Query 018152
Match_columns 360
No_of_seqs 274 out of 1386
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 06:34:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018152.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018152hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2248 3'-5' exonuclease [Rep 100.0 7.9E-44 1.7E-48 353.0 13.5 301 1-302 70-377 (380)
2 cd06143 PAN2_exo DEDDh 3'-5' e 100.0 2.9E-37 6.3E-42 276.8 13.8 147 145-294 1-174 (174)
3 cd06145 REX1_like DEDDh 3'-5' 100.0 9.2E-37 2E-41 268.2 15.8 148 145-293 1-149 (150)
4 KOG2249 3'-5' exonuclease [Rep 100.0 1.5E-36 3.4E-41 283.9 14.0 151 143-297 106-263 (280)
5 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 5E-36 1.1E-40 266.1 13.2 149 145-294 1-161 (161)
6 cd06149 ISG20 DEDDh 3'-5' exon 100.0 1.5E-35 3.2E-40 262.5 15.4 148 145-294 1-157 (157)
7 cd06144 REX4_like DEDDh 3'-5' 100.0 1.3E-32 2.8E-37 242.0 14.3 146 145-294 1-152 (152)
8 PRK05711 DNA polymerase III su 100.0 4.9E-30 1.1E-34 242.1 18.5 156 141-300 3-176 (240)
9 TIGR01406 dnaQ_proteo DNA poly 100.0 2.1E-29 4.6E-34 235.6 18.0 153 143-299 1-171 (225)
10 PRK09146 DNA polymerase III su 100.0 1.3E-28 2.9E-33 232.2 19.1 161 136-302 41-229 (239)
11 PRK07740 hypothetical protein; 100.0 8.9E-28 1.9E-32 227.2 19.0 156 140-301 57-227 (244)
12 PRK06310 DNA polymerase III su 100.0 1.4E-27 3E-32 226.6 18.2 155 140-299 5-173 (250)
13 PRK06309 DNA polymerase III su 100.0 1E-27 2.2E-32 224.9 16.9 153 142-299 2-165 (232)
14 PRK07247 DNA polymerase III su 100.0 2E-27 4.2E-32 218.0 18.4 156 141-304 4-173 (195)
15 PRK09145 DNA polymerase III su 99.9 5E-27 1.1E-31 215.4 17.9 152 141-298 28-199 (202)
16 cd06131 DNA_pol_III_epsilon_Ec 99.9 3.5E-27 7.6E-32 208.6 15.8 149 144-296 1-166 (167)
17 smart00479 EXOIII exonuclease 99.9 7.5E-27 1.6E-31 204.7 16.3 153 143-300 1-167 (169)
18 PRK07942 DNA polymerase III su 99.9 9.1E-27 2E-31 218.7 16.4 157 141-301 5-181 (232)
19 PRK06807 DNA polymerase III su 99.9 1.6E-26 3.4E-31 225.9 18.6 154 140-300 6-172 (313)
20 TIGR00573 dnaq exonuclease, DN 99.9 1.6E-26 3.5E-31 214.6 17.4 157 141-302 6-179 (217)
21 PRK07983 exodeoxyribonuclease 99.9 2.4E-26 5.1E-31 214.3 18.0 147 144-299 2-153 (219)
22 cd06136 TREX1_2 DEDDh 3'-5' ex 99.9 3.6E-27 7.8E-32 212.5 11.9 144 144-295 1-176 (177)
23 PRK08517 DNA polymerase III su 99.9 5.5E-26 1.2E-30 216.5 20.4 156 139-301 65-232 (257)
24 cd06130 DNA_pol_III_epsilon_li 99.9 2.2E-26 4.7E-31 200.5 16.1 142 144-294 1-155 (156)
25 PRK06063 DNA polymerase III su 99.9 4.1E-26 8.9E-31 223.0 19.6 154 141-302 14-181 (313)
26 KOG1275 PAB-dependent poly(A) 99.9 4.2E-28 9E-33 254.6 1.3 262 28-299 785-1091(1118)
27 PRK07748 sporulation inhibitor 99.9 2E-25 4.4E-30 205.7 16.5 155 141-300 3-180 (207)
28 PRK06195 DNA polymerase III su 99.9 2.8E-25 6.1E-30 216.7 18.3 148 143-299 2-163 (309)
29 TIGR01298 RNaseT ribonuclease 99.9 1.9E-25 4.1E-30 205.3 15.5 155 141-300 7-192 (200)
30 cd06134 RNaseT DEDDh 3'-5' exo 99.9 2.6E-25 5.6E-30 202.5 15.8 153 142-299 5-188 (189)
31 PRK05168 ribonuclease T; Provi 99.9 2.6E-25 5.6E-30 206.0 15.3 156 140-300 15-201 (211)
32 PRK07883 hypothetical protein; 99.9 1.1E-24 2.4E-29 227.5 21.0 158 139-302 12-184 (557)
33 PRK07246 bifunctional ATP-depe 99.9 6.7E-25 1.5E-29 238.0 18.9 154 141-301 6-171 (820)
34 PRK05601 DNA polymerase III su 99.9 1.5E-24 3.3E-29 214.0 17.6 155 140-299 44-248 (377)
35 COG2176 PolC DNA polymerase II 99.9 2.5E-25 5.4E-30 239.2 9.8 162 137-304 416-590 (1444)
36 PRK06722 exonuclease; Provisio 99.9 5.9E-24 1.3E-28 204.6 17.4 152 141-298 4-179 (281)
37 TIGR01407 dinG_rel DnaQ family 99.9 5.4E-24 1.2E-28 232.2 18.9 153 143-301 1-166 (850)
38 PRK08074 bifunctional ATP-depe 99.9 5.2E-24 1.1E-28 234.0 18.6 155 142-302 3-171 (928)
39 COG0847 DnaQ DNA polymerase II 99.9 1.2E-23 2.7E-28 196.9 17.2 154 142-299 13-181 (243)
40 TIGR01405 polC_Gram_pos DNA po 99.9 9.6E-24 2.1E-28 234.9 18.4 156 140-301 188-356 (1213)
41 cd06133 ERI-1_3'hExo_like DEDD 99.9 9.5E-24 2.1E-28 187.0 13.6 148 144-296 1-175 (176)
42 cd06127 DEDDh DEDDh 3'-5' exon 99.9 2.1E-23 4.6E-28 178.6 14.8 144 145-293 1-158 (159)
43 cd06138 ExoI_N N-terminal DEDD 99.9 8.5E-24 1.8E-28 191.3 12.8 144 145-293 1-182 (183)
44 PRK09182 DNA polymerase III su 99.9 1.4E-22 3.1E-27 196.5 15.7 150 141-299 36-200 (294)
45 PF00929 RNase_T: Exonuclease; 99.9 1.3E-24 2.7E-29 186.5 -0.9 145 145-293 1-164 (164)
46 PRK05359 oligoribonuclease; Pr 99.9 4E-21 8.6E-26 174.3 14.3 145 141-299 2-174 (181)
47 cd06135 Orn DEDDh 3'-5' exonuc 99.9 2.8E-21 6E-26 173.6 11.1 142 144-298 1-170 (173)
48 PRK11779 sbcB exonuclease I; P 99.9 1E-20 2.2E-25 193.8 16.3 157 141-301 5-199 (476)
49 PRK00448 polC DNA polymerase I 99.8 1.9E-20 4E-25 211.2 15.6 157 139-301 416-585 (1437)
50 PTZ00315 2'-phosphotransferase 99.8 2.3E-19 5E-24 186.0 18.0 156 142-302 56-257 (582)
51 KOG3242 Oligoribonuclease (3'- 99.4 4.4E-13 9.5E-18 119.5 8.6 147 141-301 25-200 (208)
52 COG1949 Orn Oligoribonuclease 99.4 2.4E-12 5.1E-17 113.9 9.7 147 141-301 5-179 (184)
53 cd05160 DEDDy_DNA_polB_exo DED 99.1 1.3E-09 2.8E-14 99.2 11.5 121 144-272 1-162 (199)
54 cd06139 DNA_polA_I_Ecoli_like_ 99.0 2.1E-08 4.6E-13 89.7 14.7 141 141-299 4-169 (193)
55 KOG0542 Predicted exonuclease 98.9 1E-08 2.2E-13 96.6 9.3 158 142-304 56-246 (280)
56 COG5018 KapD Inhibitor of the 98.8 6.5E-09 1.4E-13 92.8 5.7 153 142-298 4-183 (210)
57 COG2925 SbcB Exonuclease I [DN 98.7 8.8E-08 1.9E-12 94.9 11.7 156 141-300 8-201 (475)
58 PF01612 DNA_pol_A_exo1: 3'-5' 98.6 6.8E-07 1.5E-11 78.3 13.5 132 142-298 20-173 (176)
59 cd06125 DnaQ_like_exo DnaQ-lik 98.5 4.3E-07 9.3E-12 74.1 7.6 59 145-239 1-62 (96)
60 PRK05755 DNA polymerase I; Pro 98.5 1.6E-06 3.4E-11 96.0 14.0 134 141-299 314-468 (880)
61 cd06146 mut-7_like_exo DEDDy 3 98.4 8.9E-06 1.9E-10 74.5 13.6 88 210-297 70-192 (193)
62 cd00007 35EXOc 3'-5' exonuclea 98.2 9E-05 1.9E-09 63.0 14.8 104 144-273 2-111 (155)
63 cd05780 DNA_polB_Kod1_like_exo 98.2 1.4E-05 3.1E-10 73.1 10.3 116 142-273 3-156 (195)
64 cd06129 RNaseD_like DEDDy 3'-5 98.0 0.00011 2.4E-09 65.0 13.3 126 141-296 12-159 (161)
65 PF13482 RNase_H_2: RNase_H su 98.0 1.9E-05 4.2E-10 69.3 7.7 127 145-301 1-138 (164)
66 cd05781 DNA_polB_B3_exo DEDDy 97.9 0.00014 3.1E-09 66.4 12.4 106 142-272 3-144 (188)
67 cd06141 WRN_exo DEDDy 3'-5' ex 97.9 0.00018 3.9E-09 63.7 12.3 85 213-297 64-169 (170)
68 PRK10829 ribonuclease D; Provi 97.8 0.0005 1.1E-08 69.4 14.2 131 140-298 20-168 (373)
69 cd05779 DNA_polB_epsilon_exo D 97.5 0.0031 6.7E-08 58.5 14.6 128 142-272 2-168 (204)
70 PF04857 CAF1: CAF1 family rib 97.5 0.00075 1.6E-08 64.6 10.0 75 219-295 147-262 (262)
71 smart00474 35EXOc 3'-5' exonuc 97.4 0.0099 2.1E-07 51.3 15.7 87 211-297 64-168 (172)
72 cd05785 DNA_polB_like2_exo Unc 97.4 0.0019 4.1E-08 60.0 10.9 106 141-271 8-167 (207)
73 cd06142 RNaseD_exo DEDDy 3'-5' 97.3 0.0075 1.6E-07 53.1 14.2 129 142-298 12-158 (178)
74 COG0349 Rnd Ribonuclease D [Tr 97.3 0.0031 6.8E-08 63.1 12.7 132 141-298 16-164 (361)
75 cd06148 Egl_like_exo DEDDy 3'- 97.3 0.0016 3.5E-08 59.7 9.9 131 140-299 8-176 (197)
76 TIGR01388 rnd ribonuclease D. 97.3 0.0027 5.8E-08 63.9 12.2 129 141-298 17-164 (367)
77 cd05784 DNA_polB_II_exo DEDDy 97.2 0.0087 1.9E-07 55.0 13.0 114 142-272 3-153 (193)
78 cd05777 DNA_polB_delta_exo DED 97.0 0.024 5.2E-07 53.2 14.4 122 141-273 6-183 (230)
79 cd05783 DNA_polB_B1_exo DEDDy 96.5 0.04 8.8E-07 51.0 12.0 126 141-272 4-170 (204)
80 cd06140 DNA_polA_I_Bacillus_li 96.3 0.13 2.9E-06 45.4 13.6 105 142-273 3-113 (178)
81 cd05782 DNA_polB_like1_exo Unc 96.3 0.042 9E-07 51.0 10.7 66 206-272 77-169 (208)
82 PF10108 DNA_pol_B_exo2: Predi 96.1 0.14 3.1E-06 47.9 13.0 90 206-298 36-171 (209)
83 cd05778 DNA_polB_zeta_exo inac 96.0 0.21 4.6E-06 47.0 14.2 142 142-286 4-203 (231)
84 COG0749 PolA DNA polymerase I 96.0 0.045 9.7E-07 58.3 10.1 131 145-299 25-179 (593)
85 cd09018 DEDDy_polA_RNaseD_like 95.9 0.21 4.5E-06 42.4 12.5 60 214-273 45-110 (150)
86 smart00486 POLBc DNA polymeras 95.5 0.23 5E-06 50.1 12.9 144 142-296 3-220 (471)
87 PRK05762 DNA polymerase II; Re 95.2 0.35 7.7E-06 53.5 14.1 138 140-295 153-347 (786)
88 KOG4793 Three prime repair exo 95.2 0.044 9.6E-07 52.9 6.1 160 136-297 7-215 (318)
89 PTZ00166 DNA polymerase delta 95.1 0.39 8.4E-06 54.8 14.4 149 140-297 262-483 (1054)
90 cd06147 Rrp6p_like_exo DEDDy 3 95.0 0.45 9.8E-06 42.9 12.2 102 143-272 25-131 (192)
91 cd05776 DNA_polB_alpha_exo ina 95.0 0.19 4.2E-06 47.3 10.1 130 143-273 4-187 (234)
92 COG3359 Predicted exonuclease 94.7 0.79 1.7E-05 44.0 13.1 113 139-274 95-220 (278)
93 PF03104 DNA_pol_B_exo1: DNA p 94.1 0.19 4.2E-06 48.4 7.9 87 140-237 155-255 (325)
94 TIGR00593 pola DNA polymerase 93.8 0.35 7.6E-06 54.2 10.2 94 206-299 362-476 (887)
95 TIGR00592 pol2 DNA polymerase 91.6 2.1 4.4E-05 49.7 12.7 104 191-295 569-721 (1172)
96 PHA02570 dexA exonuclease; Pro 89.8 1.7 3.6E-05 41.0 8.2 93 145-238 4-125 (220)
97 PHA02528 43 DNA polymerase; Pr 89.7 1.8 3.9E-05 48.6 9.7 153 141-295 105-323 (881)
98 COG0417 PolB DNA polymerase el 86.3 11 0.00025 41.8 13.3 122 139-273 151-309 (792)
99 KOG0304 mRNA deadenylase subun 80.3 9.2 0.0002 36.2 8.1 105 191-298 109-237 (239)
100 cd06128 DNA_polA_exo DEDDy 3'- 77.3 7.7 0.00017 33.2 6.4 59 214-272 45-109 (151)
101 TIGR03491 RecB family nuclease 76.8 31 0.00068 35.7 11.7 84 207-298 328-429 (457)
102 KOG1798 DNA polymerase epsilon 73.5 48 0.001 39.5 12.6 153 141-298 245-452 (2173)
103 KOG3657 Mitochondrial DNA poly 72.2 3 6.6E-05 46.1 2.9 34 219-252 239-278 (1075)
104 PRK05761 DNA polymerase I; Rev 70.9 33 0.00072 38.3 10.8 88 206-293 209-334 (787)
105 PF00843 Arena_nucleocap: Aren 68.5 6.5 0.00014 40.6 4.2 138 139-288 369-526 (533)
106 PF13423 UCH_1: Ubiquitin carb 66.4 0.32 7E-06 46.9 -5.3 48 26-86 247-294 (295)
107 PHA02524 43A DNA polymerase su 61.9 32 0.0007 36.4 8.0 147 142-293 106-321 (498)
108 PF13017 Maelstrom: piRNA path 43.0 30 0.00064 32.3 3.8 59 161-219 10-79 (213)
109 KOG0970 DNA polymerase alpha, 38.2 1.4E+02 0.003 34.8 8.5 128 139-272 526-711 (1429)
110 PHA02563 DNA polymerase; Provi 33.2 51 0.0011 35.9 4.2 68 140-238 10-83 (630)
111 PF11491 DUF3213: Protein of u 28.3 34 0.00074 27.6 1.4 43 24-67 19-61 (88)
No 1
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=7.9e-44 Score=353.05 Aligned_cols=301 Identities=35% Similarity=0.449 Sum_probs=264.7
Q ss_pred CcchhhhHHHHHHHHHHHHHhhccccCCCCchhhHhhhhccccCC-CCCCCCcC--c-hHHHHHHhhccCcchhhHHHHH
Q 018152 1 MDQKLDTLEKKALVEIVKLIQKRRMEGTAGGWKDFLTSYDKKFGS-SLSDPARR--S-KDALSSFLKTFTKEDDLKFIAK 76 (360)
Q Consensus 1 ~~~~~~~~~~~~l~~~v~~~~~~~~~~~~~~~k~~l~~~~~~~~~-~~~d~~~~--~-~~~l~~f~~~~~~~~~~~~~~~ 76 (360)
|...++++++.+++..++..|+.++.+.+|.||.||+.|.+..+. +.++|+.. . ...+..|..+....+..+++++
T Consensus 70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~~f~~~~~~~~~~~~l~~ 149 (380)
T KOG2248|consen 70 SLVAEGNAPKIVLLSKPELKQKDYLLSFSGLSKAILNLVATNLKDVDRSDKALLPRPCSRCGSEFYVTEKGREFKDLLCK 149 (380)
T ss_pred HHHHhccCceeeeeccchhhhhhheeccCCccHHHhhhhhcccccccccCccccCchhhhhhhhhccccchhhhhhhhcc
Confidence 345677888889999999999999999999999999999999984 77777766 3 5678889888887666566777
Q ss_pred HHHHhhhHHHHHHHHhhCCCCCChhHHHHHhhhcCCCCccccCCCCCCCCceEeccCCC-CCCCCCCcEEEEEEeccCCC
Q 018152 77 VVQSHLNRDLVEQLKKTSPDDESPEQRLVRLTLQHPQYPLCYMFPSSDEGWLVTKLGKS-SKTMTSNIMYAVDCEMVLCE 155 (360)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~~t~~~~~~~~~y~~p~~~~~~~~t~~~~~-~~~~~~~~~ValD~Ettgl~ 155 (360)
+.+...++......+++.....++.+.++..+..++.|...+.+|+....|+....+.. .......+++||||||+.++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~v~~~~~i~AlDCEm~~te 229 (380)
T KOG2248|consen 150 YHPGKLIREPRRGFKDKTEDCCTPKEGLVSFLCLGPDYHVEILFPSESLDEFVQTLGAKGKAVSKSPNIFALDCEMVVTE 229 (380)
T ss_pred ccccccccchhccccccCchhhcccccCccceeecccccccccCccccccceecccccCCCCCCCCCCeEEEEeeeeeec
Confidence 77766777777777777777778999999988889999889999988766666655533 34567789999999999999
Q ss_pred CCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCCCEEEEEcchhhHHH
Q 018152 156 DGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGTILVGHSLNNDLEV 235 (360)
Q Consensus 156 ~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g~iLVGHnl~fDl~~ 235 (360)
.| .+++||++||.+++++||.+|+|..+|.||.|+++|||++|++++++++++||.+|+.+++.++|||||++++||++
T Consensus 230 ~g-~el~RVt~VD~~~~vi~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~l~~~~~~~TILVGHSLenDL~a 308 (380)
T KOG2248|consen 230 NG-LELTRVTAVDRDGKVILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKELLELISKNTILVGHSLENDLKA 308 (380)
T ss_pred cc-eeeEEeeeeeccCcEEeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHHHHhhcCcCcEEEeechhhHHHH
Confidence 99 67999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcccCCCccchHHHhhHhCC--CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHHHHHHhccc
Q 018152 236 LKLDHPRVIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRVD 302 (360)
Q Consensus 236 L~~~~~~viDT~~l~~~~~~--~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~g~~ 302 (360)
|++.|+.||||+.+|.+..+ ..+.||+.||+.|||+.||++-.+|+|.+||.|||+|+..+++.+..
T Consensus 309 LKl~H~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~~~~HdS~eDA~acm~Lv~~k~~~~~~ 377 (380)
T KOG2248|consen 309 LKLDHPSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEGVGGHDSVEDALACMKLVKLKIKNSES 377 (380)
T ss_pred HhhhCCceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhccCCCCccHHHHHHHHHHHHHHHhcccc
Confidence 99999999999999998887 47788999999999999995445899999999999999988877654
No 2
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=100.00 E-value=2.9e-37 Score=276.81 Aligned_cols=147 Identities=32% Similarity=0.497 Sum_probs=133.7
Q ss_pred EEEEEeccCCCC--------Ccc--------cEEEEEEEE----cCCcEEEEEeecCCCcccccccccCCCCHHhhcCCC
Q 018152 145 YAVDCEMVLCED--------GSE--------GLVRLCVVD----RNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVT 204 (360)
Q Consensus 145 ValD~Ettgl~~--------g~~--------~I~~VsvVd----~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap 204 (360)
|||||||+|+.+ |++ +++||++|| .+|++++|.||+|..+|.||+|++||||+++|.+++
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 588999998876 444 699999999 689999999999999999999999999999999875
Q ss_pred -----CCHHHHHHHHHHHhhCCCEEEEEcchhhHHHHcccCC--CccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCC
Q 018152 205 -----CSLAEIQKRMKKLLSNGTILVGHSLNNDLEVLKLDHP--RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKG 277 (360)
Q Consensus 205 -----~~l~eV~~~l~~~l~~g~iLVGHnl~fDl~~L~~~~~--~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~ 277 (360)
+++++++++++++++.++|||||++++||++|++.|| .+|||+.+|+... .+++||+.||+.+||++||++
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL~nDL~aL~l~hp~~~viDTa~l~~~~~-~r~~sLk~La~~~L~~~IQ~~- 158 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELFHLPG-QRKLSLRFLAWYLLGEKIQSE- 158 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccchhHHHHhcCcCCCcceEEcHHhccCCC-CCChhHHHHHHHHcCCcccCC-
Confidence 3799999999999988999999999999999999987 5999999998643 468999999999999999974
Q ss_pred CCCChHHHHHHHHHHHH
Q 018152 278 TPHNCLDDASAAMKLVL 294 (360)
Q Consensus 278 ~~H~AleDA~at~eL~~ 294 (360)
+|+|++||+|||+||+
T Consensus 159 -~HdSvEDArAam~Ly~ 174 (174)
T cd06143 159 -THDSIEDARTALKLYR 174 (174)
T ss_pred -CcCcHHHHHHHHHHhC
Confidence 8999999999999993
No 3
>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=9.2e-37 Score=268.20 Aligned_cols=148 Identities=48% Similarity=0.751 Sum_probs=136.3
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCCCEE
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGTIL 224 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g~iL 224 (360)
|+|||||||++.| ++|++|++|+.+|.++|++||+|..+|+++++++||||++||+++|.++++++++|++|++++.+|
T Consensus 1 ~~iD~E~~g~~~g-~ei~~i~~v~~~~~~~f~~lv~P~~~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~~fl~~~~vl 79 (150)
T cd06145 1 FALDCEMCYTTDG-LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79 (150)
T ss_pred CEEeeeeeeecCC-CEEEEEEEEeCCCCEEEEEeECCCCccchhccCcCCCCHHHhccCCCCHHHHHHHHHHHhCCCCEE
Confidence 5899999999988 789999999999999999999999999999999999999999999549999999999999448999
Q ss_pred EEEcchhhHHHHcccCCCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHH
Q 018152 225 VGHSLNNDLEVLKLDHPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLV 293 (360)
Q Consensus 225 VGHnl~fDl~~L~~~~~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~ 293 (360)
||||+.||++||+..+++++||+.+++...+ ..+++|+.||++|+|+.++.++.+|+|++||++|++||
T Consensus 80 VgHn~~fD~~fL~~~~~~~iDT~~l~r~~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 80 VGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred EEcChHHHHHHhhccCCCEEEcHHhccccCCCCCChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 9999999999999999999999999998765 55789999999999988874235899999999999998
No 4
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.5e-36 Score=283.89 Aligned_cols=151 Identities=37% Similarity=0.583 Sum_probs=139.1
Q ss_pred cEEEEEEeccCCCCC--cccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhC
Q 018152 143 IMYAVDCEMVLCEDG--SEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (360)
Q Consensus 143 ~~ValD~Ettgl~~g--~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~ 220 (360)
++||+||||+|+.++ .+.++||||||..|.++||.||+|..+|+||+|++|||+++.+.++. +|+.||.++.+|| .
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~-pf~~aQ~ev~klL-~ 183 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAM-PFKVAQKEVLKLL-K 183 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCc-cHHHHHHHHHHHH-h
Confidence 699999999999874 34789999999999999999999999999999999999999999999 9999999999999 9
Q ss_pred CCEEEEEcchhhHHHHcccCCC--ccchHHHhhHhC--C-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHHH
Q 018152 221 GTILVGHSLNNDLEVLKLDHPR--VIDTSLIFKYVD--E-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLA 295 (360)
Q Consensus 221 g~iLVGHnl~fDl~~L~~~~~~--viDT~~l~~~~~--~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~ 295 (360)
|+|||||.+.+||.+|+..||+ +.||+..-.... . ..++||+.|++.+||++||.| .|++++||+|||+||..
T Consensus 184 gRIlVGHaLhnDl~~L~l~hp~s~iRDTs~~~pl~k~~~~~~tpSLK~Lt~~~Lg~~IQ~G--eHsSvEDA~AtM~LY~~ 261 (280)
T KOG2249|consen 184 GRILVGHALHNDLQALKLEHPRSMIRDTSKYPPLMKLLSKKATPSLKKLTEALLGKDIQVG--EHSSVEDARATMELYKR 261 (280)
T ss_pred CCEEeccccccHHHHHhhhCchhhhcccccCchHHHHhhccCCccHHHHHHHHhchhhhcc--ccCcHHHHHHHHHHHHH
Confidence 9999999999999999999997 899998644332 3 789999999999999999975 69999999999999975
Q ss_pred HH
Q 018152 296 II 297 (360)
Q Consensus 296 ~l 297 (360)
..
T Consensus 262 vk 263 (280)
T KOG2249|consen 262 VK 263 (280)
T ss_pred HH
Confidence 43
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=5e-36 Score=266.11 Aligned_cols=149 Identities=40% Similarity=0.627 Sum_probs=135.7
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEc-CCcEEEEEeecCCCcccccccccCCCCHHhhcCCCC------CHHHHHHHHHHH
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDR-NLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTC------SLAEIQKRMKKL 217 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~------~l~eV~~~l~~~ 217 (360)
|+|||||||+++..++|++|++|+. +|++++++||+|..+|+++++++||||++||+++|. ++++++++|++|
T Consensus 1 v~lD~EttGl~~~~d~ii~Ig~V~v~~g~i~~~~~v~P~~~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~~~~~~~~~ 80 (161)
T cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKAGKTIFGWEAARAALWKF 80 (161)
T ss_pred CEEEeeeeeEcCCCCEEEEEEEEEcCCCeEEEeccccCCCCCCccceeccCCCHHHHhhhhhcCCccccHHHHHHHHHHh
Confidence 6899999999987788999999998 888889999999999999999999999999999872 246999999999
Q ss_pred hhCC-CEEEEEcchhhHHHHcccCCCccchHHHhhHhCC-C---CCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHH
Q 018152 218 LSNG-TILVGHSLNNDLEVLKLDHPRVIDTSLIFKYVDE-Y---RRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKL 292 (360)
Q Consensus 218 l~~g-~iLVGHnl~fDl~~L~~~~~~viDT~~l~~~~~~-~---~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL 292 (360)
+ ++ ++|||||+.||++||+..+++++||+.++++..+ . .+++|+.||+.++|++++.+..+|+|++||+||++|
T Consensus 81 i-~~~~vlVgHn~~fD~~fL~~~~~~~iDT~~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l 159 (161)
T cd06137 81 I-DPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGPLAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREV 159 (161)
T ss_pred c-CCCcEEEeccHHHHHHHHhCcCCCeeEehhhhhhccCCCcCCCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHH
Confidence 9 65 9999999999999999999999999999998876 3 589999999888999997533589999999999999
Q ss_pred HH
Q 018152 293 VL 294 (360)
Q Consensus 293 ~~ 294 (360)
|+
T Consensus 160 ~~ 161 (161)
T cd06137 160 VL 161 (161)
T ss_pred hC
Confidence 84
No 6
>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=1.5e-35 Score=262.53 Aligned_cols=148 Identities=36% Similarity=0.539 Sum_probs=133.7
Q ss_pred EEEEEeccCCCCC--cccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCCC
Q 018152 145 YAVDCEMVLCEDG--SEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGT 222 (360)
Q Consensus 145 ValD~Ettgl~~g--~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g~ 222 (360)
|||||||||++++ .++|++|++|+.+|.+++++||+|..+|+++++++||||++||+++| ++++++++|++|+ +|+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~~~~~~lv~P~~~i~~~~~~i~GIt~~~l~~a~-~~~~v~~~l~~~l-~~~ 78 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNAT-PFAVAQKEILKIL-KGK 78 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCCEEEEEeECCCCccCccceECCCCCHHHHhcCC-CHHHHHHHHHHHc-CCC
Confidence 6899999999986 46899999999999999999999999999999999999999999999 9999999999999 899
Q ss_pred EEEEEcchhhHHHHcccCCC--ccchHHH--hhHh--CC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHH
Q 018152 223 ILVGHSLNNDLEVLKLDHPR--VIDTSLI--FKYV--DE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVL 294 (360)
Q Consensus 223 iLVGHnl~fDl~~L~~~~~~--viDT~~l--~~~~--~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~ 294 (360)
||||||+.||++||+..++. ++||+.+ +++. .+ .++++|+.||++++|..++.++.+|+|++||+||++||+
T Consensus 79 vlV~Hn~~~D~~~l~~~~~~~~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~~ 157 (157)
T cd06149 79 VVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157 (157)
T ss_pred EEEEeCcHHHHHHhcccCCCcCEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHhC
Confidence 99999999999999999775 7999875 4433 44 467999999999988888764458999999999999984
No 7
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=100.00 E-value=1.3e-32 Score=241.98 Aligned_cols=146 Identities=41% Similarity=0.680 Sum_probs=130.6
Q ss_pred EEEEEeccCCCCCc--ccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCCC
Q 018152 145 YAVDCEMVLCEDGS--EGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGT 222 (360)
Q Consensus 145 ValD~Ettgl~~g~--~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g~ 222 (360)
|+|||||||+++.. .+|++|++++.+|.+++++||+|+.+|+++++++||||++|++++| ++++++++|.+|+ +++
T Consensus 1 v~lD~EttGl~~~~~~~~i~~v~~v~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~~~v~~a~-~~~~~~~~l~~~l-~~~ 78 (152)
T cd06144 1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAP-DFEEVQKKVAELL-KGR 78 (152)
T ss_pred CEEEEEeecccCCCCEEEEEEEEEEeCCCCEEEEEEECCCCCCCcccccCCCCCHHHHcCCC-CHHHHHHHHHHHh-CCC
Confidence 68999999999762 5788999999999989999999999999999999999999999999 9999999999999 789
Q ss_pred EEEEEcchhhHHHHcccCCC--ccchHHHhhHhCC--CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHH
Q 018152 223 ILVGHSLNNDLEVLKLDHPR--VIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVL 294 (360)
Q Consensus 223 iLVGHnl~fDl~~L~~~~~~--viDT~~l~~~~~~--~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~ 294 (360)
+|||||+.||++||+..+++ ++||..+.....+ ..++||+.||+.++|++++. .+|+|++||++|++||+
T Consensus 79 vlVgHn~~fD~~~L~~~~~~~~~~dt~~l~~~~~~~~~~~~sL~~l~~~~lgi~~~~--~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 79 ILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQE--GEHSSVEDARAAMRLYR 152 (152)
T ss_pred EEEEcCcHHHHHHhcCcCCCccEEEeEEeeccccccCCCChhHHHHHHHHcCcccCC--CCcCcHHHHHHHHHHhC
Confidence 99999999999999988764 7899876554433 47899999998889998863 38999999999999984
No 8
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.97 E-value=4.9e-30 Score=242.09 Aligned_cols=156 Identities=21% Similarity=0.278 Sum_probs=135.0
Q ss_pred CCcEEEEEEeccCCCCC-cccEEEEEEEEc-CCc---EEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDG-SEGLVRLCVVDR-NLK---VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g-~~~I~~VsvVd~-~g~---~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~ 215 (360)
..++|+||+||||+++. .++|++|++|.. ++. ..|+.||+|+++|++.++++||||++||+++| +|++|+++|.
T Consensus 3 ~~r~vvlDtETTGldp~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p-~f~ev~~~f~ 81 (240)
T PRK05711 3 IMRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKP-TFAEVADEFL 81 (240)
T ss_pred CCeEEEEEeeCCCcCCCCCCeEEEEEEEEEECCEEeccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCC-CHHHHHHHHH
Confidence 35899999999999986 567999999875 332 24899999999999999999999999999999 9999999999
Q ss_pred HHhhCCCEEEEEcchhhHHHHcccC-------------CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCCh
Q 018152 216 KLLSNGTILVGHSLNNDLEVLKLDH-------------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNC 282 (360)
Q Consensus 216 ~~l~~g~iLVGHnl~fDl~~L~~~~-------------~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~A 282 (360)
+|+ ++.+|||||+.||++||+.+. .+++||+.+++..++..++||++|| .++|++... +..|+|
T Consensus 82 ~fi-~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~-~~~gi~~~~-r~~H~A 158 (240)
T PRK05711 82 DFI-RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALC-KRYGIDNSH-RTLHGA 158 (240)
T ss_pred HHh-CCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHH-HHCCCCCCC-CCCCCH
Confidence 999 899999999999999998641 2479999999998887778999999 556887532 347999
Q ss_pred HHHHHHHHHHHHHHHHhc
Q 018152 283 LDDASAAMKLVLAIIERR 300 (360)
Q Consensus 283 leDA~at~eL~~~~l~~g 300 (360)
+.||++++++|+++..+.
T Consensus 159 L~DA~~~A~v~~~l~~~~ 176 (240)
T PRK05711 159 LLDAEILAEVYLAMTGGQ 176 (240)
T ss_pred HHHHHHHHHHHHHHHCcc
Confidence 999999999999888543
No 9
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.97 E-value=2.1e-29 Score=235.59 Aligned_cols=153 Identities=24% Similarity=0.266 Sum_probs=132.6
Q ss_pred cEEEEEEeccCCCCCc-ccEEEEEEEEc-CCc---EEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 143 IMYAVDCEMVLCEDGS-EGLVRLCVVDR-NLK---VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 143 ~~ValD~Ettgl~~g~-~~I~~VsvVd~-~g~---~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
++|+||+||||+++.. ++|++|++|.. ++. ..|+.||+|+++|++.++++||||++||+++| ++++|+++|.+|
T Consensus 1 r~vvlD~ETTGl~p~~~d~IIEIgav~~~~~~~~~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p-~f~ev~~~f~~f 79 (225)
T TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKP-KFKEIADEFLDF 79 (225)
T ss_pred CEEEEEeeCCCcCCCCCCeEEEEEEEEEECCcEecceEEEEECcCCCCCHHHHhccCCCHHHHhCCC-CHHHHHHHHHHH
Confidence 5899999999999865 67999998854 222 25899999999999999999999999999999 999999999999
Q ss_pred hhCCCEEEEEcchhhHHHHcccC-------------CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHH
Q 018152 218 LSNGTILVGHSLNNDLEVLKLDH-------------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (360)
Q Consensus 218 l~~g~iLVGHnl~fDl~~L~~~~-------------~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~Ale 284 (360)
+ ++.+|||||+.||++||+.+. .+++||..+++..++..+++|++|| .++|++... +..|+|+.
T Consensus 80 i-~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~-~~~gi~~~~-r~~H~Al~ 156 (225)
T TIGR01406 80 I-GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALC-KRFKVDNSH-RTLHGALL 156 (225)
T ss_pred h-CCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHH-HhcCCCCCC-CCCcCHHH
Confidence 9 899999999999999998641 2479999999998887789999999 556887542 34799999
Q ss_pred HHHHHHHHHHHHHHh
Q 018152 285 DASAAMKLVLAIIER 299 (360)
Q Consensus 285 DA~at~eL~~~~l~~ 299 (360)
||+++++||+++..+
T Consensus 157 DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 157 DAHLLAEVYLALTGG 171 (225)
T ss_pred HHHHHHHHHHHHHcC
Confidence 999999999987753
No 10
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.3e-28 Score=232.22 Aligned_cols=161 Identities=22% Similarity=0.268 Sum_probs=137.7
Q ss_pred CCCCCCCcEEEEEEeccCCCCCcccEEEEEEEEcCC-c----EEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHH
Q 018152 136 SKTMTSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNL-K----VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEI 210 (360)
Q Consensus 136 ~~~~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g-~----~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV 210 (360)
.......++++||+||||+++..++|++|++|..++ . ..++.+|+|+++|++.++++||||++||+++| ++.+|
T Consensus 41 ~~~~~~~~~vviD~ETTGl~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap-~~~ev 119 (239)
T PRK09146 41 DTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAP-DLERI 119 (239)
T ss_pred CCCcccCCEEEEEeECCCCCCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCC-CHHHH
Confidence 344456789999999999999888999999998743 2 24789999999999999999999999999999 99999
Q ss_pred HHHHHHHhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-C-------------CCCCHHHHHHH
Q 018152 211 QKRMKKLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-Y-------------RRPSLYNLCKS 267 (360)
Q Consensus 211 ~~~l~~~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~-------------~~~sL~~L~~~ 267 (360)
+++|.+++ ++.++||||+.||++||+... .++|||+.++++..+ . ..++|.++| .
T Consensus 120 l~~l~~~~-~~~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~-~ 197 (239)
T PRK09146 120 LDELLEAL-AGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSR-L 197 (239)
T ss_pred HHHHHHHh-CCCEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHHHHHHcccccccccchhccCCCCCCCHHHHH-H
Confidence 99999999 899999999999999998751 247999999987643 1 467899999 5
Q ss_pred HhCCccCCCCCCCChHHHHHHHHHHHHHHHHhccc
Q 018152 268 VLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRVD 302 (360)
Q Consensus 268 ~Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~g~~ 302 (360)
++|++.. .+|+|++||.+|++||++++.+..+
T Consensus 198 ~~gl~~~---~~H~Al~DA~ata~l~~~~~~~~~~ 229 (239)
T PRK09146 198 RYGLPAY---SPHHALTDAIATAELLQAQIAHHFS 229 (239)
T ss_pred HcCCCCC---CCCCcHHHHHHHHHHHHHHHHHHcC
Confidence 5688753 4899999999999999998876543
No 11
>PRK07740 hypothetical protein; Provisional
Probab=99.96 E-value=8.9e-28 Score=227.15 Aligned_cols=156 Identities=24% Similarity=0.319 Sum_probs=137.3
Q ss_pred CCCcEEEEEEeccCCCCCc-ccEEEEEEEEcCCcEE----EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHH
Q 018152 140 TSNIMYAVDCEMVLCEDGS-EGLVRLCVVDRNLKVT----IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRM 214 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~-~~I~~VsvVd~~g~~~----~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l 214 (360)
...++|+|||||||+++.. ++|++|++|..++..+ |+.+|+|+.+|+++++++||||+++|+++| ++.+++.+|
T Consensus 57 ~~~~~vv~D~ETTGl~p~~~deIIeIgaV~~~~~~i~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap-~~~evl~~f 135 (244)
T PRK07740 57 TDLPFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAP-PLAEVLHRF 135 (244)
T ss_pred cCCCEEEEEEeCCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEEeCcCCCCChhheeccCCCHHHHhCCC-CHHHHHHHH
Confidence 4568999999999999875 6899999998754333 788999999999999999999999999999 999999999
Q ss_pred HHHhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHH
Q 018152 215 KKLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLD 284 (360)
Q Consensus 215 ~~~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~Ale 284 (360)
.+|+ +++++||||+.||+.||+... .+++||..+++...+ ...+||++|| .++|++.. +.|+|++
T Consensus 136 ~~fi-~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~-~~~gi~~~---~~H~Al~ 210 (244)
T PRK07740 136 YAFI-GAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDAL-AYYGIPIP---RRHHALG 210 (244)
T ss_pred HHHh-CCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHH-HHCCcCCC---CCCCcHH
Confidence 9999 899999999999999998641 358999999998776 5689999999 67899875 3799999
Q ss_pred HHHHHHHHHHHHHHhcc
Q 018152 285 DASAAMKLVLAIIERRV 301 (360)
Q Consensus 285 DA~at~eL~~~~l~~g~ 301 (360)
||++|++||.+++..-.
T Consensus 211 Da~ata~l~~~ll~~~~ 227 (244)
T PRK07740 211 DALMTAKLWAILLVEAQ 227 (244)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999886543
No 12
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.4e-27 Score=226.58 Aligned_cols=155 Identities=21% Similarity=0.331 Sum_probs=134.9
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcE---EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~---~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
+..++|+|||||||+++..++|++|++|..++.. .++.+|+|+.+|++..+.+||||++||+++| ++.+|+++|.+
T Consensus 5 ~~~~~v~~D~ETTGl~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p-~~~ev~~~~~~ 83 (250)
T PRK06310 5 KDTEFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKP-KIAEVFPQIKG 83 (250)
T ss_pred cCCcEEEEEEeCCCCCCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCC-CHHHHHHHHHH
Confidence 4568999999999999888899999999874332 3788999999999999999999999999999 99999999999
Q ss_pred HhhCCCEEEEEcchhhHHHHcccC-----------CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHHH
Q 018152 217 LLSNGTILVGHSLNNDLEVLKLDH-----------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDD 285 (360)
Q Consensus 217 ~l~~g~iLVGHnl~fDl~~L~~~~-----------~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~AleD 285 (360)
|++++.+|||||+.||+.||+.+. .++|||..+++...+..+++|..|| .++|++.. .+|+|++|
T Consensus 84 fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~-~~~g~~~~---~aH~Al~D 159 (250)
T PRK06310 84 FFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALA-VHFNVPYD---GNHRAMKD 159 (250)
T ss_pred HhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHH-HHCCCCCC---CCcChHHH
Confidence 994459999999999999998742 3479999999875435678999999 56688864 38999999
Q ss_pred HHHHHHHHHHHHHh
Q 018152 286 ASAAMKLVLAIIER 299 (360)
Q Consensus 286 A~at~eL~~~~l~~ 299 (360)
|.+|++||..++++
T Consensus 160 a~at~~vl~~l~~~ 173 (250)
T PRK06310 160 VEINIKVFKHLCKR 173 (250)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999988864
No 13
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1e-27 Score=224.93 Aligned_cols=153 Identities=20% Similarity=0.303 Sum_probs=134.9
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCC
Q 018152 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG 221 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g 221 (360)
.++|+||+||||+++..++|++|++++......++.+|+|+.+|++.++++||||++|++++| ++.+++++|.+|++++
T Consensus 2 ~~~vv~D~ETTGl~~~~d~IIeig~v~~~~~~~f~~lv~P~~~I~~~a~~IhGIt~e~v~~~p-~f~ev~~~~~~fi~~~ 80 (232)
T PRK06309 2 PALIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAP-KFPEAYQKFIEFCGTD 80 (232)
T ss_pred CcEEEEEeeCCCCCCCCCEEEEEEEEcCccccEEEEEeCCCCCCChhHHhhcCCCHHHHhCCC-CHHHHHHHHHHHHcCC
Confidence 369999999999998888999999998655567999999999999999999999999999999 9999999999999556
Q ss_pred CEEEEEc-chhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHH
Q 018152 222 TILVGHS-LNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAM 290 (360)
Q Consensus 222 ~iLVGHn-l~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~ 290 (360)
.++|||| ..||++||+.+. .+.+||..+++...+ ..+++|.+|| .++|++.. .+|+|++||.+|+
T Consensus 81 ~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~~~iDt~~l~~~~~~~~~~~~L~~l~-~~~~~~~~---~aH~Al~Da~~t~ 156 (232)
T PRK06309 81 NILVAHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLR-QVYGFEEN---QAHRALDDVITLH 156 (232)
T ss_pred CEEEEeCCHHHHHHHHHHHHHHcCCCCCCCcEEeHHHHHHHHcCCCCCCCHHHHH-HHcCCCCC---CCCCcHHHHHHHH
Confidence 8999999 589999998752 247999999998766 4678999999 55687753 4899999999999
Q ss_pred HHHHHHHHh
Q 018152 291 KLVLAIIER 299 (360)
Q Consensus 291 eL~~~~l~~ 299 (360)
+||.+++++
T Consensus 157 ~vl~~l~~~ 165 (232)
T PRK06309 157 RVFSALVGD 165 (232)
T ss_pred HHHHHHHHH
Confidence 999998864
No 14
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=2e-27 Score=217.97 Aligned_cols=156 Identities=19% Similarity=0.270 Sum_probs=130.4
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcE--EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
...+|+|||||||+++ .++|++|++|.. +|.+ .+++||+|..+|+++++++||||++||+++| ++.+|+++|.+|
T Consensus 4 ~~~~vvlD~EtTGl~~-~~eIIeIgaV~v~~g~~~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap-~~~evl~~f~~f 81 (195)
T PRK07247 4 LETYIAFDLEFNTVNG-VSHIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAP-KVEEVLAAFKEF 81 (195)
T ss_pred CCeEEEEEeeCCCCCC-CCeEEEEEEEEEECCEEEEEEEEEECCCCCCCccceecCCCCHHHHhCCC-CHHHHHHHHHHH
Confidence 3589999999999985 457999999986 4543 4999999999999999999999999999999 999999999999
Q ss_pred hhCCCEEEEEcch-hhHHHHcccC-----CCccchHHHh--hHh--CC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 218 LSNGTILVGHSLN-NDLEVLKLDH-----PRVIDTSLIF--KYV--DE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 218 l~~g~iLVGHnl~-fDl~~L~~~~-----~~viDT~~l~--~~~--~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
+ ++.++||||+. ||+.||+... ...+||.... ++. .+ ..+++|..|| +++|++. .+|+|++||
T Consensus 82 ~-~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La-~~~gi~~----~~HrAl~DA 155 (195)
T PRK07247 82 V-GELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVA-DFLGIKG----RGHNSLEDA 155 (195)
T ss_pred H-CCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHH-HhcCCCC----CCcCCHHHH
Confidence 9 89999999997 8999998752 1347776433 221 12 4679999999 6778874 279999999
Q ss_pred HHHHHHHHHHHHhcccCC
Q 018152 287 SAAMKLVLAIIERRVDNA 304 (360)
Q Consensus 287 ~at~eL~~~~l~~g~~~~ 304 (360)
++|+.+|+++++.+....
T Consensus 156 ~~ta~v~~~ll~~~~~~~ 173 (195)
T PRK07247 156 RMTARVYESFLESDQNKE 173 (195)
T ss_pred HHHHHHHHHHHhhccchh
Confidence 999999999998776543
No 15
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=5e-27 Score=215.38 Aligned_cols=152 Identities=20% Similarity=0.258 Sum_probs=130.1
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCc-E----EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLK-V----TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~-~----~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~ 215 (360)
+.++|+||+||||+++..++|++|++|..++. . .++.+|+|..+|+++++++||||++|++++| ++.+|+++|.
T Consensus 28 ~~~~vviD~ETTGl~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~-~~~~vl~~~~ 106 (202)
T PRK09145 28 PDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGL-SEEEALRQLL 106 (202)
T ss_pred CCCEEEEEeECCCCCCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCC-CHHHHHHHHH
Confidence 45899999999999988788999999987443 2 3789999999999999999999999999999 9999999999
Q ss_pred HHhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHh----CC--CCCCCHHHHHHHHhCCccCCCCCCC
Q 018152 216 KLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYV----DE--YRRPSLYNLCKSVLGYEIRKKGTPH 280 (360)
Q Consensus 216 ~~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~----~~--~~~~sL~~L~~~~Lg~~iq~~~~~H 280 (360)
+++ ++.++||||+.||+.||+... .+.+|++.++... .+ ..+++|.+|| +++|++.. ..|
T Consensus 107 ~~i-~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~-~~~gi~~~---~~H 181 (202)
T PRK09145 107 AFI-GNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAIL-KHLDLPVL---GRH 181 (202)
T ss_pred HHH-cCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHH-HHcCCCCC---CCC
Confidence 999 899999999999999998641 2379998877432 11 3468999999 66798864 389
Q ss_pred ChHHHHHHHHHHHHHHHH
Q 018152 281 NCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 281 ~AleDA~at~eL~~~~l~ 298 (360)
+|++||++|++||+++++
T Consensus 182 ~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 182 DALNDAIMAALIFLRLRK 199 (202)
T ss_pred CcHHHHHHHHHHHHHHHh
Confidence 999999999999998765
No 16
>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=99.95 E-value=3.5e-27 Score=208.63 Aligned_cols=149 Identities=23% Similarity=0.320 Sum_probs=128.2
Q ss_pred EEEEEEeccCCCC-CcccEEEEEEEEc-CCcE---EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHh
Q 018152 144 MYAVDCEMVLCED-GSEGLVRLCVVDR-NLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLL 218 (360)
Q Consensus 144 ~ValD~Ettgl~~-g~~~I~~VsvVd~-~g~~---~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l 218 (360)
+|+||+||||+++ ..++|++|++|.. ++.. .++.+|+|..+|++.++++||||++|++++| ++.+++++|.+|+
T Consensus 1 ~v~~D~ETTGl~~~~~~~iieig~v~v~~~~~~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~-~~~~v~~~l~~~l 79 (167)
T cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKP-KFAEIADEFLDFI 79 (167)
T ss_pred CEEEEeeCCCCCCCCCCeEEEEEEEEEECCcEeccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCC-CHHHHHHHHHHHH
Confidence 5899999999997 5568999998864 3322 5789999999999999999999999999999 9999999999999
Q ss_pred hCCCEEEEEcchhhHHHHcccC------------CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 219 SNGTILVGHSLNNDLEVLKLDH------------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 219 ~~g~iLVGHnl~fDl~~L~~~~------------~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
++.++||||+.||++||+... ...+||..+++...+...++|..+| +++|++... ...|+|+.||
T Consensus 80 -~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~-~~~~i~~~~-~~~H~Al~Da 156 (167)
T cd06131 80 -RGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALC-KRFGIDNSH-RTLHGALLDA 156 (167)
T ss_pred -CCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHH-HHCCCCCCC-CCCCChHHHH
Confidence 889999999999999998641 1369999999887765678999999 666887642 2479999999
Q ss_pred HHHHHHHHHH
Q 018152 287 SAAMKLVLAI 296 (360)
Q Consensus 287 ~at~eL~~~~ 296 (360)
++|++||+++
T Consensus 157 ~~~a~l~~~l 166 (167)
T cd06131 157 ELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHh
Confidence 9999999764
No 17
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.95 E-value=7.5e-27 Score=204.74 Aligned_cols=153 Identities=35% Similarity=0.560 Sum_probs=133.6
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEcCC---cEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 143 IMYAVDCEMVLCEDGSEGLVRLCVVDRNL---KVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 143 ~~ValD~Ettgl~~g~~~I~~VsvVd~~g---~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
.+|+|||||||++++..+|++|++|..++ ...|+.||+|..+|+++++++||||++++.+++ ++.+++++|.+++
T Consensus 1 ~~v~~D~Ettg~~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~-~~~~~~~~~~~~l- 78 (169)
T smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGRIIVVFDTYVKPDRPITDYATEIHGITPEMLDDAP-TFEEVLEELLEFL- 78 (169)
T ss_pred CEEEEEeeCCCCCCCCCeEEEEEEEEEECCEeEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCC-CHHHHHHHHHHHh-
Confidence 48999999999998877899999998644 345999999999999999999999999999998 9999999999999
Q ss_pred CCCEEEEEcc-hhhHHHHcccCC----------CccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHHHHHH
Q 018152 220 NGTILVGHSL-NNDLEVLKLDHP----------RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASA 288 (360)
Q Consensus 220 ~g~iLVGHnl-~fDl~~L~~~~~----------~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~a 288 (360)
++.++||||. .||+.+|+.... +.+||..+++...+...++|..|| .++|++... ..|+|++||++
T Consensus 79 ~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~-~~~~~~~~~--~~H~A~~Da~~ 155 (169)
T smart00479 79 KGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLA-ERLGLEVIG--RAHRALDDARA 155 (169)
T ss_pred cCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHH-HHCCCCCCC--CCcCcHHHHHH
Confidence 7888888988 999999998532 269999999988775599999999 666877642 25999999999
Q ss_pred HHHHHHHHHHhc
Q 018152 289 AMKLVLAIIERR 300 (360)
Q Consensus 289 t~eL~~~~l~~g 300 (360)
|++||+++++.+
T Consensus 156 t~~l~~~~~~~~ 167 (169)
T smart00479 156 TAKLFKKLVERL 167 (169)
T ss_pred HHHHHHHHHHHh
Confidence 999999887654
No 18
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.95 E-value=9.1e-27 Score=218.65 Aligned_cols=157 Identities=24% Similarity=0.277 Sum_probs=131.6
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcC--CcE--EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRN--LKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~--g~~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
..++|+||+||||+++..++|++|++|..+ |.+ .++.||+|+.+|++.++++||||++|+.+.+.+++++.++|..
T Consensus 5 ~~~~vv~D~ETTGl~p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~vl~e~~~ 84 (232)
T PRK07942 5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGEVVESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAEVLAEIAD 84 (232)
T ss_pred cCcEEEEEeccCCCCCCCCeeEEEEEEEEeCCCccccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHHHHHHHHH
Confidence 458999999999999988889999998653 654 3788999999999999999999999998744378888888887
Q ss_pred Hhh----CCCEEEEEcchhhHHHHcccC----------CCccchHHHhhHhCC--CCCCCHHHHHHHHhCCccCCCCCCC
Q 018152 217 LLS----NGTILVGHSLNNDLEVLKLDH----------PRVIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIRKKGTPH 280 (360)
Q Consensus 217 ~l~----~g~iLVGHnl~fDl~~L~~~~----------~~viDT~~l~~~~~~--~~~~sL~~L~~~~Lg~~iq~~~~~H 280 (360)
++. ++++|||||+.||++||+.+. .+++||..+.+...+ ..+++|.+|| .++|++.. .+|
T Consensus 85 ~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~-~~~gi~~~---~aH 160 (232)
T PRK07942 85 ALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALC-EHYGVRLD---NAH 160 (232)
T ss_pred HHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHH-HHcCCCCC---CCC
Confidence 663 689999999999999998752 137999999876544 3468999999 66798864 389
Q ss_pred ChHHHHHHHHHHHHHHHHhcc
Q 018152 281 NCLDDASAAMKLVLAIIERRV 301 (360)
Q Consensus 281 ~AleDA~at~eL~~~~l~~g~ 301 (360)
+|++||.||++||+++.++.+
T Consensus 161 ~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 161 EATADALAAARVAWALARRFP 181 (232)
T ss_pred ChHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999887554
No 19
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.95 E-value=1.6e-26 Score=225.92 Aligned_cols=154 Identities=20% Similarity=0.290 Sum_probs=136.9
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
-+.++|+||+||||+++..++|++|++|.. +|.+. |+.+|+|+.+|+++++++||||++||+++| ++.+|+++|.+
T Consensus 6 ~~~~~Vv~DlETTGl~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~-~~~evl~~f~~ 84 (313)
T PRK06807 6 LPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAP-TIEEVLPLFLA 84 (313)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCC-CHHHHHHHHHH
Confidence 356899999999999998888999999986 45443 788999999999999999999999999999 99999999999
Q ss_pred HhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 217 LLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 217 ~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
|+ ++.++||||+.||++||+... .++|||..+++...+ ...++|..|| +++|++. . +|+|+.||
T Consensus 85 fl-~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~-~~lgi~~-~---~H~Al~DA 158 (313)
T PRK06807 85 FL-HTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLK-RMLGIRL-S---SHNAFDDC 158 (313)
T ss_pred HH-cCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHH-HHcCCCC-C---CcChHHHH
Confidence 99 899999999999999998742 247999999998877 5678999999 7789987 2 89999999
Q ss_pred HHHHHHHHHHHHhc
Q 018152 287 SAAMKLVLAIIERR 300 (360)
Q Consensus 287 ~at~eL~~~~l~~g 300 (360)
++|++||+++....
T Consensus 159 ~~ta~l~~~l~~~~ 172 (313)
T PRK06807 159 ITCAAVYQKCASIE 172 (313)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999888654
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=99.94 E-value=1.6e-26 Score=214.55 Aligned_cols=157 Identities=23% Similarity=0.318 Sum_probs=133.4
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEE-cCCc---EEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVD-RNLK---VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd-~~g~---~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
...+|+||+||||++++.+ |++|++|. .++. ..|+.||+|..+|++.++.+||||++||.++| ++.+|+++|.+
T Consensus 6 ~~~fvv~D~ETTGl~~~~~-IIeIgav~v~~~~~~~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p-~~~ev~~~~~~ 83 (217)
T TIGR00573 6 LDTETTGDNETTGLYAGHD-IIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKP-DFKEIAEDFAD 83 (217)
T ss_pred ecCEEEEEecCCCCCCCCC-EEEEEEEEEECCCEeeeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCC-CHHHHHHHHHH
Confidence 4589999999999999887 99999998 3332 25899999999999999999999999999999 99999999999
Q ss_pred HhhCCCEEEEEcchhhHHHHcccC----------CCccchHHHhhHhCC---CCCCCHHHHHHHHhCCccCCCCCCCChH
Q 018152 217 LLSNGTILVGHSLNNDLEVLKLDH----------PRVIDTSLIFKYVDE---YRRPSLYNLCKSVLGYEIRKKGTPHNCL 283 (360)
Q Consensus 217 ~l~~g~iLVGHnl~fDl~~L~~~~----------~~viDT~~l~~~~~~---~~~~sL~~L~~~~Lg~~iq~~~~~H~Al 283 (360)
|+ ++.++||||+.||+.||+.+. .+++||..+++...+ ..+++|..|| .++|++... +.+|+|+
T Consensus 84 ~~-~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~-~~~gl~~~~-~~~H~Al 160 (217)
T TIGR00573 84 YI-RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALC-KRYEITNSH-RALHGAL 160 (217)
T ss_pred Hh-CCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHH-HHcCCCCCC-cccCCHH
Confidence 99 889999999999999998752 136899887776544 3578999999 566887531 2489999
Q ss_pred HHHHHHHHHHHHHHHhccc
Q 018152 284 DDASAAMKLVLAIIERRVD 302 (360)
Q Consensus 284 eDA~at~eL~~~~l~~g~~ 302 (360)
.||++|++||+.++.+...
T Consensus 161 ~DA~~ta~l~~~l~~~~~~ 179 (217)
T TIGR00573 161 ADAFILAKLYLVMTGKQTK 179 (217)
T ss_pred HHHHHHHHHHHHHHhcchh
Confidence 9999999999998876543
No 21
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.94 E-value=2.4e-26 Score=214.32 Aligned_cols=147 Identities=18% Similarity=0.196 Sum_probs=126.9
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEc-CCcE--EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhC
Q 018152 144 MYAVDCEMVLCEDGSEGLVRLCVVDR-NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (360)
Q Consensus 144 ~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~ 220 (360)
+++||+||||++++ |++|++|+. +|++ .+++||+|+++|+..++++||||++|++++| ++.+++++ |+ +
T Consensus 2 ~~vlD~ETTGl~~~---IieIg~v~v~~~~i~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap-~~~ev~~~---~~-~ 73 (219)
T PRK07983 2 LRVIDTETCGLQGG---IVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKP-WIEDVIPH---YY-G 73 (219)
T ss_pred eEEEEEECCCCCCC---CEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCC-CHHHHHHH---Hc-C
Confidence 68999999999753 889988875 5554 3899999999999999999999999999999 99999886 46 7
Q ss_pred CCEEEEEcchhhHHHHcccCCCccchHHHhhHhCCCCCCCHHHHHHHHhCCccC--CCCCCCChHHHHHHHHHHHHHHHH
Q 018152 221 GTILVGHSLNNDLEVLKLDHPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIR--KKGTPHNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 221 g~iLVGHnl~fDl~~L~~~~~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq--~~~~~H~AleDA~at~eL~~~~l~ 298 (360)
+.+|||||+.||++||+....+.|||..++++..+...++|..|| .++|++.. ....+|+|+.||.+|++||+++++
T Consensus 74 ~~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~~~~~l~~L~-~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~ 152 (219)
T PRK07983 74 SEWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPGIKYSNMALY-KSRKLNVQTPPGLHHHRALYDCYITAALLIDIMN 152 (219)
T ss_pred CCEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccCCCCCHHHHH-HHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 899999999999999987767899999999998884459999999 66787642 113599999999999999999886
Q ss_pred h
Q 018152 299 R 299 (360)
Q Consensus 299 ~ 299 (360)
.
T Consensus 153 ~ 153 (219)
T PRK07983 153 T 153 (219)
T ss_pred H
Confidence 4
No 22
>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=99.94 E-value=3.6e-27 Score=212.51 Aligned_cols=144 Identities=26% Similarity=0.336 Sum_probs=118.9
Q ss_pred EEEEEEeccCCC-CCcccEEEEEEEEcCCc--------------E--EEEEeecCCCcccccccccCCCCHHhhcCCCCC
Q 018152 144 MYAVDCEMVLCE-DGSEGLVRLCVVDRNLK--------------V--TIDELVKPEKAVADYRSEITGLTADDLVGVTCS 206 (360)
Q Consensus 144 ~ValD~Ettgl~-~g~~~I~~VsvVd~~g~--------------~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~ 206 (360)
||+||+||||++ +..++|++|++|...+. + .+++||||+++|++.++++||||++|+.++| +
T Consensus 1 ~vv~D~ETTGl~~~~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~~I~~~a~~IhGIt~e~l~~~~-~ 79 (177)
T cd06136 1 FVFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKA-P 79 (177)
T ss_pred CeEEeeecCCCCCCCCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCCcCChhHHHHhCcCHHHHhcCC-C
Confidence 589999999999 57778999999975321 1 3789999999999999999999999999999 7
Q ss_pred HH-HHHHHHHHHh---hCCCEEEEEcc-hhhHHHHcccC----------CCccchHHHhhHhCCCCCCCHHHHHHHHhCC
Q 018152 207 LA-EIQKRMKKLL---SNGTILVGHSL-NNDLEVLKLDH----------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGY 271 (360)
Q Consensus 207 l~-eV~~~l~~~l---~~g~iLVGHnl-~fDl~~L~~~~----------~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~ 271 (360)
+. ++.+.+.+|+ +++.+|||||+ .||++||+.+. ..++||+.+++.+.+ +|..||++++|+
T Consensus 80 ~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~~----~L~~l~~~~~~~ 155 (177)
T cd06136 80 FDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELDQ----SLGSLYKRLFGQ 155 (177)
T ss_pred ccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhHh----hHHHHHHHHhCC
Confidence 65 3555555555 33569999998 89999998752 135899999998653 999999777898
Q ss_pred ccCCCCCCCChHHHHHHHHHHHHH
Q 018152 272 EIRKKGTPHNCLDDASAAMKLVLA 295 (360)
Q Consensus 272 ~iq~~~~~H~AleDA~at~eL~~~ 295 (360)
+.. .+|+|+.||.||+++|++
T Consensus 156 ~~~---~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 156 EPK---NSHTAEGDVLALLKCALH 176 (177)
T ss_pred Ccc---cccchHHHHHHHHHHHhh
Confidence 864 389999999999999975
No 23
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=5.5e-26 Score=216.54 Aligned_cols=156 Identities=25% Similarity=0.329 Sum_probs=137.2
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHH
Q 018152 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (360)
Q Consensus 139 ~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~ 215 (360)
.....+|+||+||||++++.++|++|++|.. +|.++ |+.||+|. +|+++++++||||++|+.++| ++.+|+++|.
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~-~ip~~~~~itGIt~e~l~~ap-~~~evl~~f~ 142 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAP-SLKEVLEEFR 142 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCC-CCChhhhhhcCcCHHHHcCCC-CHHHHHHHHH
Confidence 3567899999999999988878999999986 55543 78999996 899999999999999999999 9999999999
Q ss_pred HHhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 216 KLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 216 ~~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
+++ ++.++||||+.||++||+... .+.+||..+++...+..+++|.+|| .++|++.. .+|+|+.||
T Consensus 143 ~fl-~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~-~~lgi~~~---~~HrAl~DA 217 (257)
T PRK08517 143 LFL-GDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLK-ELLGIEIE---VHHRAYADA 217 (257)
T ss_pred HHH-CCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHH-HHcCcCCC---CCCChHHHH
Confidence 999 899999999999999998642 2479999999887766789999999 67898864 389999999
Q ss_pred HHHHHHHHHHHHhcc
Q 018152 287 SAAMKLVLAIIERRV 301 (360)
Q Consensus 287 ~at~eL~~~~l~~g~ 301 (360)
.+|++||..++.+.+
T Consensus 218 ~ata~ll~~ll~~~~ 232 (257)
T PRK08517 218 LAAYEIFKICLLNLP 232 (257)
T ss_pred HHHHHHHHHHHHHhH
Confidence 999999999887654
No 24
>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=99.94 E-value=2.2e-26 Score=200.46 Aligned_cols=142 Identities=23% Similarity=0.401 Sum_probs=124.9
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEc-CCcE--EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhC
Q 018152 144 MYAVDCEMVLCEDGSEGLVRLCVVDR-NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (360)
Q Consensus 144 ~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~ 220 (360)
+|+|||||||.. .++|++|++|.. .|++ .++.||+|+.+++++++++||||+++|++++ ++.+++++|.+++ +
T Consensus 1 ~v~~D~Ettg~~--~~~ii~ig~v~~~~~~~~~~~~~~i~p~~~~~~~~~~i~GIt~e~l~~~~-~~~~v~~~l~~~l-~ 76 (156)
T cd06130 1 FVAIDFETANAD--RASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAP-TFPEVWPEIKPFL-G 76 (156)
T ss_pred CEEEEEeCCCCC--CCceEEEEEEEEECCEEEEEEEEEeCcCCCCChhhccccCcCHHHHhcCC-CHHHHHHHHHHHh-C
Confidence 589999999976 346999999986 4443 3779999999999999999999999999999 8999999999999 7
Q ss_pred CCEEEEEcchhhHHHHcccC-------C--CccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHH
Q 018152 221 GTILVGHSLNNDLEVLKLDH-------P--RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAM 290 (360)
Q Consensus 221 g~iLVGHnl~fDl~~L~~~~-------~--~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~ 290 (360)
+.++||||+.||+++|+... + +.+||..+++...+ ..+++|..|| +++|++.+ +|+|+.||++|+
T Consensus 77 ~~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~~~~~~~~~~~~~~L~~l~-~~~g~~~~----~H~Al~Da~~ta 151 (156)
T cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVA-EHLGIELN----HHDALEDARACA 151 (156)
T ss_pred CCEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHHHHHHHhccCCCCCHHHHH-HHcCCCcc----CcCchHHHHHHH
Confidence 89999999999999997641 2 37999999998877 5789999999 56788864 799999999999
Q ss_pred HHHH
Q 018152 291 KLVL 294 (360)
Q Consensus 291 eL~~ 294 (360)
+||+
T Consensus 152 ~l~~ 155 (156)
T cd06130 152 EILL 155 (156)
T ss_pred HHHh
Confidence 9986
No 25
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.94 E-value=4.1e-26 Score=223.04 Aligned_cols=154 Identities=25% Similarity=0.332 Sum_probs=133.9
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc--CCcE--EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR--NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~--~g~~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
+.+||+||+||||++++.++|++|++|.. +|.+ .|.+||+|.. ++..+.+||||++||+++| +|.+++++|.+
T Consensus 14 ~~~fvvlD~ETTGl~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~--~~~~~~IhGIt~e~l~~ap-~f~ev~~~l~~ 90 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQARIISLAVLGLDADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQP-QFADIAGEVAE 90 (313)
T ss_pred CCCEEEEEEECCCCCCCCCEEEEEEEEEEECCceeeeEEEEEECcCC--CCCCeecCCCCHHHHhCCC-CHHHHHHHHHH
Confidence 56899999999999998889999999964 5654 3889999986 3567899999999999999 99999999999
Q ss_pred HhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 217 LLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 217 ~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
|+ ++.+|||||+.||++||+.+. ..++||+.+++...+ ..+++|..|| .++|++.. .+|+|++||
T Consensus 91 ~l-~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~-~~~gi~~~---~~H~Al~DA 165 (313)
T PRK06063 91 LL-RGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLA-AHWGVPQQ---RPHDALDDA 165 (313)
T ss_pred Hc-CCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHH-HHcCCCCC---CCCCcHHHH
Confidence 99 899999999999999998752 137999999998765 6789999999 67798854 389999999
Q ss_pred HHHHHHHHHHHHhccc
Q 018152 287 SAAMKLVLAIIERRVD 302 (360)
Q Consensus 287 ~at~eL~~~~l~~g~~ 302 (360)
++|++||..++++-..
T Consensus 166 ~ata~l~~~ll~~~~~ 181 (313)
T PRK06063 166 RVLAGILRPSLERARE 181 (313)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999988866433
No 26
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=99.94 E-value=4.2e-28 Score=254.65 Aligned_cols=262 Identities=23% Similarity=0.289 Sum_probs=204.2
Q ss_pred CCCchhhHhhhhccccCCCCCCCCcCchHHHHHHhhccCcchhhHHHHHHHHHhhhHHHHHHHHhhCCCCCChhHHHHH-
Q 018152 28 TAGGWKDFLTSYDKKFGSSLSDPARRSKDALSSFLKTFTKEDDLKFIAKVVQSHLNRDLVEQLKKTSPDDESPEQRLVR- 106 (360)
Q Consensus 28 ~~~~~k~~l~~~~~~~~~~~~d~~~~~~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~- 106 (360)
+++.++|.|++|+..++ |- ++...|++.++-....+..+ -++-=|+++|+.++.++-++++...+.-|++..
T Consensus 785 ~~~~~vYeL~a~V~~I~----d~--~~e~~lVs~Ikv~~~~~~~~-~~dsqWylFNDfLV~~ite~EAl~~~~~WKvP~I 857 (1118)
T KOG1275|consen 785 EPSAVVYELDAMVHAIG----DN--ENEVNLVSPIKVLRPYHVIK-PDDSQWYLFNDFLVSEITEEEALHFDGPWKVPAI 857 (1118)
T ss_pred CCceEEEEeeeEEEEec----cC--CCccceEEEEEccCcccccC-cCcceeEEEcceeeeeCChHHheEeccCccCcEE
Confidence 67889999999999999 44 56668888877776655444 011129999999999999999988887777665
Q ss_pred ---hhhcC-CCCccc-------cC--CCCCCCC---ceEeccC-CCCCCCCCCcEEEEEEeccCCCC--------Cc---
Q 018152 107 ---LTLQH-PQYPLC-------YM--FPSSDEG---WLVTKLG-KSSKTMTSNIMYAVDCEMVLCED--------GS--- 158 (360)
Q Consensus 107 ---~t~~~-~~~~~~-------y~--~p~~~~~---~~~t~~~-~~~~~~~~~~~ValD~Ettgl~~--------g~--- 158 (360)
|+.+. +.+... |. +.++..+ =..+-.+ ...+.+.++.+|+||.|++.+.. |.
T Consensus 858 l~Y~d~~s~~~~~V~~~~eiSd~~l~~~~~~~n~~~a~~t~~pLt~dEmPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~st 937 (1118)
T KOG1275|consen 858 LYYCDKKSKKNFDVKTPDEISDYLLLEESYALNRDGAMTTLQPLTLDEMPKSGDLVGIDAEFVTLQTEELEIRSDGKTST 937 (1118)
T ss_pred EEEeccccccCCCCCCccccchHhhhhchhhhcCCcccceeeeccccccCCCCceeeeehhheecchHHhccccCCceeE
Confidence 33331 111111 10 0111111 0111111 23456778999999999998753 22
Q ss_pred -----ccEEEEEEEEcC----CcEEEEEeecCCCcccccccccCCCCHHhhcCCC-----CCHHHHHHHHHHHhhCCCEE
Q 018152 159 -----EGLVRLCVVDRN----LKVTIDELVKPEKAVADYRSEITGLTADDLVGVT-----CSLAEIQKRMKKLLSNGTIL 224 (360)
Q Consensus 159 -----~~I~~VsvVd~~----g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap-----~~l~eV~~~l~~~l~~g~iL 224 (360)
-+++||++|+++ |.++.|.||-.+.+|.||.|+++||.++||.... +++.-++.+++-+++.|+++
T Consensus 938 IkP~~msvARiScvRGeGp~eGiPFiDDYv~T~d~VvDYLTqySGI~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviF 1017 (1118)
T KOG1275|consen 938 IKPSRMSVARISCVRGEGPNEGIPFIDDYVSTDDKVVDYLTQYSGIKPGDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIF 1017 (1118)
T ss_pred eccccceeEEEEEEcccCCCCCCccccceecchhHHHHHHHHhcCCCccccCCccCcceehhHHHHHHHHHHHHHcCcEE
Confidence 258999999984 6778999999999999999999999999999765 36899999999999999999
Q ss_pred EEEcchhhHHHHcccCCC--ccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHHHHHHh
Q 018152 225 VGHSLNNDLEVLKLDHPR--VIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 225 VGHnl~fDl~~L~~~~~~--viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~ 299 (360)
|||++++|+++||+..|+ +|||+.+|+... .+..||++||+.+||-.||.+ .||+++||+.|+.||.++++-
T Consensus 1018 VGHGL~nDFrvINi~Vp~~QiiDTv~lf~~~s-~R~LSLrfLa~~lLg~~IQ~~--~HDSIeDA~taLkLYk~Yl~l 1091 (1118)
T KOG1275|consen 1018 VGHGLQNDFRVINIHVPEEQIIDTVTLFRLGS-QRMLSLRFLAWELLGETIQME--AHDSIEDARTALKLYKKYLKL 1091 (1118)
T ss_pred EcccccccceEEEEecChhhheeeeEEEeccc-ccEEEHHHHHHHHhcchhhcc--ccccHHHHHHHHHHHHHHHHH
Confidence 999999999999999885 899999998533 588999999999999999964 999999999999999999973
No 27
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.93 E-value=2e-25 Score=205.72 Aligned_cols=155 Identities=21% Similarity=0.276 Sum_probs=128.6
Q ss_pred CCcEEEEEEeccCCCCC------cccEEEEEEEEc-CCcE--EEEEeecCCC--cccccccccCCCCHHhhcCCCCCHHH
Q 018152 141 SNIMYAVDCEMVLCEDG------SEGLVRLCVVDR-NLKV--TIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAE 209 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g------~~~I~~VsvVd~-~g~~--~~d~lV~P~~--~I~d~~t~i~GIT~e~L~~ap~~l~e 209 (360)
..++|+||+||||++.+ .++|++|++|.. +|.+ .|++||+|.. +|+++++++||||++||+++| ++.+
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap-~~~e 81 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGI-SFEE 81 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcChhhhcceECCCccCccChhhhhhcCcCHHHHccCC-CHHH
Confidence 45799999999998643 257999999976 3433 3899999987 799999999999999999999 9999
Q ss_pred HHHHHHHHhhCC-CEEEEEcchhhHHHHcccC-------C---CccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCC
Q 018152 210 IQKRMKKLLSNG-TILVGHSLNNDLEVLKLDH-------P---RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKG 277 (360)
Q Consensus 210 V~~~l~~~l~~g-~iLVGHnl~fDl~~L~~~~-------~---~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~ 277 (360)
|+++|.+|+ ++ ..+|.|+..||++||+... + +.+|+..+++...+ ...++|+.+| .++|++.. +
T Consensus 82 vl~~f~~~~-~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~-~~~gi~~~--~ 157 (207)
T PRK07748 82 LVEKLAEYD-KRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAI-EEYGKEGT--G 157 (207)
T ss_pred HHHHHHHHh-CcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHH-HHcCCCCC--C
Confidence 999999999 66 4566667899999998742 1 36888888887666 5678999999 66788853 2
Q ss_pred CCCChHHHHHHHHHHHHHHHHhc
Q 018152 278 TPHNCLDDASAAMKLVLAIIERR 300 (360)
Q Consensus 278 ~~H~AleDA~at~eL~~~~l~~g 300 (360)
.+|+|+.||++|++||.++.+++
T Consensus 158 ~~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 158 KHHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred CCcChHHHHHHHHHHHHHHHhCc
Confidence 47999999999999999988765
No 28
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=2.8e-25 Score=216.68 Aligned_cols=148 Identities=21% Similarity=0.299 Sum_probs=128.9
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCC-cccccccccCCCCHHhhcCCCCCHHHHHHHHHHHh
Q 018152 143 IMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEK-AVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLL 218 (360)
Q Consensus 143 ~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~-~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l 218 (360)
++|+||+||||.. .++|++|++|.. +|.++ +++||+|.. .+++..+++||||++||+++| +|.+|+++|.+|+
T Consensus 2 ~~vviD~ETTg~~--~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap-~f~ev~~~~~~fl 78 (309)
T PRK06195 2 NFVAIDFETANEK--RNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDEL-EFDKIWEKIKHYF 78 (309)
T ss_pred cEEEEEEeCCCCC--CCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCC-CHHHHHHHHHHHh
Confidence 6899999999754 457999999986 55443 889999985 678889999999999999999 9999999999999
Q ss_pred hCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHH
Q 018152 219 SNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASA 288 (360)
Q Consensus 219 ~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~a 288 (360)
++.+|||||+.||++||+... .+.+||..+++...+ ..+++|..|| .++|++. .+|+|++||++
T Consensus 79 -~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~-~~~gi~~----~~H~Al~DA~a 152 (309)
T PRK06195 79 -NNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVN-NFLGYEF----KHHDALADAMA 152 (309)
T ss_pred -CCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHH-HHcCCCC----cccCCHHHHHH
Confidence 899999999999999998752 247999999998877 5789999999 6678874 28999999999
Q ss_pred HHHHHHHHHHh
Q 018152 289 AMKLVLAIIER 299 (360)
Q Consensus 289 t~eL~~~~l~~ 299 (360)
|++||..++++
T Consensus 153 ta~l~~~l~~~ 163 (309)
T PRK06195 153 CSNILLNISKE 163 (309)
T ss_pred HHHHHHHHHHH
Confidence 99999988865
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=99.93 E-value=1.9e-25 Score=205.28 Aligned_cols=155 Identities=24% Similarity=0.317 Sum_probs=127.6
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc----CCcE----EEEEeecC--CCcccccccccCCCCHH-hhcCCCCCHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLKV----TIDELVKP--EKAVADYRSEITGLTAD-DLVGVTCSLAE 209 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~----~g~~----~~d~lV~P--~~~I~d~~t~i~GIT~e-~L~~ap~~l~e 209 (360)
...+|+||+||||+++..++|++|++|.. +|.+ .|+++|+| +++|+..++++||||++ |+.+++ +.++
T Consensus 7 ~~~~vv~D~ETTGl~~~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~-~~~~ 85 (200)
T TIGR01298 7 GYLPVVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAV-SEYE 85 (200)
T ss_pred CCeeEEEEeeCCCCCCCCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCc-chHH
Confidence 45789999999999987778999999864 3443 38899997 47999999999999976 699998 8888
Q ss_pred HHHHHHHHhh--------CCCEEEEEcchhhHHHHcccC--------C----CccchHHHhhHhCCCCCCCHHHHHHHHh
Q 018152 210 IQKRMKKLLS--------NGTILVGHSLNNDLEVLKLDH--------P----RVIDTSLIFKYVDEYRRPSLYNLCKSVL 269 (360)
Q Consensus 210 V~~~l~~~l~--------~g~iLVGHnl~fDl~~L~~~~--------~----~viDT~~l~~~~~~~~~~sL~~L~~~~L 269 (360)
++.+++.++. ++.+|||||+.||++||+... + +++||..+++...+ ..+|..|| +++
T Consensus 86 ~~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~~~~--~~~L~~l~-~~~ 162 (200)
T TIGR01298 86 ALHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGLAYG--QTVLAKAC-QAA 162 (200)
T ss_pred HHHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHcC--cccHHHHH-HHc
Confidence 8888777762 578999999999999998641 1 27999999987764 45899999 567
Q ss_pred CCccCCCCCCCChHHHHHHHHHHHHHHHHhc
Q 018152 270 GYEIRKKGTPHNCLDDASAAMKLVLAIIERR 300 (360)
Q Consensus 270 g~~iq~~~~~H~AleDA~at~eL~~~~l~~g 300 (360)
|++... ..+|+|+.||.+|++||.+++++.
T Consensus 163 gi~~~~-~~~H~Al~Da~ata~lf~~l~~~~ 192 (200)
T TIGR01298 163 GXDFDS-TQAHSALYDTEKTAELFCEIVNRW 192 (200)
T ss_pred CCCccc-cchhhhHHhHHHHHHHHHHHHHHH
Confidence 988632 248999999999999999988654
No 30
>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=99.93 E-value=2.6e-25 Score=202.53 Aligned_cols=153 Identities=22% Similarity=0.253 Sum_probs=121.7
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEc----CCc----EEEEEeecC--CCcccccccccCCCCHHh-hcCCCCCHHHH
Q 018152 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLK----VTIDELVKP--EKAVADYRSEITGLTADD-LVGVTCSLAEI 210 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~~~I~~VsvVd~----~g~----~~~d~lV~P--~~~I~d~~t~i~GIT~e~-L~~ap~~l~eV 210 (360)
-..|+||+||||+++..++|++|++|.. +|. ..|++||+| +.+|++.++++||||++| +++++ ..+++
T Consensus 5 ~~~vv~D~ETTGl~~~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~-~~~~~ 83 (189)
T cd06134 5 FLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAV-DEKEA 83 (189)
T ss_pred ceeEEEEecCCCCCCCCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhcccc-chHHH
Confidence 3578999999999988888999999965 243 258999999 579999999999999987 55555 55555
Q ss_pred HHHHHHHhh--------CCCEEEEEcchhhHHHHcccC--------C----CccchHHHhhHhCCCCCCCHHHHHHHHhC
Q 018152 211 QKRMKKLLS--------NGTILVGHSLNNDLEVLKLDH--------P----RVIDTSLIFKYVDEYRRPSLYNLCKSVLG 270 (360)
Q Consensus 211 ~~~l~~~l~--------~g~iLVGHnl~fDl~~L~~~~--------~----~viDT~~l~~~~~~~~~~sL~~L~~~~Lg 270 (360)
..++++++. ++.+|||||+.||+.||+... + +++||..+++...+ ..+|..+| .++|
T Consensus 84 ~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~--~~~L~~l~-~~~g 160 (189)
T cd06134 84 LKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG--QTVLAKAC-QAAG 160 (189)
T ss_pred HHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC--CCcHHHHH-HHCC
Confidence 555555442 378999999999999998641 1 36999999998765 45899999 5679
Q ss_pred CccCCCCCCCChHHHHHHHHHHHHHHHHh
Q 018152 271 YEIRKKGTPHNCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 271 ~~iq~~~~~H~AleDA~at~eL~~~~l~~ 299 (360)
+++.. ..+|+|+.||.+|++||.+++++
T Consensus 161 i~~~~-~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 161 IEFDN-KEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred CCCCC-CCCcChHHHHHHHHHHHHHHHHh
Confidence 88642 24899999999999999988753
No 31
>PRK05168 ribonuclease T; Provisional
Probab=99.93 E-value=2.6e-25 Score=205.96 Aligned_cols=156 Identities=22% Similarity=0.297 Sum_probs=129.7
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc----CCc----EEEEEeecC--CCcccccccccCCCCHHh-hcCCCCCHH
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLK----VTIDELVKP--EKAVADYRSEITGLTADD-LVGVTCSLA 208 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~----~g~----~~~d~lV~P--~~~I~d~~t~i~GIT~e~-L~~ap~~l~ 208 (360)
+...+|+||+||||+++..++|++|++|.. +|. ..|++||+| +.+|+++++++||||+++ +++++ +..
T Consensus 15 ~~~~~vv~D~ETTGl~~~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~-~~~ 93 (211)
T PRK05168 15 RGFLPVVIDVETAGFNAKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAV-SEK 93 (211)
T ss_pred cCCceEEEEeeCCCCCCCCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCC-ChH
Confidence 456799999999999988888999999964 343 258999999 578999999999999986 78888 888
Q ss_pred HHHHHHHHHhh--------CCCEEEEEcchhhHHHHcccC-----------C-CccchHHHhhHhCCCCCCCHHHHHHHH
Q 018152 209 EIQKRMKKLLS--------NGTILVGHSLNNDLEVLKLDH-----------P-RVIDTSLIFKYVDEYRRPSLYNLCKSV 268 (360)
Q Consensus 209 eV~~~l~~~l~--------~g~iLVGHnl~fDl~~L~~~~-----------~-~viDT~~l~~~~~~~~~~sL~~L~~~~ 268 (360)
++..++++++. +++++||||+.||++||+.+. + +++||..+++...+ ..+|..+| .+
T Consensus 94 ~~l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~~~~--~~~L~~l~-~~ 170 (211)
T PRK05168 94 EALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGLALG--QTVLAKAC-QA 170 (211)
T ss_pred HHHHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHHHcC--CCCHHHHH-HH
Confidence 88888888763 378999999999999998741 1 47999999998764 35899999 56
Q ss_pred hCCccCCCCCCCChHHHHHHHHHHHHHHHHhc
Q 018152 269 LGYEIRKKGTPHNCLDDASAAMKLVLAIIERR 300 (360)
Q Consensus 269 Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~g 300 (360)
+|+++.. ..+|+|++||.+|++||.+++++.
T Consensus 171 ~gl~~~~-~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 171 AGIEFDN-KEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred CCCCCCC-CCCCChHHHHHHHHHHHHHHHHHH
Confidence 7988642 248999999999999999888653
No 32
>PRK07883 hypothetical protein; Validated
Probab=99.93 E-value=1.1e-24 Score=227.46 Aligned_cols=158 Identities=22% Similarity=0.339 Sum_probs=139.0
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHH
Q 018152 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (360)
Q Consensus 139 ~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~ 215 (360)
....++|+||+||||+++..++|++|++|.. .|.++ |+.+|+|+.+|+++++++||||++||+++| ++++++++|.
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap-~~~evl~~f~ 90 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAP-PIEEVLPAFL 90 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCC-CHHHHHHHHH
Confidence 3456899999999999988788999999987 45444 889999999999999999999999999999 9999999999
Q ss_pred HHhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC---CCCCCHHHHHHHHhCCccCCCCCCCChH
Q 018152 216 KLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE---YRRPSLYNLCKSVLGYEIRKKGTPHNCL 283 (360)
Q Consensus 216 ~~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~---~~~~sL~~L~~~~Lg~~iq~~~~~H~Al 283 (360)
+|+ +++++||||+.||+.||+... ...+||..+++...+ ..+++|.+|| .++|++.. .+|+|+
T Consensus 91 ~fl-~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~-~~~gi~~~---~~H~Al 165 (557)
T PRK07883 91 EFA-RGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLA-RLFGATTT---PTHRAL 165 (557)
T ss_pred HHh-cCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHH-HHCCcccC---CCCCHH
Confidence 999 899999999999999998742 247999999988664 5788999999 67899864 389999
Q ss_pred HHHHHHHHHHHHHHHhccc
Q 018152 284 DDASAAMKLVLAIIERRVD 302 (360)
Q Consensus 284 eDA~at~eL~~~~l~~g~~ 302 (360)
+||.+|++||..++++-..
T Consensus 166 ~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 166 DDARATVDVLHGLIERLGN 184 (557)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 9999999999998876543
No 33
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.93 E-value=6.7e-25 Score=238.05 Aligned_cols=154 Identities=18% Similarity=0.281 Sum_probs=135.9
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcE--EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
..++|+||+||||+++. ++|++|++|.. +|++ .|++||+|+.+|+++++++||||++||+++| ++++|+++|.++
T Consensus 6 ~~~~vvvD~ETTGl~~~-d~IIeIgaV~v~~g~i~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap-~~~ev~~~~~~~ 83 (820)
T PRK07246 6 LRKYAVVDLEATGAGPN-ASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAP-DFSQVARHIYDL 83 (820)
T ss_pred CCCEEEEEEecCCcCCC-CeEEEEEEEEEECCEEEEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCC-CHHHHHHHHHHH
Confidence 46799999999999874 67999999986 4544 3788999999999999999999999999999 999999999999
Q ss_pred hhCCCEEEEEcchhhHHHHcccC--------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHH
Q 018152 218 LSNGTILVGHSLNNDLEVLKLDH--------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASA 288 (360)
Q Consensus 218 l~~g~iLVGHnl~fDl~~L~~~~--------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~a 288 (360)
+ +++++||||+.||+.||+... .+.+||..+++...+ ..+++|..|| .++|++.. .+|+|++||++
T Consensus 84 l-~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~-~~lgl~~~---~~H~Al~DA~a 158 (820)
T PRK07246 84 I-EDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLS-RELNIDLA---DAHTAIADARA 158 (820)
T ss_pred h-CCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHH-HHcCCCCC---CCCCHHHHHHH
Confidence 9 899999999999999998641 246999999998887 5789999999 66798864 38999999999
Q ss_pred HHHHHHHHHHhcc
Q 018152 289 AMKLVLAIIERRV 301 (360)
Q Consensus 289 t~eL~~~~l~~g~ 301 (360)
|++||..++++-.
T Consensus 159 ta~L~~~l~~~l~ 171 (820)
T PRK07246 159 TAELFLKLLQKIE 171 (820)
T ss_pred HHHHHHHHHHHHh
Confidence 9999998887643
No 34
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.92 E-value=1.5e-24 Score=213.97 Aligned_cols=155 Identities=15% Similarity=0.237 Sum_probs=131.4
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc--CCcE--EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHH
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR--NLKV--TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~--~g~~--~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~ 215 (360)
...+||+||+||||+++..++|++|++|.. +|.+ .|++||||+.++.+ ..+||||++||+++| +|++|+++|.
T Consensus 44 ~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p--~~LHGIT~e~La~AP-~f~eVl~el~ 120 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGP--FHLHGLSAEEFAQGK-RFSQILKPLD 120 (377)
T ss_pred CCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCC--ccccCCCHHHHhcCC-CHHHHHHHHH
Confidence 456899999999999998889999999864 4654 59999999986554 479999999999999 9999999999
Q ss_pred HHhhCCCEEEEEcchhhHHHHcccC------------------------------------CCccchHHHhhHhCC-CCC
Q 018152 216 KLLSNGTILVGHSLNNDLEVLKLDH------------------------------------PRVIDTSLIFKYVDE-YRR 258 (360)
Q Consensus 216 ~~l~~g~iLVGHnl~fDl~~L~~~~------------------------------------~~viDT~~l~~~~~~-~~~ 258 (360)
+|+ +|++|||||+.||++||+.+. ..++||+.++++..+ ..+
T Consensus 121 ~fL-~g~vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LARrl~p~l~~ 199 (377)
T PRK05601 121 RLI-DGRTLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATARRQGVALDD 199 (377)
T ss_pred HHh-CCCEEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHHHHcCCCCC
Confidence 999 899999999999999997741 136999999999987 689
Q ss_pred CCHHHHHHHHhCCccCC-------CCCCCChH--HHHHHHHHHHHHHHHh
Q 018152 259 PSLYNLCKSVLGYEIRK-------KGTPHNCL--DDASAAMKLVLAIIER 299 (360)
Q Consensus 259 ~sL~~L~~~~Lg~~iq~-------~~~~H~Al--eDA~at~eL~~~~l~~ 299 (360)
++|..|| .+||++... ....|+++ +||+.+++||.+..+.
T Consensus 200 ~rL~~La-~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~~ 248 (377)
T PRK05601 200 IRIRGVA-HTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRAS 248 (377)
T ss_pred CCHHHHH-HHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhcc
Confidence 9999999 667998711 12478988 6999999999876433
No 35
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.92 E-value=2.5e-25 Score=239.25 Aligned_cols=162 Identities=21% Similarity=0.366 Sum_probs=145.3
Q ss_pred CCCCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHH
Q 018152 137 KTMTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKR 213 (360)
Q Consensus 137 ~~~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~ 213 (360)
.......||+||+||||+++..++|+++++|.. +|+++ ++.||||++||+..+|++||||++||++++ ++.+|..+
T Consensus 416 ~~l~datyVVfDiETTGLs~~~d~iIE~aAvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~-~i~~vL~k 494 (1444)
T COG2176 416 QKLDDATYVVFDIETTGLSPVYDEIIEIAAVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAP-EIEEVLEK 494 (1444)
T ss_pred cccccccEEEEEeecCCcCcccchhhhheeeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCc-cHHHHHHH
Confidence 445678899999999999999999999999986 67665 789999999999999999999999999999 99999999
Q ss_pred HHHHhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChH
Q 018152 214 MKKLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCL 283 (360)
Q Consensus 214 l~~~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~Al 283 (360)
|.+|+ +|+|||+||++||++||+... .++|||+.++|.++| .++++|..||+ -||+.+. .+|+|.
T Consensus 495 f~~~~-~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~k-k~~v~le---~hHRA~ 569 (1444)
T COG2176 495 FREFI-GDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCK-KLGVELE---RHHRAD 569 (1444)
T ss_pred HHHHh-cCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHH-HhCccHH---Hhhhhh
Confidence 99999 999999999999999999852 248999999999998 89999999995 5588884 389999
Q ss_pred HHHHHHHHHHHHHHHhcccCC
Q 018152 284 DDASAAMKLVLAIIERRVDNA 304 (360)
Q Consensus 284 eDA~at~eL~~~~l~~g~~~~ 304 (360)
-||.|++.+|..+++.-.+.+
T Consensus 570 yDaeat~~vf~~f~~~~ke~G 590 (1444)
T COG2176 570 YDAEATAKVFFVFLKDLKEKG 590 (1444)
T ss_pred hhHHHHHHHHHHHHHHHHHhc
Confidence 999999999999887644443
No 36
>PRK06722 exonuclease; Provisional
Probab=99.92 E-value=5.9e-24 Score=204.63 Aligned_cols=152 Identities=25% Similarity=0.337 Sum_probs=125.4
Q ss_pred CCcEEEEEEeccCCCCC----cccEEEEEEEEc-CC--cEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDG----SEGLVRLCVVDR-NL--KVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQ 211 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g----~~~I~~VsvVd~-~g--~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~ 211 (360)
...+|+||+|||| ++. .++|++|++|.. +| +++ |++||+|+.+|+++++++||||++||+++| ++++|+
T Consensus 4 ~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP-~f~eVl 81 (281)
T PRK06722 4 ATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVE-KFPQII 81 (281)
T ss_pred CCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCC-CHHHHH
Confidence 4689999999995 432 257999999976 33 443 999999999999999999999999999999 999999
Q ss_pred HHHHHHhhCCCEEEEEcchhhHHHHcccC-------C-----CccchHHHhhHhCC---CCCCCHHHHHHHHhCCccCCC
Q 018152 212 KRMKKLLSNGTILVGHSLNNDLEVLKLDH-------P-----RVIDTSLIFKYVDE---YRRPSLYNLCKSVLGYEIRKK 276 (360)
Q Consensus 212 ~~l~~~l~~g~iLVGHnl~fDl~~L~~~~-------~-----~viDT~~l~~~~~~---~~~~sL~~L~~~~Lg~~iq~~ 276 (360)
++|.+|+ ++.++|+||..||++||+... | +.+|+..++....+ ...+||..|| +++|++..
T Consensus 82 ~ef~~fi-g~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~-~~lgL~~~-- 157 (281)
T PRK06722 82 EKFIQFI-GEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAV-EQLGLIWE-- 157 (281)
T ss_pred HHHHHHH-CCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHH-HHCCCCCC--
Confidence 9999999 777788888899999999852 1 13788877654332 3557999999 77798864
Q ss_pred CCCCChHHHHHHHHHHHHHHHH
Q 018152 277 GTPHNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 277 ~~~H~AleDA~at~eL~~~~l~ 298 (360)
+..|+|++||.+|++||+.++.
T Consensus 158 g~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 158 GKQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCCcCcHHHHHHHHHHHHHHhc
Confidence 3489999999999999998874
No 37
>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=99.91 E-value=5.4e-24 Score=232.20 Aligned_cols=153 Identities=22% Similarity=0.300 Sum_probs=136.7
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 143 IMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 143 ~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
+||+||+||||++++.++|++|++|.. +|+++ |+++|+|+.+|+++++++||||++|++++| ++++++++|.+++
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 RYAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAP-YFSQVAQEIYDLL- 78 (850)
T ss_pred CEEEEEEECCCCCCCCCeEEEEEEEEEECCEEEEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCC-CHHHHHHHHHHHh-
Confidence 489999999999988889999999986 56544 899999999999999999999999999999 9999999999999
Q ss_pred CCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHH
Q 018152 220 NGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAA 289 (360)
Q Consensus 220 ~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at 289 (360)
+++++||||+.||+.||+.+. ...+||..+++...+ ..+++|.+|| +++|++.. .+|+|++||.+|
T Consensus 79 ~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~-~~~gi~~~---~~H~Al~DA~at 154 (850)
T TIGR01407 79 EDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELS-EALGLTHE---NPHRADSDAQAT 154 (850)
T ss_pred CCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHH-HHCCCCCC---CCCChHHHHHHH
Confidence 899999999999999998641 147999999998887 6789999999 66798864 389999999999
Q ss_pred HHHHHHHHHhcc
Q 018152 290 MKLVLAIIERRV 301 (360)
Q Consensus 290 ~eL~~~~l~~g~ 301 (360)
++||++++.+-.
T Consensus 155 a~l~~~l~~~~~ 166 (850)
T TIGR01407 155 AELLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHHHH
Confidence 999998876543
No 38
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.91 E-value=5.2e-24 Score=234.03 Aligned_cols=155 Identities=20% Similarity=0.333 Sum_probs=136.9
Q ss_pred CcEEEEEEeccCCCCCc-ccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 142 NIMYAVDCEMVLCEDGS-EGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~-~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
.++|+||+||||+++.. ++|++|++|.. +|+++ |+.||+|+.+|+++++++||||++||+++| ++++|+++|.+|
T Consensus 3 ~~~vvvD~ETTG~~p~~~d~IIeigav~v~~~~i~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap-~f~ev~~~l~~~ 81 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAP-LFEDVAPEIVEL 81 (928)
T ss_pred CCEEEEEEeCCCCCCCCCCcEEEEEEEEEECCEEEEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCC-CHHHHHHHHHHH
Confidence 46999999999998654 57999999986 55543 889999999999999999999999999999 999999999999
Q ss_pred hhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHH
Q 018152 218 LSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDAS 287 (360)
Q Consensus 218 l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~ 287 (360)
+ +++++||||+.||++||+... .+.|||..+++...| ...++|..|| .++|++.. .+|+|++||.
T Consensus 82 l-~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~-~~l~i~~~---~~H~Al~DA~ 156 (928)
T PRK08074 82 L-EGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLS-EELGLEHD---QPHRADSDAE 156 (928)
T ss_pred h-CCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHH-HhCCCCCC---CCCChHHHHH
Confidence 9 899999999999999998741 247999999998887 6789999999 66788754 4899999999
Q ss_pred HHHHHHHHHHHhccc
Q 018152 288 AAMKLVLAIIERRVD 302 (360)
Q Consensus 288 at~eL~~~~l~~g~~ 302 (360)
+|++||.+++++-..
T Consensus 157 ata~l~~~l~~~~~~ 171 (928)
T PRK08074 157 VTAELFLQLLNKLER 171 (928)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999876543
No 39
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.91 E-value=1.2e-23 Score=196.94 Aligned_cols=154 Identities=23% Similarity=0.321 Sum_probs=135.9
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEc-CCcE---EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~---~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
.++|+||+||||.++..++|++|++|.. ++.+ .++.||+|+.+|+++++++||||.+||.++| .+.++++++.++
T Consensus 13 ~~~vv~D~ETtg~~~~~~~iieIgav~~~~~~i~~~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p-~~~~v~~~~~~~ 91 (243)
T COG0847 13 TRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAP-KFAEVLPEFLDF 91 (243)
T ss_pred CcEEEEecccCCCCCCCCceEEEEeEEEECCeeecceeEEEECCCCCCChhhhhhcCCCHHHHhcCC-CHHHHHHHHHHH
Confidence 5899999999999986678999999986 4432 3889999999999999999999999999999 999999999999
Q ss_pred hhCC-CEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCCC-CCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 218 LSNG-TILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDEY-RRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 218 l~~g-~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~~-~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
+ ++ .++||||+.||+.||+... ..++||..+.+...+. ..++|+.|| .++|++.. ....|+|+.||
T Consensus 92 i-~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~-~~~gi~~~-~~~~H~Al~Da 168 (243)
T COG0847 92 I-GGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALA-ERLGIDRN-PFHPHRALFDA 168 (243)
T ss_pred H-CCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHH-HHcCCCcC-CcCCcchHHHH
Confidence 9 66 9999999999999998752 2368999999999885 899999999 57798854 23479999999
Q ss_pred HHHHHHHHHHHHh
Q 018152 287 SAAMKLVLAIIER 299 (360)
Q Consensus 287 ~at~eL~~~~l~~ 299 (360)
.+++++|+.+..+
T Consensus 169 ~~~a~~~~~~~~~ 181 (243)
T COG0847 169 LALAELFLLLQTG 181 (243)
T ss_pred HHHHHHHHHHHhc
Confidence 9999999988874
No 40
>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=99.91 E-value=9.6e-24 Score=234.94 Aligned_cols=156 Identities=23% Similarity=0.391 Sum_probs=139.8
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
+..++|+||+||||+++..++|++|++|.. +|.++ |+.||+|+.+|+++++++||||++||+++| ++++|+++|.+
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap-~~~evl~~f~~ 266 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAP-EIEEVLEKFKE 266 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCC-CHHHHHHHHHH
Confidence 567999999999999998889999999986 55544 899999999999999999999999999999 99999999999
Q ss_pred HhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 217 LLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 217 ~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
|+ ++++|||||+.||+.||+... .+++||+.+++...+ ...++|..|| .++|++... +|+|+.||
T Consensus 267 fl-~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~La-k~lgi~~~~---~HrAl~DA 341 (1213)
T TIGR01405 267 FF-KDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNIC-KKLGVDLDD---HHRADYDA 341 (1213)
T ss_pred Hh-CCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHH-HHcCCCCCC---CcCHHHHH
Confidence 99 899999999999999998742 247999999998876 7889999999 556988753 89999999
Q ss_pred HHHHHHHHHHHHhcc
Q 018152 287 SAAMKLVLAIIERRV 301 (360)
Q Consensus 287 ~at~eL~~~~l~~g~ 301 (360)
.+|+++|..+++...
T Consensus 342 ~aTa~I~~~ll~~l~ 356 (1213)
T TIGR01405 342 EATAKVFKVMVEQLK 356 (1213)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999886543
No 41
>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=99.91 E-value=9.5e-24 Score=187.04 Aligned_cols=148 Identities=25% Similarity=0.309 Sum_probs=125.3
Q ss_pred EEEEEEeccCCCCCc-----ccEEEEEEEEc--CCc---EEEEEeecCCC--cccccccccCCCCHHhhcCCCCCHHHHH
Q 018152 144 MYAVDCEMVLCEDGS-----EGLVRLCVVDR--NLK---VTIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEIQ 211 (360)
Q Consensus 144 ~ValD~Ettgl~~g~-----~~I~~VsvVd~--~g~---~~~d~lV~P~~--~I~d~~t~i~GIT~e~L~~ap~~l~eV~ 211 (360)
||+|||||||++++. ++|++|++|.. ++. ..|+.||+|.. +|+++++++||||++|+.++| ++.+|+
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~-~~~~vl 79 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAP-SFPEVL 79 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCC-CHHHHH
Confidence 589999999999764 68999999964 332 35899999998 999999999999999999998 999999
Q ss_pred HHHHHHhhCCC--EEEEEcchhhHHHHccc------------CCCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCC
Q 018152 212 KRMKKLLSNGT--ILVGHSLNNDLEVLKLD------------HPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKK 276 (360)
Q Consensus 212 ~~l~~~l~~g~--iLVGHnl~fDl~~L~~~------------~~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~ 276 (360)
++|.+++ ++. .+++|+..||.++|... ..+.+|+..+++...+ ...++|..+| .++|++..
T Consensus 80 ~~~~~~l-~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~-~~~gi~~~-- 155 (176)
T cd06133 80 KEFLEWL-GKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKAL-EYLGLEFE-- 155 (176)
T ss_pred HHHHHHH-HhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHH-HHCCCCCC--
Confidence 9999999 665 55566669999877653 1137999999998887 4699999999 67798875
Q ss_pred CCCCChHHHHHHHHHHHHHH
Q 018152 277 GTPHNCLDDASAAMKLVLAI 296 (360)
Q Consensus 277 ~~~H~AleDA~at~eL~~~~ 296 (360)
+..|+|+.||++++++++++
T Consensus 156 ~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 156 GRHHRGLDDARNIARILKRL 175 (176)
T ss_pred CCCcCcHHHHHHHHHHHHHh
Confidence 35999999999999999875
No 42
>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=99.91 E-value=2.1e-23 Score=178.65 Aligned_cols=144 Identities=22% Similarity=0.303 Sum_probs=126.0
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcCC----cEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhC
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDRNL----KVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~~g----~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~ 220 (360)
|++||||||+++...+|++|+++..++ ...++.||+|+..++++.+.+||||++++++++ ++.++..+|.+++ .
T Consensus 1 v~~D~Ettg~~~~~~~iiei~~v~~~~~~~~~~~~~~~i~p~~~~~~~~~~~~gi~~~~~~~~~-~~~~~~~~~~~~l-~ 78 (159)
T cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAP-PFEEVLPEFLEFL-G 78 (159)
T ss_pred CeEEeeCCCcCCCCCeEEEEEEEEEECCcChhhhhheeeCcCCcCCHhheeccCCCHHHHhcCC-CHHHHHHHHHHHH-C
Confidence 579999999998777899999998643 245899999999999999999999999999998 9999999999999 7
Q ss_pred CCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHH
Q 018152 221 GTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAM 290 (360)
Q Consensus 221 g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~ 290 (360)
+.++||||+.||..+|+... .+.+||..+++...+ ...++|..+...++|.+.. ..|+|+.||++++
T Consensus 79 ~~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~~~~~~~~~~~~~~l~~~~~~~~~~~~~---~~H~Al~Da~~t~ 155 (159)
T cd06127 79 GRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLE---GAHRALADALATA 155 (159)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHHHHHHHcCCCCcCchHHHHHHHcCCCCC---CCCCcHHHHHHHH
Confidence 79999999999999998752 247999999998887 6778999983367777653 4899999999999
Q ss_pred HHH
Q 018152 291 KLV 293 (360)
Q Consensus 291 eL~ 293 (360)
+||
T Consensus 156 ~l~ 158 (159)
T cd06127 156 ELL 158 (159)
T ss_pred HHh
Confidence 998
No 43
>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=99.91 E-value=8.5e-24 Score=191.32 Aligned_cols=144 Identities=18% Similarity=0.215 Sum_probs=117.9
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcC--CcE--EEEEeecCCC--cccccccccCCCCHHhhcC-CCCCHHHHHHHHHHH
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDRN--LKV--TIDELVKPEK--AVADYRSEITGLTADDLVG-VTCSLAEIQKRMKKL 217 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~~--g~~--~~d~lV~P~~--~I~d~~t~i~GIT~e~L~~-ap~~l~eV~~~l~~~ 217 (360)
++||+||||+++..++|++|++|..+ +.+ .++.+|+|.. ++++..+.+||||++||.+ +| ++.+++++|..|
T Consensus 1 ~~~D~ETTGl~~~~d~Iieig~v~v~~~~~~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~-~~~~~l~~~~~~ 79 (183)
T cd06138 1 LFYDYETFGLNPSFDQILQFAAIRTDENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGL-SEYEFIAKIHRL 79 (183)
T ss_pred CEEEeecCCCCCCCCceEEEEEEEECCCCCCccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCC-CHHHHHHHHHHH
Confidence 47999999999988889999999753 333 3889999874 6777899999999999999 78 999999999999
Q ss_pred hh-CCCEEEEEc-chhhHHHHcccCC---------------CccchHHHhhHhC--------------CCCCCCHHHHHH
Q 018152 218 LS-NGTILVGHS-LNNDLEVLKLDHP---------------RVIDTSLIFKYVD--------------EYRRPSLYNLCK 266 (360)
Q Consensus 218 l~-~g~iLVGHn-l~fDl~~L~~~~~---------------~viDT~~l~~~~~--------------~~~~~sL~~L~~ 266 (360)
+. +++++|||| +.||++||+.... ..+||..+++... +..+++|.+||
T Consensus 80 ~~~~~~~lVahn~~~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~- 158 (183)
T cd06138 80 FNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLA- 158 (183)
T ss_pred HccCCCcEEeeCchhhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHH-
Confidence 95 368999997 8999999987521 2378887766432 12468899999
Q ss_pred HHhCCccCCCCCCCChHHHHHHHHHHH
Q 018152 267 SVLGYEIRKKGTPHNCLDDASAAMKLV 293 (360)
Q Consensus 267 ~~Lg~~iq~~~~~H~AleDA~at~eL~ 293 (360)
+++|++.. .+|+|+.||++|++|.
T Consensus 159 ~~~gi~~~---~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 159 QANGIEHS---NAHDALSDVEATIALA 182 (183)
T ss_pred HHCCCCcc---ccccHHHHHHHHHHHh
Confidence 56798864 4899999999999985
No 44
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.89 E-value=1.4e-22 Score=196.51 Aligned_cols=150 Identities=16% Similarity=0.255 Sum_probs=120.0
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc----CCcE-----EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR----NLKV-----TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQ 211 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~----~g~~-----~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~ 211 (360)
...+|+||+||||+++..++|++|++|.. +|.+ .++.||+|+.+|++.++++||||++|+.+++...
T Consensus 36 ~~~~vvlD~ETTGLd~~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~---- 111 (294)
T PRK09182 36 VRLGVILDTETTGLDPRKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDP---- 111 (294)
T ss_pred CCeEEEEEeeCCCCCCCCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcH----
Confidence 45799999999999998889999999965 3532 3889999999999999999999999999999333
Q ss_pred HHHHHHhhCCCEEEEEcchhhHHHHcccCC-----CccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHH
Q 018152 212 KRMKKLLSNGTILVGHSLNNDLEVLKLDHP-----RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDD 285 (360)
Q Consensus 212 ~~l~~~l~~g~iLVGHnl~fDl~~L~~~~~-----~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleD 285 (360)
+.|..|+..+.+|||||+.||++||+...+ ...||........+ ..+++|.+|| ..+|... .+|+|+.|
T Consensus 112 ~~l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La-~~~g~~~----~aHrAl~D 186 (294)
T PRK09182 112 AAVDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLA-GQAGFFH----EGHRAVDD 186 (294)
T ss_pred HHHHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHH-HHcCCCC----CCcChHHH
Confidence 346777755579999999999999987532 34677655444333 5789999999 5567332 48999999
Q ss_pred HHHHHHHHHHHHHh
Q 018152 286 ASAAMKLVLAIIER 299 (360)
Q Consensus 286 A~at~eL~~~~l~~ 299 (360)
|.||++|+..++..
T Consensus 187 a~Ata~ll~~~l~~ 200 (294)
T PRK09182 187 CQALLELLARPLPE 200 (294)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999976643
No 45
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.88 E-value=1.3e-24 Score=186.48 Aligned_cols=145 Identities=25% Similarity=0.419 Sum_probs=120.6
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEc---C--CcEEEEEeecCCCc--ccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDR---N--LKVTIDELVKPEKA--VADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~---~--g~~~~d~lV~P~~~--I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
|+|||||||+++...+|++|++|.. . +...++.||+|..+ |+++++++||||.++|++++ ++.+++++|.++
T Consensus 1 v~~D~Ettg~~~~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~-~~~~~~~~~~~~ 79 (164)
T PF00929_consen 1 VVFDTETTGLDPRQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAP-SFEEALDEFEEF 79 (164)
T ss_dssp EEEEEEESSSTTTTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHC-EHHHHHHHHHHH
T ss_pred cEEEeEcCCCCCCCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCC-cHHHHHHhhhhh
Confidence 6899999999987778999999875 2 23569999999998 99999999999999999999 999999999999
Q ss_pred hhCCCEEEEEcchhhHHHHccc--------CC---CccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHH
Q 018152 218 LSNGTILVGHSLNNDLEVLKLD--------HP---RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDD 285 (360)
Q Consensus 218 l~~g~iLVGHnl~fDl~~L~~~--------~~---~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleD 285 (360)
+.++.++||||+.||..+++.. ++ .++||..+.+...+ ...++|+.|| +++|.+... .+|+|++|
T Consensus 80 ~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~~--~~H~Al~D 156 (164)
T PF00929_consen 80 LKKNDILVGHNASFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFPNRKKYSLDDLA-EYFGIPFDG--TAHDALDD 156 (164)
T ss_dssp HHHHTEEEETTCCHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHHHHHHHSHHHHH-HHTTSSSTS--TTTSHHHH
T ss_pred hhcccccccccccchhhHHHHhhhhcccccccccchhhhhhHHHHHHhhccccCCHHHHH-HHcCCCCCC--CCcChHHH
Confidence 9668999999999998666442 23 36788777666544 3448999999 566777653 27999999
Q ss_pred HHHHHHHH
Q 018152 286 ASAAMKLV 293 (360)
Q Consensus 286 A~at~eL~ 293 (360)
|++|++||
T Consensus 157 a~~t~~l~ 164 (164)
T PF00929_consen 157 ARATAELF 164 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHhCcC
Confidence 99999987
No 46
>PRK05359 oligoribonuclease; Provisional
Probab=99.86 E-value=4e-21 Score=174.26 Aligned_cols=145 Identities=15% Similarity=0.208 Sum_probs=116.3
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCC--cE---EEEEeecCCCc----ccccccccC---CCCHHhhcCCCCCHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNL--KV---TIDELVKPEKA----VADYRSEIT---GLTADDLVGVTCSLA 208 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g--~~---~~d~lV~P~~~----I~d~~t~i~---GIT~e~L~~ap~~l~ 208 (360)
..++|+|||||||+++..++|++|++|..++ .+ .++.+|+|... ++++++.+| |||+++++++| ++.
T Consensus 2 ~~~~vvlD~ETTGLdp~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~-~~~ 80 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTV-SEA 80 (181)
T ss_pred CCcEEEEEeecCCCCCCCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCC-CHH
Confidence 3579999999999999888999999997644 22 38899999865 467788887 99999999999 999
Q ss_pred HHHHHHHHHhh-----CCCEEEEEcchhhHHHHcccC--------CCccc--hH-HHhhHhCCCCCCCHHHHHHHHhCCc
Q 018152 209 EIQKRMKKLLS-----NGTILVGHSLNNDLEVLKLDH--------PRVID--TS-LIFKYVDEYRRPSLYNLCKSVLGYE 272 (360)
Q Consensus 209 eV~~~l~~~l~-----~g~iLVGHnl~fDl~~L~~~~--------~~viD--T~-~l~~~~~~~~~~sL~~L~~~~Lg~~ 272 (360)
++..+|.+|+. ++++|||||+.||+.||+... .+++| |. .++++..| .+ +++++
T Consensus 81 e~~~~~l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~~~l~~~~~Dv~tl~~l~r~~~P----~~------~~~~~ 150 (181)
T PRK05359 81 EAEAQTLEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELEAYFHYRNLDVSTLKELARRWKP----EI------LNGFK 150 (181)
T ss_pred HHHHHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhcccCCCcccchhHHHHHHHHhCh----hh------hhCCC
Confidence 99999999995 368999999999999999863 35677 44 46666554 11 23444
Q ss_pred cCCCCCCCChHHHHHHHHHHHHHHHHh
Q 018152 273 IRKKGTPHNCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 273 iq~~~~~H~AleDA~at~eL~~~~l~~ 299 (360)
.. ..|+|++||+++.++|.++.+.
T Consensus 151 ~~---~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 151 KQ---GTHRALADIRESIAELKYYREH 174 (181)
T ss_pred Cc---CCcccHHHHHHHHHHHHHHHHH
Confidence 32 3799999999999999988764
No 47
>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=99.85 E-value=2.8e-21 Score=173.64 Aligned_cols=142 Identities=16% Similarity=0.241 Sum_probs=111.6
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEcCCc--E---EEEEeecCCCccc----cccccc---CCCCHHhhcCCCCCHHHHH
Q 018152 144 MYAVDCEMVLCEDGSEGLVRLCVVDRNLK--V---TIDELVKPEKAVA----DYRSEI---TGLTADDLVGVTCSLAEIQ 211 (360)
Q Consensus 144 ~ValD~Ettgl~~g~~~I~~VsvVd~~g~--~---~~d~lV~P~~~I~----d~~t~i---~GIT~e~L~~ap~~l~eV~ 211 (360)
+++||+||||+++..++|++|++|..++. . .|+.+|+|..+++ ++..++ ||||++|++++| ++.+++
T Consensus 1 lv~iD~ETTGl~p~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~-~~~~vl 79 (173)
T cd06135 1 LVWIDLEMTGLDPEKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTV-TLAQAE 79 (173)
T ss_pred CEEEEEecCCCCCCCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCC-CHHHHH
Confidence 48999999999987788999999976442 2 3899999998665 344555 599999999999 999999
Q ss_pred HHHHHHhhC-----CCEEEEEcchhhHHHHcccC--------CCccch---HHHhhHhCCCCCCCHHHHHHHHhCCccCC
Q 018152 212 KRMKKLLSN-----GTILVGHSLNNDLEVLKLDH--------PRVIDT---SLIFKYVDEYRRPSLYNLCKSVLGYEIRK 275 (360)
Q Consensus 212 ~~l~~~l~~-----g~iLVGHnl~fDl~~L~~~~--------~~viDT---~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~ 275 (360)
++|.+|+.. +.++||||+.||+.||+... .+.+|| ..+++.+.+. +.. +++..
T Consensus 80 ~~~~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~~~~~~~~~~D~~~l~~l~~~l~p~----~~~-----~~~~~-- 148 (173)
T cd06135 80 AELLEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDVSSIKELARRWYPE----IYR-----KAPKK-- 148 (173)
T ss_pred HHHHHHHHHhcCCCCCceeecchhhCHHHHHHHHHHHhccCCcchhhHHHHHHHHHHhCcH----hhh-----cCCCC--
Confidence 999999942 37999999999999998753 346887 3466655541 111 23332
Q ss_pred CCCCCChHHHHHHHHHHHHHHHH
Q 018152 276 KGTPHNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 276 ~~~~H~AleDA~at~eL~~~~l~ 298 (360)
+..|+|+.||++++.+|.++++
T Consensus 149 -~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 149 -KGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred -CCCcchHHHHHHHHHHHHHHHH
Confidence 2489999999999999998875
No 48
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.85 E-value=1e-20 Score=193.85 Aligned_cols=157 Identities=17% Similarity=0.185 Sum_probs=126.0
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCC--cE---EEEEeecCCCc--ccccccccCCCCHHhhcCCCCCHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNL--KV---TIDELVKPEKA--VADYRSEITGLTADDLVGVTCSLAEIQKR 213 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g--~~---~~d~lV~P~~~--I~d~~t~i~GIT~e~L~~ap~~l~eV~~~ 213 (360)
..++|++|+||||+++..++|++|++|..++ .. .++.||+|... +++.++.+||||++|+.+++.+..++.++
T Consensus 5 ~~~fvv~D~ETTGLdP~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e~~~~ 84 (476)
T PRK11779 5 QPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAEFAAR 84 (476)
T ss_pred CCcEEEEEEECCCCCCCCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHHHHHH
Confidence 4579999999999999888999999997532 22 38899999863 45678999999999998888789999999
Q ss_pred HHHHhh-CCCEEEEEc-chhhHHHHcccCC------------------CccchHHHhhHhCC-----------CCCCCHH
Q 018152 214 MKKLLS-NGTILVGHS-LNNDLEVLKLDHP------------------RVIDTSLIFKYVDE-----------YRRPSLY 262 (360)
Q Consensus 214 l~~~l~-~g~iLVGHn-l~fDl~~L~~~~~------------------~viDT~~l~~~~~~-----------~~~~sL~ 262 (360)
|.+++. +|+++|||| +.||..||+.... .++|++.++....+ ..+++|.
T Consensus 85 i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe 164 (476)
T PRK11779 85 IHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLE 164 (476)
T ss_pred HHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHH
Confidence 999993 489999997 7999999877421 13566666554321 2569999
Q ss_pred HHHHHHhCCccCCCCCCCChHHHHHHHHHHHHHHHHhcc
Q 018152 263 NLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRV 301 (360)
Q Consensus 263 ~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~g~ 301 (360)
.|| ..+|++.. .+|+|+.||.+|++|++.+.++.+
T Consensus 165 ~L~-~~~gI~~~---~AHdALsDa~aT~~la~~l~~~qP 199 (476)
T PRK11779 165 HLT-KANGIEHE---NAHDAMSDVYATIAMAKLIKQKQP 199 (476)
T ss_pred HHH-HHcCCCCC---CCCCcHHHHHHHHHHHHHHHHhCh
Confidence 999 55688754 489999999999999988776533
No 49
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.84 E-value=1.9e-20 Score=211.20 Aligned_cols=157 Identities=20% Similarity=0.328 Sum_probs=137.9
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEE--EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHH
Q 018152 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVT--IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (360)
Q Consensus 139 ~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~--~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~ 215 (360)
....++|++|+||||+++..++|+++++|.. +|.+. |+.||+|+.+|+++++++||||++|+.+++ ++.+|+++|.
T Consensus 416 L~~~~~VVfDLETTGL~~~~deIIEIgAV~V~~G~iie~F~~~V~P~~~I~~~~~~LTGIT~e~L~~ap-s~~EaL~~f~ 494 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAP-SIEEVLPKFK 494 (1437)
T ss_pred hccCcEEEEEhhhcCCCCchhhhheeeeEEEeCCeEeeeEEEEECCCCCCCHHHHHHhCCCHHHHcCCC-CHHHHHHHHH
Confidence 3456899999999999988888999998875 55543 899999999999999999999999999999 9999999999
Q ss_pred HHhhCCCEEEEEcchhhHHHHcccC---------CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHH
Q 018152 216 KLLSNGTILVGHSLNNDLEVLKLDH---------PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDD 285 (360)
Q Consensus 216 ~~l~~g~iLVGHnl~fDl~~L~~~~---------~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleD 285 (360)
+|+ +|.++||||+.||+.||+... ..++||+.+++...+ ..+++|..|| ..+|+... .+|+|+.|
T Consensus 495 ~fi-gg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LA-k~lGL~~~---~~HrAl~D 569 (1437)
T PRK00448 495 EFC-GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLA-KKFGVELE---HHHRADYD 569 (1437)
T ss_pred HHh-CCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHH-HHcCCCCC---CCcChHHH
Confidence 999 899999999999999986531 247999999998887 7899999999 56688875 37999999
Q ss_pred HHHHHHHHHHHHHhcc
Q 018152 286 ASAAMKLVLAIIERRV 301 (360)
Q Consensus 286 A~at~eL~~~~l~~g~ 301 (360)
|.+|++||.++++...
T Consensus 570 A~aTa~lf~~ll~~l~ 585 (1437)
T PRK00448 570 AEATAYLLIKFLKDLK 585 (1437)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999886543
No 50
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.82 E-value=2.3e-19 Score=186.03 Aligned_cols=156 Identities=16% Similarity=0.241 Sum_probs=125.8
Q ss_pred CcEEEEEEeccCCCCC---cccEEEEEEEEc---CCcE--EEEEeecCCC--cccccccccCCCCHHhhcCCCCCHHHHH
Q 018152 142 NIMYAVDCEMVLCEDG---SEGLVRLCVVDR---NLKV--TIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEIQ 211 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g---~~~I~~VsvVd~---~g~~--~~d~lV~P~~--~I~d~~t~i~GIT~e~L~~ap~~l~eV~ 211 (360)
..+|+||+||||.++. .++|++|++|.. +|++ .|++||+|.. +|+++++++||||++||+++| +|.+|+
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap-~F~eVl 134 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRAD-PFPVVY 134 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCC-CHHHHH
Confidence 6899999999998753 358999999975 5654 3899999987 799999999999999999999 999999
Q ss_pred HHHHHHhhCCC----------EEEEEcchhhHH-HHccc--------CC----CccchH-HHhhHhCC------------
Q 018152 212 KRMKKLLSNGT----------ILVGHSLNNDLE-VLKLD--------HP----RVIDTS-LIFKYVDE------------ 255 (360)
Q Consensus 212 ~~l~~~l~~g~----------iLVGHnl~fDl~-~L~~~--------~~----~viDT~-~l~~~~~~------------ 255 (360)
.+|.+|+ .+. .+|+||..||+. ||..+ .+ ..+|.. .+.+..++
T Consensus 135 ~ef~~fL-~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e~~~~~~~g~p~~f~~widLk~~lar~l~p~~~~~~~~~~~~ 213 (582)
T PTZ00315 135 CEALQFL-AEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQMRVSGQQGTPLSFQRWCNLKKYMSQLGFGNGSGCGGGATPP 213 (582)
T ss_pred HHHHHHH-hccccccccccCceEEEeccHHHHHHHHHHHHHHhhhcCCCcccceEEEhHHHHHHHhCccccccccccccc
Confidence 9999999 443 699999999995 77532 11 245543 33343332
Q ss_pred CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHHHHHHhccc
Q 018152 256 YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERRVD 302 (360)
Q Consensus 256 ~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~g~~ 302 (360)
...++|.+++ .++|++.. |..|+|++||+.+++|+.++++.|.-
T Consensus 214 ~~~~~L~~al-~~lgL~~e--Gr~HrAlDDA~ntA~L~~~Ll~~g~~ 257 (582)
T PTZ00315 214 LGPSDMPDML-QMLGLPLQ--GRHHSGIDDCRNIAAVLCELLRRGLV 257 (582)
T ss_pred cCCcCHHHHH-HHCCCCCC--CCCcCcHHHHHHHHHHHHHHHHcCCE
Confidence 3568999999 67798875 45899999999999999999988753
No 51
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.42 E-value=4.4e-13 Score=119.51 Aligned_cols=147 Identities=22% Similarity=0.308 Sum_probs=113.5
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCC--cEE---EEEeecCCC----cccccccc---cCCCCHHhhcCCCCCHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNL--KVT---IDELVKPEK----AVADYRSE---ITGLTADDLVGVTCSLA 208 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g--~~~---~d~lV~P~~----~I~d~~t~---i~GIT~e~L~~ap~~l~ 208 (360)
..++|.|||||||++-+.+.|++|+.+--+| .++ .|..|+... .+.++... -+|+|..-++..- +++
T Consensus 25 ~q~lVWiD~EMTGLdvekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~-tl~ 103 (208)
T KOG3242|consen 25 KQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKI-TLA 103 (208)
T ss_pred cCceEEEeeeccccccccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhc-cHH
Confidence 4589999999999999999999999885433 332 677777654 34455443 3689999999997 999
Q ss_pred HHHHHHHHHhh-----CCCEEEEEcchhhHHHHccc--------CCCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCC
Q 018152 209 EIQKRMKKLLS-----NGTILVGHSLNNDLEVLKLD--------HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK 275 (360)
Q Consensus 209 eV~~~l~~~l~-----~g~iLVGHnl~fDl~~L~~~--------~~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~ 275 (360)
++-.++++|+. +.++|-|.++.-|..||..+ |.|+||++ +.+.||++++- .++.
T Consensus 104 ~aEnevl~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~~~lhyrivDVS------------tIkeL~~Rw~P-~~~~ 170 (208)
T KOG3242|consen 104 DAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLIKHLHYRIVDVS------------TIKELARRWYP-DIKA 170 (208)
T ss_pred HHHHHHHHHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHHHhcceeeeeHH------------HHHHHHHHhCc-hhhc
Confidence 99999999984 56899999999999999886 44688988 56778877643 2321
Q ss_pred ----CCCCCChHHHHHHHHHHHHHHHHhcc
Q 018152 276 ----KGTPHNCLDDASAAMKLVLAIIERRV 301 (360)
Q Consensus 276 ----~~~~H~AleDA~at~eL~~~~l~~g~ 301 (360)
....|+|++|.+....-.+++.+.-+
T Consensus 171 ~aPkK~~~HrAldDI~ESI~ELq~Yr~nif 200 (208)
T KOG3242|consen 171 RAPKKKATHRALDDIRESIKELQYYRENIF 200 (208)
T ss_pred cCcccccccchHHHHHHHHHHHHHHHHHhc
Confidence 23489999999999888777776544
No 52
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.37 E-value=2.4e-12 Score=113.87 Aligned_cols=147 Identities=22% Similarity=0.282 Sum_probs=109.9
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEE--cCCcEE---EEEeecCC----Cccccccccc---CCCCHHhhcCCCCCHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVD--RNLKVT---IDELVKPE----KAVADYRSEI---TGLTADDLVGVTCSLA 208 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd--~~g~~~---~d~lV~P~----~~I~d~~t~i---~GIT~e~L~~ap~~l~ 208 (360)
..++|.|||||||++++.++|++|+.+- .+.+++ .+.-|... ..+.+++++- +|++..-.+... +.+
T Consensus 5 ~~nLiWIDlEMTGLd~~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~-t~~ 83 (184)
T COG1949 5 KNNLIWIDLEMTGLDPERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTV-TEA 83 (184)
T ss_pred CCceEEEeeeeccCCcCcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhc-cHH
Confidence 4689999999999999999999999884 333333 33344433 2556777765 578887777776 999
Q ss_pred HHHHHHHHHhh-----CCCEEEEEcchhhHHHHcccCC--------CccchHHHhhHhCCCCCCCHHHHHHHHhCCccCC
Q 018152 209 EIQKRMKKLLS-----NGTILVGHSLNNDLEVLKLDHP--------RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK 275 (360)
Q Consensus 209 eV~~~l~~~l~-----~g~iLVGHnl~fDl~~L~~~~~--------~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~ 275 (360)
++-.++++|+. +-.++-|.++..|.+||-...| |.+|++ +|+.||+++ ..+|..
T Consensus 84 ~aE~~~l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~yfHYR~lDVS------------TlKELa~RW-~P~i~~ 150 (184)
T COG1949 84 EAEAQTLDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAYFHYRYLDVS------------TLKELARRW-NPEILA 150 (184)
T ss_pred HHHHHHHHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHHhhhHhhhHH------------HHHHHHHhh-CcHhhh
Confidence 99999888884 3578999999999999988755 456666 688888665 444442
Q ss_pred ---CCCCCChHHHHHHHHHHHHHHHHhcc
Q 018152 276 ---KGTPHNCLDDASAAMKLVLAIIERRV 301 (360)
Q Consensus 276 ---~~~~H~AleDA~at~eL~~~~l~~g~ 301 (360)
++..|.|++|.+-+..-..++.+...
T Consensus 151 ~~~K~~~H~Al~DI~ESI~EL~~YR~~f~ 179 (184)
T COG1949 151 GFKKGGTHRALDDIRESIAELRYYREHFL 179 (184)
T ss_pred ccccccchhHHHHHHHHHHHHHHHHHHhc
Confidence 24689999999998887777776543
No 53
>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=99.06 E-value=1.3e-09 Score=99.24 Aligned_cols=121 Identities=17% Similarity=0.125 Sum_probs=93.9
Q ss_pred EEEEEEeccCC----CCCcccEEEEEEEEc-CCcEE-EEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 144 MYAVDCEMVLC----EDGSEGLVRLCVVDR-NLKVT-IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 144 ~ValD~Ettgl----~~g~~~I~~VsvVd~-~g~~~-~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
++++|+||+|. ++..++|+.|+++.. +|... +.....+.... .. ||+..++...+ +..+++.+|.++
T Consensus 1 v~~~DIEt~~~~~~p~~~~d~Ii~I~~~~~~~g~~~~~~~~~~~~~~~---~~---~i~~~~v~~~~-~E~~lL~~f~~~ 73 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDRDPIICITYADSFDGVKVVFLLKTSTVGDD---IE---FIDGIEVEYFA-DEKELLKRFFDI 73 (199)
T ss_pred CccEEEeecCCCCCcCCCCCCEEEEEEEEeeCCceeeEEEeecccCCc---CC---CCCCceEEEeC-CHHHHHHHHHHH
Confidence 36899999998 667788999999986 66543 22222222211 11 89999999999 999999999999
Q ss_pred hhCC---CEEEEEcc-hhhHHHHccc-------C-----------------------CC-ccchHHHhhHhCCCCCCCHH
Q 018152 218 LSNG---TILVGHSL-NNDLEVLKLD-------H-----------------------PR-VIDTSLIFKYVDEYRRPSLY 262 (360)
Q Consensus 218 l~~g---~iLVGHnl-~fDl~~L~~~-------~-----------------------~~-viDT~~l~~~~~~~~~~sL~ 262 (360)
+ +. .++||||. .||+.+|... . .+ ++|+..+++...+..+++|+
T Consensus 74 i-~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~~l~sy~L~ 152 (199)
T cd05160 74 I-REYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDFKLKSYTLD 152 (199)
T ss_pred H-HhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhcCcccCCHH
Confidence 9 44 59999999 8999998642 2 12 58999999887777889999
Q ss_pred HHHHHHhCCc
Q 018152 263 NLCKSVLGYE 272 (360)
Q Consensus 263 ~L~~~~Lg~~ 272 (360)
.+|+.+||..
T Consensus 153 ~v~~~~l~~~ 162 (199)
T cd05160 153 AVAEELLGEG 162 (199)
T ss_pred HHHHHHhCCC
Confidence 9999888764
No 54
>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=98.95 E-value=2.1e-08 Score=89.67 Aligned_cols=141 Identities=21% Similarity=0.216 Sum_probs=99.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhC
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~ 220 (360)
..+.+++|+|++|+++....|+.+++....+..++ + | +.+ +.+ .+.+ +..++.+.|.+++..
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~---~-~---~~~--~~~--------~~~~-~~~~~~~~l~~~l~~ 65 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYY---I-P---LGH--DYG--------GEQL-PREEVLAALKPLLED 65 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEE---E-e---cCC--Ccc--------ccCC-CHHHHHHHHHHHHhC
Confidence 35689999999999876667888888866553322 1 1 110 001 1344 788899999999943
Q ss_pred C-CEEEEEcchhhHHHHcccC----CCccchHHHhhHhCCCC-CCCHHHHHHHHhCCccCC------C--------C---
Q 018152 221 G-TILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYR-RPSLYNLCKSVLGYEIRK------K--------G--- 277 (360)
Q Consensus 221 g-~iLVGHnl~fDl~~L~~~~----~~viDT~~l~~~~~~~~-~~sL~~L~~~~Lg~~iq~------~--------~--- 277 (360)
. .++||||+.||+.+|+... ..+.||..++....+.. +++|+.+|++|+|..+.. . .
T Consensus 66 ~~~~~v~hn~k~d~~~l~~~gi~~~~~~~Dt~l~a~ll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~k~~~~~~~~~~~~ 145 (193)
T cd06139 66 PSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLASYLLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQVPL 145 (193)
T ss_pred CCCcEEeeccHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCCCCHHHHHHHHhCCCCccHHHHcCCCcCcCCccccCH
Confidence 3 3799999999999997653 24799999998888744 679999999998765210 0 0
Q ss_pred --CCCChHHHHHHHHHHHHHHHHh
Q 018152 278 --TPHNCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 278 --~~H~AleDA~at~eL~~~~l~~ 299 (360)
..|.|..||.++.+|+..+.+.
T Consensus 146 ~~~~~ya~~d~~~~~~l~~~l~~~ 169 (193)
T cd06139 146 EKAAEYAAEDADITLRLYELLKPK 169 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1235788899999999877654
No 55
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=98.86 E-value=1e-08 Score=96.64 Aligned_cols=158 Identities=16% Similarity=0.288 Sum_probs=119.2
Q ss_pred CcEEEEEEeccCCCCCc----ccEEEEEEEEc----CCcE--EEEEeecCCC--cccccccccCCCCHHhhcCCCCCHHH
Q 018152 142 NIMYAVDCEMVLCEDGS----EGLVRLCVVDR----NLKV--TIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAE 209 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~----~~I~~VsvVd~----~g~~--~~d~lV~P~~--~I~d~~t~i~GIT~e~L~~ap~~l~e 209 (360)
.-+++||.|+|.-+.+. .+|++..+|-. .+.+ .|++||+|.. ..++|++.+|||..++++.+| +|.+
T Consensus 56 dYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~-~f~~ 134 (280)
T KOG0542|consen 56 DYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAP-TFPQ 134 (280)
T ss_pred ceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCC-CHHH
Confidence 46789999999876443 37999888832 3332 4899999965 778999999999999999999 9999
Q ss_pred HHHHHHHHhhCC--------CEEEEEcchhhHH-HHccc-------CC----CccchHHHhhHhCCC-CCCCHHHHHHHH
Q 018152 210 IQKRMKKLLSNG--------TILVGHSLNNDLE-VLKLD-------HP----RVIDTSLIFKYVDEY-RRPSLYNLCKSV 268 (360)
Q Consensus 210 V~~~l~~~l~~g--------~iLVGHnl~fDl~-~L~~~-------~~----~viDT~~l~~~~~~~-~~~sL~~L~~~~ 268 (360)
|+++|..++... .-+|- .-.-|+. ||..+ .| ..||.-+.|+..+.. .+-++..+- ++
T Consensus 135 vl~~f~~Wlr~~~~~~k~~~~Afvt-dg~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk~~y~~~~~t~it~mL-e~ 212 (280)
T KOG0542|consen 135 VLSEFDSWLRKDSLGDKNGKFAFVT-DGDWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYKNFYNRPAPTNITGML-EH 212 (280)
T ss_pred HHHHHHHHHHHhhcccccCceEEEe-CchhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHHHHhcCccccCHHHHH-HH
Confidence 999999988421 11221 2234553 44433 22 258988888876653 577888877 77
Q ss_pred hCCccCCCCCCCChHHHHHHHHHHHHHHHHhcccCC
Q 018152 269 LGYEIRKKGTPHNCLDDASAAMKLVLAIIERRVDNA 304 (360)
Q Consensus 269 Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~g~~~~ 304 (360)
+|.+.+ |..|+.++||+-.+++.++|++.|....
T Consensus 213 ~gL~f~--Gr~HsGiDDa~Nia~I~~kM~~dg~~~~ 246 (280)
T KOG0542|consen 213 YGLQFE--GRAHSGIDDARNIARIAQKMIRDGAEFR 246 (280)
T ss_pred hCCccc--CCcccCchhHHHHHHHHHHHHhCCcEEE
Confidence 788877 5799999999999999999998776543
No 56
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=98.80 E-value=6.5e-09 Score=92.81 Aligned_cols=153 Identities=23% Similarity=0.276 Sum_probs=115.6
Q ss_pred CcEEEEEEeccCCCCCc----ccEEEEEEE--Ec-C--CcEEEEEeecCCC--cccccccccCCCCHHhhcCCCCCHHHH
Q 018152 142 NIMYAVDCEMVLCEDGS----EGLVRLCVV--DR-N--LKVTIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEI 210 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~----~~I~~VsvV--d~-~--g~~~~d~lV~P~~--~I~d~~t~i~GIT~e~L~~ap~~l~eV 210 (360)
..+.+||+|.|--+.+- -+|++|.+. +. + -...|++||+|.+ ..++++..++|||...++.+| -|..|
T Consensus 4 ~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~ap-ifs~v 82 (210)
T COG5018 4 NSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAP-IFSMV 82 (210)
T ss_pred ceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccc-hHHHH
Confidence 45789999999765332 257666543 32 2 2234889999986 677899999999999999999 99999
Q ss_pred HHHHHHHhhCCCE----EEEEcchhhHHHHccc----C-C------CccchHHHhhHhCC-CCCCCHHHHHHHHhCCccC
Q 018152 211 QKRMKKLLSNGTI----LVGHSLNNDLEVLKLD----H-P------RVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIR 274 (360)
Q Consensus 211 ~~~l~~~l~~g~i----LVGHnl~fDl~~L~~~----~-~------~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq 274 (360)
+++|..++.+..+ -.+-.-..|++.|++. + + +.+|...-|+..++ .+..+|.... +.+|...+
T Consensus 83 ~E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~al-e~~G~sf~ 161 (210)
T COG5018 83 FEDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKAL-EEYGDSFT 161 (210)
T ss_pred HHHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHH-HHhccccC
Confidence 9999999964322 2233446789888874 1 1 35899988988887 5668899888 55688887
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHH
Q 018152 275 KKGTPHNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 275 ~~~~~H~AleDA~at~eL~~~~l~ 298 (360)
|..|+|++||+.+++|+..+..
T Consensus 162 --G~~HraldDArn~~rl~klv~~ 183 (210)
T COG5018 162 --GTHHRALDDARNAYRLFKLVEQ 183 (210)
T ss_pred --CchhhhHHHHHHHHHHHHHHcc
Confidence 5699999999999999976553
No 57
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=98.73 E-value=8.8e-08 Score=94.93 Aligned_cols=156 Identities=17% Similarity=0.169 Sum_probs=116.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc--CCcEE---EEEeecCCCccc--ccccccCCCCHHhhcCCCCCHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR--NLKVT---IDELVKPEKAVA--DYRSEITGLTADDLVGVTCSLAEIQKR 213 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~--~g~~~---~d~lV~P~~~I~--d~~t~i~GIT~e~L~~ap~~l~eV~~~ 213 (360)
...++..|.||.|.++..++.+.++.|+- +-.++ +.-|++|....- +..+-||||||+.....+++-.+....
T Consensus 8 ~~tF~~yDYETfG~~Pa~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~F~~~ 87 (475)
T COG2925 8 QPTFLFYDYETFGVHPALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAAFAAR 87 (475)
T ss_pred CCcEEEEehhhcCCCcccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHHHHHH
Confidence 45799999999999999999999999975 32322 678999976433 468899999999999888888888888
Q ss_pred HHH-HhhCCCEEEEEc-chhhHHHHcccC----------------CC--ccchHHHhhHhCC-----------CCCCCHH
Q 018152 214 MKK-LLSNGTILVGHS-LNNDLEVLKLDH----------------PR--VIDTSLIFKYVDE-----------YRRPSLY 262 (360)
Q Consensus 214 l~~-~l~~g~iLVGHn-l~fDl~~L~~~~----------------~~--viDT~~l~~~~~~-----------~~~~sL~ 262 (360)
|.. |..+++.+||+| ++||=.+-+... .| ++|.+.....+.| ..+.+|.
T Consensus 88 I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkLE 167 (475)
T COG2925 88 IHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLE 167 (475)
T ss_pred HHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchhhH
Confidence 775 556899999995 899977666431 12 5677665443332 3567788
Q ss_pred HHHHHHhCCccCCCCCCCChHHHHHHHHHHHHHHHHhc
Q 018152 263 NLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIERR 300 (360)
Q Consensus 263 ~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~~l~~g 300 (360)
.|+ ..-|++-. .+|+|++|.+||..+.+...+..
T Consensus 168 hLt-~ANgieH~---nAHdAmsDVyATIamAklvk~~Q 201 (475)
T COG2925 168 HLT-KANGIEHS---NAHDAMSDVYATIAMAKLVKTAQ 201 (475)
T ss_pred HHh-hccccccc---hhhHHHHHHHHHHHHHHHHHhhC
Confidence 998 44466643 59999999999999997555443
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=98.64 E-value=6.8e-07 Score=78.34 Aligned_cols=132 Identities=26% Similarity=0.253 Sum_probs=82.8
Q ss_pred CcEEEEEEeccCCCC--CcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 142 NIMYAVDCEMVLCED--GSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 142 ~~~ValD~Ettgl~~--g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
.++++||||+++++. ....++.|++-..++..+++ |-.. .+. . +.+.|.+++.
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~----~~~~-~~~-----------------~---~~~~l~~ll~ 74 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIID----PIDL-GDN-----------------W---ILDALKELLE 74 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEEC----GTTS-TTT-----------------T---HHHHHHHHHT
T ss_pred CCeEEEEEEECCCCccccCCeEEEEEEecCCCceeee----eccc-ccc-----------------c---hHHHHHHHHh
Confidence 359999999999987 33345555555553332221 1110 000 0 5666777772
Q ss_pred -CCCEEEEEcchhhHHHHccc----CCCccchHHHhhHhCCCCCCCHHHHHHHHhC-CccCCC---CCCC--C-------
Q 018152 220 -NGTILVGHSLNNDLEVLKLD----HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLG-YEIRKK---GTPH--N------- 281 (360)
Q Consensus 220 -~g~iLVGHnl~fDl~~L~~~----~~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg-~~iq~~---~~~H--~------- 281 (360)
.+.+.||||+.||+..|... ...+.||...+....+.+.++|+.|+..++| .....+ +... +
T Consensus 75 ~~~i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~~~l~~~~~~~L~~L~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~ 154 (176)
T PF01612_consen 75 DPNIIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAAYLLDPTRSYSLKDLAEEYLGNIDLDKKEQMSDWRKARPLSEEQI 154 (176)
T ss_dssp TTTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTTSTTSSHHHHHHHHHSEEE-GHCCTTSSTTTSSS-HHHHH
T ss_pred CCCccEEEEEEechHHHHHHHhccccCCccchhhhhhcccccccccHHHHHHHHhhhccCcHHHhhccCCcCCCChHHHH
Confidence 35689999999999999884 3358999444444444444999999999999 433211 1111 2
Q ss_pred --hHHHHHHHHHHHHHHHH
Q 018152 282 --CLDDASAAMKLVLAIIE 298 (360)
Q Consensus 282 --AleDA~at~eL~~~~l~ 298 (360)
|-.||..+.+||..+..
T Consensus 155 ~YAa~D~~~~~~l~~~l~~ 173 (176)
T PF01612_consen 155 EYAAQDAVVTFRLYEKLKP 173 (176)
T ss_dssp HHHHHHHHTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 55699999999976553
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=98.50 E-value=4.3e-07 Score=74.12 Aligned_cols=59 Identities=25% Similarity=0.382 Sum_probs=45.5
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcC-CcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCC--
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDRN-LKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG-- 221 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~~-g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g-- 221 (360)
+++|+||+|+++..++|+.|++.+.+ +...+ .. |.+++.+.
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~----~~--------------------------------f~~~l~~~~~ 44 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAV----ID--------------------------------LKDILRDKPL 44 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEE----eh--------------------------------HHHHHhhCCC
Confidence 47999999999888889999999873 43221 11 66666332
Q ss_pred CEEEEEcchhhHHHHccc
Q 018152 222 TILVGHSLNNDLEVLKLD 239 (360)
Q Consensus 222 ~iLVGHnl~fDl~~L~~~ 239 (360)
.++||||+.||+.||+..
T Consensus 45 ~v~V~hn~~fD~~fL~~~ 62 (96)
T cd06125 45 AILVGHNGSFDLPFLNNR 62 (96)
T ss_pred CEEEEeCcHHhHHHHHHH
Confidence 599999999999999875
No 60
>PRK05755 DNA polymerase I; Provisional
Probab=98.48 E-value=1.6e-06 Score=96.01 Aligned_cols=134 Identities=23% Similarity=0.243 Sum_probs=97.1
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhC
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~ 220 (360)
...++++|+||+|+++....|+.|++-..+|...+ |.+ +++ + . ++...|.+++..
T Consensus 314 ~~~~~a~DtEt~~l~~~~~~i~~i~ls~~~g~~~~---ip~-----------~~i--------~--~-~~l~~l~~~L~d 368 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAY---IPL-----------DQL--------D--R-EVLAALKPLLED 368 (880)
T ss_pred ccCeEEEEeccCCCCcccccEEEEEEEeCCCcEEE---Eec-----------ccc--------c--H-HHHHHHHHHHhC
Confidence 46789999999999987777888887655664322 211 111 1 1 577778888843
Q ss_pred CC-EEEEEcchhhHHHHcccC----CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCC-------C---------CCC
Q 018152 221 GT-ILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK-------K---------GTP 279 (360)
Q Consensus 221 g~-iLVGHnl~fDl~~L~~~~----~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~-------~---------~~~ 279 (360)
.. ++||||+.||+.+|.... .++.||..++....+...++|+.|++.|+|.+.-. + ...
T Consensus 369 ~~v~kV~HNakfDl~~L~~~gi~~~~~~~DT~iAa~Ll~~~~~~~L~~L~~~ylg~~~~~~~~~~gk~~~~~~~ple~~~ 448 (880)
T PRK05755 369 PAIKKVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTISFEEVAGKQLTFAQVDLEEAA 448 (880)
T ss_pred CCCcEEEeccHhHHHHHHhCCCCcCCCcccHHHHHHHcCCCCCCCHHHHHHHHhCCCccchHHhcCCCCCccccCHHHHH
Confidence 33 489999999999998642 24799999888777633489999999998876310 0 013
Q ss_pred CChHHHHHHHHHHHHHHHHh
Q 018152 280 HNCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 280 H~AleDA~at~eL~~~~l~~ 299 (360)
|.|..|+..+++||..+.+.
T Consensus 449 ~YAa~Dv~~~~~L~~~L~~~ 468 (880)
T PRK05755 449 EYAAEDADVTLRLHEVLKPK 468 (880)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 67999999999999887764
No 61
>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=98.36 E-value=8.9e-06 Score=74.48 Aligned_cols=88 Identities=19% Similarity=0.299 Sum_probs=65.2
Q ss_pred HHHHHHHHhhCC-CEEEEEcchhhHHHHcccC----------CCccchHHHhhHhCC-----------CCCCCHHHHHHH
Q 018152 210 IQKRMKKLLSNG-TILVGHSLNNDLEVLKLDH----------PRVIDTSLIFKYVDE-----------YRRPSLYNLCKS 267 (360)
Q Consensus 210 V~~~l~~~l~~g-~iLVGHnl~fDl~~L~~~~----------~~viDT~~l~~~~~~-----------~~~~sL~~L~~~ 267 (360)
+.+.+.+++... .+.|||++.+|+++|...+ ..++||..+++...+ ....||..||+.
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 445566777333 4569999999999998643 248999988876542 357899999999
Q ss_pred HhCCccCCCC-------------CCCChHHHHHHHHHHHHHHH
Q 018152 268 VLGYEIRKKG-------------TPHNCLDDASAAMKLVLAII 297 (360)
Q Consensus 268 ~Lg~~iq~~~-------------~~H~AleDA~at~eL~~~~l 297 (360)
+||.++.+.. .-+-|..||.++.+||.++.
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 9998876421 11457789999999998764
No 62
>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=98.17 E-value=9e-05 Score=62.98 Aligned_cols=104 Identities=28% Similarity=0.270 Sum_probs=70.5
Q ss_pred EEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCC-C
Q 018152 144 MYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG-T 222 (360)
Q Consensus 144 ~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g-~ 222 (360)
.+++|+|+.+..+....|..+++... +...+ +..... ...+.+.+.+++... .
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~~~~---i~~~~~----------------------~~~~~~~l~~~l~~~~~ 55 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATA-GEAAY---IPDELE----------------------LEEDLEALKELLEDEDI 55 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEEC-CcEEE---EEcCCC----------------------HHHHHHHHHHHHcCCCC
Confidence 57899998877632334666666654 32221 110000 145667777888323 4
Q ss_pred EEEEEcchhhHHHHcccC----CCccchHHHhhHhCCCC-CCCHHHHHHHHhCCcc
Q 018152 223 ILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYR-RPSLYNLCKSVLGYEI 273 (360)
Q Consensus 223 iLVGHnl~fDl~~L~~~~----~~viDT~~l~~~~~~~~-~~sL~~L~~~~Lg~~i 273 (360)
.+||||+.+|+.+|.... ..+.||..++....+.. +.+|+.|+++|++..+
T Consensus 56 ~~v~~~~k~d~~~L~~~~~~~~~~~~D~~~~ayll~~~~~~~~l~~l~~~~l~~~~ 111 (155)
T cd00007 56 TKVGHDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIEL 111 (155)
T ss_pred cEEeccHHHHHHHHHHCCCCCCCCcccHHHHHHHhCCCCCcCCHHHHHHHHcCCCC
Confidence 599999999999997542 24789999888888744 6799999999988774
No 63
>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=98.16 E-value=1.4e-05 Score=73.09 Aligned_cols=116 Identities=16% Similarity=0.141 Sum_probs=82.5
Q ss_pred CcEEEEEEecc---CC-CCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 142 NIMYAVDCEMV---LC-EDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 142 ~~~ValD~Ett---gl-~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
-++++||+||+ |. ++..+.|+.|+++...+..++. + ++.. ...+.... +-.++..+|.++
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~-~-~~~~-------------~~~v~~~~-~E~~lL~~F~~~ 66 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVIT-W-KKFD-------------LPFVEVVK-TEKEMIKRFIEI 66 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEE-e-cCCC-------------CCeEEEeC-CHHHHHHHHHHH
Confidence 47899999998 44 4556789999998865543321 1 1110 01233334 678999999999
Q ss_pred hhC--CCEEEEEcc-hhhHHHHccc-------C-----------------------CC-ccchHHHhhHhCCCCCCCHHH
Q 018152 218 LSN--GTILVGHSL-NNDLEVLKLD-------H-----------------------PR-VIDTSLIFKYVDEYRRPSLYN 263 (360)
Q Consensus 218 l~~--g~iLVGHnl-~fDl~~L~~~-------~-----------------------~~-viDT~~l~~~~~~~~~~sL~~ 263 (360)
+.. -.++||||. .||+.+|... . .+ .+|+..+++......+++|++
T Consensus 67 i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~~~l~sy~L~~ 146 (195)
T cd05780 67 VKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLER 146 (195)
T ss_pred HHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhhCCCCcCcHHH
Confidence 954 479999996 5899988542 0 12 588888888766678999999
Q ss_pred HHHHHhCCcc
Q 018152 264 LCKSVLGYEI 273 (360)
Q Consensus 264 L~~~~Lg~~i 273 (360)
+|+.+||.+-
T Consensus 147 v~~~~Lg~~k 156 (195)
T cd05780 147 VYEELFGIEK 156 (195)
T ss_pred HHHHHhCCCC
Confidence 9999999863
No 64
>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=98.04 E-value=0.00011 Score=64.96 Aligned_cols=126 Identities=21% Similarity=0.147 Sum_probs=81.3
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc--C-CcE-EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR--N-LKV-TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~--~-g~~-~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
..++|+||||........ .+|+++-. . +.+ ++|..- ... . .+.|.+
T Consensus 12 ~~~~ig~D~E~~~~~~~~---~~~~liQl~~~~~~~~l~d~~~-~~~-------------------~-------~~~L~~ 61 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYY---GEVALIQLCVSEEKCYLFDPLS-LSV-------------------D-------WQGLKM 61 (161)
T ss_pred CCCEEEEECCccCCCCCC---CceEEEEEEECCCCEEEEeccc-Ccc-------------------C-------HHHHHH
Confidence 568999999999875422 23555532 2 222 333211 100 1 123444
Q ss_pred Hhh-CCCEEEEEcchhhHHHHcccC----CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCC-------------C
Q 018152 217 LLS-NGTILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKG-------------T 278 (360)
Q Consensus 217 ~l~-~g~iLVGHnl~fDl~~L~~~~----~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~-------------~ 278 (360)
++. ++.+.|||++..|+..|...+ ..++||...+....+..+.+|+.|+++++|..+.+.. .
T Consensus 62 lL~d~~i~Kvg~~~k~D~~~L~~~~gi~~~~~~D~~~aa~ll~~~~~~~L~~l~~~~lg~~l~K~~~~s~W~~rpLt~~q 141 (161)
T cd06129 62 LLENPSIVKALHGIEGDLWKLLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQ 141 (161)
T ss_pred HhCCCCEEEEEeccHHHHHHHHHHcCCCcccHhHHHHHHHHhCCCCCchHHHHHHHHhCCCCCccceeccCCCCCCCHHH
Confidence 552 234679999999999997532 2479999988776554567999999999998774311 1
Q ss_pred CCChHHHHHHHHHHHHHH
Q 018152 279 PHNCLDDASAAMKLVLAI 296 (360)
Q Consensus 279 ~H~AleDA~at~eL~~~~ 296 (360)
-|-|..||.++.+||.++
T Consensus 142 i~YAa~Da~~l~~l~~~l 159 (161)
T cd06129 142 KLYAAADVYALLIIYTKL 159 (161)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 255778999999999754
No 65
>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=98.01 E-value=1.9e-05 Score=69.30 Aligned_cols=127 Identities=23% Similarity=0.139 Sum_probs=63.7
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEc-CCc-EEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCCC
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDR-NLK-VTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNGT 222 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~-~g~-~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g~ 222 (360)
+.||+||+|++++.+.|..|++... ++. ..+..+.-.+. .-++...++.+++.+..
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~----------------------~ee~~~~~~~~~l~~~~ 58 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDP----------------------DEEEIILEFFELLDEAD 58 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGH----------------------HHHHHHHH--HHHHTT-
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCc----------------------HHHHHHHHHHHHHhcCC
Confidence 5799999999987777888888864 222 22333332211 11223333225665788
Q ss_pred EEEEEc-chhhHHHHcccCC--------CccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHH
Q 018152 223 ILVGHS-LNNDLEVLKLDHP--------RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLV 293 (360)
Q Consensus 223 iLVGHn-l~fDl~~L~~~~~--------~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~ 293 (360)
.+|+|| .+||+.+|+.... +.+|+...++.... .++||+.++ .++|++.+ .--.+...+.++|
T Consensus 59 ~iv~yng~~FD~p~L~~~~~~~~~~~~~~~iDl~~~~~~~~~-~~~~Lk~ve-~~lg~~~~------~~~~~G~~~~~~~ 130 (164)
T PF13482_consen 59 NIVTYNGKNFDIPFLKRRAKRYGLPPPFNHIDLLKIIKKHFL-ESYSLKNVE-KFLGIERR------DDDISGSESVKLY 130 (164)
T ss_dssp -EEESSTTTTHHHHHHHHH-HHHH--GGGEEEHHHHHT-TTS-CCTT--SHH-H-----------------HHHHHHHHH
T ss_pred eEEEEeCcccCHHHHHHHHHHcCCCcccchhhHHHHHHhccC-CCCCHHHHh-hhcccccc------cCCCCHHHHHHHH
Confidence 999998 6999999987431 36899888865444 778999999 55787743 1224455567778
Q ss_pred HHHHHhcc
Q 018152 294 LAIIERRV 301 (360)
Q Consensus 294 ~~~l~~g~ 301 (360)
..++..+.
T Consensus 131 ~~~~~~~~ 138 (164)
T PF13482_consen 131 KEYLETGD 138 (164)
T ss_dssp H---TTGG
T ss_pred HHHHhcCC
Confidence 77665544
No 66
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=97.94 E-value=0.00014 Score=66.37 Aligned_cols=106 Identities=19% Similarity=0.140 Sum_probs=77.2
Q ss_pred CcEEEEEEecc---CC-CCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 142 NIMYAVDCEMV---LC-EDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 142 ~~~ValD~Ett---gl-~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
-+.++||+||+ |. +++.+.|+.|++...+|...+=. .... +-.++..+|.++
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~d~Ii~Is~~~~~g~~~~~~-----------------------~~~~-~E~~lL~~F~~~ 58 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLATSNGDVEFIL-----------------------AEGL-DDRKIIREFVKY 58 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCCCCEEEEEEEeCCCCEEEEE-----------------------ecCC-CHHHHHHHHHHH
Confidence 47899999999 43 56667899999998766532100 1124 778999999999
Q ss_pred hhCC--CEEEEEcc-hhhHHHHccc-------C---------C------------C-ccchHHHhhHhCCCCCCCHHHHH
Q 018152 218 LSNG--TILVGHSL-NNDLEVLKLD-------H---------P------------R-VIDTSLIFKYVDEYRRPSLYNLC 265 (360)
Q Consensus 218 l~~g--~iLVGHnl-~fDl~~L~~~-------~---------~------------~-viDT~~l~~~~~~~~~~sL~~L~ 265 (360)
+..- .+++|||. .||+.+|..- . + + .+|...+.+......+++|+++|
T Consensus 59 i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~~y~L~~Va 138 (188)
T cd05781 59 VKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENVA 138 (188)
T ss_pred HHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhCCCCCCCHHHHH
Confidence 9644 68999995 6899997541 0 0 1 57887777765557889999999
Q ss_pred HHHhCCc
Q 018152 266 KSVLGYE 272 (360)
Q Consensus 266 ~~~Lg~~ 272 (360)
+ +||..
T Consensus 139 ~-~Lg~~ 144 (188)
T cd05781 139 E-YLGVM 144 (188)
T ss_pred H-HHCCC
Confidence 5 68863
No 67
>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=97.91 E-value=0.00018 Score=63.66 Aligned_cols=85 Identities=29% Similarity=0.341 Sum_probs=62.8
Q ss_pred HHHHHhh-CCCEEEEEcchhhHHHHcccC----CCccchHHHhhHhCCC-CCCCHHHHHHHHhCCccC--CCC-------
Q 018152 213 RMKKLLS-NGTILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEY-RRPSLYNLCKSVLGYEIR--KKG------- 277 (360)
Q Consensus 213 ~l~~~l~-~g~iLVGHnl~fDl~~L~~~~----~~viDT~~l~~~~~~~-~~~sL~~L~~~~Lg~~iq--~~~------- 277 (360)
.|.+++. .+.+.|||++.+|+..|...+ ..++||..++....+. ...+|..||..++|..+. ...
T Consensus 64 ~l~~ll~~~~i~kv~~~~k~D~~~L~~~~g~~~~~~~Dl~~aa~ll~~~~~~~~l~~l~~~~l~~~~~k~k~~~~s~W~~ 143 (170)
T cd06141 64 SLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEA 143 (170)
T ss_pred HHHHHhcCCCeeEEEeeeHHHHHHHHhHcCCCCCCeeeHHHHHHHhCCCcCCccHHHHHHHHcCcccCCCCCcccCCCCC
Confidence 4555563 345679999999999997543 3479999998887763 457999999999999876 210
Q ss_pred ------CCCChHHHHHHHHHHHHHHH
Q 018152 278 ------TPHNCLDDASAAMKLVLAII 297 (360)
Q Consensus 278 ------~~H~AleDA~at~eL~~~~l 297 (360)
.-|-|..||..+.+||..+.
T Consensus 144 rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 144 RPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 12557789999999997653
No 68
>PRK10829 ribonuclease D; Provisional
Probab=97.77 E-value=0.0005 Score=69.39 Aligned_cols=131 Identities=18% Similarity=0.191 Sum_probs=83.8
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
...+.++||+|+.....-...++=|-+-.+++. .+|.|-. +.+ ...|.+++.
T Consensus 20 ~~~~~lalDtEf~~~~ty~~~l~LiQl~~~~~~----~LiD~l~-~~d-----------------------~~~L~~ll~ 71 (373)
T PRK10829 20 RAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQL----SLIDPLG-ITD-----------------------WSPFKALLR 71 (373)
T ss_pred hcCCeEEEecccccCccCCCceeEEEEecCCce----EEEecCC-ccc-----------------------hHHHHHHHc
Confidence 456789999999987653332222222233332 2333321 111 123555554
Q ss_pred CCCE-EEEEcchhhHHHHccc----CCCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCC-------------CC
Q 018152 220 NGTI-LVGHSLNNDLEVLKLD----HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTP-------------HN 281 (360)
Q Consensus 220 ~g~i-LVGHnl~fDl~~L~~~----~~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~-------------H~ 281 (360)
...| -|+|++.+|+.+|... ...+.||...++.+....+.+|..|++.++|+.+.++... +-
T Consensus 72 ~~~ivKV~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa~~lg~~~~~gl~~Lv~~~lgv~ldK~~~~sDW~~RPLs~~ql~Y 151 (373)
T PRK10829 72 DPQVTKFLHAGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEY 151 (373)
T ss_pred CCCeEEEEeChHhHHHHHHHHcCCCcCCeeeHHHHHHHcCCCccccHHHHHHHHhCCccCcccccCCCCCCCCCHHHHHH
Confidence 4444 4899999999998553 2358999877765533457899999999999987653111 34
Q ss_pred hHHHHHHHHHHHHHHHH
Q 018152 282 CLDDASAAMKLVLAIIE 298 (360)
Q Consensus 282 AleDA~at~eL~~~~l~ 298 (360)
|..|+....+||..+..
T Consensus 152 Aa~Dv~~L~~l~~~L~~ 168 (373)
T PRK10829 152 AAADVFYLLPIAAKLMA 168 (373)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 67899999999987664
No 69
>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=97.53 E-value=0.0031 Score=58.54 Aligned_cols=128 Identities=16% Similarity=0.148 Sum_probs=76.6
Q ss_pred CcEEEEEEeccCC-----CCCcccEEEEEEEEc-CCcEEEE-EeecCCCcccccc--cccCCCCHHhhcCCCCCHHHHHH
Q 018152 142 NIMYAVDCEMVLC-----EDGSEGLVRLCVVDR-NLKVTID-ELVKPEKAVADYR--SEITGLTADDLVGVTCSLAEIQK 212 (360)
Q Consensus 142 ~~~ValD~Ettgl-----~~g~~~I~~VsvVd~-~g~~~~d-~lV~P~~~I~d~~--t~i~GIT~e~L~~ap~~l~eV~~ 212 (360)
.+++++|+|+.+. ++..+.|+.||++.. .|..+.. .++.+...--.+. -.+.|. -.+.... +-.+++.
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~v~~~~-~E~~lL~ 78 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQGYLIVNREIVSEDIEDFEYTPKPEYEGP--FKVFNEP-DEKALLQ 78 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCCEEEecccccccccccccccCCCCCCCc--eEEecCC-CHHHHHH
Confidence 4789999999863 344568999999864 4532211 1111100000000 011111 0111233 7789999
Q ss_pred HHHHHhhCC--CEEEEEcc-hhhHHHHccc---C----C-----------------C-ccchHHHhhHhCC--CCCCCHH
Q 018152 213 RMKKLLSNG--TILVGHSL-NNDLEVLKLD---H----P-----------------R-VIDTSLIFKYVDE--YRRPSLY 262 (360)
Q Consensus 213 ~l~~~l~~g--~iLVGHnl-~fDl~~L~~~---~----~-----------------~-viDT~~l~~~~~~--~~~~sL~ 262 (360)
+|.+++..- .+++|||. .||+.+|..- + . + .+|...+++.... ...++|+
T Consensus 79 ~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sysLd 158 (204)
T cd05779 79 RFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQGLK 158 (204)
T ss_pred HHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCccHH
Confidence 999999543 39999985 7899987541 0 0 1 3777777765322 4689999
Q ss_pred HHHHHHhCCc
Q 018152 263 NLCKSVLGYE 272 (360)
Q Consensus 263 ~L~~~~Lg~~ 272 (360)
+.|+.+||..
T Consensus 159 ~Va~~~Lg~~ 168 (204)
T cd05779 159 AVTKAKLGYD 168 (204)
T ss_pred HHHHHHhCCC
Confidence 9998899974
No 70
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=97.47 E-value=0.00075 Score=64.65 Aligned_cols=75 Identities=25% Similarity=0.215 Sum_probs=54.9
Q ss_pred hCCCEEEEEcchhhHHHHccc-------------------CCCccchHHHhhHhCCCCCCCHHHHHHHHhCCcc------
Q 018152 219 SNGTILVGHSLNNDLEVLKLD-------------------HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEI------ 273 (360)
Q Consensus 219 ~~g~iLVGHnl~fDl~~L~~~-------------------~~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~i------ 273 (360)
....++||||.-.|+.+|-.. .|+++||-.|+.... ....+|..|+ ..++..-
T Consensus 147 ~~~~p~Vghn~~~Dl~~l~~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~~-~~~~~L~~l~-~~l~~~~~~~~~~ 224 (262)
T PF04857_consen 147 SSKKPIVGHNGLYDLMYLYKKFIGPLPETLEEFKELLRELFPRIYDTKYLAEECP-GKSTSLQELA-EELGIRRNPSSIS 224 (262)
T ss_dssp CC-SEEEESSTHHHHHHHHHHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTSTT-TS-SSHHHHH-HHTTSTT----EE
T ss_pred ccCCcEEEeChHhHHHHHHHHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhcc-ccccCHHHHH-HHhCCCccccccc
Confidence 345899999999999886432 467899998887544 3678999999 5566543
Q ss_pred ----------------CCCCCCCChHHHHHHHHHHHHH
Q 018152 274 ----------------RKKGTPHNCLDDASAAMKLVLA 295 (360)
Q Consensus 274 ----------------q~~~~~H~AleDA~at~eL~~~ 295 (360)
..+...|.|=-||..|+.+|.+
T Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~HeAGyDA~mTg~~F~~ 262 (262)
T PF04857_consen 225 SPEGFPSYDEEKNNFPMFGEKAHEAGYDAYMTGCVFIK 262 (262)
T ss_dssp E-TTS-------------SS-TTSHHHHHHHHHHHHHH
T ss_pred cccccccccccccccccCCCCCCCcchHHHHHHHHHcC
Confidence 1222389999999999999863
No 71
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=97.42 E-value=0.0099 Score=51.32 Aligned_cols=87 Identities=28% Similarity=0.290 Sum_probs=57.7
Q ss_pred HHHHHHHhh-CCCEEEEEcchhhHHHHccc---CCCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCC-CC------
Q 018152 211 QKRMKKLLS-NGTILVGHSLNNDLEVLKLD---HPRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKK-GT------ 278 (360)
Q Consensus 211 ~~~l~~~l~-~g~iLVGHnl~fDl~~L~~~---~~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~-~~------ 278 (360)
...|.+++. .+...||||+.+|+.+|+.. .+.+.||...+....+ ....+|+.++..++|..+... +.
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~k~~~~~L~~~gi~~~~~~D~~laayll~p~~~~~~l~~l~~~~l~~~~~~~~~~~~~~~~ 143 (172)
T smart00474 64 LEILKDLLEDETITKVGHNAKFDLHVLARFGIELENIFDTMLAAYLLLGGPSKHGLATLLKEYLGVELDKEEQKSDWGAR 143 (172)
T ss_pred HHHHHHHhcCCCceEEEechHHHHHHHHHCCCcccchhHHHHHHHHHcCCCCcCCHHHHHHHHhCCCCCcccCccccccC
Confidence 344556663 34569999999999999642 2235899988877777 333699999999998875310 00
Q ss_pred --CC----ChHHHHHHHHHHHHHHH
Q 018152 279 --PH----NCLDDASAAMKLVLAII 297 (360)
Q Consensus 279 --~H----~AleDA~at~eL~~~~l 297 (360)
.. -|..||.++.+|+..+.
T Consensus 144 ~l~~~~~~ya~~~a~~~~~L~~~l~ 168 (172)
T smart00474 144 PLSEEQLQYAAEDADALLRLYEKLE 168 (172)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 00 15566777777775544
No 72
>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=97.35 E-value=0.0019 Score=60.01 Aligned_cols=106 Identities=17% Similarity=0.266 Sum_probs=72.9
Q ss_pred CCcEEEEEEeccCCC--------CCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHH
Q 018152 141 SNIMYAVDCEMVLCE--------DGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQK 212 (360)
Q Consensus 141 ~~~~ValD~Ettgl~--------~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~ 212 (360)
+-++++||+|+.... +..+.|+.|++.+..|.... +.. ... +-.+++.
T Consensus 8 ~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~---~~~--------------------~~~-~E~~lL~ 63 (207)
T cd05785 8 DLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEV---LHA--------------------EDA-AEKELLE 63 (207)
T ss_pred CceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceee---ecc--------------------CCC-CHHHHHH
Confidence 458999999997642 23357999998876552111 100 134 7889999
Q ss_pred HHHHHhhCC--CEEEEEcc-hhhHHHHccc-------CC-------------------------------C-ccchHHHh
Q 018152 213 RMKKLLSNG--TILVGHSL-NNDLEVLKLD-------HP-------------------------------R-VIDTSLIF 250 (360)
Q Consensus 213 ~l~~~l~~g--~iLVGHnl-~fDl~~L~~~-------~~-------------------------------~-viDT~~l~ 250 (360)
+|.+++..- .|+||||. .||+.+|... .+ + ++|+..++
T Consensus 64 ~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~iDl~~~~ 143 (207)
T cd05785 64 ELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIPGRHVIDTYFLV 143 (207)
T ss_pred HHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEecCEEEEEcHHHH
Confidence 999999543 79999998 8999987531 10 2 27888877
Q ss_pred hHh----CCCCCCCHHHHHHHHhCC
Q 018152 251 KYV----DEYRRPSLYNLCKSVLGY 271 (360)
Q Consensus 251 ~~~----~~~~~~sL~~L~~~~Lg~ 271 (360)
++. ....++||+++|+. +|.
T Consensus 144 ~~~~~~~~~l~sysL~~Va~~-~g~ 167 (207)
T cd05785 144 QLFDVSSRDLPSYGLKAVAKH-FGL 167 (207)
T ss_pred HhhcccccCCCCCCHHHHHHH-hcc
Confidence 752 22568899999965 454
No 73
>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=97.34 E-value=0.0075 Score=53.07 Aligned_cols=129 Identities=24% Similarity=0.253 Sum_probs=79.3
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh-C
Q 018152 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-N 220 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~-~ 220 (360)
...+++|+|+.+..+....+..+++-.. +.+. +|.+. .+ . +...|..++. .
T Consensus 12 ~~~l~~~~e~~~~~~~~~~~~~i~l~~~-~~~~---~i~~~----------------~~-~-------~~~~l~~ll~~~ 63 (178)
T cd06142 12 AGVIAVDTEFMRLNTYYPRLCLIQISTG-GEVY---LIDPL----------------AI-G-------DLSPLKELLADP 63 (178)
T ss_pred CCeEEEECCccCCCcCCCceEEEEEeeC-CCEE---EEeCC----------------Cc-c-------cHHHHHHHHcCC
Confidence 3589999998766543334665665544 3222 12111 00 0 2333455552 3
Q ss_pred CCEEEEEcchhhHHHHccc----CCCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCC---C-C---------CChH
Q 018152 221 GTILVGHSLNNDLEVLKLD----HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKG---T-P---------HNCL 283 (360)
Q Consensus 221 g~iLVGHnl~fDl~~L~~~----~~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~---~-~---------H~Al 283 (360)
+...||||+.+|+.+|... ...+.||...+....+..+.+|+.+++.|+|..+.... . + +-+.
T Consensus 64 ~i~kv~~d~K~~~~~L~~~~gi~~~~~~D~~laayLl~p~~~~~l~~l~~~~l~~~~~~~~~~~~w~~~~l~~~~~~yaa 143 (178)
T cd06142 64 NIVKVFHAAREDLELLKRDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAA 143 (178)
T ss_pred CceEEEeccHHHHHHHHHHcCCCCCCcccHHHHHHHhCCCccccHHHHHHHHhCCCCCcccccccCCCCCCCHHHHHHHH
Confidence 4679999999999999644 22468998777666664456999999999988732110 0 0 1256
Q ss_pred HHHHHHHHHHHHHHH
Q 018152 284 DDASAAMKLVLAIIE 298 (360)
Q Consensus 284 eDA~at~eL~~~~l~ 298 (360)
.||.++.+|+..+.+
T Consensus 144 ~~a~~l~~L~~~l~~ 158 (178)
T cd06142 144 LDVRYLLPLYEKLKE 158 (178)
T ss_pred HhHHHHHHHHHHHHH
Confidence 677778888776554
No 74
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=97.33 E-value=0.0031 Score=63.08 Aligned_cols=132 Identities=21% Similarity=0.233 Sum_probs=86.2
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhC
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSN 220 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~ 220 (360)
..++|+||+||.+..+-..+++=|-+-++++ ..+|.|-.++.+ .+ .|..+.. +.
T Consensus 16 ~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~----~~lIdpl~~~~d---------------~~-~l~~Ll~------d~ 69 (361)
T COG0349 16 GSKAIAIDTEFMRLRTYYPRLCLIQISDGEG----ASLIDPLAGILD---------------LP-PLVALLA------DP 69 (361)
T ss_pred CCCceEEecccccccccCCceEEEEEecCCC----ceEecccccccc---------------cc-hHHHHhc------CC
Confidence 3569999999999987666555455555555 345555443222 22 2222221 13
Q ss_pred CCEEEEEcchhhHHHHcccC---C-CccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCC----CCC---------hH
Q 018152 221 GTILVGHSLNNDLEVLKLDH---P-RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGT----PHN---------CL 283 (360)
Q Consensus 221 g~iLVGHnl~fDl~~L~~~~---~-~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~----~H~---------Al 283 (360)
+-+=|-|+++||+.+|.... | .++||-...+...-..+++|++||++++|+++.++.. +++ |.
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 34448899999999998752 3 4899987777644344999999999999999975311 244 34
Q ss_pred HHHHHHHHHHHHHHH
Q 018152 284 DDASAAMKLVLAIIE 298 (360)
Q Consensus 284 eDA~at~eL~~~~l~ 298 (360)
.|..-...||.++.+
T Consensus 150 ~DV~yL~~l~~~L~~ 164 (361)
T COG0349 150 ADVEYLLPLYDKLTE 164 (361)
T ss_pred HHHHHHHHHHHHHHH
Confidence 566667777766553
No 75
>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=97.32 E-value=0.0016 Score=59.65 Aligned_cols=131 Identities=22% Similarity=0.220 Sum_probs=78.6
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEc--C-CcE-EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHH
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDR--N-LKV-TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMK 215 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~--~-g~~-~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~ 215 (360)
...++|+||||+++... . .+|++|-. . +.+ ++|.+--+. . . ....|.
T Consensus 8 ~~~~~i~~D~E~~~~~~-~---~~~~LiQia~~~~~v~l~D~~~~~~---------------------~-~---~~~~L~ 58 (197)
T cd06148 8 KKQKVIGLDCEGVNLGR-K---GKLCLVQIATRTGQIYLFDILKLGS---------------------I-V---FINGLK 58 (197)
T ss_pred hhCCEEEEEcccccCCC-C---CCEEEEEEeeCCCcEEEEEhhhccc---------------------h-h---HHHHHH
Confidence 45789999999987654 2 23555542 2 222 334321110 0 1 123444
Q ss_pred HHhh-CCCEEEEEcchhhHHHHccc----CCCccchHHHhhHhCC--------CCCCCHHHHHHHHhCCccCC-------
Q 018152 216 KLLS-NGTILVGHSLNNDLEVLKLD----HPRVIDTSLIFKYVDE--------YRRPSLYNLCKSVLGYEIRK------- 275 (360)
Q Consensus 216 ~~l~-~g~iLVGHnl~fDl~~L~~~----~~~viDT~~l~~~~~~--------~~~~sL~~L~~~~Lg~~iq~------- 275 (360)
+++. .+.+-|||++.+|+.+|... ...+.||...+....+ ....+|+.+++.++|.++..
T Consensus 59 ~iLe~~~i~Kv~h~~k~D~~~L~~~~gi~~~~~fDt~iA~~lL~~~~~~~~~~~~~~~L~~l~~~~l~~~~~k~~~~~~~ 138 (197)
T cd06148 59 DILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEQETGGFNPDRVISLVQLLDKYLYISISLKEDVKKL 138 (197)
T ss_pred HHhcCCCccEEEEechhHHHHHHHhcCccccceeeHHHHHHHHHHHhcCCccccccccHHHHHHHhhCCChHHHHHHHHH
Confidence 5553 23456999999999999432 2347899866544332 12469999999999987621
Q ss_pred -----C----C-----CCCChHHHHHHHHHHHHHHHHh
Q 018152 276 -----K----G-----TPHNCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 276 -----~----~-----~~H~AleDA~at~eL~~~~l~~ 299 (360)
. + .-.-|..||..+..||..+...
T Consensus 139 ~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~ 176 (197)
T cd06148 139 MREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDA 176 (197)
T ss_pred HhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 0 0 0133567888888888777653
No 76
>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=97.31 E-value=0.0027 Score=63.94 Aligned_cols=129 Identities=22% Similarity=0.230 Sum_probs=80.7
Q ss_pred CCcEEEEEEeccCCCCCcccEEEEEEEEc-CCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 141 SNIMYAVDCEMVLCEDGSEGLVRLCVVDR-NLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 141 ~~~~ValD~Ettgl~~g~~~I~~VsvVd~-~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
..++|+||+|++....-.. ++|+|-. ++... .+|.|-.. . . ...|.+++.
T Consensus 17 ~~~~ia~DtE~~~~~~y~~---~l~LiQia~~~~~--~liD~~~~-~-------------------~----~~~L~~lL~ 67 (367)
T TIGR01388 17 TFPFVALDTEFVRERTFWP---QLGLIQVADGEQL--ALIDPLVI-I-------------------D----WSPLKELLR 67 (367)
T ss_pred cCCEEEEeccccCCCCCCC---cceEEEEeeCCeE--EEEeCCCc-c-------------------c----HHHHHHHHC
Confidence 3579999999998754322 2344432 22222 24444211 0 0 122344442
Q ss_pred -CCCEEEEEcchhhHHHHccc---CC-CccchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCC----CCC---------
Q 018152 220 -NGTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGT----PHN--------- 281 (360)
Q Consensus 220 -~g~iLVGHnl~fDl~~L~~~---~~-~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~----~H~--------- 281 (360)
.+.+.|+|++.+|+.+|... .+ .+.||...+..+.+..+.+|..|++.|||+.+..+.. ..+
T Consensus 68 d~~i~KV~h~~k~Dl~~L~~~~~~~~~~~fDtqlAa~lL~~~~~~~l~~Lv~~~Lg~~l~K~~~~sdW~~rPL~~~q~~Y 147 (367)
T TIGR01388 68 DESVVKVLHAASEDLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEY 147 (367)
T ss_pred CCCceEEEeecHHHHHHHHHHhCCCCCCcccHHHHHHHhCCCCCccHHHHHHHHcCCCCCcccccccCCCCCCCHHHHHH
Confidence 34557999999999999754 22 4799988776655545679999999999998754210 122
Q ss_pred hHHHHHHHHHHHHHHHH
Q 018152 282 CLDDASAAMKLVLAIIE 298 (360)
Q Consensus 282 AleDA~at~eL~~~~l~ 298 (360)
|..||.....||..+.+
T Consensus 148 Aa~Dv~~L~~L~~~L~~ 164 (367)
T TIGR01388 148 AAADVTYLLPLYAKLME 164 (367)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 67788888888876653
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=97.17 E-value=0.0087 Score=55.03 Aligned_cols=114 Identities=18% Similarity=0.182 Sum_probs=74.2
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhhCC
Q 018152 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLSNG 221 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~~g 221 (360)
-++++||+|+++-. .|..|+..+..-+.++- +=.+ .++. |. .+.-.+ +-.++..+|.+++..-
T Consensus 3 l~~~~fDIE~~~~~----~i~~i~~~~~~~~~i~~-~~~~-~~~~-------~~---~v~~~~-~E~~lL~~f~~~i~~~ 65 (193)
T cd05784 3 LKVVSLDIETSMDG----ELYSIGLYGEGQERVLM-VGDP-EDDA-------PD---NIEWFA-DEKSLLLALIAWFAQY 65 (193)
T ss_pred ccEEEEEeecCCCC----CEEEEEeecCCCCEEEE-ECCC-CCCC-------CC---EEEEEC-CHHHHHHHHHHHHHhh
Confidence 47899999998643 58888887753332221 1111 1111 11 122234 6778999999999544
Q ss_pred --CEEEEEcc-hhhHHHHccc-------CC-------------------------C-ccchHHHhhH-hCCCCCCCHHHH
Q 018152 222 --TILVGHSL-NNDLEVLKLD-------HP-------------------------R-VIDTSLIFKY-VDEYRRPSLYNL 264 (360)
Q Consensus 222 --~iLVGHnl-~fDl~~L~~~-------~~-------------------------~-viDT~~l~~~-~~~~~~~sL~~L 264 (360)
.|++|||. .||+.+|..- .. | ++|+..+.+. .....+++|+++
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 58999996 5699887431 10 1 4788777765 344789999999
Q ss_pred HHHHhCCc
Q 018152 265 CKSVLGYE 272 (360)
Q Consensus 265 ~~~~Lg~~ 272 (360)
|+.+||..
T Consensus 146 a~~~Lg~~ 153 (193)
T cd05784 146 AQELLGEG 153 (193)
T ss_pred HHHHhCCC
Confidence 99999864
No 78
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic
Probab=96.99 E-value=0.024 Score=53.20 Aligned_cols=122 Identities=17% Similarity=0.187 Sum_probs=79.4
Q ss_pred CCcEEEEEEeccCC-----CCCcccEEEEEEEEc-CCc--EEEEE-e-ecCCCcccccccccCCCCHHhhcCCCCCHHHH
Q 018152 141 SNIMYAVDCEMVLC-----EDGSEGLVRLCVVDR-NLK--VTIDE-L-VKPEKAVADYRSEITGLTADDLVGVTCSLAEI 210 (360)
Q Consensus 141 ~~~~ValD~Ettgl-----~~g~~~I~~VsvVd~-~g~--~~~d~-l-V~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV 210 (360)
+-+.+++|+|+..- ++..+.|+.|+++.. +|. ..... + +++..+++ | ..+.... +-.+.
T Consensus 6 ~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~-------~---~~v~~~~-~E~eL 74 (230)
T cd05777 6 PLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIV-------G---AQVFSFE-TEEEL 74 (230)
T ss_pred CceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCC-------C---CEEEEEC-CHHHH
Confidence 45799999999853 345678999999854 342 11111 1 23322222 1 1222334 77899
Q ss_pred HHHHHHHhhCC--CEEEEEcc-hhhHHHHccc-------C-----------------------------------CC-cc
Q 018152 211 QKRMKKLLSNG--TILVGHSL-NNDLEVLKLD-------H-----------------------------------PR-VI 244 (360)
Q Consensus 211 ~~~l~~~l~~g--~iLVGHnl-~fDl~~L~~~-------~-----------------------------------~~-vi 244 (360)
..+|.+++..- .|++|||+ .||+.+|..- . .| ++
T Consensus 75 L~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~i 154 (230)
T cd05777 75 LLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQF 154 (230)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEEee
Confidence 99999999532 69999996 5699886321 0 01 36
Q ss_pred chHHHhhHhCCCCCCCHHHHHHHHhCCcc
Q 018152 245 DTSLIFKYVDEYRRPSLYNLCKSVLGYEI 273 (360)
Q Consensus 245 DT~~l~~~~~~~~~~sL~~L~~~~Lg~~i 273 (360)
|+..++++.....+++|+++|+.+||...
T Consensus 155 D~~~~~~~~~kl~sy~L~~Va~~~Lg~~k 183 (230)
T cd05777 155 DLLQVIQRDYKLRSYSLNSVSAHFLGEQK 183 (230)
T ss_pred eHHHHHHHhcCcccCcHHHHHHHHhCCCC
Confidence 77777766555789999999999999654
No 79
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=96.51 E-value=0.04 Score=51.03 Aligned_cols=126 Identities=19% Similarity=0.127 Sum_probs=76.0
Q ss_pred CCcEEEEEEeccCCC----CC--c--ccEEEEEEEEcCCcEEEEEeecC-CCcccccccccCCCCHHhhcCCCCCHHHHH
Q 018152 141 SNIMYAVDCEMVLCE----DG--S--EGLVRLCVVDRNLKVTIDELVKP-EKAVADYRSEITGLTADDLVGVTCSLAEIQ 211 (360)
Q Consensus 141 ~~~~ValD~Ettgl~----~g--~--~~I~~VsvVd~~g~~~~d~lV~P-~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~ 211 (360)
+-++++||+||+.-. |. . +.|+.|++...+|...+ .+++. .....+.-. .-| ..+.... +-.++.
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v-~~~~~~~~~~~~~~~-~~~---~~v~~~~-~E~~lL 77 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRV-LVLKREGVEGLEGLL-PEG---AEVEFFD-SEKELI 77 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEE-EEEecCCcccccccC-CCC---CeEEecC-CHHHHH
Confidence 358999999998521 21 2 47999999864453211 11221 111000000 001 1122334 788999
Q ss_pred HHHHHHhhCCCEEEEEcc-hhhHHHHccc-----CC-----------------C-ccchHHHhhHh------C--CCCCC
Q 018152 212 KRMKKLLSNGTILVGHSL-NNDLEVLKLD-----HP-----------------R-VIDTSLIFKYV------D--EYRRP 259 (360)
Q Consensus 212 ~~l~~~l~~g~iLVGHnl-~fDl~~L~~~-----~~-----------------~-viDT~~l~~~~------~--~~~~~ 259 (360)
.+|.+++..-.++||+|. .||+.+|..- .+ + .+|....+... + ...++
T Consensus 78 ~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~~~~~ 157 (204)
T cd05783 78 REAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNKYREY 157 (204)
T ss_pred HHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccccccC
Confidence 999999987789999985 6899987541 11 1 36776654431 1 24789
Q ss_pred CHHHHHHHHhCCc
Q 018152 260 SLYNLCKSVLGYE 272 (360)
Q Consensus 260 sL~~L~~~~Lg~~ 272 (360)
+|+++|+.+||..
T Consensus 158 ~L~~Va~~~lg~~ 170 (204)
T cd05783 158 TLDAVAKALLGEG 170 (204)
T ss_pred cHHHHHHHhcCCC
Confidence 9999998898874
No 80
>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=96.30 E-value=0.13 Score=45.41 Aligned_cols=105 Identities=23% Similarity=0.195 Sum_probs=71.7
Q ss_pred CcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh-C
Q 018152 142 NIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-N 220 (360)
Q Consensus 142 ~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~-~ 220 (360)
...+++|+|++|.++....+..+++-..+ ... ||.+... + .+.+.+.+++. .
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~---~i~~~~~----------~-------------~~~~~l~~~l~~~ 55 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGG-GAY---YIPLELA----------L-------------LDLAALKEWLEDE 55 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCC-cEE---EEeccch----------H-------------HHHHHHHHHHhCC
Confidence 35679999999999766667777776543 222 3332211 0 13444556663 3
Q ss_pred CCEEEEEcchhhHHHHccc---CC-CccchHHHhhHhCCCC-CCCHHHHHHHHhCCcc
Q 018152 221 GTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDEYR-RPSLYNLCKSVLGYEI 273 (360)
Q Consensus 221 g~iLVGHnl~fDl~~L~~~---~~-~viDT~~l~~~~~~~~-~~sL~~L~~~~Lg~~i 273 (360)
+...|+||+.+|+.+|... .+ .+.||...+.-+.+.. .++|+.++++|++.++
T Consensus 56 ~~~ki~~d~K~~~~~l~~~gi~~~~~~fDt~laaYLL~p~~~~~~l~~l~~~yl~~~~ 113 (178)
T cd06140 56 KIPKVGHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGREL 113 (178)
T ss_pred CCceeccchhHHHHHHHHCCCcCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCCC
Confidence 4579999999999999653 22 3589998887777733 4799999999998874
No 81
>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=96.29 E-value=0.042 Score=51.03 Aligned_cols=66 Identities=27% Similarity=0.343 Sum_probs=49.2
Q ss_pred CHHHHHHHHHHHhhC-CCEEEEEcc-hhhHHHHccc-------CC------------------CccchHHHhhHhCCCCC
Q 018152 206 SLAEIQKRMKKLLSN-GTILVGHSL-NNDLEVLKLD-------HP------------------RVIDTSLIFKYVDEYRR 258 (360)
Q Consensus 206 ~l~eV~~~l~~~l~~-g~iLVGHnl-~fDl~~L~~~-------~~------------------~viDT~~l~~~~~~~~~ 258 (360)
+-.++.++|++++.. +.+|||||. .||+.+|... .+ +.+|+..+.+......+
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 446899999999965 568999996 8999998752 11 25788877654322579
Q ss_pred CCHHHHHHHHhCCc
Q 018152 259 PSLYNLCKSVLGYE 272 (360)
Q Consensus 259 ~sL~~L~~~~Lg~~ 272 (360)
.+|+.+| .+||++
T Consensus 157 ~~L~~va-~~lG~~ 169 (208)
T cd05782 157 ASLDLLA-KLLGIP 169 (208)
T ss_pred CCHHHHH-HHhCCC
Confidence 9999999 577874
No 82
>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=96.08 E-value=0.14 Score=47.87 Aligned_cols=90 Identities=24% Similarity=0.264 Sum_probs=64.4
Q ss_pred CHHHHHHHHHHHhhC-CCEEEEEc-chhhHHHHccc-------CC-------------------CccchHHHhhHhCCCC
Q 018152 206 SLAEIQKRMKKLLSN-GTILVGHS-LNNDLEVLKLD-------HP-------------------RVIDTSLIFKYVDEYR 257 (360)
Q Consensus 206 ~l~eV~~~l~~~l~~-g~iLVGHn-l~fDl~~L~~~-------~~-------------------~viDT~~l~~~~~~~~ 257 (360)
+-+++.+.|++++.+ ...||+|| -.||+.+|... .| +-+|++.+...-.+..
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 467899999999954 34899998 68999998652 11 1377776644322367
Q ss_pred CCCHHHHHHHHhCCccCCCCCC------------------CChHHHHHHHHHHHHHHHH
Q 018152 258 RPSLYNLCKSVLGYEIRKKGTP------------------HNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 258 ~~sL~~L~~~~Lg~~iq~~~~~------------------H~AleDA~at~eL~~~~l~ 298 (360)
+.||+.|| ..+|++= + .+- .-+..|+.+|+.||+++..
T Consensus 116 ~~sLd~la-~~lgiPg-K-~~idGs~V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 116 RTSLDELA-ALLGIPG-K-DDIDGSQVAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred cCCHHHHH-HHcCCCC-C-CCCCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999 7889873 2 112 2345899999999987663
No 83
>cd05778 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Probab=96.02 E-value=0.21 Score=47.04 Aligned_cols=142 Identities=15% Similarity=0.131 Sum_probs=85.1
Q ss_pred CcEEEEEEeccCC-----CCCcccEEEEEEEEc-CCcEE-E-----E-EeecCCCcccccccccCCCCHHhhcCCCCCHH
Q 018152 142 NIMYAVDCEMVLC-----EDGSEGLVRLCVVDR-NLKVT-I-----D-ELVKPEKAVADYRSEITGLTADDLVGVTCSLA 208 (360)
Q Consensus 142 ~~~ValD~Ettgl-----~~g~~~I~~VsvVd~-~g~~~-~-----d-~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~ 208 (360)
-++.++|+|+.+- +|..+.|..|+.+-. +.... . . -++.+...-........++....+.-.+ +-.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~v~~~~-~E~ 82 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKSNASNGRIRSGLSGIPVEVVE-SEL 82 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccchhhhhccccCCCCCeEEEeC-CHH
Confidence 4688999998753 244568988887743 22111 1 1 2233322111111112233333444455 777
Q ss_pred HHHHHHHHHhh--CCCEEEEEcc-hhhHHHHccc----------------------------------C-------CC-c
Q 018152 209 EIQKRMKKLLS--NGTILVGHSL-NNDLEVLKLD----------------------------------H-------PR-V 243 (360)
Q Consensus 209 eV~~~l~~~l~--~g~iLVGHnl-~fDl~~L~~~----------------------------------~-------~~-v 243 (360)
+...+|.+++. .-.|++|||+ .||+.+|-.- + .| +
T Consensus 83 ~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi~ 162 (231)
T cd05778 83 ELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRHI 162 (231)
T ss_pred HHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEEE
Confidence 88888888874 2379999998 5788765320 0 01 3
Q ss_pred cchHHHhhHhCCCCCCCHHHHHHHHhCCccCCCCCCCChHHHH
Q 018152 244 IDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKKGTPHNCLDDA 286 (360)
Q Consensus 244 iDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA 286 (360)
+|+..+.++.....++||..+|..+||..... -.|..+.+.
T Consensus 163 lD~~~~~r~~~kl~sYsL~~V~~~~L~~~k~~--~~~~~i~~~ 203 (231)
T cd05778 163 LNVWRLMRSELALTNYTLENVVYHVLHQRIPL--YSNKTLTEW 203 (231)
T ss_pred eEhHHHHHHHcCcccCCHHHHHHHHhCCCCCC--CCHHHHHHH
Confidence 67777777655578999999999999987542 345555554
No 84
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=95.95 E-value=0.045 Score=58.27 Aligned_cols=131 Identities=25% Similarity=0.288 Sum_probs=87.3
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh-CCCE
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-NGTI 223 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~-~g~i 223 (360)
+++|+||+|+++-...++.+++.... +..| | | -.|+ + ..-++...+..++. .+..
T Consensus 25 ~a~~~et~~l~~~~~~lvg~s~~~~~-~~~y---i-~---------~~~~---------~-~~~~~~~~l~~~l~~~~~~ 80 (593)
T COG0749 25 IAFDTETDGLDPHGADLVGLSVASEE-EAAY---I-P---------LLHG---------P-EQLNVLAALKPLLEDEGIK 80 (593)
T ss_pred ceeeccccccCcccCCeeEEEeeccc-ccee---E-e---------eccc---------h-hhhhhHHHHHHHhhCcccc
Confidence 99999999999854457777766554 2111 1 1 1111 1 11126677777772 2346
Q ss_pred EEEEcchhhHHHHcccC---CCccchHHHhhHhCC-CCCCCHHHHHHHHhCCccCCC------CC-------------CC
Q 018152 224 LVGHSLNNDLEVLKLDH---PRVIDTSLIFKYVDE-YRRPSLYNLCKSVLGYEIRKK------GT-------------PH 280 (360)
Q Consensus 224 LVGHnl~fDl~~L~~~~---~~viDT~~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~------~~-------------~H 280 (360)
.||||+.+|+.+|.... +..-||+...--+.+ ...+.++.|+++|++...... +. .-
T Consensus 81 kv~~~~K~d~~~l~~~Gi~~~~~~DtmlasYll~~~~~~~~~~~l~~r~l~~~~~~~~~i~~kg~~~~~~~~~~~~~~~~ 160 (593)
T COG0749 81 KVGQNLKYDYKVLANLGIEPGVAFDTMLASYLLNPGAGAHNLDDLAKRYLGLETITFEDIAGKGKKQLTFADVKLEKATE 160 (593)
T ss_pred hhccccchhHHHHHHcCCcccchHHHHHHHhccCcCcCcCCHHHHHHHhcCCccchhHHhhccccccCccccchHHHHHH
Confidence 99999999999998865 345788766555554 567999999999988765320 00 12
Q ss_pred ChHHHHHHHHHHHHHHHHh
Q 018152 281 NCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 281 ~AleDA~at~eL~~~~l~~ 299 (360)
.+.+||.++.+|+..+...
T Consensus 161 y~a~~a~~~~~L~~~l~~~ 179 (593)
T COG0749 161 YAAEDADATLRLESILEPE 179 (593)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3568999999999877643
No 85
>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=95.90 E-value=0.21 Score=42.39 Aligned_cols=60 Identities=25% Similarity=0.265 Sum_probs=45.0
Q ss_pred HHHHhh-CCCEEEEEcchhhHHHHccc---CC-CccchHHHhhHhCCCC-CCCHHHHHHHHhCCcc
Q 018152 214 MKKLLS-NGTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDEYR-RPSLYNLCKSVLGYEI 273 (360)
Q Consensus 214 l~~~l~-~g~iLVGHnl~fDl~~L~~~---~~-~viDT~~l~~~~~~~~-~~sL~~L~~~~Lg~~i 273 (360)
|.+++. .+...||||+..|+.+|... .+ .+.||...+..+.+.. +.+|+.|+++|++.++
T Consensus 45 l~~~l~~~~~~kv~~d~K~~~~~L~~~~~~~~~~~~D~~laayLl~p~~~~~~l~~l~~~~l~~~~ 110 (150)
T cd09018 45 LKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFDTMLEAYILNSVAGRWDMDSLVERWLGHKL 110 (150)
T ss_pred HHHHhcCCCCceeeecHHHHHHHHHHcCCccCCcchhHHHHHHHhCCCCCCCCHHHHHHHHhCCCc
Confidence 444552 34668999999999999653 22 3689998887777743 5699999999988773
No 86
>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=95.46 E-value=0.23 Score=50.09 Aligned_cols=144 Identities=19% Similarity=0.210 Sum_probs=89.4
Q ss_pred CcEEEEEEeccCCCC-----C--cccEEEEEEEEcCCcE----E-EEEeecCCCcccccccccCCCCHHhhcCCCCCHHH
Q 018152 142 NIMYAVDCEMVLCED-----G--SEGLVRLCVVDRNLKV----T-IDELVKPEKAVADYRSEITGLTADDLVGVTCSLAE 209 (360)
Q Consensus 142 ~~~ValD~Ettgl~~-----g--~~~I~~VsvVd~~g~~----~-~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~e 209 (360)
.+++++|+||+.-.. . .+.|+.++++...+.. . ......+...+. |+. +.... +-.+
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~---~~~~~-~E~~ 71 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCKEID-------GVE---VYEFN-NEKE 71 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcCCCC-------CCe---EEecC-CHHH
Confidence 478999999986431 1 3578999988753321 1 111223333322 222 22222 5567
Q ss_pred HHHHHHHHhhCC--CEEEEEcch-hhHHHHccc-------C----------------------------------CC-cc
Q 018152 210 IQKRMKKLLSNG--TILVGHSLN-NDLEVLKLD-------H----------------------------------PR-VI 244 (360)
Q Consensus 210 V~~~l~~~l~~g--~iLVGHnl~-fDl~~L~~~-------~----------------------------------~~-vi 244 (360)
...+|.+++..- .+++|||.. ||+.+|... . .+ .+
T Consensus 72 lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 151 (471)
T smart00486 72 LLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLVI 151 (471)
T ss_pred HHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEEE
Confidence 888888877432 599999985 899887431 0 01 37
Q ss_pred chHHHhhHhCCCCCCCHHHHHHHHhCCccCCC-C----------------CCCChHHHHHHHHHHHHHH
Q 018152 245 DTSLIFKYVDEYRRPSLYNLCKSVLGYEIRKK-G----------------TPHNCLDDASAAMKLVLAI 296 (360)
Q Consensus 245 DT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~~-~----------------~~H~AleDA~at~eL~~~~ 296 (360)
|+..+++......+++|+.+++.+||..-..- . ...-++.||.++.+|+.++
T Consensus 152 Dl~~~~~~~~kl~~~~L~~va~~~l~~~k~d~~~~~i~~~~~~~~~~~~~~~~Y~~~D~~l~~~l~~~l 220 (471)
T smart00486 152 DLYNLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNLNYKLRDELLEYCIQDAVLTLKLFNKL 220 (471)
T ss_pred EhHHHHHHHhCcccCCHHHHHHHHhCCCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88888777666789999999998888432210 0 0112356999999998775
No 87
>PRK05762 DNA polymerase II; Reviewed
Probab=95.18 E-value=0.35 Score=53.45 Aligned_cols=138 Identities=18% Similarity=0.215 Sum_probs=88.4
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
.+-++++||+|+..- .+|..|++.......++ .+.+..+.+ .+.+...+ +-.+.+.+|.+++.
T Consensus 153 p~lrvlsfDIE~~~~----~~i~sI~~~~~~~~~vi--~ig~~~~~~----------~~~v~~~~-sE~~LL~~F~~~i~ 215 (786)
T PRK05762 153 PPLKVVSLDIETSNK----GELYSIGLEGCGQRPVI--MLGPPNGEA----------LDFLEYVA-DEKALLEKFNAWFA 215 (786)
T ss_pred CCCeEEEEEEEEcCC----CceEEeeecCCCCCeEE--EEECCCCCC----------cceEEEcC-CHHHHHHHHHHHHH
Confidence 356999999999853 25878887633222111 122221110 11144445 78899999999995
Q ss_pred CC--CEEEEEcc-hhhHHHHccc-------C--------------C------------C-ccchHHHhhHhC-CCCCCCH
Q 018152 220 NG--TILVGHSL-NNDLEVLKLD-------H--------------P------------R-VIDTSLIFKYVD-EYRRPSL 261 (360)
Q Consensus 220 ~g--~iLVGHnl-~fDl~~L~~~-------~--------------~------------~-viDT~~l~~~~~-~~~~~sL 261 (360)
.- .|++|||+ .||+.+|..- . + + ++|+..+.+... ...+++|
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 42 59999996 5899887431 0 1 1 477777776644 3679999
Q ss_pred HHHHHHHhCCccCCCCCCC-------------------ChHHHHHHHHHHHHH
Q 018152 262 YNLCKSVLGYEIRKKGTPH-------------------NCLDDASAAMKLVLA 295 (360)
Q Consensus 262 ~~L~~~~Lg~~iq~~~~~H-------------------~AleDA~at~eL~~~ 295 (360)
+++|+.+||..-.. ...| -++.||..+.+|+.+
T Consensus 296 ~~Va~~~Lg~~K~~-~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~k 347 (786)
T PRK05762 296 EYVSQRLLGEGKAI-DDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEK 347 (786)
T ss_pred HHHHHHHhCCCeec-cCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999865321 0111 257899999999974
No 88
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=95.17 E-value=0.044 Score=52.90 Aligned_cols=160 Identities=19% Similarity=0.161 Sum_probs=102.4
Q ss_pred CCCCCCCcEEEEEEeccCCCCCcccEEEEEEEEc-----CCc---------------EE---EEEeecCCCccccccccc
Q 018152 136 SKTMTSNIMYAVDCEMVLCEDGSEGLVRLCVVDR-----NLK---------------VT---IDELVKPEKAVADYRSEI 192 (360)
Q Consensus 136 ~~~~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~-----~g~---------------~~---~d~lV~P~~~I~d~~t~i 192 (360)
++.++-..++.+|.|+||+..-...|+++++.+. +|. .+ +..++.|.....+...++
T Consensus 7 se~pr~~tf~fldleat~lp~~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~v~~p~aeei 86 (318)
T KOG4793|consen 7 SEVPRLRTFSFLDLEATGLPGWIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVPVTRPIAEEI 86 (318)
T ss_pred CcCCceeEEEeeeeccccCCcccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcCCcChhhhhh
Confidence 4455567899999999999865556888877642 222 12 335677777777778899
Q ss_pred CCCCHHhhcCCC--CCHHHHHHHHHHHhh---CCCEEEEEc-chhhHHHHccc-------CCC---ccchHHHhhHh---
Q 018152 193 TGLTADDLVGVT--CSLAEIQKRMKKLLS---NGTILVGHS-LNNDLEVLKLD-------HPR---VIDTSLIFKYV--- 253 (360)
Q Consensus 193 ~GIT~e~L~~ap--~~l~eV~~~l~~~l~---~g~iLVGHn-l~fDl~~L~~~-------~~~---viDT~~l~~~~--- 253 (360)
+|++...+.-.. .--.++.+-|..|++ .---||+|| -.+|+..|.++ .++ ++|+...++..
T Consensus 87 tgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald~a 166 (318)
T KOG4793|consen 87 TGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALDRA 166 (318)
T ss_pred cccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHhhh
Confidence 999986655322 112234444445552 234599998 46787777664 232 57877665432
Q ss_pred -----CC--CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHHHHH
Q 018152 254 -----DE--YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAII 297 (360)
Q Consensus 254 -----~~--~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~~l 297 (360)
.+ .+.++|..+-.+|.+-. +. ..+|.+..|.-+..-.++...
T Consensus 167 ~s~~tr~~~~~~~~l~~If~ry~~q~-ep-pa~~~~e~d~~~l~~~fqf~~ 215 (318)
T KOG4793|consen 167 NSMVTRPEVRRMYSLGSIFLRYVEQR-EP-PAGHVAEGDVNGLLFIFQFRI 215 (318)
T ss_pred cCcccCCCCCcccccchHHHhhhccc-CC-CcceeeecccchhHHHHHHHH
Confidence 11 56788888877776543 21 248999888777666665444
No 89
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=95.10 E-value=0.39 Score=54.84 Aligned_cols=149 Identities=16% Similarity=0.230 Sum_probs=92.3
Q ss_pred CCCcEEEEEEeccCCC------CCcccEEEEEEE-EcCCcE---EEEEeecCCCcccccccccCCCCHHhhcCCCCCHHH
Q 018152 140 TSNIMYAVDCEMVLCE------DGSEGLVRLCVV-DRNLKV---TIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAE 209 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~------~g~~~I~~VsvV-d~~g~~---~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~e 209 (360)
.+-++++||+||.+.+ +..+.|+.|+.+ ...|.. ....++-+.. ...+.|. .+..-. +-.+
T Consensus 262 pplrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~~~~~r~vftl~~-----c~~i~g~---~V~~f~-sE~e 332 (1054)
T PTZ00166 262 APLRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEEEPLTKFIFTLKE-----CASIAGA---NVLSFE-TEKE 332 (1054)
T ss_pred CCcEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCccCCcceEEEecCc-----cccCCCc---eEEEeC-CHHH
Confidence 3568999999998643 234689999987 334431 2222222221 1112221 222234 6778
Q ss_pred HHHHHHHHhh--CCCEEEEEcc-hhhHHHHcc-------c----------C-------------------------CC-c
Q 018152 210 IQKRMKKLLS--NGTILVGHSL-NNDLEVLKL-------D----------H-------------------------PR-V 243 (360)
Q Consensus 210 V~~~l~~~l~--~g~iLVGHnl-~fDl~~L~~-------~----------~-------------------------~~-v 243 (360)
.+.+|.+++. .-.|++|||+ .||+.+|-. . . .| +
T Consensus 333 LL~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~~ 412 (1054)
T PTZ00166 333 LLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRIQ 412 (1054)
T ss_pred HHHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEEE
Confidence 8888888874 2479999997 579877532 0 0 01 3
Q ss_pred cchHHHhhHhCCCCCCCHHHHHHHHhCCccCC----------CCCC-------CChHHHHHHHHHHHHHHH
Q 018152 244 IDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK----------KGTP-------HNCLDDASAAMKLVLAII 297 (360)
Q Consensus 244 iDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~----------~~~~-------H~AleDA~at~eL~~~~l 297 (360)
+|+..++++.....+++|+++|..+||..... .+.. .-++.||..+++|+.++.
T Consensus 413 iDl~~~~~~~~kl~sYsL~~Vs~~~Lg~~K~dv~~~~i~~~~~~~~~~~~~l~~Y~l~Da~L~~~L~~kl~ 483 (1054)
T PTZ00166 413 FDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETRRRIAVYCLKDAILPLRLLDKLL 483 (1054)
T ss_pred EEHHHHHHHhcCcCcCCHHHHHHHHhCCCCCCCCHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 67777777665578999999999999965321 0011 124689999999887653
No 90
>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=95.04 E-value=0.45 Score=42.94 Aligned_cols=102 Identities=18% Similarity=0.089 Sum_probs=65.6
Q ss_pred cEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh-CC
Q 018152 143 IMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS-NG 221 (360)
Q Consensus 143 ~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~-~g 221 (360)
..+++|+|+....+-...+..+++-..++. . ||.+ +. .......|.+++. .+
T Consensus 25 ~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~-~---~i~~------------------l~-----~~~~~~~L~~~L~~~~ 77 (192)
T cd06147 25 KEIAVDLEHHSYRSYLGFTCLMQISTREED-Y---IVDT------------------LK-----LRDDMHILNEVFTDPN 77 (192)
T ss_pred CeEEEEeEecCCccCCCceEEEEEecCCCc-E---EEEe------------------cc-----cccchHHHHHHhcCCC
Confidence 488999987655532334666777655442 1 2221 01 1112233555553 34
Q ss_pred CEEEEEcchhhHHHHc-cc---CCCccchHHHhhHhCCCCCCCHHHHHHHHhCCc
Q 018152 222 TILVGHSLNNDLEVLK-LD---HPRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYE 272 (360)
Q Consensus 222 ~iLVGHnl~fDl~~L~-~~---~~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~ 272 (360)
...|||++..|+..|+ .. ...+.||...+..+.+. +.+|+.|+++|++..
T Consensus 78 i~kv~~d~K~~~~~L~~~~gi~~~~~fD~~laaYLL~p~-~~~l~~l~~~yl~~~ 131 (192)
T cd06147 78 ILKVFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-RHSLAYLLQKYCNVD 131 (192)
T ss_pred ceEEEechHHHHHHHHHHhCCCcCchHHHHHHHHHhCCC-cccHHHHHHHHhCCC
Confidence 6789999999999996 22 12248999888877776 569999999998876
No 91
>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=95.03 E-value=0.19 Score=47.32 Aligned_cols=130 Identities=22% Similarity=0.231 Sum_probs=81.1
Q ss_pred cEEEEEEeccCCCC-CcccEEEEEEEEc-----CC-------cEEEEEeecCCCc--ccccccccCCCCHHhhcCCCCCH
Q 018152 143 IMYAVDCEMVLCED-GSEGLVRLCVVDR-----NL-------KVTIDELVKPEKA--VADYRSEITGLTADDLVGVTCSL 207 (360)
Q Consensus 143 ~~ValD~Ettgl~~-g~~~I~~VsvVd~-----~g-------~~~~d~lV~P~~~--I~d~~t~i~GIT~e~L~~ap~~l 207 (360)
.+++|-+=|+--.. ...+|+.|+++-. ++ ...+-.+++|... .++.....-......+.-.+ +-
T Consensus 4 ~v~sls~~T~~n~k~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~-~E 82 (234)
T cd05776 4 TVMSLSIKTVLNSKTNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFE-NE 82 (234)
T ss_pred EEEEEEeEEEecCcCCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeC-CH
Confidence 45666666654333 2467999888732 11 1124456677543 22222222222222234444 77
Q ss_pred HHHHHHHHHHhhC--CCEEEEEcc-hhhHHHHccc-------C----------------------------CC-ccchHH
Q 018152 208 AEIQKRMKKLLSN--GTILVGHSL-NNDLEVLKLD-------H----------------------------PR-VIDTSL 248 (360)
Q Consensus 208 ~eV~~~l~~~l~~--g~iLVGHnl-~fDl~~L~~~-------~----------------------------~~-viDT~~ 248 (360)
.+....|..++.. -.|+||||+ .||+.+|-.- + .| ++|+..
T Consensus 83 ~~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~ 162 (234)
T cd05776 83 RALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYL 162 (234)
T ss_pred HHHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHH
Confidence 7888888888843 379999999 8899886321 0 01 478888
Q ss_pred HhhHhCCCCCCCHHHHHHHHhCCcc
Q 018152 249 IFKYVDEYRRPSLYNLCKSVLGYEI 273 (360)
Q Consensus 249 l~~~~~~~~~~sL~~L~~~~Lg~~i 273 (360)
.++......+++|.++|..+||.+.
T Consensus 163 ~~k~~~~~~sY~L~~va~~~Lg~~k 187 (234)
T cd05776 163 SAKELIRCKSYDLTELSQQVLGIER 187 (234)
T ss_pred HHHHHhCCCCCChHHHHHHHhCcCc
Confidence 8877766789999999999999753
No 92
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=94.72 E-value=0.79 Score=43.97 Aligned_cols=113 Identities=11% Similarity=0.002 Sum_probs=73.6
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEcC-CcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHH
Q 018152 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDRN-LKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKL 217 (360)
Q Consensus 139 ~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~~-g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~ 217 (360)
....+++.||+||||++.....|+-++.-... +....-...- ++|-.-..|.+.|...
T Consensus 95 ~~~e~~~FFDiETTGL~~ag~~I~~~g~a~~~~~~~~Vrq~~l---------------------p~p~~E~avle~fl~~ 153 (278)
T COG3359 95 YEAEDVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVRQHFL---------------------PAPEEEVAVLENFLHD 153 (278)
T ss_pred ccccceEEEeeeccccCCCCCeEEEEEEEEccCceEEEEeecC---------------------CCcchhhHHHHHHhcC
Confidence 45678999999999999744445555555553 3322222222 2221122366777777
Q ss_pred hhCCCEEEEEc-chhhHHHHcc---cCC-----C-ccchHHHhhHhCC--CCCCCHHHHHHHHhCCccC
Q 018152 218 LSNGTILVGHS-LNNDLEVLKL---DHP-----R-VIDTSLIFKYVDE--YRRPSLYNLCKSVLGYEIR 274 (360)
Q Consensus 218 l~~g~iLVGHn-l~fDl~~L~~---~~~-----~-viDT~~l~~~~~~--~~~~sL~~L~~~~Lg~~iq 274 (360)
. ..+.||-.| ..||.-|++. .+. . =+|.....|++.+ ..+-+|+..- +.||+.-.
T Consensus 154 ~-~~~~lvsfNGkaFD~PfikR~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VE-r~LGi~R~ 220 (278)
T COG3359 154 P-DFNMLVSFNGKAFDIPFIKRMVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVE-RILGIRRE 220 (278)
T ss_pred C-CcceEEEecCcccCcHHHHHHHhcccccCccccchhhhhhhhhhhhccCCCCChhhHH-HHhCcccc
Confidence 7 677888886 8999999993 211 1 2777777777665 6788999987 48898744
No 93
>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=94.08 E-value=0.19 Score=48.43 Aligned_cols=87 Identities=16% Similarity=0.229 Sum_probs=55.9
Q ss_pred CCCcEEEEEEeccCCC-----CCcccEEEEEEE-EcC-----CcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHH
Q 018152 140 TSNIMYAVDCEMVLCE-----DGSEGLVRLCVV-DRN-----LKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLA 208 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~-----~g~~~I~~VsvV-d~~-----g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~ 208 (360)
.+.++++||+||..-. +..++|..|+++ ... ....+-.+..+.. +.+ ...+.-.+ +-.
T Consensus 155 p~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~~-~~~---------~~~v~~~~-~E~ 223 (325)
T PF03104_consen 155 PPLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCDS-IED---------NVEVIYFD-SEK 223 (325)
T ss_dssp GGSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSCC-TTC---------TTEEEEES-SHH
T ss_pred cccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCCC-CCC---------CcEEEEEC-CHH
Confidence 3568999999999765 345689999974 222 2222333333332 221 23333344 778
Q ss_pred HHHHHHHHHhhC--CCEEEEEcch-hhHHHHc
Q 018152 209 EIQKRMKKLLSN--GTILVGHSLN-NDLEVLK 237 (360)
Q Consensus 209 eV~~~l~~~l~~--g~iLVGHnl~-fDl~~L~ 237 (360)
+++..|.+++.. -.|++|||+. ||+.+|-
T Consensus 224 ~lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~ 255 (325)
T PF03104_consen 224 ELLEAFLDIIQEYDPDIITGYNIDGFDLPYLI 255 (325)
T ss_dssp HHHHHHHHHHHHHS-SEEEESSTTTTHHHHHH
T ss_pred HHHHHHHHHHHhcCCcEEEEecccCCCHHHHH
Confidence 888888888753 3599999975 8998874
No 94
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.84 E-value=0.35 Score=54.24 Aligned_cols=94 Identities=19% Similarity=0.173 Sum_probs=66.2
Q ss_pred CHHHHHHHHHHHhhC-CCEEEEEcchhhHHHHcccC----CCccchHHHhhHhCCCCCCCHHHHHHHHhCCccCC-----
Q 018152 206 SLAEIQKRMKKLLSN-GTILVGHSLNNDLEVLKLDH----PRVIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK----- 275 (360)
Q Consensus 206 ~l~eV~~~l~~~l~~-g~iLVGHnl~fDl~~L~~~~----~~viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~----- 275 (360)
....+...|..++.. +...||||+.||+.+|.... ..+.||...+..+.+..+.+|+.|+.+|++.....
T Consensus 362 ~~~~~~~~l~~~l~~~~~~~v~~n~K~d~~~l~~~gi~~~~~~~Dt~la~yll~~~~~~~l~~la~~yl~~~~~~~~~~~ 441 (887)
T TIGR00593 362 LTILTDDKFARWLLNEQIKKIGHDAKFLMHLLKREGIELGGVIFDTMLAAYLLDPAQVSTLDTLARRYLVEELILDEKIG 441 (887)
T ss_pred hhHHHHHHHHHHHhCCCCcEEEeeHHHHHHHHHhCCCCCCCcchhHHHHHHHcCCCCCCCHHHHHHHHcCcccccHHHhc
Confidence 345667778887732 24589999999999997542 24689998887777745569999999998865211
Q ss_pred -CCCC----------CChHHHHHHHHHHHHHHHHh
Q 018152 276 -KGTP----------HNCLDDASAAMKLVLAIIER 299 (360)
Q Consensus 276 -~~~~----------H~AleDA~at~eL~~~~l~~ 299 (360)
.+.. .-|..||.+++.||..+...
T Consensus 442 ~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~ 476 (887)
T TIGR00593 442 GKLAKFAFPPLEEATEYLARRAAATKRLAEELLKE 476 (887)
T ss_pred cCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 0000 13667899999999876543
No 95
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.57 E-value=2.1 Score=49.66 Aligned_cols=104 Identities=17% Similarity=0.210 Sum_probs=73.0
Q ss_pred ccCCCCHHhhcCCCCCHHHHHHHHHHHhh--CCCEEEEEcc-hhhHHHHccc----------------------------
Q 018152 191 EITGLTADDLVGVTCSLAEIQKRMKKLLS--NGTILVGHSL-NNDLEVLKLD---------------------------- 239 (360)
Q Consensus 191 ~i~GIT~e~L~~ap~~l~eV~~~l~~~l~--~g~iLVGHnl-~fDl~~L~~~---------------------------- 239 (360)
..-|+.+..|..-. +-.+.+..+++++. .-.+++|||+ .||+.+|-.-
T Consensus 569 ~~~~~~~~~L~~~~-sEr~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~ 647 (1172)
T TIGR00592 569 EFPGKKPSLVEDLA-TERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGER 647 (1172)
T ss_pred hhhccCCcEEEEec-CHHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccce
Confidence 44566666677766 77888888888885 5689999996 6688876331
Q ss_pred -CCC-ccchHHHhhHhCCCCCCCHHHHHHHHhCCccCC-----------C-----CCCCChHHHHHHHHHHHHH
Q 018152 240 -HPR-VIDTSLIFKYVDEYRRPSLYNLCKSVLGYEIRK-----------K-----GTPHNCLDDASAAMKLVLA 295 (360)
Q Consensus 240 -~~~-viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~iq~-----------~-----~~~H~AleDA~at~eL~~~ 295 (360)
..| ++|+...++......+++|..+|+.+||.+-.. . .-.+.++.||..+++|+.+
T Consensus 648 ~~Grl~~D~~~~~k~~~~~~sy~L~~v~~~~L~~~k~~~~~~~i~~~~~~~~~~~~~~~y~~~Da~l~~~L~~~ 721 (1172)
T TIGR00592 648 TCGRMICDVEISAKELIRCKSYDLSELVQQILKTERKVIPIDNINNMYSESSSLTYLLEHTWKDAMFILQIMCE 721 (1172)
T ss_pred ECCEEEEEHHHHHHHHhCcCCCCHHHHHHHHhCCCCcccCHHHHHHHHhCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 112 578888887776678999999999999853221 0 0013456788888887754
No 96
>PHA02570 dexA exonuclease; Provisional
Probab=89.79 E-value=1.7 Score=41.04 Aligned_cols=93 Identities=17% Similarity=0.129 Sum_probs=56.3
Q ss_pred EEEEEeccCCCCCcccEEEEEEEEc--C-C-cEEEEEeecCCC------------ccccccc--ccCCCCHHh---hcC-
Q 018152 145 YAVDCEMVLCEDGSEGLVRLCVVDR--N-L-KVTIDELVKPEK------------AVADYRS--EITGLTADD---LVG- 202 (360)
Q Consensus 145 ValD~Ettgl~~g~~~I~~VsvVd~--~-g-~~~~d~lV~P~~------------~I~d~~t--~i~GIT~e~---L~~- 202 (360)
+.||+||.|..+.- .|+.|++|-. + | ...|..+|..+. .+++..| .+-.-++|- |.+
T Consensus 4 lMIDlETmG~~p~A-aIisIgAV~Fdp~~~~g~tF~elV~~~~~~k~d~~sq~g~~~~d~~TI~WW~kQS~EAR~~L~~s 82 (220)
T PHA02570 4 FIIDFETFGNTPDG-AVIDLAVIAFEHDPHNPPTFEELVSRGRRIKFDLKSQKGKRLFDKSTIEWWKNQSPEARKNLKPS 82 (220)
T ss_pred EEEEeeccCCCCCc-eEEEEEEEEecCCCCccccHHHHhhcccccccchhhccCCCccCchHHHHHHhCCHHHHHhccCC
Confidence 67999999998753 6999999943 2 1 123455554221 1222111 222222221 211
Q ss_pred -CCCCHHHHHHHHHHHhhCCC------EEEEEcchhhHHHHcc
Q 018152 203 -VTCSLAEIQKRMKKLLSNGT------ILVGHSLNNDLEVLKL 238 (360)
Q Consensus 203 -ap~~l~eV~~~l~~~l~~g~------iLVGHnl~fDl~~L~~ 238 (360)
..+++.+++.+|.+||.... .+=|-+.+||...|+.
T Consensus 83 ~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~~ 125 (220)
T PHA02570 83 DEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILVD 125 (220)
T ss_pred CccccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHHH
Confidence 12479999999999996433 4667789999999854
No 97
>PHA02528 43 DNA polymerase; Provisional
Probab=89.65 E-value=1.8 Score=48.64 Aligned_cols=153 Identities=10% Similarity=-0.030 Sum_probs=89.1
Q ss_pred CCcEEEEEEeccCCC----CC--cccEEEEEEEEcCCcEEEEEeecCCCc---ccccccccCCCCHHhhcCCCCCHHHHH
Q 018152 141 SNIMYAVDCEMVLCE----DG--SEGLVRLCVVDRNLKVTIDELVKPEKA---VADYRSEITGLTADDLVGVTCSLAEIQ 211 (360)
Q Consensus 141 ~~~~ValD~Ettgl~----~g--~~~I~~VsvVd~~g~~~~d~lV~P~~~---I~d~~t~i~GIT~e~L~~ap~~l~eV~ 211 (360)
.-++++||+||+.-+ +. .+.|+.|++.+..+..++-..+....+ ..+.... .-...-.+.... +-.+.+
T Consensus 105 ~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~-~~~~~v~~~~~~-sE~eLL 182 (881)
T PHA02528 105 KIRIANLDIEVTAEDGFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQ-EILDKVVYMPFD-TEREML 182 (881)
T ss_pred CccEEEEEEEECCCCCCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccc-cccCCeeEEEcC-CHHHHH
Confidence 468999999997521 22 457999999877665322222211000 0000000 000001111134 778899
Q ss_pred HHHHHHhhC--CCEEEEEcc-hhhHHHHccc---C---------C-------------------------C-ccchHHHh
Q 018152 212 KRMKKLLSN--GTILVGHSL-NNDLEVLKLD---H---------P-------------------------R-VIDTSLIF 250 (360)
Q Consensus 212 ~~l~~~l~~--g~iLVGHnl-~fDl~~L~~~---~---------~-------------------------~-viDT~~l~ 250 (360)
.+|.+++.. -.|++|||+ .||+.+|..- . . + ++|...++
T Consensus 183 ~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD~~dl~ 262 (881)
T PHA02528 183 LEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILDYLDLY 262 (881)
T ss_pred HHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEeHHHHH
Confidence 999999842 269999995 6799876321 0 0 1 24555566
Q ss_pred hHhC--CCCCCCHHHHHHHHhCCccCCC-C-------------CCCChHHHHHHHHHHHHH
Q 018152 251 KYVD--EYRRPSLYNLCKSVLGYEIRKK-G-------------TPHNCLDDASAAMKLVLA 295 (360)
Q Consensus 251 ~~~~--~~~~~sL~~L~~~~Lg~~iq~~-~-------------~~H~AleDA~at~eL~~~ 295 (360)
+... ...++||++.|+.+||..-..- . -.+-++.||..+.+|+.+
T Consensus 263 k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 263 KKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 6532 2578999999998999753210 0 013346899999999976
No 98
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=86.29 E-value=11 Score=41.82 Aligned_cols=122 Identities=18% Similarity=0.116 Sum_probs=76.7
Q ss_pred CCCCcEEEEEEeccCCCC-----CcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHH
Q 018152 139 MTSNIMYAVDCEMVLCED-----GSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKR 213 (360)
Q Consensus 139 ~~~~~~ValD~Ettgl~~-----g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~ 213 (360)
..+.++++||+|+..... ..+.+..|+.....+.... ..+ ..+...|.. +.... +-.+++..
T Consensus 151 ~p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~---~~~------~~~~~~~~~---v~~~~-~e~e~l~~ 217 (792)
T COG0417 151 RPPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI---EVF------IYTSGEGFS---VEVVI-SEAELLER 217 (792)
T ss_pred CCCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc---ccc------cccCCCCce---eEEec-CHHHHHHH
Confidence 356789999999998642 2345777777765322111 111 111111111 33343 66678888
Q ss_pred HHHHhh--CCCEEEEEcch-hhHHHHccc-------C--------------------CC-ccchHHHhhH-hCCCCCCCH
Q 018152 214 MKKLLS--NGTILVGHSLN-NDLEVLKLD-------H--------------------PR-VIDTSLIFKY-VDEYRRPSL 261 (360)
Q Consensus 214 l~~~l~--~g~iLVGHnl~-fDl~~L~~~-------~--------------------~~-viDT~~l~~~-~~~~~~~sL 261 (360)
|..++. ...|+||||.. ||+.+|..- . .+ .+|....++. ......++|
T Consensus 218 ~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~~~~~~~~ysl 297 (792)
T COG0417 218 FVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRRRPLNLKSYSL 297 (792)
T ss_pred HHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhhhhcccccccH
Confidence 887774 34699999987 899988642 0 12 4777777773 444789999
Q ss_pred HHHHHHHhCCcc
Q 018152 262 YNLCKSVLGYEI 273 (360)
Q Consensus 262 ~~L~~~~Lg~~i 273 (360)
...+..+++..-
T Consensus 298 ~~v~~~~l~~~k 309 (792)
T COG0417 298 EAVSEALLGEGK 309 (792)
T ss_pred HHHHHHhccccc
Confidence 999988887654
No 99
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=80.31 E-value=9.2 Score=36.21 Aligned_cols=105 Identities=17% Similarity=0.243 Sum_probs=76.5
Q ss_pred ccCCCCHHhhcCCCCCHHHHHHHHH---HHhhCCCEEEEEcchhhHHHHccc--------------------CCCccchH
Q 018152 191 EITGLTADDLVGVTCSLAEIQKRMK---KLLSNGTILVGHSLNNDLEVLKLD--------------------HPRVIDTS 247 (360)
Q Consensus 191 ~i~GIT~e~L~~ap~~l~eV~~~l~---~~l~~g~iLVGHnl~fDl~~L~~~--------------------~~~viDT~ 247 (360)
+-+||.-+-....++...+-.+.+. -.++++-..|-.+...|+..|=.. .|.+-|+-
T Consensus 109 r~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~fp~vYDiK 188 (239)
T KOG0304|consen 109 RRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLPETEEEFFEIVRQLFPFVYDVK 188 (239)
T ss_pred HHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCcchHHHHHHHHHHHcchhhhHH
Confidence 5689988888777765554444433 344456778888889999876431 24567887
Q ss_pred HHhhHhCC-CCCCCHHHHHHHHhCCccCCCCCCCChHHHHHHHHHHHHHHHH
Q 018152 248 LIFKYVDE-YRRPSLYNLCKSVLGYEIRKKGTPHNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 248 ~l~~~~~~-~~~~sL~~L~~~~Lg~~iq~~~~~H~AleDA~at~eL~~~~l~ 298 (360)
.+++...+ ..+.+|..+| ..|+++-. |..|.|=.|+..|+..|.++.+
T Consensus 189 ~l~~~c~~~~l~~GL~~lA-~~L~~~Rv--G~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 189 YLMKFCEGLSLKGGLQRLA-DLLGLKRV--GIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred HHHHhhhhhhhhcCHHHHH-HHhCCCee--ecccccCcHHHHHHHHHHHHHh
Confidence 77776655 5678999999 77787753 4699999999999999987654
No 100
>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=77.35 E-value=7.7 Score=33.19 Aligned_cols=59 Identities=24% Similarity=0.218 Sum_probs=42.6
Q ss_pred HHHHhh-CCCEEEEEcchhhHHHHccc---CC-CccchHHHhhHhCCCCC-CCHHHHHHHHhCCc
Q 018152 214 MKKLLS-NGTILVGHSLNNDLEVLKLD---HP-RVIDTSLIFKYVDEYRR-PSLYNLCKSVLGYE 272 (360)
Q Consensus 214 l~~~l~-~g~iLVGHnl~fDl~~L~~~---~~-~viDT~~l~~~~~~~~~-~sL~~L~~~~Lg~~ 272 (360)
|.+++. .+...+|||+.+++.+|+.. .. .+.||...+--+.|.++ .+|+.|+++||+..
T Consensus 45 l~~~l~~~~~~ki~~d~K~~~~~l~~~gi~l~~~~fD~~LAaYLL~p~~~~~~l~~la~~yl~~~ 109 (151)
T cd06128 45 LKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAYLLDPVAGRHDMDSLAERWLKEK 109 (151)
T ss_pred HHHHHcCCCCCEEeeehHHHHHHHHHCCCCCCCcchhHHHHHHHcCCCCCCCCHHHHHHHHcCCC
Confidence 445552 23458999999999999643 22 35799977777777332 49999999998877
No 101
>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=76.78 E-value=31 Score=35.74 Aligned_cols=84 Identities=14% Similarity=0.100 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHhh--CCCEEEEEcchhhHHHHccc---CC-----------CccchHHHhhHh--CCCCCCCHHHHHHHH
Q 018152 207 LAEIQKRMKKLLS--NGTILVGHSLNNDLEVLKLD---HP-----------RVIDTSLIFKYV--DEYRRPSLYNLCKSV 268 (360)
Q Consensus 207 l~eV~~~l~~~l~--~g~iLVGHnl~fDl~~L~~~---~~-----------~viDT~~l~~~~--~~~~~~sL~~L~~~~ 268 (360)
-.+++.+|++++. ++..++-+| .+...+|+.- ++ +.+|.-.+.+.. .|..++|||.++ .+
T Consensus 328 E~~~~~~f~~~l~~~~~~~i~hY~-~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~-~~ 405 (457)
T TIGR03491 328 EELAWQQFLQLLQSYPDAPIYHYG-ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIA-RW 405 (457)
T ss_pred HHHHHHHHHHHHHHCCCCeEEeeC-HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHH-HH
Confidence 3456667777664 445677777 7888887753 11 346666554432 236789999999 77
Q ss_pred hCCccCCCCCCCChHHHHHHHHHHHHHHHH
Q 018152 269 LGYEIRKKGTPHNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 269 Lg~~iq~~~~~H~AleDA~at~eL~~~~l~ 298 (360)
+|.+.. +...|.-.++..|..++.
T Consensus 406 lg~~~~------~~~~~G~~ai~~y~~~~~ 429 (457)
T TIGR03491 406 LGFEWR------QKEASGAKSLLWYRQWKK 429 (457)
T ss_pred hCcccC------CCCCCHHHHHHHHHHHHH
Confidence 788754 223444566777776654
No 102
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=73.51 E-value=48 Score=39.54 Aligned_cols=153 Identities=18% Similarity=0.197 Sum_probs=88.5
Q ss_pred CCcEEEEEEeccCCC-----CCcccEEEEEEE-EcCCcEEEEE-eecCCCccccc--cc--ccCCCCHHhhcCCCCCHHH
Q 018152 141 SNIMYAVDCEMVLCE-----DGSEGLVRLCVV-DRNLKVTIDE-LVKPEKAVADY--RS--EITGLTADDLVGVTCSLAE 209 (360)
Q Consensus 141 ~~~~ValD~Ettgl~-----~g~~~I~~VsvV-d~~g~~~~d~-lV~P~~~I~d~--~t--~i~GIT~e~L~~ap~~l~e 209 (360)
..++.|||+|||-+. ...+.|.-|+.. |+.|--+.+. .|- ..|.|+ .- ++-|- =.+-+.+ .-..
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISYMiDGqGfLItNREiVs--~DIedfEYTPKpE~eG~--F~v~Ne~-dEv~ 319 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISYMIDGQGFLITNREIVS--EDIEDFEYTPKPEYEGP--FCVFNEP-DEVG 319 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEEEecCceEEEechhhhc--cchhhcccCCccccccc--eEEecCC-cHHH
Confidence 458999999999874 334578888764 6666433221 111 111111 00 00000 0012344 5556
Q ss_pred HHHHHHHHhh--CCCEEEEEc-chhhHHHHccc---CC--------Cccc-----------hHHHhhHhC-----CCCCC
Q 018152 210 IQKRMKKLLS--NGTILVGHS-LNNDLEVLKLD---HP--------RVID-----------TSLIFKYVD-----EYRRP 259 (360)
Q Consensus 210 V~~~l~~~l~--~g~iLVGHn-l~fDl~~L~~~---~~--------~viD-----------T~~l~~~~~-----~~~~~ 259 (360)
+.+++.+-+. +-.|+|-+| --||.-|+... |. -..| -+.-|++.. |..+.
T Consensus 320 Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDSYLPqGSq 399 (2173)
T KOG1798|consen 320 LLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDSYLPQGSQ 399 (2173)
T ss_pred HHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcccCCCccc
Confidence 6666666553 446888887 45699998652 11 0122 122344432 25788
Q ss_pred CHHHHHHHHhCCccCC--------------CCCCCChHHHHHHHHHHHHHHHH
Q 018152 260 SLYNLCKSVLGYEIRK--------------KGTPHNCLDDASAAMKLVLAIIE 298 (360)
Q Consensus 260 sL~~L~~~~Lg~~iq~--------------~~~~H~AleDA~at~eL~~~~l~ 298 (360)
+|++.++.-||.+--+ ...+--|+.||.||.-||.++..
T Consensus 400 gLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVh 452 (2173)
T KOG1798|consen 400 GLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVH 452 (2173)
T ss_pred chhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhh
Confidence 9999999999975321 01245678999999999998884
No 103
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=72.21 E-value=3 Score=46.13 Aligned_cols=34 Identities=21% Similarity=0.328 Sum_probs=26.2
Q ss_pred hCCCEEEEEcchhhHHHHcccC------CCccchHHHhhH
Q 018152 219 SNGTILVGHSLNNDLEVLKLDH------PRVIDTSLIFKY 252 (360)
Q Consensus 219 ~~g~iLVGHnl~fDl~~L~~~~------~~viDT~~l~~~ 252 (360)
+++.++||||+.||..-++.+. -+++||+.|.-.
T Consensus 239 ~ke~liVGHNVsfDRaRirEeY~i~~Sk~rFlDTMSlHia 278 (1075)
T KOG3657|consen 239 GKEQLIVGHNVSFDRARIREEYNINGSKIRFLDTMSLHIA 278 (1075)
T ss_pred CCCceEEeccccchHHHHHHHHhccccceeeeechhhhhh
Confidence 3789999999999999888652 247999765433
No 104
>PRK05761 DNA polymerase I; Reviewed
Probab=70.92 E-value=33 Score=38.27 Aligned_cols=88 Identities=22% Similarity=0.195 Sum_probs=59.3
Q ss_pred CHHHHHHHHHHHhhCCCEEEEEcc-hhhHHHHcccC----------CC------c-cchHHHhhHh-------CC---CC
Q 018152 206 SLAEIQKRMKKLLSNGTILVGHSL-NNDLEVLKLDH----------PR------V-IDTSLIFKYV-------DE---YR 257 (360)
Q Consensus 206 ~l~eV~~~l~~~l~~g~iLVGHnl-~fDl~~L~~~~----------~~------v-iDT~~l~~~~-------~~---~~ 257 (360)
+-.+++.+|.+++..-.+.|++|. +||+..|..-. ++ . +|....+... .+ .+
T Consensus 209 ~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~~ 288 (787)
T PRK05761 209 SEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRHR 288 (787)
T ss_pred CHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeecc
Confidence 788999999999988788888985 58998875420 01 1 5554444321 01 23
Q ss_pred CCCHHHHHHHHhCCccCC-------C---CCCCChHHHHHHHHHHH
Q 018152 258 RPSLYNLCKSVLGYEIRK-------K---GTPHNCLDDASAAMKLV 293 (360)
Q Consensus 258 ~~sL~~L~~~~Lg~~iq~-------~---~~~H~AleDA~at~eL~ 293 (360)
.++|+..++.+||..-.. . .-+.-++.||..+++|.
T Consensus 289 ~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 289 EARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred cCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 789999999999975210 0 01234689999999984
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=68.53 E-value=6.5 Score=40.65 Aligned_cols=138 Identities=22% Similarity=0.282 Sum_probs=77.2
Q ss_pred CCCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCC--cccccccccCCCCHHhhcCCCCCHHHHHHHHHH
Q 018152 139 MTSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEK--AVADYRSEITGLTADDLVGVTCSLAEIQKRMKK 216 (360)
Q Consensus 139 ~~~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~--~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~ 216 (360)
..+..-.+||+|-.-.+ -+++++...+...-+|.|=+|.. ...+..---|||--.||.++. + -+...+.+
T Consensus 369 Ldp~~ttWiDIEG~p~D-----PVElAiyQP~sg~YiHcyR~P~D~K~FK~~SKysHGillkDl~~aq-P--GL~S~vi~ 440 (533)
T PF00843_consen 369 LDPNATTWIDIEGPPND-----PVELAIYQPSSGNYIHCYREPHDEKQFKNQSKYSHGILLKDLENAQ-P--GLTSAVIE 440 (533)
T ss_dssp S-TTS-EEEEEESETTS-----ESEEEEEETTTTEEEEEE---S-HHHHHHHHHHTT-B-GGGCTTB--T--THHHHHHH
T ss_pred CCCCCCeeEecCCCCCC-----CeEEEEeccCCCcEEEEecCCcchhhhcccccccccccHHHHhhhc-c--chHHHHHH
Confidence 34566788999976443 47799998755457899999965 445556667999999999886 3 57788899
Q ss_pred HhhCCCEEEEEcchhhHHHHcccCCC----ccchHH------HhhHhCCCCCCCHHHHHHHHhCCccCCC--C------C
Q 018152 217 LLSNGTILVGHSLNNDLEVLKLDHPR----VIDTSL------IFKYVDEYRRPSLYNLCKSVLGYEIRKK--G------T 278 (360)
Q Consensus 217 ~l~~g~iLVGHnl~fDl~~L~~~~~~----viDT~~------l~~~~~~~~~~sL~~L~~~~Lg~~iq~~--~------~ 278 (360)
.++.+-||-..+.. |++-|=..|.| +||... .|.. .-.-..+.||+.+-|+-+... | .
T Consensus 441 ~LP~~MVlT~QGsD-DIrkLld~hGRrDiKlvDV~lt~eqaR~FEd---~VWd~f~~LC~~H~GvVv~KKKkg~~~~~t~ 516 (533)
T PF00843_consen 441 LLPKNMVLTCQGSD-DIRKLLDMHGRRDIKLVDVKLTSEQARKFED---QVWDRFGHLCKKHTGVVVKKKKKGKKPESTN 516 (533)
T ss_dssp HS-TT-EEEESSHH-HHHHHHHCTT-TTSEEEE----HHHHTTTHH---HHHHHHGGG---B-S-EEE--SSSS-EEE--
T ss_pred hCCcCcEEEeeChH-HHHHHHHhcCCCcceEEEeecCHHHHHHHHH---HHHHHHHHHHHhcCceEEecccCCCCCCCCC
Confidence 99888888887765 55554444443 788753 2222 123345678988888866531 1 3
Q ss_pred CCChHHHHHH
Q 018152 279 PHNCLDDASA 288 (360)
Q Consensus 279 ~H~AleDA~a 288 (360)
+|.|+-|+..
T Consensus 517 PHCALlDCiM 526 (533)
T PF00843_consen 517 PHCALLDCIM 526 (533)
T ss_dssp ---HHHHHHH
T ss_pred chHHHHHHHH
Confidence 7999999864
No 106
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=66.39 E-value=0.32 Score=46.92 Aligned_cols=48 Identities=27% Similarity=0.239 Sum_probs=37.3
Q ss_pred cCCCCchhhHhhhhccccCCCCCCCCcCchHHHHHHhhccCcchhhHHHHHHHHHhhhHHH
Q 018152 26 EGTAGGWKDFLTSYDKKFGSSLSDPARRSKDALSSFLKTFTKEDDLKFIAKVVQSHLNRDL 86 (360)
Q Consensus 26 ~~~~~~~k~~l~~~~~~~~~~~~d~~~~~~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (360)
++..+++||.|.+++..++ |. ..+..||+|++.....+ .. |+++|+.+
T Consensus 247 ~~~~~~~~Y~L~~~V~~i~----~~--~~~~HlVs~vrv~~~~~--~~-----W~lFNDfl 294 (295)
T PF13423_consen 247 EGESGIFKYELRSMVCHIG----DS--IESGHLVSLVRVGPSDD--SQ-----WYLFNDFL 294 (295)
T ss_pred cCCCCceEEEEEEEEEEec----CC--CCCCceEEEEEcCCCCC--Cc-----EEEECcEe
Confidence 4899999999999999999 43 34667999999886322 23 89998764
No 107
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=61.92 E-value=32 Score=36.39 Aligned_cols=147 Identities=14% Similarity=0.091 Sum_probs=85.5
Q ss_pred CcEEEEEEeccCCC-C----CcccEEEEEEEEcC-CcE---EEEEeecCCCcccccccccCCCCHHhhcC-----CCCCH
Q 018152 142 NIMYAVDCEMVLCE-D----GSEGLVRLCVVDRN-LKV---TIDELVKPEKAVADYRSEITGLTADDLVG-----VTCSL 207 (360)
Q Consensus 142 ~~~ValD~Ettgl~-~----g~~~I~~VsvVd~~-g~~---~~d~lV~P~~~I~d~~t~i~GIT~e~L~~-----ap~~l 207 (360)
-++..||+|.++-. | ...+|..|+.-|.. +.. +|+.+ +. ...+-....=...+.+.+ -+ +-
T Consensus 106 i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~~~~~~~~~~~~--~~--~~~~~~~~~~~~~~~~~~v~v~~f~-sE 180 (498)
T PHA02524 106 VVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHNGKKTYYIFDLV--KD--VGHWDPKKSVLEKYILDNVVYMPFE-DE 180 (498)
T ss_pred ceEEEEEEEecCCCCCChhhcCCceEEEEeeecccCCccEEEEecc--cc--ccCCCcccccccccccCCeEEEEeC-CH
Confidence 47999999997643 1 12268888887752 221 23333 11 111111110011111222 23 77
Q ss_pred HHHHHHHHHHhhC--CCEEEEEcc-hhhHHHHcc--------c-------C---------------------CC-ccchH
Q 018152 208 AEIQKRMKKLLSN--GTILVGHSL-NNDLEVLKL--------D-------H---------------------PR-VIDTS 247 (360)
Q Consensus 208 ~eV~~~l~~~l~~--g~iLVGHnl-~fDl~~L~~--------~-------~---------------------~~-viDT~ 247 (360)
.+.+.++.+++.. -.|++|||+ +||+..|.. . . .+ ++|..
T Consensus 181 ~eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl~ 260 (498)
T PHA02524 181 VDLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDYM 260 (498)
T ss_pred HHHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeEHH
Confidence 8999999999943 289999996 679866421 0 0 01 36777
Q ss_pred HHhhHh--CCCCCCCHHHHHHHHhCCccCCCC-------------CCCChHHHHHHHHHHH
Q 018152 248 LIFKYV--DEYRRPSLYNLCKSVLGYEIRKKG-------------TPHNCLDDASAAMKLV 293 (360)
Q Consensus 248 ~l~~~~--~~~~~~sL~~L~~~~Lg~~iq~~~-------------~~H~AleDA~at~eL~ 293 (360)
.++++. ....++||++.+..+||..--.-. -++-++.||..+..|.
T Consensus 261 ~l~kk~s~~~l~sYsL~~Vs~~~Lg~~K~d~~~~I~~l~~~d~~rla~YclkDa~L~~~L~ 321 (498)
T PHA02524 261 DVFKKFSFTPMPDYKLGNVGYREVKADKLDYEGPINKFRKADHQRYVDYCVRDTDIILLID 321 (498)
T ss_pred HHHHHhhhccCCCCCHHHHHHHhcCCccccchhhHHHHhcCchHHHHHHHHHHHHHHHHHH
Confidence 788764 337899999999888875432100 0122467899887776
No 108
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=42.99 E-value=30 Score=32.27 Aligned_cols=59 Identities=10% Similarity=0.173 Sum_probs=42.7
Q ss_pred EEEEEEEEc---CCcE-EEEEeecCCCccccccc-------ccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 161 LVRLCVVDR---NLKV-TIDELVKPEKAVADYRS-------EITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 161 I~~VsvVd~---~g~~-~~d~lV~P~~~I~d~~t-------~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
.++++++.. +|.. .|+++|+|+..+..++. .-|+|...-.+.....+..+..+|.+||.
T Consensus 10 PaEiai~~fSL~~GI~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~ 79 (213)
T PF13017_consen 10 PAEIAICKFSLKEGIIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLK 79 (213)
T ss_pred eEEEEEEEEecCCccchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhh
Confidence 577888875 4532 49999999965544432 44787766556565579999999999994
No 109
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=38.21 E-value=1.4e+02 Score=34.85 Aligned_cols=128 Identities=16% Similarity=0.190 Sum_probs=76.0
Q ss_pred CCCCcEEEEEEeccCCCC-CcccEEEEEEEEc--------CCc----EEEEEeecCCCccccccc------ccCCCCHHh
Q 018152 139 MTSNIMYAVDCEMVLCED-GSEGLVRLCVVDR--------NLK----VTIDELVKPEKAVADYRS------EITGLTADD 199 (360)
Q Consensus 139 ~~~~~~ValD~Ettgl~~-g~~~I~~VsvVd~--------~g~----~~~d~lV~P~~~I~d~~t------~i~GIT~e~ 199 (360)
+.+..+.+|-++|+--.. ...+|+.|++.-. .+. ..+..+++|...+-++-- ..++
T Consensus 526 ~Ppl~llsL~i~T~~N~k~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~~fP~g~~ela~~k~~~----- 600 (1429)
T KOG0970|consen 526 PPPLTLLSLNIRTSMNPKQNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGTSFPLGLKELAKQKLSK----- 600 (1429)
T ss_pred CCCeeEEEeeeeehhccccchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCCcCCchHHHHHHhccCc-----
Confidence 345567778888775432 2347888877642 111 247789999875555411 1112
Q ss_pred hcCCCCCHHHHHHHHHHHhh--CCCEEEEEc-chhhHHHH-------cc-----------cC-----------------C
Q 018152 200 LVGVTCSLAEIQKRMKKLLS--NGTILVGHS-LNNDLEVL-------KL-----------DH-----------------P 241 (360)
Q Consensus 200 L~~ap~~l~eV~~~l~~~l~--~g~iLVGHn-l~fDl~~L-------~~-----------~~-----------------~ 241 (360)
+.-.. +-...+..|+..+. .-.++|||| ..|+|.+| ++ .. .
T Consensus 601 v~~~~-sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aG 679 (1429)
T KOG0970|consen 601 VVLHN-SERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAG 679 (1429)
T ss_pred eEEec-CHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccc
Confidence 11111 34455666666553 347999999 77888887 11 10 1
Q ss_pred C-ccchHHHhhHhCCCCCCCHHHHHHHHhCCc
Q 018152 242 R-VIDTSLIFKYVDEYRRPSLYNLCKSVLGYE 272 (360)
Q Consensus 242 ~-viDT~~l~~~~~~~~~~sL~~L~~~~Lg~~ 272 (360)
| +-|+-...+.+.+.+.++|..|++..|+.+
T Consensus 680 Rl~CD~~~~a~~lik~~S~~LseL~q~~l~~e 711 (1429)
T KOG0970|consen 680 RLMCDLNLAARELIKAQSYSLSELSQQILKEE 711 (1429)
T ss_pred eEEeehHHHHHhhhccccccHHHHHHHHHhhh
Confidence 2 245533444444578999999999999883
No 110
>PHA02563 DNA polymerase; Provisional
Probab=33.18 E-value=51 Score=35.94 Aligned_cols=68 Identities=12% Similarity=0.059 Sum_probs=41.4
Q ss_pred CCCcEEEEEEeccCCCCCcccEEEEEEEEcCCcEEEEEeecCCCcccccccccCCCCHHhhcCCCCCHHHHHHHHHHHhh
Q 018152 140 TSNIMYAVDCEMVLCEDGSEGLVRLCVVDRNLKVTIDELVKPEKAVADYRSEITGLTADDLVGVTCSLAEIQKRMKKLLS 219 (360)
Q Consensus 140 ~~~~~ValD~Ettgl~~g~~~I~~VsvVd~~g~~~~d~lV~P~~~I~d~~t~i~GIT~e~L~~ap~~l~eV~~~l~~~l~ 219 (360)
.+..+++.|+||++.+.... ....+++++ . .+.+|.- .+..++|.+++.
T Consensus 10 ~~~~~~~~DfET~t~~~~~~-~~~~~~~d~--~-~~~s~~~---------------------------~~~~~~f~~~i~ 58 (630)
T PHA02563 10 KPRKILACDFETTTINKDCR-RWFWGEIDV--E-DFPSYYG---------------------------GNSFDEFLQWIE 58 (630)
T ss_pred ccceEEEEEEEecccCCcce-eeeeeEecc--c-eeceeec---------------------------cccHHHHHHHHh
Confidence 35689999999998865332 222333332 2 1222211 122346666663
Q ss_pred ------CCCEEEEEcchhhHHHHcc
Q 018152 220 ------NGTILVGHSLNNDLEVLKL 238 (360)
Q Consensus 220 ------~g~iLVGHnl~fDl~~L~~ 238 (360)
.+.++--||+.||..||-.
T Consensus 59 ~~~~k~~~~~vYfHN~~FD~~Fil~ 83 (630)
T PHA02563 59 DTTYKETECIIYFHNLKFDGSFILK 83 (630)
T ss_pred hccccccceEEEEecCCccHHHHHH
Confidence 3789999999999999865
No 111
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=28.34 E-value=34 Score=27.60 Aligned_cols=43 Identities=21% Similarity=0.448 Sum_probs=20.8
Q ss_pred cccCCCCchhhHhhhhccccCCCCCCCCcCchHHHHHHhhccCc
Q 018152 24 RMEGTAGGWKDFLTSYDKKFGSSLSDPARRSKDALSSFLKTFTK 67 (360)
Q Consensus 24 ~~~~~~~~~k~~l~~~~~~~~~~~~d~~~~~~~~l~~f~~~~~~ 67 (360)
.|.-+.+.|..|+|+|.+. +--.=||++-+.+-|..++..|..
T Consensus 19 eLsk~~~vyRvFiNgYar~-g~VifDe~kl~~e~lL~~le~~kp 61 (88)
T PF11491_consen 19 ELSKNEAVYRVFINGYARN-GFVIFDESKLSKEELLEMLEEFKP 61 (88)
T ss_dssp TTTTTTTB------TTSS---EEE--B-S-SHHHH---HHHTTT
T ss_pred Hhhcccceeeeeecccccc-eEEEECcccCCHHHHHHHHHhcCh
Confidence 3567789999999999885 444558888888888777777665
Done!