE---GRILVGHAL-HNDLKAL 173 (275)
Q Consensus 144 ~~~ev~~~l~~~l~---~~ilVgHn~-~fDl~~L 173 (275)
+-.+++..|.+|+. -.+|+|||+ .||+.+|
T Consensus 179 sE~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL 212 (498)
T PHA02524 179 DEVDLLLNYIQLWKANTPDLVFGWNSEGFDIPYI 212 (498)
T ss_pred CHHHHHHHHHHHHHHhCCCEEEeCCCcccCHHHH
Confidence 78999999999995 489999998 9999887
No 97
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=95.54 E-value=0.24 Score=42.12 Aligned_cols=60 Identities=20% Similarity=0.149 Sum_probs=42.0
Q ss_pred HHHHHhC--CCEEEEEcchhhHHHhc--ccCCCCceeehhccchhhcCCCCccHHHHHHHHcCCc
Q 023906 151 KVAELIE--GRILVGHALHNDLKALL--LTHSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVE 211 (275)
Q Consensus 151 ~l~~~l~--~~ilVgHn~~fDl~~L~--~~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~ 211 (275)
.|..++. +...|+|++..|+.+|. ....-..++|++.....+... ..+|+.++.+++|..
T Consensus 68 ~L~~~L~~~~i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~~~l~~l~~~yl~~~ 131 (192)
T cd06147 68 ILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-RHSLAYLLQKYCNVD 131 (192)
T ss_pred HHHHHhcCCCceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-cccHHHHHHHHhCCC
Confidence 3556665 46789999999999984 222111238998777666444 459999988888775
No 98
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=95.42 E-value=0.29 Score=50.94 Aligned_cols=74 Identities=16% Similarity=0.084 Sum_probs=50.4
Q ss_pred HcCCCCHHHHHHHHHHHh---CCCEEEEEcc-hhhHHHhc-------ccCC-------------------CCceeehhcc
Q 023906 139 LRKAKDFPTVQKKVAELI---EGRILVGHAL-HNDLKALL-------LTHS-------------------KKDLRDTSEY 188 (275)
Q Consensus 139 l~~a~~~~ev~~~l~~~l---~~~ilVgHn~-~fDl~~L~-------~~~~-------------------~~~~iDt~~l 188 (275)
+....+-.+++..|..++ +..++||||. .||+.+|. +... ....+|....
T Consensus 205 v~~~~~e~e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~ 284 (792)
T COG0417 205 VEVVISEAELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPA 284 (792)
T ss_pred eEEecCHHHHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHH
Confidence 444567788889998887 4689999999 59999985 1111 1234555544
Q ss_pred ch-hhcCCCCccHHHHHHHHcCCcC
Q 023906 189 QP-FLKNGRSKALRHLAAEILAVEI 212 (275)
Q Consensus 189 ~~-~~~~~~~~sL~~l~~~~lgi~~ 212 (275)
.. .......++|...+..+++..-
T Consensus 285 ~~~~~~~~~~ysl~~v~~~~l~~~k 309 (792)
T COG0417 285 LRRRPLNLKSYSLEAVSEALLGEGK 309 (792)
T ss_pred HhhhhcccccccHHHHHHHhccccc
Confidence 44 2345678899998777777665
No 99
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=94.59 E-value=0.0081 Score=60.69 Aligned_cols=135 Identities=16% Similarity=0.219 Sum_probs=77.7
Q ss_pred CCCcEEEEEEeecCCC---C----CCeeEEEEEEEEeCCCcEEE-EEE-ecCCccccccceeecCCCHHHHcCCCC---H
Q 023906 78 SLTDVVAMDCEMVGIS---Q----GNKSALGRVSLVNKWGNLIY-DEF-VRPLERVVDFRTRISGIRPRDLRKAKD---F 145 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~---~----~~iieIaav~v~d~~g~~i~-~~~-V~P~~~i~~~~~~ihGIt~e~l~~a~~---~ 145 (275)
.+-++..||+|+.|.. | +.+|+||-+...-+++...+ +.+ ++|-.+ |.-.++-.-.. +
T Consensus 272 APlrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~pf~rnvf~l~~cap----------I~G~~V~~~~~e~el 341 (1066)
T KOG0969|consen 272 APLRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEPFVRNVFTLKTCAP----------IVGSNVHSYETEKEL 341 (1066)
T ss_pred ccccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCchHHHhhhcccCcCC----------CCCceeEEeccHHHH
Confidence 3567899999999986 2 35778886655544444431 222 222223 22223322222 3
Q ss_pred HHHHHHHHHHhCCCEEEEEcc-hhhHHHhc-------c-cCC--------CCceeehhccchhh----------------
Q 023906 146 PTVQKKVAELIEGRILVGHAL-HNDLKALL-------L-THS--------KKDLRDTSEYQPFL---------------- 192 (275)
Q Consensus 146 ~ev~~~l~~~l~~~ilVgHn~-~fDl~~L~-------~-~~~--------~~~~iDt~~l~~~~---------------- 192 (275)
-+.|..|..-++-.+|+|||+ .||+..|- + .+| +..+.|+..-.+.+
T Consensus 342 L~~W~~firevDPDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqf 421 (1066)
T KOG0969|consen 342 LESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQF 421 (1066)
T ss_pred HHHHHHHHHhcCCCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeee
Confidence 345555555567899999999 99997762 1 111 11233432211110
Q ss_pred ---------cCCCCccHHHHHHHHcCCcCCCCCCChHHH
Q 023906 193 ---------KNGRSKALRHLAAEILAVEIQNGEHCPIDD 222 (275)
Q Consensus 193 ---------~~~~~~sL~~l~~~~lgi~~~~~~H~Al~D 222 (275)
...++|+|...+..+||..-+.-+|+-+.|
T Consensus 422 Dllqvi~Rd~KLrSytLNaVs~hFL~EQKEDV~~siItd 460 (1066)
T KOG0969|consen 422 DLLQVILRDYKLRSYTLNAVSAHFLGEQKEDVHHSIITD 460 (1066)
T ss_pred hHHHHHHHhhhhhhcchhhhHHHhhhhhcccccccchhh
Confidence 135689999998899998777556766543
No 100
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.20 E-value=0.17 Score=53.22 Aligned_cols=93 Identities=18% Similarity=0.058 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHhCC--CEEEEEcchhhHHHhc---ccCCCCceeehhccchhhcCCCCccHHHHHHHHcCCcCCC-----
Q 023906 145 FPTVQKKVAELIEG--RILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQN----- 214 (275)
Q Consensus 145 ~~ev~~~l~~~l~~--~ilVgHn~~fDl~~L~---~~~~~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~----- 214 (275)
...+...|..|+.+ ...||||+.||+.+|. +.... .+.||+...-.+......+|++++.++++.....
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~-~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~ 441 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGG-VIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIG 441 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCC-cchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhc
Confidence 45667778888864 4589999999999996 22322 4679987766664444469999988887754210
Q ss_pred -C-----C-------CChHHHHHHHHHHHHHhHHHHH
Q 023906 215 -G-----E-------HCPIDDARAAMLLYMKNRKQWE 238 (275)
Q Consensus 215 -~-----~-------H~Al~DA~ata~L~~~l~~~~e 238 (275)
. . .-|..||.++..||..+..+.+
T Consensus 442 ~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 442 GKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred cCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 0 0 1356788889999988866543
No 101
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.79 E-value=2.2 Score=46.47 Aligned_cols=83 Identities=23% Similarity=0.252 Sum_probs=57.8
Q ss_pred eecCCCHHHHcCCCCHHHHHHHHHHHh---CCCEEEEEcc-hhhHHHhc-----ccCC----------------------
Q 023906 130 RISGIRPRDLRKAKDFPTVQKKVAELI---EGRILVGHAL-HNDLKALL-----LTHS---------------------- 178 (275)
Q Consensus 130 ~ihGIt~e~l~~a~~~~ev~~~l~~~l---~~~ilVgHn~-~fDl~~L~-----~~~~---------------------- 178 (275)
..-|+.+..|..-.+-.+.+..+..++ +-.+++|||+ .||+.+|- +..+
T Consensus 569 ~~~~~~~~~L~~~~sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~ 648 (1172)
T TIGR00592 569 EFPGKKPSLVEDLATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERT 648 (1172)
T ss_pred hhhccCCcEEEEecCHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceE
Confidence 344666666666777888888888887 4689999998 99999873 1111
Q ss_pred -CCceeehhccchhhcCCCCccHHHHHHHHcCCcC
Q 023906 179 -KKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEI 212 (275)
Q Consensus 179 -~~~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~ 212 (275)
..-++|+....+......+++|..++..+||.+-
T Consensus 649 ~Grl~~D~~~~~k~~~~~~sy~L~~v~~~~L~~~k 683 (1172)
T TIGR00592 649 CGRMICDVEISAKELIRCKSYDLSELVQQILKTER 683 (1172)
T ss_pred CCEEEEEHHHHHHHHhCcCCCCHHHHHHHHhCCCC
Confidence 1124555554444445788999999999998643
No 102
>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=93.30 E-value=1.6 Score=42.53 Aligned_cols=126 Identities=13% Similarity=0.143 Sum_probs=73.4
Q ss_pred CcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcE--EEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHHhC
Q 023906 80 TDVVAMDCEMVGISQGNKSALGRVSLVNKWGNL--IYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIE 157 (275)
Q Consensus 80 ~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~--i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~l~ 157 (275)
...++||+||+. +.+-...+|.+.. + .|.. .|..|+.... ....+++.+|.+|+.
T Consensus 284 ~~~~ffDiEt~P-~~~~~yL~G~~~~-~-~~~~~~~~~~fla~~~--------------------~~E~~~~~~f~~~l~ 340 (457)
T TIGR03491 284 PGELIFDIESDP-DENLDYLHGFLVV-D-KGQENEKYRPFLAEDP--------------------NTEELAWQQFLQLLQ 340 (457)
T ss_pred CccEEEEecCCC-CCCCceEEEEEEe-c-CCCCCcceeeeecCCc--------------------hHHHHHHHHHHHHHH
Confidence 567899999994 2233457775332 2 2322 1544443321 124556666766664
Q ss_pred ---CCEEEEEcchhhHHHhc-----ccCCC-------Cceeehhccch--hhcCCCCccHHHHHHHHcCCcCCCCCCChH
Q 023906 158 ---GRILVGHALHNDLKALL-----LTHSK-------KDLRDTSEYQP--FLKNGRSKALRHLAAEILAVEIQNGEHCPI 220 (275)
Q Consensus 158 ---~~ilVgHn~~fDl~~L~-----~~~~~-------~~~iDt~~l~~--~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al 220 (275)
+..|+.|| .|...+|+ +..+. .+++|.....+ ++-+..++||+.+ ..++|.+... ..
T Consensus 341 ~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v-~~~lg~~~~~----~~ 414 (457)
T TIGR03491 341 SYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSI-ARWLGFEWRQ----KE 414 (457)
T ss_pred HCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHH-HHHhCcccCC----CC
Confidence 55788888 88888876 22221 14677764432 2234578999999 6899987652 23
Q ss_pred HHHHHHHHHHHHhH
Q 023906 221 DDARAAMLLYMKNR 234 (275)
Q Consensus 221 ~DA~ata~L~~~l~ 234 (275)
.|.-.++..|..+.
T Consensus 415 ~~G~~ai~~y~~~~ 428 (457)
T TIGR03491 415 ASGAKSLLWYRQWK 428 (457)
T ss_pred CCHHHHHHHHHHHH
Confidence 44445566666553
No 103
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=93.23 E-value=0.21 Score=51.15 Aligned_cols=32 Identities=25% Similarity=0.361 Sum_probs=25.5
Q ss_pred CCCEEEEEcchhhHHHhc----ccCCCCceeehhcc
Q 023906 157 EGRILVGHALHNDLKALL----LTHSKKDLRDTSEY 188 (275)
Q Consensus 157 ~~~ilVgHn~~fDl~~L~----~~~~~~~~iDt~~l 188 (275)
++.++||||+.||..-++ +.-.+.+++||+.+
T Consensus 240 ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSl 275 (1075)
T KOG3657|consen 240 KEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSL 275 (1075)
T ss_pred CCceEEeccccchHHHHHHHHhccccceeeeechhh
Confidence 368999999999999887 34445678899766
No 104
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=92.96 E-value=0.26 Score=43.12 Aligned_cols=148 Identities=20% Similarity=0.175 Sum_probs=82.9
Q ss_pred CcEEEEEEeecCCC--C-------------------C--CeeEEEEEEEEeCCCcEE-------EEEEecCCcccc-ccc
Q 023906 80 TDVVAMDCEMVGIS--Q-------------------G--NKSALGRVSLVNKWGNLI-------YDEFVRPLERVV-DFR 128 (275)
Q Consensus 80 ~~~vviD~EtTGl~--~-------------------~--~iieIaav~v~d~~g~~i-------~~~~V~P~~~i~-~~~ 128 (275)
=++|.+|+|..|.- | + .||+|| +++.|.+|+.- |+.-..|...+- ...
T Consensus 42 Yn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlG-lsLSDe~GN~P~~~sTWQFNF~F~l~~dmya~ES 120 (299)
T COG5228 42 YNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLG-LSLSDENGNKPNGPSTWQFNFEFDLKKDMYATES 120 (299)
T ss_pred CCceeeccccCceeecccccccccchHHHHHHhcccchhhhhhee-eeeccccCCCCCCCceeEEEEEecchhhhcchHH
Confidence 36899999999874 1 1 488999 88988887642 444455554221 111
Q ss_pred ee---ecCCCHHHH-cCCCCHHHHHHHHHHHh--------CCCEEEEEcchhhHHHhc-----ccCCCC-----------
Q 023906 129 TR---ISGIRPRDL-RKAKDFPTVQKKVAELI--------EGRILVGHALHNDLKALL-----LTHSKK----------- 180 (275)
Q Consensus 129 ~~---ihGIt~e~l-~~a~~~~ev~~~l~~~l--------~~~ilVgHn~~fDl~~L~-----~~~~~~----------- 180 (275)
.+ -+||.-+.- .-+.... +|.+++ +.-++|.++..+|+++|- .+.|..
T Consensus 121 ieLL~ksgIdFkkHe~~GI~v~----eF~elLm~SGLvm~e~VtWitfHsaYDfgyLikilt~~plP~~~EdFy~~l~~y 196 (299)
T COG5228 121 IELLRKSGIDFKKHENLGIDVF----EFSELLMDSGLVMDESVTWITFHSAYDFGYLIKILTNDPLPNNKEDFYWWLHQY 196 (299)
T ss_pred HHHHHHcCCChhhHhhcCCCHH----HHHHHHhccCceeccceEEEEeecchhHHHHHHHHhcCCCCccHHHHHHHHHHH
Confidence 11 134443222 1122222 233333 345788999999999874 233321
Q ss_pred --ceeehhccchhhcCCCCccHHHHHHHHcCCcCCCCCCChHHHHHHHHHHHHHhH
Q 023906 181 --DLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQNGEHCPIDDARAAMLLYMKNR 234 (275)
Q Consensus 181 --~~iDt~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~ata~L~~~l~ 234 (275)
.+.|...+..-. -..+-.|.+. +.-+++...+..|.|-.||..|+..|-..+
T Consensus 197 fP~fYDik~v~ks~-~~~~KglQei-~ndlql~r~g~QhQagsdaLlTa~~ff~~R 250 (299)
T COG5228 197 FPNFYDIKLVYKSV-LNNSKGLQEI-KNDLQLQRSGQQHQAGSDALLTADEFFLPR 250 (299)
T ss_pred CccccchHHHHHhh-hhhhhHHHHh-cCcHhhhccchhhhccchhhhhhHHhcchh
Confidence 122322211110 0112345555 455666666668999999999999886554
No 105
>PF00843 Arena_nucleocap: Arenavirus nucleocapsid protein; InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. The arenavirus S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired "hairpin" structure. The mature glycoproteins that result are G1 and G2 and the N protein []. This family represents the nucleocapsid protein that encapsulates the viral ssRNA [].; GO: 0019013 viral nucleocapsid; PDB: 3MX5_A 3MX2_C 3MWT_C 3Q7C_A 3MWP_B 3Q7B_A 3T5Q_E 3T5N_A 3R3L_B.
Probab=92.44 E-value=0.15 Score=48.67 Aligned_cols=142 Identities=17% Similarity=0.216 Sum_probs=75.8
Q ss_pred CCCCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCc--cccccceeecCCCHHHHcCCCCHHHHHHHHHH
Q 023906 77 FSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLE--RVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE 154 (275)
Q Consensus 77 ~~~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~--~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~ 154 (275)
..+..-.+||+|-. ++..+|||.. ..+.....+.|=+|.+ .+.+....-|||--.||.++.| -+...+..
T Consensus 369 Ldp~~ttWiDIEG~---p~DPVElAiy---QP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aqP--GL~S~vi~ 440 (533)
T PF00843_consen 369 LDPNATTWIDIEGP---PNDPVELAIY---QPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQP--GLTSAVIE 440 (533)
T ss_dssp S-TTS-EEEEEESE---TTSESEEEEE---ETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB-T--THHHHHHH
T ss_pred CCCCCCeeEecCCC---CCCCeEEEEe---ccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhcc--chHHHHHH
Confidence 45677899999966 5566888844 3333344566667775 4555667779999999998855 45677788
Q ss_pred HhCCCEEEEEcchhhHHHhcccCCCC--ceeehhccc---hhhcCCCCccHHHHHHHHcCCcCCC----------CCCCh
Q 023906 155 LIEGRILVGHALHNDLKALLLTHSKK--DLRDTSEYQ---PFLKNGRSKALRHLAAEILAVEIQN----------GEHCP 219 (275)
Q Consensus 155 ~l~~~ilVgHn~~fDl~~L~~~~~~~--~~iDt~~l~---~~~~~~~~~sL~~l~~~~lgi~~~~----------~~H~A 219 (275)
.+....++.--..-|++-|--.|.+. .++|...-. +.+...-.-....||..+-|+-+.. ++|+|
T Consensus 441 ~LP~~MVlT~QGsDDIrkLld~hGRrDiKlvDV~lt~eqaR~FEd~VWd~f~~LC~~H~GvVv~KKKkg~~~~~t~PHCA 520 (533)
T PF00843_consen 441 LLPKNMVLTCQGSDDIRKLLDMHGRRDIKLVDVKLTSEQARKFEDQVWDRFGHLCKKHTGVVVKKKKKGKKPESTNPHCA 520 (533)
T ss_dssp HS-TT-EEEESSHHHHHHHHHCTT-TTSEEEE----HHHHTTTHHHHHHHHGGG---B-S-EEE--SSSS-EEE-----H
T ss_pred hCCcCcEEEeeChHHHHHHHHhcCCCcceEEEeecCHHHHHHHHHHHHHHHHHHHHhcCceEEecccCCCCCCCCCchHH
Confidence 88766665555578888877666654 367765432 2221112234556777777765431 37999
Q ss_pred HHHHHHH
Q 023906 220 IDDARAA 226 (275)
Q Consensus 220 l~DA~at 226 (275)
|-||++-
T Consensus 521 LlDCiMf 527 (533)
T PF00843_consen 521 LLDCIMF 527 (533)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9999863
No 106
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=91.40 E-value=1.2 Score=35.50 Aligned_cols=59 Identities=22% Similarity=0.132 Sum_probs=42.2
Q ss_pred HHHHhC--CCEEEEEcchhhHHHhcc---cCCCCceeehhccchhhcCCC-CccHHHHHHHHcCCc
Q 023906 152 VAELIE--GRILVGHALHNDLKALLL---THSKKDLRDTSEYQPFLKNGR-SKALRHLAAEILAVE 211 (275)
Q Consensus 152 l~~~l~--~~ilVgHn~~fDl~~L~~---~~~~~~~iDt~~l~~~~~~~~-~~sL~~l~~~~lgi~ 211 (275)
|.+++. +...|+||+.+|+.+|.. ..+ ..+.|++..+..+.... +.+|+.++.+++|.+
T Consensus 45 l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~-~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKALKVGQNLKYDRGILLNYFIELR-GIAFDTMLEAYILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCCceeeecHHHHHHHHHHcCCccC-CcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence 556664 466899999999999852 222 23589987766664432 469999988888876
No 107
>PRK05761 DNA polymerase I; Reviewed
Probab=90.01 E-value=3.1 Score=43.40 Aligned_cols=88 Identities=15% Similarity=0.067 Sum_probs=56.3
Q ss_pred CCHHHHHHHHHHHhC-CCEEEEEcc-hhhHHHhc-----ccCC-----C----Cc-eeehhccchhh--------c--CC
Q 023906 143 KDFPTVQKKVAELIE-GRILVGHAL-HNDLKALL-----LTHS-----K----KD-LRDTSEYQPFL--------K--NG 195 (275)
Q Consensus 143 ~~~~ev~~~l~~~l~-~~ilVgHn~-~fDl~~L~-----~~~~-----~----~~-~iDt~~l~~~~--------~--~~ 195 (275)
.+-.+++..|.+|+. -.+.|++|. .||+.+|. +..+ . .. .+|....+... . ..
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~ 287 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRH 287 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeec
Confidence 678899999999996 567778998 89999984 1111 0 00 13432222110 0 12
Q ss_pred CCccHHHHHHHHcCCcCCCC------------CCChHHHHHHHHHHH
Q 023906 196 RSKALRHLAAEILAVEIQNG------------EHCPIDDARAAMLLY 230 (275)
Q Consensus 196 ~~~sL~~l~~~~lgi~~~~~------------~H~Al~DA~ata~L~ 230 (275)
++++|+..+..+||..-..- +.=.+.||..|..|+
T Consensus 288 ~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 288 REARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 36899999888999764210 123578999999884
No 108
>PHA02563 DNA polymerase; Provisional
Probab=81.24 E-value=4.9 Score=40.80 Aligned_cols=68 Identities=18% Similarity=0.177 Sum_probs=41.5
Q ss_pred CCCCCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHHHHHHHHHHH
Q 023906 76 DFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAEL 155 (275)
Q Consensus 76 ~~~~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ev~~~l~~~ 155 (275)
...+..+++.|+||++.+.+. ...+ +.+.| |.. +.+|.-- ..+ ++|..|
T Consensus 8 k~~~~~~~~~DfET~t~~~~~-~~~~-~~~~d--~~~-~~s~~~~----------------------~~~----~~f~~~ 56 (630)
T PHA02563 8 KHKPRKILACDFETTTINKDC-RRWF-WGEID--VED-FPSYYGG----------------------NSF----DEFLQW 56 (630)
T ss_pred ccccceEEEEEEEecccCCcc-eeee-eeEec--cce-eceeecc----------------------ccH----HHHHHH
Confidence 345678999999999997432 1222 23434 433 2232210 112 255555
Q ss_pred hC-------CCEEEEEcchhhHHHhc
Q 023906 156 IE-------GRILVGHALHNDLKALL 174 (275)
Q Consensus 156 l~-------~~ilVgHn~~fDl~~L~ 174 (275)
+. +.++..||+.||..||.
T Consensus 57 i~~~~~k~~~~~vYfHN~~FD~~Fil 82 (630)
T PHA02563 57 IEDTTYKETECIIYFHNLKFDGSFIL 82 (630)
T ss_pred HhhccccccceEEEEecCCccHHHHH
Confidence 54 67999999999999985
No 109
>PHA03036 DNA polymerase; Provisional
Probab=78.76 E-value=19 Score=38.57 Aligned_cols=101 Identities=12% Similarity=-0.072 Sum_probs=56.1
Q ss_pred CCCCCCCCCcEEEEEEeecCCC--C----CCeeEEEEEEEEeCCCcEEEEEEecCCccc--cccceeecCCC---H-HHH
Q 023906 72 PINDDFSLTDVVAMDCEMVGIS--Q----GNKSALGRVSLVNKWGNLIYDEFVRPLERV--VDFRTRISGIR---P-RDL 139 (275)
Q Consensus 72 p~~~~~~~~~~vviD~EtTGl~--~----~~iieIaav~v~d~~g~~i~~~~V~P~~~i--~~~~~~ihGIt---~-e~l 139 (275)
|.+.-.-+..+++||+|+-.-+ | +-|+.|+. .+++..|...--++++..... ......+-|+. . .++
T Consensus 152 ~i~~~~~~~~~lsfDIEC~~~g~FPs~~~~pvshIs~-~~~~~~~~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (1004)
T PHA03036 152 KIPRFDIPRSYLFLDIECHFDKKFPSVFINPVSHISC-CYIDLSGKEKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDM 230 (1004)
T ss_pred cCCCccCcceeEEEEEEeccCCCCCCcccCcceEEEE-EEEecCCCeeEEEEeccccccccccccceeeeeecccccccc
Confidence 3333344678999999998643 3 36778884 566666655433455443211 11122222221 1 111
Q ss_pred cC-----CCCHHHHHHHHHHHh---CCCEEEEEcc-hhhHHHhc
Q 023906 140 RK-----AKDFPTVQKKVAELI---EGRILVGHAL-HNDLKALL 174 (275)
Q Consensus 140 ~~-----a~~~~ev~~~l~~~l---~~~ilVgHn~-~fDl~~L~ 174 (275)
.. -.+..+++ .+.+++ +-.+++|+|. .||++.|.
T Consensus 231 ~~~~~~~~~sE~~ml-~~~~~i~~~d~D~i~~yNg~nFD~~Yi~ 273 (1004)
T PHA03036 231 DYSKELILCSEIVLL-RIAKKLLELEFDYVVTFNGHNFDLRYIS 273 (1004)
T ss_pred CCceeeecCCHHHHH-HHHHHHHhcCCCEEEeccCCCcchHHHH
Confidence 21 23445544 555555 3689999998 99998763
No 110
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=68.17 E-value=14 Score=36.84 Aligned_cols=58 Identities=19% Similarity=0.161 Sum_probs=39.7
Q ss_pred eeehhccchhhcCCC---CccHHHHHHHHcCCcCCCCC--------------CChHHHHHHHHHHHHHhHHHHHH
Q 023906 182 LRDTSEYQPFLKNGR---SKALRHLAAEILAVEIQNGE--------------HCPIDDARAAMLLYMKNRKQWEK 239 (275)
Q Consensus 182 ~iDt~~l~~~~~~~~---~~sL~~l~~~~lgi~~~~~~--------------H~Al~DA~ata~L~~~l~~~~e~ 239 (275)
++||.....++.... ..+|..++..++++...... .=|..|+..+..||..+..+.++
T Consensus 72 ~fDT~LAa~lL~~~~~~~~~~l~~la~~~l~~~l~k~~~~sdw~rpls~~q~~YAa~Dv~~l~~L~~~L~~qL~~ 146 (553)
T PRK14975 72 CHDLMLASQLLLGSEGRAGSSLSAAAARALGEGLDKPPQTSALSDPPDEEQLLYAAADADVLLELYAVLADQLNR 146 (553)
T ss_pred CchHHHHHHHcCCCCCcCCCCHHHHHHHHhCCCCCChhhhccccccchHHHHHHHHHHhHHHHHHHHHHHHHHHh
Confidence 678887777665443 67899998888888854311 12566777788888777666543
No 111
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=63.90 E-value=19 Score=28.82 Aligned_cols=59 Identities=22% Similarity=0.161 Sum_probs=40.5
Q ss_pred HHHHhC--CCEEEEEcchhhHHHhc---ccCCCCceeehhccchhhcCCCC-ccHHHHHHHHcCCc
Q 023906 152 VAELIE--GRILVGHALHNDLKALL---LTHSKKDLRDTSEYQPFLKNGRS-KALRHLAAEILAVE 211 (275)
Q Consensus 152 l~~~l~--~~ilVgHn~~fDl~~L~---~~~~~~~~iDt~~l~~~~~~~~~-~sL~~l~~~~lgi~ 211 (275)
|.+|+. +...++||+..++.+|. +.... ...|++...-.+.+..+ .+|++++.++++..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~-~~fD~~LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRG-IAFDTMLEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCC-cchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 556675 35589999999999984 33332 24788866655544332 49999988887766
No 112
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=59.33 E-value=31 Score=37.30 Aligned_cols=154 Identities=13% Similarity=0.146 Sum_probs=84.3
Q ss_pred CCCcEEEEEEeecCCCC---CCeeEEEEEEEEeCC-----CcEE----EEEEecCCccccccceeecCCCHHH---HcCC
Q 023906 78 SLTDVVAMDCEMVGISQ---GNKSALGRVSLVNKW-----GNLI----YDEFVRPLERVVDFRTRISGIRPRD---LRKA 142 (275)
Q Consensus 78 ~~~~~vviD~EtTGl~~---~~iieIaav~v~d~~-----g~~i----~~~~V~P~~~i~~~~~~ihGIt~e~---l~~a 142 (275)
++-.+.+|-++|+--.. .+|+.|++...-+.+ +... |..+++|...+-|...+ -+.... +.-.
T Consensus 527 Ppl~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~--ela~~k~~~v~~~ 604 (1429)
T KOG0970|consen 527 PPLTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLK--ELAKQKLSKVVLH 604 (1429)
T ss_pred CCeeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHH--HHHHhccCceEEe
Confidence 34567888888887652 356666644433221 1111 66677887643332110 011111 2222
Q ss_pred CCHHHHHHHHHHHh---CCCEEEEEc-chhhHHHhc-------c-----------cCCC---------------Cc-eee
Q 023906 143 KDFPTVQKKVAELI---EGRILVGHA-LHNDLKALL-------L-----------THSK---------------KD-LRD 184 (275)
Q Consensus 143 ~~~~ev~~~l~~~l---~~~ilVgHn-~~fDl~~L~-------~-----------~~~~---------------~~-~iD 184 (275)
.+...++..|...+ +-.++|||| ..|++.+|- + .++. -+ +.|
T Consensus 605 ~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~CD 684 (1429)
T KOG0970|consen 605 NSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMCD 684 (1429)
T ss_pred cCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccceEEee
Confidence 34556666666655 468999999 499998882 1 1110 01 223
Q ss_pred hhccchhhcCCCCccHHHHHHHHcCCcCCCC------------C------CChHHHHHHHHHHHHHh
Q 023906 185 TSEYQPFLKNGRSKALRHLAAEILAVEIQNG------------E------HCPIDDARAAMLLYMKN 233 (275)
Q Consensus 185 t~~l~~~~~~~~~~sL~~l~~~~lgi~~~~~------------~------H~Al~DA~ata~L~~~l 233 (275)
+-...+-+....+++|.+|+...++.+...- . .+...|+...++|+.++
T Consensus 685 ~~~~a~~lik~~S~~LseL~q~~l~~eR~~i~~~~i~~~y~~s~~L~~ll~~~~~d~~~~l~i~~~l 751 (1429)
T KOG0970|consen 685 LNLAARELIKAQSYSLSELSQQILKEERKEINANEIPKMYEDSKSLTYLLEHTITDAELILQIMFRL 751 (1429)
T ss_pred hHHHHHhhhccccccHHHHHHHHHhhhcccCCHhHhhhhccChHHHHHHHHHHhHHHHHHHHHHHHh
Confidence 3222334444678999999888888732210 1 12345788888887665
No 113
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=58.27 E-value=11 Score=32.84 Aligned_cols=62 Identities=10% Similarity=0.193 Sum_probs=43.9
Q ss_pred CeeEEEEEEEEeCCCcEE-EEEEecCCcccccc-------ceeecCCCHHHHcCCC-CHHHHHHHHHHHhC
Q 023906 96 NKSALGRVSLVNKWGNLI-YDEFVRPLERVVDF-------RTRISGIRPRDLRKAK-DFPTVQKKVAELIE 157 (275)
Q Consensus 96 ~iieIaav~v~d~~g~~i-~~~~V~P~~~i~~~-------~~~ihGIt~e~l~~a~-~~~ev~~~l~~~l~ 157 (275)
-.+|||.+...-.+|-+- |+++|+|......+ ...-|+|.......+. .+..++.+|.+|++
T Consensus 9 ~PaEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~ 79 (213)
T PF13017_consen 9 VPAEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLK 79 (213)
T ss_pred EeEEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhh
Confidence 457899888876666322 99999998633323 2344777766555554 79999999999995
No 114
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=56.10 E-value=41 Score=27.01 Aligned_cols=33 Identities=9% Similarity=-0.096 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHhC-C-CEEEEEcchhhHHHhc
Q 023906 142 AKDFPTVQKKVAELIE-G-RILVGHALHNDLKALL 174 (275)
Q Consensus 142 a~~~~ev~~~l~~~l~-~-~ilVgHn~~fDl~~L~ 174 (275)
..+..+.+..|.+.++ . ..+|+||..|....|+
T Consensus 54 ~DPr~~~~~~L~~~i~~~~g~ivvyN~sfE~~rL~ 88 (130)
T PF11074_consen 54 EDPRRELIEALIKAIGSIYGSIVVYNKSFEKTRLK 88 (130)
T ss_pred CCchHHHHHHHHHHhhhhcCeEEEechHHHHHHHH
Confidence 4567788888888886 5 7999999999998886
No 115
>KOG0968 consensus DNA polymerase zeta, catalytic subunit [Replication, recombination and repair]
Probab=40.85 E-value=84 Score=34.29 Aligned_cols=94 Identities=20% Similarity=0.159 Sum_probs=55.7
Q ss_pred CCCCCCCC-CCCCCcEEEEEEeecCCCCCCeeEEEEEEEEeCCCcEEEEEEecCCccccccceeecCCCHHHHcCCCCHH
Q 023906 68 SPLTPIND-DFSLTDVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLRKAKDFP 146 (275)
Q Consensus 68 ~~~~p~~~-~~~~~~~vviD~EtTGl~~~~iieIaav~v~d~~g~~i~~~~V~P~~~i~~~~~~ihGIt~e~l~~a~~~~ 146 (275)
..+.|.+. +.-..=+.+++-+|--++-+.|...| |.|+|... |.- ....+-.+||+.-.|.-..+..
T Consensus 671 ~dl~PDP~~D~V~~l~~~vq~dtp~pd~~si~~~g-v~Vv~~~~---------~ds--~~~t~~~~~~~~~~V~~~~sE~ 738 (1488)
T KOG0968|consen 671 GDLEPDPVFDSVASLFLCVQEDTPMPDADSIVSVG-VIVVDKVC---------PDS--HVQTTTLGGIYGCRVVVMESEL 738 (1488)
T ss_pred CCCCCCcccccchhhhhhhccCCCCCcccceeeee-EEEEeccC---------ccc--cccccccCCcCCceEEEehhHH
Confidence 44555554 33334467778887777655544455 55554211 211 1112222777755555566677
Q ss_pred HHHHHHHHHh---CCCEEEEEcc-hhhHHHh
Q 023906 147 TVQKKVAELI---EGRILVGHAL-HNDLKAL 173 (275)
Q Consensus 147 ev~~~l~~~l---~~~ilVgHn~-~fDl~~L 173 (275)
+++.+|.+++ +-.||.||.+ .+-+++|
T Consensus 739 elf~ev~~~i~q~DPDIl~GyEi~~~SWGyl 769 (1488)
T KOG0968|consen 739 ELFEEVAKLIVQYDPDILLGYEIHNLSWGYL 769 (1488)
T ss_pred HHHHHHHHHHHhcCcceeeeeeecccchHHH
Confidence 7888888877 5789999987 6677776
No 116
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.49 E-value=65 Score=35.40 Aligned_cols=33 Identities=15% Similarity=0.114 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHHhC---CCEEEEEcc-hhhHHHhc
Q 023906 142 AKDFPTVQKKVAELIE---GRILVGHAL-HNDLKALL 174 (275)
Q Consensus 142 a~~~~ev~~~l~~~l~---~~ilVgHn~-~fDl~~L~ 174 (275)
.++..+.+..+.+++. ..+++|+|+ .||+..|.
T Consensus 267 ~~~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~ 303 (1172)
T TIGR00592 267 VSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLA 303 (1172)
T ss_pred ccchHHHHhhHHHHHhhcCcchhcccccccCccceec
Confidence 4566777777777773 468999998 99997663
Done!