Query 010297
Match_columns 513
No_of_seqs 200 out of 1247
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 22:52:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010297.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010297hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2176 PolC DNA polymerase II 100.0 1.4E-37 3E-42 349.4 8.0 218 4-231 417-642 (1444)
2 PRK09146 DNA polymerase III su 100.0 1.6E-32 3.5E-37 271.0 23.0 176 3-184 42-230 (239)
3 TIGR00573 dnaq exonuclease, DN 100.0 4.3E-32 9.4E-37 263.1 22.6 194 5-219 4-205 (217)
4 PRK05711 DNA polymerase III su 100.0 5E-32 1.1E-36 267.9 22.7 168 6-180 2-175 (240)
5 PRK07942 DNA polymerase III su 100.0 7E-32 1.5E-36 264.8 22.6 174 3-182 1-181 (232)
6 TIGR01406 dnaQ_proteo DNA poly 100.0 1.1E-31 2.4E-36 262.7 22.3 165 9-180 1-171 (225)
7 PRK06807 DNA polymerase III su 100.0 1.9E-31 4.2E-36 272.8 24.0 172 1-181 1-172 (313)
8 PRK07748 sporulation inhibitor 100.0 1.3E-31 2.9E-36 257.7 21.1 172 6-181 2-180 (207)
9 smart00479 EXOIII exonuclease 100.0 4.7E-31 1E-35 239.9 23.5 166 9-182 1-168 (169)
10 cd06131 DNA_pol_III_epsilon_Ec 100.0 2.7E-31 6E-36 244.3 22.0 161 10-177 1-166 (167)
11 PRK08517 DNA polymerase III su 100.0 2.9E-31 6.2E-36 264.9 23.2 168 4-182 64-232 (257)
12 cd06130 DNA_pol_III_epsilon_li 100.0 2.5E-31 5.3E-36 240.6 20.3 155 10-175 1-155 (156)
13 PRK06195 DNA polymerase III su 100.0 3.9E-31 8.4E-36 269.4 22.8 166 8-183 1-166 (309)
14 PRK07740 hypothetical protein; 100.0 4.6E-31 1E-35 261.1 22.2 172 5-183 56-228 (244)
15 PRK06310 DNA polymerase III su 100.0 7.1E-31 1.5E-35 260.6 23.3 167 6-181 5-174 (250)
16 PRK06063 DNA polymerase III su 100.0 4E-31 8.7E-36 270.3 21.8 168 7-184 14-182 (313)
17 TIGR01405 polC_Gram_pos DNA po 100.0 2.3E-31 5E-36 309.4 20.7 216 6-231 188-411 (1213)
18 PRK09145 DNA polymerase III su 100.0 2.4E-30 5.3E-35 247.6 22.6 167 6-179 27-199 (202)
19 TIGR01298 RNaseT ribonuclease 100.0 3.6E-30 7.8E-35 247.4 22.2 174 4-184 4-195 (200)
20 PRK06309 DNA polymerase III su 100.0 3.3E-30 7.1E-35 252.7 21.9 163 8-181 2-166 (232)
21 cd06136 TREX1_2 DEDDh 3'-5' ex 100.0 1.1E-30 2.3E-35 246.0 17.5 158 10-176 1-176 (177)
22 PRK07247 DNA polymerase III su 100.0 3.7E-30 7.9E-35 247.4 21.3 162 8-181 5-169 (195)
23 PRK07883 hypothetical protein; 100.0 4.3E-30 9.3E-35 280.4 24.2 186 3-197 10-197 (557)
24 PRK05168 ribonuclease T; Provi 100.0 6.4E-30 1.4E-34 247.6 22.7 173 4-183 13-203 (211)
25 PRK06722 exonuclease; Provisio 100.0 1E-29 2.2E-34 256.7 22.2 170 6-179 3-179 (281)
26 cd06134 RNaseT DEDDh 3'-5' exo 100.0 1.6E-29 3.5E-34 240.6 21.0 167 7-180 4-188 (189)
27 cd06133 ERI-1_3'hExo_like DEDD 100.0 2.2E-29 4.7E-34 231.7 20.0 166 10-177 1-175 (176)
28 PRK07246 bifunctional ATP-depe 100.0 6.6E-29 1.4E-33 281.4 23.7 169 3-182 2-171 (820)
29 cd06138 ExoI_N N-terminal DEDD 100.0 6.2E-29 1.3E-33 234.8 18.4 160 11-174 1-182 (183)
30 PRK08074 bifunctional ATP-depe 100.0 1.8E-28 3.9E-33 281.1 24.1 168 7-182 2-170 (928)
31 cd06127 DEDDh DEDDh 3'-5' exon 100.0 3.9E-28 8.4E-33 215.1 18.1 157 11-175 1-159 (159)
32 TIGR01407 dinG_rel DnaQ family 100.0 6.3E-28 1.4E-32 274.3 23.6 165 9-182 1-166 (850)
33 PRK05601 DNA polymerase III su 100.0 1.1E-27 2.3E-32 248.7 22.2 164 5-177 43-245 (377)
34 PRK07983 exodeoxyribonuclease 100.0 2.8E-27 6E-32 231.2 21.0 147 10-181 2-154 (219)
35 PRK00448 polC DNA polymerase I 100.0 4.4E-28 9.5E-33 285.3 16.2 217 5-231 416-640 (1437)
36 cd06137 DEDDh_RNase DEDDh 3'-5 100.0 4E-28 8.6E-33 225.2 12.0 144 11-174 1-160 (161)
37 COG0847 DnaQ DNA polymerase II 99.9 2.9E-26 6.2E-31 223.5 20.8 164 8-180 13-181 (243)
38 cd06149 ISG20 DEDDh 3'-5' exon 99.9 6E-27 1.3E-31 217.1 13.5 149 11-175 1-157 (157)
39 PRK05359 oligoribonuclease; Pr 99.9 2.8E-26 6.2E-31 217.8 18.3 162 7-184 2-178 (181)
40 cd06135 Orn DEDDh 3'-5' exonuc 99.9 1.3E-26 2.7E-31 217.8 15.6 156 10-180 1-171 (173)
41 cd06144 REX4_like DEDDh 3'-5' 99.9 8E-27 1.7E-31 214.4 13.4 148 11-175 1-152 (152)
42 PRK09182 DNA polymerase III su 99.9 6.6E-26 1.4E-30 230.4 20.5 160 7-180 36-200 (294)
43 PTZ00315 2'-phosphotransferase 99.9 9E-26 2E-30 245.2 22.7 171 8-180 56-254 (582)
44 cd06145 REX1_like DEDDh 3'-5' 99.9 2.5E-26 5.4E-31 211.4 14.1 143 11-175 1-150 (150)
45 PF00929 RNase_T: Exonuclease; 99.9 4E-28 8.7E-33 215.0 0.2 160 11-174 1-164 (164)
46 PRK11779 sbcB exonuclease I; P 99.9 1.1E-24 2.4E-29 233.9 21.4 174 5-180 3-197 (476)
47 KOG0542 Predicted exonuclease 99.7 1.7E-17 3.8E-22 164.0 12.2 170 8-180 56-241 (280)
48 COG5018 KapD Inhibitor of the 99.7 4.6E-17 1E-21 153.1 9.0 171 7-180 3-184 (210)
49 COG1949 Orn Oligoribonuclease 99.7 2.1E-16 4.6E-21 147.9 11.0 166 3-183 1-180 (184)
50 KOG3242 Oligoribonuclease (3'- 99.6 3E-15 6.4E-20 141.5 9.8 164 6-184 24-202 (208)
51 KOG2249 3'-5' exonuclease [Rep 99.5 6.8E-14 1.5E-18 139.6 12.8 156 9-181 106-266 (280)
52 cd05160 DEDDy_DNA_polB_exo DED 99.5 1.1E-12 2.3E-17 124.6 14.5 156 11-181 2-191 (199)
53 COG2925 SbcB Exonuclease I [DN 99.5 6.6E-13 1.4E-17 138.0 13.5 173 5-179 6-199 (475)
54 cd06143 PAN2_exo DEDDh 3'-5' e 99.4 1.1E-11 2.3E-16 118.1 14.3 152 8-175 5-174 (174)
55 cd06125 DnaQ_like_exo DnaQ-lik 99.1 6.1E-10 1.3E-14 95.7 11.6 79 11-133 1-83 (96)
56 cd05780 DNA_polB_Kod1_like_exo 98.9 3.2E-08 6.9E-13 94.9 14.5 127 9-161 4-159 (195)
57 PF13482 RNase_H_2: RNase_H su 98.9 4.1E-09 8.8E-14 96.8 7.8 115 11-158 1-116 (164)
58 KOG2248 3'-5' exonuclease [Rep 98.8 2.5E-08 5.4E-13 105.4 10.7 154 5-179 213-373 (380)
59 cd05781 DNA_polB_B3_exo DEDDy 98.8 1.7E-07 3.8E-12 89.9 14.6 116 8-157 3-144 (188)
60 COG3359 Predicted exonuclease 98.7 2.1E-07 4.5E-12 93.0 14.4 122 6-157 96-218 (278)
61 cd05779 DNA_polB_epsilon_exo D 98.7 5.6E-07 1.2E-11 87.8 15.4 145 8-158 2-169 (204)
62 cd06139 DNA_polA_I_Ecoli_like_ 98.6 1.5E-06 3.3E-11 80.9 16.6 144 6-183 3-172 (193)
63 cd05785 DNA_polB_like2_exo Unc 98.6 1.2E-06 2.5E-11 85.5 15.7 126 2-157 3-168 (207)
64 KOG4793 Three prime repair exo 98.6 1.1E-07 2.5E-12 95.7 7.0 177 4-184 9-221 (318)
65 PHA02570 dexA exonuclease; Pro 98.5 1.2E-06 2.5E-11 86.5 11.9 166 11-191 4-209 (220)
66 cd05777 DNA_polB_delta_exo DED 98.4 1.7E-05 3.7E-10 78.1 16.5 138 6-157 5-182 (230)
67 PRK05755 DNA polymerase I; Pro 98.3 6.5E-06 1.4E-10 95.5 14.8 135 7-183 314-471 (880)
68 cd05782 DNA_polB_like1_exo Unc 98.2 2.6E-05 5.6E-10 76.2 14.4 75 81-157 78-169 (208)
69 cd05783 DNA_polB_B1_exo DEDDy 98.2 3.8E-05 8.2E-10 74.9 14.5 161 8-180 5-193 (204)
70 PF10108 DNA_pol_B_exo2: Predi 98.1 7.9E-05 1.7E-09 73.4 14.9 127 25-179 7-171 (209)
71 cd05784 DNA_polB_II_exo DEDDy 98.1 9.2E-05 2E-09 71.7 13.9 124 9-158 4-154 (193)
72 PF04857 CAF1: CAF1 family rib 98.0 0.00011 2.3E-09 74.0 14.7 161 8-176 22-262 (262)
73 cd05778 DNA_polB_zeta_exo inac 98.0 0.00017 3.7E-09 71.5 15.2 172 8-183 4-225 (231)
74 PF01612 DNA_pol_A_exo1: 3'-5' 97.9 0.00064 1.4E-08 62.0 16.0 135 7-181 19-175 (176)
75 PF03104 DNA_pol_B_exo1: DNA p 97.8 0.00021 4.5E-09 72.1 12.2 131 7-150 156-325 (325)
76 PTZ00166 DNA polymerase delta 97.8 0.00037 8.1E-09 82.7 15.9 135 8-156 264-440 (1054)
77 smart00486 POLBc DNA polymeras 97.6 0.0013 2.7E-08 69.3 14.0 135 8-156 3-177 (471)
78 PRK05762 DNA polymerase II; Re 97.5 0.0018 3.9E-08 74.8 15.6 144 7-176 154-347 (786)
79 PHA02528 43 DNA polymerase; Pr 97.3 0.005 1.1E-07 72.0 16.1 163 7-176 105-323 (881)
80 cd05776 DNA_polB_alpha_exo ina 97.2 0.0025 5.5E-08 63.2 10.9 145 10-157 5-186 (234)
81 TIGR03491 RecB family nuclease 97.2 0.0039 8.5E-08 67.7 12.5 120 7-157 283-409 (457)
82 PHA02524 43A DNA polymerase su 96.6 0.01 2.2E-07 65.5 10.2 143 8-154 106-283 (498)
83 cd06146 mut-7_like_exo DEDDy 3 96.6 0.023 5E-07 54.7 11.2 143 5-178 19-192 (193)
84 KOG1275 PAB-dependent poly(A) 96.2 0.0044 9.6E-08 71.4 4.5 161 4-179 906-1090(1118)
85 cd06141 WRN_exo DEDDy 3'-5' ex 96.2 0.085 1.9E-06 48.8 12.3 129 7-178 17-169 (170)
86 KOG0304 mRNA deadenylase subun 96.0 0.096 2.1E-06 52.3 12.1 171 7-179 23-237 (239)
87 cd00007 35EXOc 3'-5' exonuclea 95.8 0.093 2E-06 46.3 10.4 66 82-155 40-107 (155)
88 cd06129 RNaseD_like DEDDy 3'-5 95.8 0.098 2.1E-06 48.6 10.8 129 7-178 12-160 (161)
89 COG0349 Rnd Ribonuclease D [Tr 95.6 0.15 3.1E-06 54.4 12.3 141 7-191 16-176 (361)
90 COG0417 PolB DNA polymerase el 95.3 0.2 4.2E-06 58.4 13.1 131 6-156 152-306 (792)
91 PRK10829 ribonuclease D; Provi 95.2 0.54 1.2E-05 50.3 15.2 137 5-186 19-175 (373)
92 TIGR00592 pol2 DNA polymerase 95.1 0.44 9.6E-06 57.9 15.8 143 9-154 505-678 (1172)
93 TIGR01388 rnd ribonuclease D. 94.6 1.4 3.1E-05 46.8 16.4 134 6-184 16-169 (367)
94 KOG1798 DNA polymerase epsilon 94.6 0.47 1E-05 58.0 13.5 162 7-180 245-453 (2173)
95 PHA03036 DNA polymerase; Provi 93.6 0.84 1.8E-05 54.5 13.1 140 8-153 160-352 (1004)
96 cd06140 DNA_polA_I_Bacillus_li 93.3 3.1 6.6E-05 38.6 14.1 104 8-154 3-108 (178)
97 PRK05761 DNA polymerase I; Rev 92.9 0.48 1E-05 55.3 9.8 96 79-174 208-334 (787)
98 KOG4793 Three prime repair exo 92.9 0.15 3.2E-06 52.5 4.9 151 25-183 128-293 (318)
99 cd06148 Egl_like_exo DEDDy 3'- 92.8 1.5 3.2E-05 42.4 11.6 139 5-184 7-180 (197)
100 smart00474 35EXOc 3'-5' exonuc 92.0 2.2 4.8E-05 38.3 11.1 88 85-181 64-171 (172)
101 KOG0969 DNA polymerase delta, 90.0 0.073 1.6E-06 61.1 -0.7 145 8-166 274-460 (1066)
102 COG0749 PolA DNA polymerase I 87.6 5.1 0.00011 45.5 11.5 134 9-183 23-182 (593)
103 cd06142 RNaseD_exo DEDDy 3'-5' 86.4 9.5 0.00021 35.0 10.9 90 86-184 54-163 (178)
104 PHA02563 DNA polymerase; Provi 82.3 9.4 0.0002 43.9 10.6 34 85-119 50-90 (630)
105 TIGR00593 pola DNA polymerase 82.2 9.1 0.0002 45.6 10.9 93 81-182 363-478 (887)
106 PF13017 Maelstrom: piRNA path 75.2 2.4 5.1E-05 42.0 2.8 95 26-121 7-115 (213)
107 COG5228 POP2 mRNA deadenylase 74.8 11 0.00025 38.2 7.4 169 8-187 42-259 (299)
108 cd06147 Rrp6p_like_exo DEDDy 3 66.2 77 0.0017 30.0 10.9 88 88-185 69-176 (192)
109 PF11074 DUF2779: Domain of un 58.2 45 0.00097 30.8 7.4 57 79-137 55-118 (130)
110 KOG3657 Mitochondrial DNA poly 57.4 8.7 0.00019 45.3 3.1 37 93-134 240-276 (1075)
111 cd09018 DEDDy_polA_RNaseD_like 53.1 63 0.0014 28.5 7.4 62 88-157 45-109 (150)
112 KOG0970 DNA polymerase alpha, 40.5 1.6E+02 0.0034 36.6 9.7 142 8-154 529-707 (1429)
113 cd06128 DNA_polA_exo DEDDy 3'- 29.4 2.2E+02 0.0048 25.5 7.2 59 88-154 45-105 (151)
114 TIGR00592 pol2 DNA polymerase 25.7 31 0.00067 42.5 1.1 38 75-112 264-304 (1172)
No 1
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.4e-37 Score=349.39 Aligned_cols=218 Identities=18% Similarity=0.263 Sum_probs=205.8
Q ss_pred CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHH
Q 010297 4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (513)
Q Consensus 4 t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~E 83 (513)
...+.+|||||+|||||++ ..+.|||||||++.+| +++++|+.||+|.. +++..++++||||++||+++++..+
T Consensus 417 ~l~datyVVfDiETTGLs~--~~d~iIE~aAvKikng--~iId~f~~Fi~P~~--pl~~~~telTgITdeml~~a~~i~~ 490 (1444)
T COG2176 417 KLDDATYVVFDIETTGLSP--VYDEIIEIAAVKIKNG--RIIDKFQFFIKPGR--PLSATITELTGITDEMLENAPEIEE 490 (1444)
T ss_pred ccccccEEEEEeecCCcCc--ccchhhhheeeeeeCC--cchHHHHHhcCCCC--cCchhhhhccccCHHHHcCCccHHH
Confidence 4567889999999999998 8899999999999998 67899999999999 9999999999999999999999999
Q ss_pred HHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCC
Q 010297 84 IADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHR 162 (513)
Q Consensus 84 Vl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHR 162 (513)
|+.+|.+|++++++||||+ .||++||+..+.++|+++..+ ++||||.++| .+.|..++|+|..||+.||+. ++|||
T Consensus 491 vL~kf~~~~~d~IlVAHNa-sFD~gFl~~~~~k~~~~~~~~-pvIDTL~lar-~L~P~~ksh~Lg~l~kk~~v~le~hHR 567 (1444)
T COG2176 491 VLEKFREFIGDSILVAHNA-SFDMGFLNTNYEKYGLEPLTN-PVIDTLELAR-ALNPEFKSHRLGTLCKKLGVELERHHR 567 (1444)
T ss_pred HHHHHHHHhcCcEEEeccC-ccchhHHHHHHHHhCCccccC-chhhHHHHHH-HhChhhhhcchHHHHHHhCccHHHhhh
Confidence 9999999999999999999 999999999999999986654 7999999997 688999999999999999999 89999
Q ss_pred hHHHHHHHHHHHHHHHHHhhcccCCCCcccccccc-CCCccccccCCccccC---CCCCCC---CCCCCCcccccc
Q 010297 163 SLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWV-SPNATTRSRSNAKSSP---EGTSQN---LSTPSSKFKFEN 231 (513)
Q Consensus 163 ALdDA~aTA~Ll~~ll~~L~~~~~~P~v~~~~~l~-~~~~~~r~r~~h~~~~---~~~~~~---~~s~~~~~~~~~ 231 (513)
|.+||.+|+++|..+++.+.+. ++.++.++|..+ +...++|.|++|++.+ |.|+|| ++|-|...||.+
T Consensus 568 A~yDaeat~~vf~~f~~~~ke~-Gi~~l~eln~~l~~~~~ykr~r~~h~~i~vknq~GlKnLykLvS~s~~kyf~~ 642 (1444)
T COG2176 568 ADYDAEATAKVFFVFLKDLKEK-GITNLSELNDKLSSEDLYKRLRPKHATIYVKNQVGLKNLYKLVSISHTKYFYG 642 (1444)
T ss_pred hhhhHHHHHHHHHHHHHHHHHh-chhhHHHHhHhhhhhHHHhhccccceEEEEechHhHHHHHHHHHHHHHHhhcc
Confidence 9999999999999999999998 899999999855 7778999999999888 899999 999999999999
No 2
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=1.6e-32 Score=271.05 Aligned_cols=176 Identities=19% Similarity=0.249 Sum_probs=155.1
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 3 ~t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
..+.+..|++||+||||+++ ..|+|||||+|.++++.+...+.|+.+|+|.. ++++.+.++||||++||+++++|.
T Consensus 42 ~~~~~~~~vviD~ETTGl~p--~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~--~i~~~~~~IhGIt~e~l~~ap~~~ 117 (239)
T PRK09146 42 TPLSEVPFVALDFETTGLDA--EQDAIVSIGLVPFTLQRIRCRQARHWVVKPRR--PLEEESVVIHGITHSELQDAPDLE 117 (239)
T ss_pred CCcccCCEEEEEeECCCCCC--CCCcEEEEEEEEEECCeEeecceEEEEECCCC--CCChhhhhhcCCCHHHHhCCCCHH
Confidence 45677899999999999998 68999999999999886555689999999998 899999999999999999999999
Q ss_pred HHHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCC------------CCCCCHHHH
Q 010297 83 DIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRR------------AGDMKMASL 150 (513)
Q Consensus 83 EVl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~pr------------l~s~kL~~L 150 (513)
+++.+|.+|+++.++||||+ .||++||++++++++...+. .+++||+.++++.+... .++++|.++
T Consensus 118 evl~~l~~~~~~~~lVaHna-~FD~~fL~~~l~~~~~~~~~-~~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l 195 (239)
T PRK09146 118 RILDELLEALAGKVVVVHYR-RIERDFLDQALRNRIGEGIE-FPVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADS 195 (239)
T ss_pred HHHHHHHHHhCCCEEEEECH-HHHHHHHHHHHHHhcCCCCC-CceechHHHHHHHcccccccccchhccCCCCCCCHHHH
Confidence 99999999999999999999 99999999999876443332 36999999998643211 267899999
Q ss_pred HHHhCCC-CCCCChHHHHHHHHHHHHHHHHHhhcc
Q 010297 151 ATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 151 Ak~fGI~-~~aHRALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
+++||++ ..+|||++||++|+++|.++++.++..
T Consensus 196 ~~~~gl~~~~~H~Al~DA~ata~l~~~~~~~~~~~ 230 (239)
T PRK09146 196 RLRYGLPAYSPHHALTDAIATAELLQAQIAHHFSP 230 (239)
T ss_pred HHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 9999999 689999999999999999999988653
No 3
>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=100.00 E-value=4.3e-32 Score=263.06 Aligned_cols=194 Identities=19% Similarity=0.218 Sum_probs=161.8
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
....+||+||+||||+++ ..+ |||||||++.++. .+.++|+++|+|.. ++++.+.++||||++||+++++|.++
T Consensus 4 l~~~~fvv~D~ETTGl~~--~~~-IIeIgav~v~~~~-~~~~~f~~li~P~~--~i~~~a~~ihGIt~e~l~~~p~~~ev 77 (217)
T TIGR00573 4 LVLDTETTGDNETTGLYA--GHD-IIEIGAVEIINRR-ITGNKFHTYIKPDR--PIDPDAIKIHGITDDMLKDKPDFKEI 77 (217)
T ss_pred EEecCEEEEEecCCCCCC--CCC-EEEEEEEEEECCC-EeeeEEEEEECcCC--CCCHHHHhhcCCCHHHHcCCCCHHHH
Confidence 356789999999999987 567 9999999987664 45789999999997 89999999999999999999999999
Q ss_pred HHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCC--CCCCHHHHHHHhCCC-C--C
Q 010297 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRA--GDMKMASLATYFGLG-Q--Q 159 (513)
Q Consensus 85 l~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl--~s~kL~~LAk~fGI~-~--~ 159 (513)
+.+|.+|+++.++||||+ .||+.||++++++++...+....++||+.+++. +.+.. .+++|..++++||++ . .
T Consensus 78 ~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~-~~~~~~~~~~~L~~l~~~~gl~~~~~~ 155 (217)
T TIGR00573 78 AEDFADYIRGAELVIHNA-SFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQY-ARPEFPGKRNTLDALCKRYEITNSHRA 155 (217)
T ss_pred HHHHHHHhCCCEEEEecc-HHHHHHHHHHHHHhcCCCCCccceecHHHHHHH-HHHhCCCCCCCHHHHHHHcCCCCCCcc
Confidence 999999999999999999 999999999999987654444468999998874 33332 467999999999998 3 6
Q ss_pred CCChHHHHHHHHHHHHHHHHHhhcccCCCCccccccccCCCccccccCCccccC---CCCCCC
Q 010297 160 THRSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWVSPNATTRSRSNAKSSP---EGTSQN 219 (513)
Q Consensus 160 aHRALdDA~aTA~Ll~~ll~~L~~~~~~P~v~~~~~l~~~~~~~r~r~~h~~~~---~~~~~~ 219 (513)
+|+|++||++|+++|.+++++.-... .+ . .++.|.+|++.. +.|++|
T Consensus 156 ~H~Al~DA~~ta~l~~~l~~~~~~~~-------~~----~--~~~~~~~~~~~~~~~~~~l~~ 205 (217)
T TIGR00573 156 LHGALADAFILAKLYLVMTGKQTKYG-------EN----E--GQQSRPYHAIKSIVKKDMLLK 205 (217)
T ss_pred cCCHHHHHHHHHHHHHHHHhcchhhc-------cc----c--ccccCCccceEeeeccccccc
Confidence 89999999999999999988753321 11 1 157788998665 556565
No 4
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=5e-32 Score=267.93 Aligned_cols=168 Identities=26% Similarity=0.389 Sum_probs=147.5
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHH
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl 85 (513)
..+++|+||+||||+++. ..++|||||||.+.++.. ..+.|+.+|+|.. ++++.+.++||||++||+++|.|++++
T Consensus 2 ~~~r~vvlDtETTGldp~-~~drIIEIGaV~v~~~~~-~~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev~ 77 (240)
T PRK05711 2 AIMRQIVLDTETTGLNQR-EGHRIIEIGAVELINRRL-TGRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEVA 77 (240)
T ss_pred CCCeEEEEEeeCCCcCCC-CCCeEEEEEEEEEECCEE-eccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHHH
Confidence 357899999999999872 279999999999998743 4578999999987 899999999999999999999999999
Q ss_pred HHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCC---CCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC---C
Q 010297 86 DTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPE---PKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ---Q 159 (513)
Q Consensus 86 ~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~---~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~---~ 159 (513)
++|.+|+++.++||||+ .||++||+++++++|...+. ...++||+.++++.+ |. ..++|+.||++||++. .
T Consensus 78 ~~f~~fi~~~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~-p~-~~~~L~aL~~~~gi~~~~r~ 154 (240)
T PRK05711 78 DEFLDFIRGAELIIHNA-PFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMF-PG-KRNSLDALCKRYGIDNSHRT 154 (240)
T ss_pred HHHHHHhCCCEEEEEcc-HHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHc-CC-CCCCHHHHHHHCCCCCCCCC
Confidence 99999999999999999 99999999999999865442 246999999998654 44 4679999999999983 4
Q ss_pred CCChHHHHHHHHHHHHHHHHH
Q 010297 160 THRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 160 aHRALdDA~aTA~Ll~~ll~~ 180 (513)
.|+|+.||+++++||..+.+.
T Consensus 155 ~H~AL~DA~~~A~v~~~l~~~ 175 (240)
T PRK05711 155 LHGALLDAEILAEVYLAMTGG 175 (240)
T ss_pred CCCHHHHHHHHHHHHHHHHCc
Confidence 699999999999999998753
No 5
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=100.00 E-value=7e-32 Score=264.82 Aligned_cols=174 Identities=20% Similarity=0.206 Sum_probs=152.4
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcC-CCCH
Q 010297 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTF 81 (513)
Q Consensus 3 ~t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~-Apsf 81 (513)
|++.+.+||+||+||||+++ ..++|||||+|+++.++ .+++.|+.+|+|.. +|++.++++||||++|+++ ++++
T Consensus 1 ~~~~~~~~vv~D~ETTGl~p--~~d~Iieig~v~v~~~g-~~~~~~~~lv~P~~--~i~~~a~~IhGIt~e~l~~~g~~~ 75 (232)
T PRK07942 1 MSWHPGPLAAFDLETTGVDP--ETARIVTAALVVVDADG-EVVESREWLADPGV--EIPEEASAVHGITTEYARAHGRPA 75 (232)
T ss_pred CCcccCcEEEEEeccCCCCC--CCCeeEEEEEEEEeCCC-ccccceEEEECCCC--CCCHHHHHHhCCCHHHHHhhCCCH
Confidence 57889999999999999998 67999999999998532 45789999999998 8999999999999999975 7888
Q ss_pred HHHHHHHHHHH-----cCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 010297 82 ADIADTVFDIL-----HGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGL 156 (513)
Q Consensus 82 ~EVl~ef~efL-----~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI 156 (513)
++++.+|.+++ ++.++||||+ .||++||+++++++|...+...+++||+.+.+.....+.++++|.+|+++||+
T Consensus 76 ~~vl~e~~~~l~~~~~~~~~lVahNa-~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi 154 (232)
T PRK07942 76 AEVLAEIADALREAWARGVPVVVFNA-PYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGV 154 (232)
T ss_pred HHHHHHHHHHHHHHhhcCCEEEEeCc-HhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCC
Confidence 99999998887 4789999999 99999999999999987654446899999887433333467899999999999
Q ss_pred C-CCCCChHHHHHHHHHHHHHHHHHhh
Q 010297 157 G-QQTHRSLDDVRMNLEVLKYCATVLF 182 (513)
Q Consensus 157 ~-~~aHRALdDA~aTA~Ll~~ll~~L~ 182 (513)
+ .++|||++||++|++||.++++++.
T Consensus 155 ~~~~aH~Al~Da~ata~l~~~l~~~~~ 181 (232)
T PRK07942 155 RLDNAHEATADALAAARVAWALARRFP 181 (232)
T ss_pred CCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 9 6899999999999999999988765
No 6
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=100.00 E-value=1.1e-31 Score=262.67 Aligned_cols=165 Identities=24% Similarity=0.326 Sum_probs=144.5
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHH
Q 010297 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (513)
Q Consensus 9 ~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef 88 (513)
++|+||+||||+++. ..++|||||||.+.++. ...++|+.+|+|.. ++++.++++||||++||+++|+|++++.+|
T Consensus 1 r~vvlD~ETTGl~p~-~~d~IIEIgav~~~~~~-~~~~~f~~~i~P~~--~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f 76 (225)
T TIGR01406 1 RQIILDTETTGLDPK-GGHRIVEIGAVELVNRM-LTGDNFHVYVNPER--DMPAEAAKVHGITDEFLADKPKFKEIADEF 76 (225)
T ss_pred CEEEEEeeCCCcCCC-CCCeEEEEEEEEEECCc-EecceEEEEECcCC--CCCHHHHhccCCCHHHHhCCCCHHHHHHHH
Confidence 589999999999872 34899999999998763 34579999999998 899999999999999999999999999999
Q ss_pred HHHHcCCeEEEeCcchHHHHHHHHHHHHcCC--CCC-CCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC---CCCC
Q 010297 89 FDILHGRIWAGHNILRFDCARIREAFAEIGR--PAP-EPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ---QTHR 162 (513)
Q Consensus 89 ~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi--~~p-~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~---~aHR 162 (513)
.+|+++.++||||+ .||++||+.++.++|. +.+ ....++||+.++++.+ |. .+++|+.||++||++. ..|+
T Consensus 77 ~~fi~~~~lVaHNa-~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~-p~-~~~~L~~L~~~~gi~~~~r~~H~ 153 (225)
T TIGR01406 77 LDFIGGSELVIHNA-AFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERF-PG-QRNSLDALCKRFKVDNSHRTLHG 153 (225)
T ss_pred HHHhCCCEEEEEec-HHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHc-CC-CCCCHHHHHHhcCCCCCCCCCcC
Confidence 99999999999999 9999999999999994 322 2247999999998654 44 4689999999999982 5799
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 010297 163 SLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 163 ALdDA~aTA~Ll~~ll~~ 180 (513)
|+.||+++++||.++.+.
T Consensus 154 Al~DA~~~a~v~~~l~~~ 171 (225)
T TIGR01406 154 ALLDAHLLAEVYLALTGG 171 (225)
T ss_pred HHHHHHHHHHHHHHHHcC
Confidence 999999999999998763
No 7
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=100.00 E-value=1.9e-31 Score=272.79 Aligned_cols=172 Identities=23% Similarity=0.362 Sum_probs=158.6
Q ss_pred CCCCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCC
Q 010297 1 MGPTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPT 80 (513)
Q Consensus 1 m~~t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Aps 80 (513)
|+-.....+||+||+||||+++ ..++|||||||.++++ +++++|+.+|+|.. ++++.++++||||++||+++++
T Consensus 1 ~~~~~~~~~~Vv~DlETTGl~p--~~~eIIEIgaV~v~~g--~i~~~f~~lVkP~~--~I~~~a~~ihGIT~e~l~~~~~ 74 (313)
T PRK06807 1 MGNISLPLDYVVIDFETTGFNP--YNDKIIQVAAVKYRNH--ELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPT 74 (313)
T ss_pred CCCcCCCCCEEEEEEECCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEECcCC--CCCHhhhccCCCCHHHHhCCCC
Confidence 5666778899999999999987 6789999999999976 67899999999998 8999999999999999999999
Q ss_pred HHHHHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCC
Q 010297 81 FADIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQT 160 (513)
Q Consensus 81 f~EVl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~~a 160 (513)
|.+|+.+|.+|+++.++||||+ .||+.||.+.+.++|++.+.. +++||+.++++ +.+..++++|.+|+++||++.++
T Consensus 75 ~~evl~~f~~fl~~~~lVaHNa-~FD~~fL~~~~~~~gl~~~~~-~~iDtl~la~~-~~~~~~~~kL~~L~~~lgi~~~~ 151 (313)
T PRK06807 75 IEEVLPLFLAFLHTNVIVAHNA-SFDMRFLKSNVNMLGLPEPKN-KVIDTVFLAKK-YMKHAPNHKLETLKRMLGIRLSS 151 (313)
T ss_pred HHHHHHHHHHHHcCCeEEEEcH-HHHHHHHHHHHHHcCCCCCCC-CEeeHHHHHHH-HhCCCCCCCHHHHHHHcCCCCCC
Confidence 9999999999999999999999 999999999999999987654 69999999874 55667889999999999999889
Q ss_pred CChHHHHHHHHHHHHHHHHHh
Q 010297 161 HRSLDDVRMNLEVLKYCATVL 181 (513)
Q Consensus 161 HRALdDA~aTA~Ll~~ll~~L 181 (513)
|||++||++|+++|.++....
T Consensus 152 H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 152 HNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred cChHHHHHHHHHHHHHHHHhh
Confidence 999999999999999998765
No 8
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=100.00 E-value=1.3e-31 Score=257.71 Aligned_cols=172 Identities=19% Similarity=0.215 Sum_probs=148.4
Q ss_pred CCCcEEEEEEecCCCCCC----CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCH
Q 010297 6 DRSEIAFFDVETTVPTRP----GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~----g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf 81 (513)
...+||+||+||||+++. +..++|||||||+++++ ++.++|+.||+|....+++++++++||||++||++||+|
T Consensus 2 ~~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~--~i~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~ 79 (207)
T PRK07748 2 DEQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGC--EVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISF 79 (207)
T ss_pred CcceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecC--cChhhhcceECCCccCccChhhhhhcCcCHHHHccCCCH
Confidence 457899999999997641 12579999999999977 567899999999875579999999999999999999999
Q ss_pred HHHHHHHHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC--C
Q 010297 82 ADIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG--Q 158 (513)
Q Consensus 82 ~EVl~ef~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~--~ 158 (513)
.+|+++|.+|+++ ..+++|++ .||+.||+++|+++|++.++...++|++.+.++ +.+....++|.+++++||++ .
T Consensus 80 ~evl~~f~~~~~~~~~~iv~~~-~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~-~~~~~~~~~L~~~~~~~gi~~~~ 157 (207)
T PRK07748 80 EELVEKLAEYDKRCKPTIVTWG-NMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKK-FFGERNQTGLWKAIEEYGKEGTG 157 (207)
T ss_pred HHHHHHHHHHhCcCCeEEEEEC-HHHHHHHHHHHHHcCCCCcccccceeHHHHHHH-HhCcCCCCCHHHHHHHcCCCCCC
Confidence 9999999999998 46666777 999999999999999987765578999887764 44444678999999999999 3
Q ss_pred CCCChHHHHHHHHHHHHHHHHHh
Q 010297 159 QTHRSLDDVRMNLEVLKYCATVL 181 (513)
Q Consensus 159 ~aHRALdDA~aTA~Ll~~ll~~L 181 (513)
++|||++||++|+++|.++++..
T Consensus 158 ~~H~Al~DA~~ta~l~~~l~~~~ 180 (207)
T PRK07748 158 KHHCALDDAMTTYNIFKLVEKDK 180 (207)
T ss_pred CCcChHHHHHHHHHHHHHHHhCc
Confidence 68999999999999999998773
No 9
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=100.00 E-value=4.7e-31 Score=239.94 Aligned_cols=166 Identities=27% Similarity=0.416 Sum_probs=149.8
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHH
Q 010297 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (513)
Q Consensus 9 ~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef 88 (513)
.||+||+||||+++ ..++|||||||+++++. +.+.|+.+|+|.. +++++++++||||++++++++++.+|+.+|
T Consensus 1 ~~v~~D~Ettg~~~--~~~~Iieig~v~~~~~~--~~~~f~~~v~p~~--~i~~~~~~~~Git~~~l~~~~~~~~~~~~~ 74 (169)
T smart00479 1 TLVVIDCETTGLDP--GKDEIIEIAAVDVDGGR--IIVVFDTYVKPDR--PITDYATEIHGITPEMLDDAPTFEEVLEEL 74 (169)
T ss_pred CEEEEEeeCCCCCC--CCCeEEEEEEEEEECCE--eEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHHHHH
Confidence 48999999999987 57899999999999983 6789999999976 899999999999999999999999999999
Q ss_pred HHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CC-CCChHHH
Q 010297 89 FDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQ-THRSLDD 166 (513)
Q Consensus 89 ~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~-aHRALdD 166 (513)
.+|+++.++++||+..||+.+|++.+.++|++.+....++|++.+++..+ +.. +++|.+++++||++ .. +|+|++|
T Consensus 75 ~~~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~-~~~-~~~L~~l~~~~~~~~~~~~H~A~~D 152 (169)
T smart00479 75 LEFLKGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALN-PGR-KYSLKKLAERLGLEVIGRAHRALDD 152 (169)
T ss_pred HHHhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHC-CCC-CCCHHHHHHHCCCCCCCCCcCcHHH
Confidence 99999999999999899999999999999988776667999999987544 332 89999999999998 34 5999999
Q ss_pred HHHHHHHHHHHHHHhh
Q 010297 167 VRMNLEVLKYCATVLF 182 (513)
Q Consensus 167 A~aTA~Ll~~ll~~L~ 182 (513)
|++|+++|++++++.+
T Consensus 153 a~~t~~l~~~~~~~~~ 168 (169)
T smart00479 153 ARATAKLFKKLVERLL 168 (169)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999987654
No 10
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=100.00 E-value=2.7e-31 Score=244.35 Aligned_cols=161 Identities=25% Similarity=0.380 Sum_probs=141.5
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHH
Q 010297 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVF 89 (513)
Q Consensus 10 ~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~ 89 (513)
||+||+||||+++ ...++|||||||+++++.. ..+.|+.+|+|.. ++++.++++||||++++++++++.+++.+|.
T Consensus 1 ~v~~D~ETTGl~~-~~~~~iieig~v~v~~~~~-~~~~~~~~v~P~~--~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~ 76 (167)
T cd06131 1 QIVLDTETTGLDP-REGHRIIEIGCVELINRRL-TGNTFHVYINPER--DIPEEAFKVHGITDEFLADKPKFAEIADEFL 76 (167)
T ss_pred CEEEEeeCCCCCC-CCCCeEEEEEEEEEECCcE-eccEEEEEECCCC--CCCHHHHHHhCCCHHHHhcCCCHHHHHHHHH
Confidence 6899999999986 2468999999999988643 4568999999998 7999999999999999999999999999999
Q ss_pred HHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCC--CCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC---CCCChH
Q 010297 90 DILHGRIWAGHNILRFDCARIREAFAEIGRPAP--EPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ---QTHRSL 164 (513)
Q Consensus 90 efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p--~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~---~aHRAL 164 (513)
+|+++.++||||+ .||+.||++++.++|+..+ .+..++||+.++++.+ +. ..++|++++++||++. ++|+|+
T Consensus 77 ~~l~~~~lv~hn~-~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~-~~-~~~~L~~l~~~~~i~~~~~~~H~Al 153 (167)
T cd06131 77 DFIRGAELVIHNA-SFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKF-PG-KPNSLDALCKRFGIDNSHRTLHGAL 153 (167)
T ss_pred HHHCCCeEEEeCh-HHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHc-CC-CCCCHHHHHHHCCCCCCCCCCCChH
Confidence 9999999999999 9999999999999877543 2347999999987544 43 4679999999999982 579999
Q ss_pred HHHHHHHHHHHHH
Q 010297 165 DDVRMNLEVLKYC 177 (513)
Q Consensus 165 dDA~aTA~Ll~~l 177 (513)
+||++++++|.++
T Consensus 154 ~Da~~~a~l~~~l 166 (167)
T cd06131 154 LDAELLAEVYLEL 166 (167)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999875
No 11
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=2.9e-31 Score=264.86 Aligned_cols=168 Identities=20% Similarity=0.356 Sum_probs=152.4
Q ss_pred CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHH
Q 010297 4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (513)
Q Consensus 4 t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~E 83 (513)
.+.+..||+||+||||+++ ..++|||||||+++++ .++++|+.+|+|. ++++.++++||||++|+++++++.+
T Consensus 64 ~~~~~~~vv~DiETTG~~~--~~~~IIEIGAv~v~~g--~i~~~f~~~v~p~---~ip~~~~~itGIt~e~l~~ap~~~e 136 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKP--KKHQIIEIGAVKVKNG--EIIDRFESFVKAK---EVPEYITELTGITYEDLENAPSLKE 136 (257)
T ss_pred CCCCCCEEEEEEeCCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEECCC---CCChhhhhhcCcCHHHHcCCCCHHH
Confidence 3567899999999999987 6789999999999976 6779999999996 5899999999999999999999999
Q ss_pred HHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCC
Q 010297 84 IADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHR 162 (513)
Q Consensus 84 Vl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHR 162 (513)
|+.+|.+|++++++||||+ .||+.||++++.++|.+...+ +++||+.++++.+ + ..+++|++|+++||++ .++||
T Consensus 137 vl~~f~~fl~~~v~VaHNa-~FD~~fL~~~l~r~g~~~~~~-~~ldtl~la~~~~-~-~~~~~L~~L~~~lgi~~~~~Hr 212 (257)
T PRK08517 137 VLEEFRLFLGDSVFVAHNV-NFDYNFISRSLEEIGLGPLLN-RKLCTIDLAKRTI-E-SPRYGLSFLKELLGIEIEVHHR 212 (257)
T ss_pred HHHHHHHHHCCCeEEEECH-HHHHHHHHHHHHHcCCCCCCC-CcEehHHHHHHHc-c-CCCCCHHHHHHHcCcCCCCCCC
Confidence 9999999999999999999 999999999999999886654 6999999987544 3 2678999999999999 58999
Q ss_pred hHHHHHHHHHHHHHHHHHhh
Q 010297 163 SLDDVRMNLEVLKYCATVLF 182 (513)
Q Consensus 163 ALdDA~aTA~Ll~~ll~~L~ 182 (513)
|++||.+|++||..++.++.
T Consensus 213 Al~DA~ata~ll~~ll~~~~ 232 (257)
T PRK08517 213 AYADALAAYEIFKICLLNLP 232 (257)
T ss_pred hHHHHHHHHHHHHHHHHHhH
Confidence 99999999999999998764
No 12
>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=99.98 E-value=2.5e-31 Score=240.57 Aligned_cols=155 Identities=25% Similarity=0.418 Sum_probs=141.9
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHH
Q 010297 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVF 89 (513)
Q Consensus 10 ~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~ 89 (513)
||+||+||||.. .++|||||||.++.+ +++++|+.+|+|.. ++++.++++||||++++++++++.+++.+|.
T Consensus 1 ~v~~D~Ettg~~----~~~ii~ig~v~~~~~--~~~~~~~~~i~p~~--~~~~~~~~i~GIt~e~l~~~~~~~~v~~~l~ 72 (156)
T cd06130 1 FVAIDFETANAD----RASACSIGLVKVRDG--QIVDTFYTLIRPPT--RFDPFNIAIHGITPEDVADAPTFPEVWPEIK 72 (156)
T ss_pred CEEEEEeCCCCC----CCceEEEEEEEEECC--EEEEEEEEEeCcCC--CCChhhccccCcCHHHHhcCCCHHHHHHHHH
Confidence 689999999974 478999999999976 66799999999998 8999999999999999999999999999999
Q ss_pred HHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHHHH
Q 010297 90 DILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDVRM 169 (513)
Q Consensus 90 efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~~aHRALdDA~a 169 (513)
+|+++.++||||+ +||.+||++.++++|+..+. .+++||+.++++ +.+..++++|.+++++||++..+|||++||++
T Consensus 73 ~~l~~~~lv~hn~-~fD~~~l~~~~~~~g~~~~~-~~~idt~~~~~~-~~~~~~~~~L~~l~~~~g~~~~~H~Al~Da~~ 149 (156)
T cd06130 73 PFLGGSLVVAHNA-SFDRSVLRAALEAYGLPPPP-YQYLCTVRLARR-VWPLLPNHKLNTVAEHLGIELNHHDALEDARA 149 (156)
T ss_pred HHhCCCEEEEeCh-HHhHHHHHHHHHHcCCCCCC-CCEEEHHHHHHH-HhccCCCCCHHHHHHHcCCCccCcCchHHHHH
Confidence 9999999999999 99999999999999998764 479999999875 45567899999999999999339999999999
Q ss_pred HHHHHH
Q 010297 170 NLEVLK 175 (513)
Q Consensus 170 TA~Ll~ 175 (513)
|+++|.
T Consensus 150 ta~l~~ 155 (156)
T cd06130 150 CAEILL 155 (156)
T ss_pred HHHHHh
Confidence 999985
No 13
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=3.9e-31 Score=269.42 Aligned_cols=166 Identities=19% Similarity=0.297 Sum_probs=150.7
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHH
Q 010297 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~e 87 (513)
++||+||+||||. ..++|||||||+++++ .++++|+++|+|.. ..+++.++++||||++||+++|+|.+++.+
T Consensus 1 ~~~vviD~ETTg~----~~d~IieIgav~v~~g--~i~~~f~~lv~P~~-~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~ 73 (309)
T PRK06195 1 MNFVAIDFETANE----KRNSPCSIGIVVVKDG--EIVEKVHYLIKPKE-MRFMPINIGIHGIRPHMVEDELEFDKIWEK 73 (309)
T ss_pred CcEEEEEEeCCCC----CCCceEEEEEEEEECC--EEEEEEEEEECCCC-CCCChhheeccCcCHHHHhCCCCHHHHHHH
Confidence 4799999999986 4589999999999877 56799999999985 257888999999999999999999999999
Q ss_pred HHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCCChHHHH
Q 010297 88 VFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTHRSLDDV 167 (513)
Q Consensus 88 f~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~~aHRALdDA 167 (513)
|.+|+++.++||||+ .||+.||+++++++|++.+.+ .++||+.+++ .+++..++++|.+|+++||++..+|||++||
T Consensus 74 ~~~fl~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~-~~idT~~lar-~l~~~~~~~~L~~L~~~~gi~~~~H~Al~DA 150 (309)
T PRK06195 74 IKHYFNNNLVIAHNA-SFDISVLRKTLELYNIPMPSF-EYICTMKLAK-NFYSNIDNARLNTVNNFLGYEFKHHDALADA 150 (309)
T ss_pred HHHHhCCCEEEEECc-HHHHHHHHHHHHHhCCCCCCC-CEEEHHHHHH-HHcCCCCcCCHHHHHHHcCCCCcccCCHHHH
Confidence 999999999999999 999999999999999987765 6999999997 4667778999999999999997799999999
Q ss_pred HHHHHHHHHHHHHhhc
Q 010297 168 RMNLEVLKYCATVLFL 183 (513)
Q Consensus 168 ~aTA~Ll~~ll~~L~~ 183 (513)
++|+++|.++++++..
T Consensus 151 ~ata~l~~~l~~~~~~ 166 (309)
T PRK06195 151 MACSNILLNISKELNS 166 (309)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 9999999999887643
No 14
>PRK07740 hypothetical protein; Provisional
Probab=99.98 E-value=4.6e-31 Score=261.08 Aligned_cols=172 Identities=22% Similarity=0.295 Sum_probs=152.1
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
....+|||||+||||+++ ...++|||||||+++++.. +.++|+.+|+|.. ++++.+.++||||+++|++++++.++
T Consensus 56 ~~~~~~vv~D~ETTGl~p-~~~deIIeIgaV~~~~~~i-~~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev 131 (244)
T PRK07740 56 LTDLPFVVFDLETTGFSP-QQGDEILSIGAVKTKGGEV-ETDTFYSLVKPKR--PIPEHILELTGITAEDVAFAPPLAEV 131 (244)
T ss_pred ccCCCEEEEEEeCCCCCC-CCCCeEEEEEEEEEECCEE-EEEEEEEEeCcCC--CCChhheeccCCCHHHHhCCCCHHHH
Confidence 356789999999999987 2348999999999998743 4799999999998 89999999999999999999999999
Q ss_pred HHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCCh
Q 010297 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRS 163 (513)
Q Consensus 85 l~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHRA 163 (513)
+.+|.+|++++++||||+ .||..||++++.+.... ++...++||+.+++ .+.+..++++|++++++||++ ..+|+|
T Consensus 132 l~~f~~fi~~~~lVahna-~fD~~fL~~~~~~~~~~-~~~~~~iDt~~l~r-~l~~~~~~~sL~~l~~~~gi~~~~~H~A 208 (244)
T PRK07740 132 LHRFYAFIGAGVLVAHHA-GHDKAFLRHALWRTYRQ-PFTHRLIDTMFLTK-LLAHERDFPTLDDALAYYGIPIPRRHHA 208 (244)
T ss_pred HHHHHHHhCCCEEEEeCH-HHHHHHHHHHHHHhcCC-CcCCCeechHHHHH-HHcCCCCCCCHHHHHHHCCcCCCCCCCc
Confidence 999999999999999999 99999999998775433 33447999999987 456666789999999999999 678999
Q ss_pred HHHHHHHHHHHHHHHHHhhc
Q 010297 164 LDDVRMNLEVLKYCATVLFL 183 (513)
Q Consensus 164 LdDA~aTA~Ll~~ll~~L~~ 183 (513)
++||++|++||.+++..+..
T Consensus 209 l~Da~ata~l~~~ll~~~~~ 228 (244)
T PRK07740 209 LGDALMTAKLWAILLVEAQQ 228 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999988764
No 15
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.98 E-value=7.1e-31 Score=260.60 Aligned_cols=167 Identities=23% Similarity=0.355 Sum_probs=151.2
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHH
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl 85 (513)
+++.||+||+||||+++ ..++|||||+|+++.+ .+++.|+.+|+|.. +|++.+.++||||++||+++|++.+++
T Consensus 5 ~~~~~v~~D~ETTGl~~--~~d~IIEIa~v~v~~~--~~~~~~~~li~P~~--~I~~~a~~ihgIt~e~v~~~p~~~ev~ 78 (250)
T PRK06310 5 KDTEFVCLDCETTGLDV--KKDRIIEFAAIRFTFD--EVIDSVEFLINPER--VVSAESQRIHHISDAMLRDKPKIAEVF 78 (250)
T ss_pred cCCcEEEEEEeCCCCCC--CCCeEEEEEEEEEECC--eEEEEEEEEECcCC--CCCHhhhhccCcCHHHHhCCCCHHHHH
Confidence 45789999999999987 6799999999999977 56789999999998 899999999999999999999999999
Q ss_pred HHHHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCCCCC-CCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCC
Q 010297 86 DTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPE-PKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHR 162 (513)
Q Consensus 86 ~ef~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~-~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHR 162 (513)
.+|.+|+++ .++||||+ .||+.||++++.++|.+.+. ...+|||+.++++ + +...+++|..|+++||++ ..+||
T Consensus 79 ~~~~~fl~~~~~lvghn~-~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~-~-~~~~~~~L~~l~~~~g~~~~~aH~ 155 (250)
T PRK06310 79 PQIKGFFKEGDYIVGHSV-GFDLQVLSQESERIGETFLSKHYYIIDTLRLAKE-Y-GDSPNNSLEALAVHFNVPYDGNHR 155 (250)
T ss_pred HHHHHHhCCCCEEEEECH-HHHHHHHHHHHHHcCCCccccCCcEEehHHHHHh-c-ccCCCCCHHHHHHHCCCCCCCCcC
Confidence 999999986 89999999 99999999999999988653 2479999999873 4 445689999999999999 67999
Q ss_pred hHHHHHHHHHHHHHHHHHh
Q 010297 163 SLDDVRMNLEVLKYCATVL 181 (513)
Q Consensus 163 ALdDA~aTA~Ll~~ll~~L 181 (513)
|++||.+|+++|.++++++
T Consensus 156 Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 156 AMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred hHHHHHHHHHHHHHHHHhc
Confidence 9999999999999998754
No 16
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.98 E-value=4e-31 Score=270.32 Aligned_cols=168 Identities=23% Similarity=0.342 Sum_probs=151.3
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
..+||+||+||||+++ ..++|||||+|+++.++ .+++.|+++|+|.. ++..+.+||||++||+++|+|.+++.
T Consensus 14 ~~~fvvlD~ETTGl~p--~~d~IIeIgav~v~~~g-~i~~~~~~lv~P~~----~~~~~~IhGIt~e~l~~ap~f~ev~~ 86 (313)
T PRK06063 14 PRGWAVVDVETSGFRP--GQARIISLAVLGLDADG-NVEQSVVTLLNPGV----DPGPTHVHGLTAEMLEGQPQFADIAG 86 (313)
T ss_pred CCCEEEEEEECCCCCC--CCCEEEEEEEEEEECCc-eeeeEEEEEECcCC----CCCCeecCCCCHHHHhCCCCHHHHHH
Confidence 4689999999999997 67999999999998643 57799999999975 34568899999999999999999999
Q ss_pred HHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHH
Q 010297 87 TVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSLD 165 (513)
Q Consensus 87 ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHRALd 165 (513)
+|.+|++++++||||+ .||+.||+++|+++|++.+.. .++||+.++++ +.+..++++|++||++||++ .++|||++
T Consensus 87 ~l~~~l~~~~lVaHNa-~FD~~fL~~~~~r~g~~~~~~-~~ldTl~lar~-~~~~~~~~kL~~l~~~~gi~~~~~H~Al~ 163 (313)
T PRK06063 87 EVAELLRGRTLVAHNV-AFDYSFLAAEAERAGAELPVD-QVMCTVELARR-LGLGLPNLRLETLAAHWGVPQQRPHDALD 163 (313)
T ss_pred HHHHHcCCCEEEEeCH-HHHHHHHHHHHHHcCCCCCCC-CEEehHHHHHH-hccCCCCCCHHHHHHHcCCCCCCCCCcHH
Confidence 9999999999999999 999999999999999887754 59999999874 56667899999999999999 68999999
Q ss_pred HHHHHHHHHHHHHHHhhcc
Q 010297 166 DVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 166 DA~aTA~Ll~~ll~~L~~~ 184 (513)
||++|+++|.++++++...
T Consensus 164 DA~ata~l~~~ll~~~~~~ 182 (313)
T PRK06063 164 DARVLAGILRPSLERARER 182 (313)
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 9999999999999887654
No 17
>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=99.97 E-value=2.3e-31 Score=309.39 Aligned_cols=216 Identities=22% Similarity=0.331 Sum_probs=190.3
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHH
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl 85 (513)
++.+||+||+||||+++ ..++|||||||+++++ .++++|+.+|+|.. ++++.++++||||++||++++++.+|+
T Consensus 188 ~~~~~VVfDiETTGL~~--~~d~IIEIGAVkv~~g--~iid~f~~~V~P~~--~I~~~~~~ltGIT~e~L~~ap~~~evl 261 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSP--QYDEIIEFGAVKVKNG--RIIDKFQFFIKPHE--PLSAFVTELTGITQDMLENAPEIEEVL 261 (1213)
T ss_pred cCCcEEEEEeEecCCCC--CCCeEEEEEEEEEECC--eEEEEEEEEECCCC--CCCHHHHHHhCCCHHHHhCCCCHHHHH
Confidence 46789999999999988 7899999999999987 67899999999998 899999999999999999999999999
Q ss_pred HHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChH
Q 010297 86 DTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSL 164 (513)
Q Consensus 86 ~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHRAL 164 (513)
.+|.+|+++.++||||+ .||++||++.++++|+++.. .+++||+.+++ .+.|..++++|++||++||++ .++|||+
T Consensus 262 ~~f~~fl~~~iLVaHNa-~FD~~fL~~~~~r~g~~~~~-~~~IDTl~lar-~l~p~~k~~kL~~Lak~lgi~~~~~HrAl 338 (1213)
T TIGR01405 262 EKFKEFFKDSILVAHNA-SFDIGFLNTNFEKVGLEPLE-NPVIDTLELAR-ALNPEYKSHRLGNICKKLGVDLDDHHRAD 338 (1213)
T ss_pred HHHHHHhCCCeEEEECh-HHHHHHHHHHHHHcCCCccC-CCEeEHHHHHH-HHhccCCCCCHHHHHHHcCCCCCCCcCHH
Confidence 99999999999999999 99999999999999997443 47999999987 466778899999999999999 6899999
Q ss_pred HHHHHHHHHHHHHHHHhhcccCCCCcccccccc-CCCccccccCCccccC---CCCCCC---CCCCCCcccccc
Q 010297 165 DDVRMNLEVLKYCATVLFLESSLPDIFTVNSWV-SPNATTRSRSNAKSSP---EGTSQN---LSTPSSKFKFEN 231 (513)
Q Consensus 165 dDA~aTA~Ll~~ll~~L~~~~~~P~v~~~~~l~-~~~~~~r~r~~h~~~~---~~~~~~---~~s~~~~~~~~~ 231 (513)
+||.+|+++|..+++.+... ++..+..+|..+ ....+++.|++|.+++ +.|.+| ++|-+...+|..
T Consensus 339 ~DA~aTa~I~~~ll~~l~~~-~i~~~~~l~~~~~~~~~~~k~~~~hl~lLAkn~~G~~nL~kLvS~a~~~~f~~ 411 (1213)
T TIGR01405 339 YDAEATAKVFKVMVEQLKEK-GITNLEELNNKLSSEELYKRLRPNHIIIYAKNQAGLKNLYKLVSISLTKYFYT 411 (1213)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCccHHHHHHhhccchhhhhcCCcceEEEEechhhHHHHHHHHHHHHHcCCCC
Confidence 99999999999999988764 667777776554 4467889999998777 778888 666666555544
No 18
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=2.4e-30 Score=247.62 Aligned_cols=167 Identities=19% Similarity=0.248 Sum_probs=145.4
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHH
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl 85 (513)
.+..||+||+||||+++ ..++|||||||+++++.+...+.|+.+|+|.. ++++.++++||||++||++++++.+|+
T Consensus 27 ~~~~~vviD~ETTGl~~--~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~--~i~~~~~~ihGIt~~~l~~~~~~~~vl 102 (202)
T PRK09145 27 PPDEWVALDCETTGLDP--RRAEIVSIAAVKIRGNRILTSERLELLVRPPQ--SLSAESIKIHRLRHQDLEDGLSEEEAL 102 (202)
T ss_pred CCCCEEEEEeECCCCCC--CCCceEEEEEEEEECCEEeecCceEEEECCCC--CCCHhHhhhcCcCHHHHhcCCCHHHHH
Confidence 45789999999999987 67899999999999875544578999999997 899999999999999999999999999
Q ss_pred HHHHHHHcCCeEEEeCcchHHHHHHHHHHHHc-CCCCCCCCcceeHHHHHHHHh----cCCCCCCCHHHHHHHhCCC-CC
Q 010297 86 DTVFDILHGRIWAGHNILRFDCARIREAFAEI-GRPAPEPKGTIDSLALLTQRF----GRRAGDMKMASLATYFGLG-QQ 159 (513)
Q Consensus 86 ~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~-Gi~~p~~~~~IDTL~Lar~~l----~prl~s~kL~~LAk~fGI~-~~ 159 (513)
.+|.+|+++.++||||+ .||..||++++++. |.+.+ ..++|+..++.... .+..++++|++++++||++ ..
T Consensus 103 ~~~~~~i~~~~lv~hn~-~fD~~fL~~~~~~~~~~~~~--~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~ 179 (202)
T PRK09145 103 RQLLAFIGNRPLVGYYL-EFDVAMLNRYVRPLLGIPLP--NPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLG 179 (202)
T ss_pred HHHHHHHcCCeEEEeCH-HHHHHHHHHHHHHhcCCCCC--CCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCC
Confidence 99999999999999999 99999999999874 55544 35899988764322 2223578999999999998 67
Q ss_pred CCChHHHHHHHHHHHHHHHH
Q 010297 160 THRSLDDVRMNLEVLKYCAT 179 (513)
Q Consensus 160 aHRALdDA~aTA~Ll~~ll~ 179 (513)
+|+|++||++|+++|.++.+
T Consensus 180 ~H~Al~DA~ata~l~~~l~~ 199 (202)
T PRK09145 180 RHDALNDAIMAALIFLRLRK 199 (202)
T ss_pred CCCcHHHHHHHHHHHHHHHh
Confidence 89999999999999998764
No 19
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.97 E-value=3.6e-30 Score=247.42 Aligned_cols=174 Identities=21% Similarity=0.170 Sum_probs=145.7
Q ss_pred CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeC---CceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHH-HHcCCC
Q 010297 4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCP---KKLEELHNYSTLVRPADPELISSLSVRCNGITPD-AVVSSP 79 (513)
Q Consensus 4 t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~---g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~E-mLa~Ap 79 (513)
.+....+++||+||||+++ ..++|||||||++.. +.+...++|+.+|+|....+|++.+.++||||++ |+++++
T Consensus 4 ~~~~~~~vv~D~ETTGl~~--~~d~IieIgav~v~~~~~g~i~~~~~f~~~v~p~p~~~i~~~a~~ihGIt~~~~~~~~~ 81 (200)
T TIGR01298 4 RFRGYLPVVVDVETGGFNA--KTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTGIDLDHPLRGAV 81 (200)
T ss_pred hhcCCeeEEEEeeCCCCCC--CCCeEEEEEEEEEEEcCCCcEeecceeEEEEcCCCCCCCCHHHHHccCCChhhhhhcCc
Confidence 3567789999999999998 679999999999973 3222346799999985323899999999999976 699999
Q ss_pred CHHHHHHHHHHHH---------cCCeEEEeCcchHHHHHHHHHHHHcCCCC-CC-CCcceeHHHHHHHHhcCCCCCCCHH
Q 010297 80 TFADIADTVFDIL---------HGRIWAGHNILRFDCARIREAFAEIGRPA-PE-PKGTIDSLALLTQRFGRRAGDMKMA 148 (513)
Q Consensus 80 sf~EVl~ef~efL---------~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~-p~-~~~~IDTL~Lar~~l~prl~s~kL~ 148 (513)
++++++.++..++ ++.++||||+ .||+.||+++++++|... +. ...++||+.+++. ++ +.++|.
T Consensus 82 ~~~~~~~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~lDTl~lar~-~~---~~~~L~ 156 (200)
T TIGR01298 82 SEYEALHEIFKVVRKAMKASGCQRAILVGHNA-NFDLGFLNAAVERTSLKRNPFHPFSTFDTATLAGL-AY---GQTVLA 156 (200)
T ss_pred chHHHHHHHHHHHHHHHHhcccCCCEEEEECc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHH-Hc---CcccHH
Confidence 9999999988887 5789999999 999999999999998753 21 2258999999875 33 346899
Q ss_pred HHHHHhCCC---CCCCChHHHHHHHHHHHHHHHHHhhcc
Q 010297 149 SLATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 149 ~LAk~fGI~---~~aHRALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
.++++||++ .++|||++||++|+++|.++++++.+.
T Consensus 157 ~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~~~ 195 (200)
T TIGR01298 157 KACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWKRL 195 (200)
T ss_pred HHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHHHc
Confidence 999999998 379999999999999999999988654
No 20
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.3e-30 Score=252.68 Aligned_cols=163 Identities=27% Similarity=0.370 Sum_probs=146.9
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHH
Q 010297 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~e 87 (513)
.++||||+||||+++ ..|+|||||++ +. ...+.|+.+|+|.. +|++.++++||||++||+++|+|.+++.+
T Consensus 2 ~~~vv~D~ETTGl~~--~~d~IIeig~v--~~---~~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~~ 72 (232)
T PRK06309 2 PALIFYDTETTGTQI--DKDRIIEIAAY--NG---VTSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQK 72 (232)
T ss_pred CcEEEEEeeCCCCCC--CCCEEEEEEEE--cC---ccccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 469999999999987 68999999996 22 23578999999998 89999999999999999999999999999
Q ss_pred HHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHH
Q 010297 88 VFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSLD 165 (513)
Q Consensus 88 f~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHRALd 165 (513)
|.+|+++ .++||||+..||++||+++++++|++.+.. .++||+.+++ .+.+..++++|..++++||++ ..+|||++
T Consensus 73 ~~~fi~~~~~lVaHN~~~FD~~~L~~e~~r~g~~~~~~-~~iDt~~l~~-~~~~~~~~~~L~~l~~~~~~~~~~aH~Al~ 150 (232)
T PRK06309 73 FIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPPTL-RTIDSLKWAQ-KYRPDLPKHNLQYLRQVYGFEENQAHRALD 150 (232)
T ss_pred HHHHHcCCCEEEEeCCHHHHHHHHHHHHHHcCCCCCCC-cEEeHHHHHH-HHcCCCCCCCHHHHHHHcCCCCCCCCCcHH
Confidence 9999985 699999953899999999999999987764 6999999987 466777789999999999998 78999999
Q ss_pred HHHHHHHHHHHHHHHh
Q 010297 166 DVRMNLEVLKYCATVL 181 (513)
Q Consensus 166 DA~aTA~Ll~~ll~~L 181 (513)
||.+|++||.++++++
T Consensus 151 Da~~t~~vl~~l~~~~ 166 (232)
T PRK06309 151 DVITLHRVFSALVGDL 166 (232)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999998876
No 21
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.97 E-value=1.1e-30 Score=246.05 Aligned_cols=158 Identities=25% Similarity=0.299 Sum_probs=132.9
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCce-----------eEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCC
Q 010297 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKL-----------EELHNYSTLVRPADPELISSLSVRCNGITPDAVVSS 78 (513)
Q Consensus 10 ~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~-----------eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~A 78 (513)
||+||+||||++++ ..++|||||||++++++. +++++|+++|+|.. +|++.++++||||++|++++
T Consensus 1 ~vv~D~ETTGl~~~-~~d~Iiei~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~--~I~~~a~~IhGIt~e~l~~~ 77 (177)
T cd06136 1 FVFLDLETTGLPKH-NRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR--AISPGASEITGLSNDLLEHK 77 (177)
T ss_pred CeEEeeecCCCCCC-CCCceEEEEEEEEecccccccccccccccceeeeeeEEeCCCC--cCChhHHHHhCcCHHHHhcC
Confidence 68999999999832 579999999999997642 24678999999998 89999999999999999999
Q ss_pred CCHHH-HHHHHHHHH---cC-CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHH
Q 010297 79 PTFAD-IADTVFDIL---HG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATY 153 (513)
Q Consensus 79 psf~E-Vl~ef~efL---~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~ 153 (513)
+++.+ +++.+.+|+ .+ .++||||+..||++||+++++++|+.++....++||+.++++.. + +|.+|+++
T Consensus 78 ~~~~~~~~~~l~~f~~~~~~~~~lVaHNa~~FD~~fL~~~~~r~~~~~~~~~~~iDtl~l~r~~~-~-----~L~~l~~~ 151 (177)
T cd06136 78 APFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRELD-Q-----SLGSLYKR 151 (177)
T ss_pred CCccHHHHHHHHHHHHhcCCCCEEEEcCCcccCHHHHHHHHHHcCCCCCCCCEEEEeHHHHhhhH-h-----hHHHHHHH
Confidence 88763 445555555 43 58999997469999999999999998764446899999988543 3 89999885
Q ss_pred -hCCC-CCCCChHHHHHHHHHHHHH
Q 010297 154 -FGLG-QQTHRSLDDVRMNLEVLKY 176 (513)
Q Consensus 154 -fGI~-~~aHRALdDA~aTA~Ll~~ 176 (513)
||++ ..+|||++||.+|+++|++
T Consensus 152 ~~~~~~~~~H~A~~Da~at~~v~~~ 176 (177)
T cd06136 152 LFGQEPKNSHTAEGDVLALLKCALH 176 (177)
T ss_pred HhCCCcccccchHHHHHHHHHHHhh
Confidence 8999 6899999999999999875
No 22
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.97 E-value=3.7e-30 Score=247.44 Aligned_cols=162 Identities=19% Similarity=0.243 Sum_probs=139.8
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHH
Q 010297 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~e 87 (513)
..||+||+||||+++ .++|||||||+++++ .++++|+.+|+|.. ++++.++++||||++||+++|++.+++.+
T Consensus 5 ~~~vvlD~EtTGl~~---~~eIIeIgaV~v~~g--~~~~~f~~lv~P~~--~i~~~~~~lhGIt~~~v~~ap~~~evl~~ 77 (195)
T PRK07247 5 ETYIAFDLEFNTVNG---VSHIIQVSAVKYDDH--KEVDSFDSYVYTDV--PLQSFINGLTGITADKIADAPKVEEVLAA 77 (195)
T ss_pred CeEEEEEeeCCCCCC---CCeEEEEEEEEEECC--EEEEEEEEEECCCC--CCCccceecCCCCHHHHhCCCCHHHHHHH
Confidence 589999999999974 578999999999987 56789999999998 89999999999999999999999999999
Q ss_pred HHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHH-Hh--cCCCCCCCHHHHHHHhCCCCCCCChH
Q 010297 88 VFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQ-RF--GRRAGDMKMASLATYFGLGQQTHRSL 164 (513)
Q Consensus 88 f~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~-~l--~prl~s~kL~~LAk~fGI~~~aHRAL 164 (513)
|.+|+++.++||||+..||+.||++ .|...... .++|++..+.. .. .+..++|+|.+||++||++..+|||+
T Consensus 78 f~~f~~~~~lVaHNa~~fD~~fL~~----~g~~~~~~-~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~~~HrAl 152 (195)
T PRK07247 78 FKEFVGELPLIGYNAQKSDLPILAE----NGLDLSDQ-YQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKGRGHNSL 152 (195)
T ss_pred HHHHHCCCeEEEEeCcHhHHHHHHH----cCCCcCCC-ceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCCCCcCCH
Confidence 9999999999999993389999964 46654432 47888865422 22 35568899999999999997789999
Q ss_pred HHHHHHHHHHHHHHHHh
Q 010297 165 DDVRMNLEVLKYCATVL 181 (513)
Q Consensus 165 dDA~aTA~Ll~~ll~~L 181 (513)
+||++|+++|.++++.-
T Consensus 153 ~DA~~ta~v~~~ll~~~ 169 (195)
T PRK07247 153 EDARMTARVYESFLESD 169 (195)
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 99999999999998753
No 23
>PRK07883 hypothetical protein; Validated
Probab=99.97 E-value=4.3e-30 Score=280.41 Aligned_cols=186 Identities=27% Similarity=0.392 Sum_probs=163.7
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 3 ~t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
....+..||+||+||||+++ ..++|||||||+++++ .++++|+.+|+|.. ++++.++++||||++||++++++.
T Consensus 10 ~~~~~~~~Vv~D~ETTGl~p--~~~~IIEIgaV~v~~g--~iv~~f~~lV~P~~--~i~~~~~~itGIt~e~l~~ap~~~ 83 (557)
T PRK07883 10 TPLRDVTFVVVDLETTGGSP--AGDAITEIGAVKVRGG--EVLGEFATLVNPGR--PIPPFITVLTGITTAMVAGAPPIE 83 (557)
T ss_pred CCCcCCCEEEEEEecCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEECCCC--CCChhHHhhcCCCHHHHhCCCCHH
Confidence 45667899999999999987 6799999999999977 57799999999988 899999999999999999999999
Q ss_pred HHHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcC-CCCCCCHHHHHHHhCCC-CCC
Q 010297 83 DIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGR-RAGDMKMASLATYFGLG-QQT 160 (513)
Q Consensus 83 EVl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~p-rl~s~kL~~LAk~fGI~-~~a 160 (513)
+++.+|.+|+++.++||||+ .||++||+++|+++|++.+.+ .++||+.++++.+.+ ..++++|.+|+++||++ ..+
T Consensus 84 evl~~f~~fl~~~~lVaHNa-~FD~~fL~~~~~r~g~~~~~~-~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~~~ 161 (557)
T PRK07883 84 EVLPAFLEFARGAVLVAHNA-PFDIGFLRAAAARCGYPWPGP-PVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTTPT 161 (557)
T ss_pred HHHHHHHHHhcCCEEEEeCc-HHHHHHHHHHHHHcCCCCCCC-CcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccCCC
Confidence 99999999999999999999 999999999999999987754 699999999854432 56899999999999999 789
Q ss_pred CChHHHHHHHHHHHHHHHHHhhcccCCCCcccccccc
Q 010297 161 HRSLDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWV 197 (513)
Q Consensus 161 HRALdDA~aTA~Ll~~ll~~L~~~~~~P~v~~~~~l~ 197 (513)
|||++||++|+++|.+++.++.. .+...+..+..++
T Consensus 162 H~Al~DA~ata~l~~~l~~~~~~-~~~~~~~~l~~~~ 197 (557)
T PRK07883 162 HRALDDARATVDVLHGLIERLGN-LGVHTLEELLTYL 197 (557)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHh-cCCCCHHHHHHhh
Confidence 99999999999999999998863 3444444443343
No 24
>PRK05168 ribonuclease T; Provisional
Probab=99.97 E-value=6.4e-30 Score=247.56 Aligned_cols=173 Identities=20% Similarity=0.176 Sum_probs=146.6
Q ss_pred CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeC---CceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHH-HcCCC
Q 010297 4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCP---KKLEELHNYSTLVRPADPELISSLSVRCNGITPDA-VVSSP 79 (513)
Q Consensus 4 t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~---g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~Em-La~Ap 79 (513)
...+..+|+||+||||+++ ..++|||||||++.. +.+.+.++|+.+|+|....++++.++++||||+++ +++++
T Consensus 13 ~~~~~~~vv~D~ETTGl~~--~~d~IieIgaV~v~~d~~g~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~e~~~~~~~ 90 (211)
T PRK05168 13 RFRGFLPVVIDVETAGFNA--KTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFNGIDPDNPLRGAV 90 (211)
T ss_pred HhcCCceEEEEeeCCCCCC--CCCEEEEEeEEEEEecCCCcEeccceEEEEECCCCCCCCCHHHHhhcCCCchhhhhcCC
Confidence 3456789999999999998 689999999999973 33335689999999953237999999999999986 89999
Q ss_pred CHHHHHHHHHHHHc---------CCeEEEeCcchHHHHHHHHHHHHcCCCCC--CCCcceeHHHHHHHHhcCCCCCCCHH
Q 010297 80 TFADIADTVFDILH---------GRIWAGHNILRFDCARIREAFAEIGRPAP--EPKGTIDSLALLTQRFGRRAGDMKMA 148 (513)
Q Consensus 80 sf~EVl~ef~efL~---------g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p--~~~~~IDTL~Lar~~l~prl~s~kL~ 148 (513)
++.+++.+|.+|+. +.++||||+ .||+.||+++++++|+... ...+++||+.+++. +.+ .++|.
T Consensus 91 ~~~~~l~~~~~~l~~~~~~~~~~~~~lVaHNa-~FD~~fL~~~~~r~~~~~~~~~~~~~iDt~~lar~-~~~---~~~L~ 165 (211)
T PRK05168 91 SEKEALHEIFKMVRKGIKASGCNRAILVAHNA-HFDLSFLMAAAERAGLKRNPFHPFSTFDTATLSGL-ALG---QTVLA 165 (211)
T ss_pred ChHHHHHHHHHHHHHHHHhcccCCceEEEecc-HHhHHHHHHHHHHhCCCCCCCCCCcEeeHHHHHHH-HcC---CCCHH
Confidence 99999999998875 679999999 9999999999999987422 12258999999875 433 45899
Q ss_pred HHHHHhCCC---CCCCChHHHHHHHHHHHHHHHHHhhc
Q 010297 149 SLATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLFL 183 (513)
Q Consensus 149 ~LAk~fGI~---~~aHRALdDA~aTA~Ll~~ll~~L~~ 183 (513)
++++++|++ ..+|||++||++|+++|.++++++..
T Consensus 166 ~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~~~ 203 (211)
T PRK05168 166 KACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRWKR 203 (211)
T ss_pred HHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence 999999998 36999999999999999999998754
No 25
>PRK06722 exonuclease; Provisional
Probab=99.97 E-value=1e-29 Score=256.72 Aligned_cols=170 Identities=16% Similarity=0.244 Sum_probs=146.8
Q ss_pred CCCcEEEEEEecCCCCCC-CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 6 DRSEIAFFDVETTVPTRP-GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~-g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
+...|+|||+||||.... ...++|||||||+++++.++++++|+.+|+|.. +++++++++||||++||++||+|++|
T Consensus 3 ~~~~~vViD~ETT~~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~--~I~~~i~~LTGIT~emV~~AP~f~eV 80 (281)
T PRK06722 3 NATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGA--RLTRHTTKLTGITKKDLIGVEKFPQI 80 (281)
T ss_pred CCCEEEEEEeeCCCCCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCC--cCCHhHhhhcCCCHHHHcCCCCHHHH
Confidence 348999999999964221 134899999999999887788899999999998 89999999999999999999999999
Q ss_pred HHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCC--CcceeHHHHHHHHhcCCC--CCCCHHHHHHHhCCC--C
Q 010297 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEP--KGTIDSLALLTQRFGRRA--GDMKMASLATYFGLG--Q 158 (513)
Q Consensus 85 l~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~--~~~IDTL~Lar~~l~prl--~s~kL~~LAk~fGI~--~ 158 (513)
+.+|.+|+++.++|+||+ .||++||+++++++|++.|.. ..++|+.++++..+ ++. ..++|.+++++||++ .
T Consensus 81 l~ef~~fig~~~lvahna-~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~-~~l~~~~~sL~~l~~~lgL~~~g 158 (281)
T PRK06722 81 IEKFIQFIGEDSIFVTWG-KEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAY-EELFEHTPSLQSAVEQLGLIWEG 158 (281)
T ss_pred HHHHHHHHCCCcEEEEEe-HHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHh-hhhccCCCCHHHHHHHCCCCCCC
Confidence 999999999888888998 999999999999999876642 24789988876433 332 356899999999999 3
Q ss_pred CCCChHHHHHHHHHHHHHHHH
Q 010297 159 QTHRSLDDVRMNLEVLKYCAT 179 (513)
Q Consensus 159 ~aHRALdDA~aTA~Ll~~ll~ 179 (513)
++|||++||++||++|.++++
T Consensus 159 ~~HrAL~DA~~TA~L~l~l~~ 179 (281)
T PRK06722 159 KQHRALADAENTANILLKAYS 179 (281)
T ss_pred CCcCcHHHHHHHHHHHHHHhc
Confidence 799999999999999999884
No 26
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.97 E-value=1.6e-29 Score=240.59 Aligned_cols=167 Identities=21% Similarity=0.205 Sum_probs=138.6
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCC---ceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHH-HcCCCCHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPK---KLEELHNYSTLVRPADPELISSLSVRCNGITPDA-VVSSPTFA 82 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g---~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~Em-La~Apsf~ 82 (513)
.-.+|+||+||||+++ ..++|||||||+++.+ .+.+.++|+++|+|....++++.+.++||||+++ ++.++...
T Consensus 4 ~~~~vv~D~ETTGl~~--~~d~Iieigav~v~~~~~~~i~~~~~f~~lv~P~~~~~i~~~~~~ihGIt~~~~~~~~~~~~ 81 (189)
T cd06134 4 GFLPVVVDVETGGFNP--QTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDEK 81 (189)
T ss_pred cceeEEEEecCCCCCC--CCCeEEEEEEEEEEECCCCceeccceEEEEEcCCCCCCCCHHHHhhcCCCchhhhccccchH
Confidence 3468999999999998 6899999999999743 2345689999999953238999999999999986 67788777
Q ss_pred HHHHHHHHHHc---------CCeEEEeCcchHHHHHHHHHHHHcCCC-CCC-CCcceeHHHHHHHHhcCCCCCCCHHHHH
Q 010297 83 DIADTVFDILH---------GRIWAGHNILRFDCARIREAFAEIGRP-APE-PKGTIDSLALLTQRFGRRAGDMKMASLA 151 (513)
Q Consensus 83 EVl~ef~efL~---------g~vLVAHNa~~FD~~FL~~~f~r~Gi~-~p~-~~~~IDTL~Lar~~l~prl~s~kL~~LA 151 (513)
+++.+|.+++. +.++||||+ .||+.||+++++++|+. .++ ...++||+.+++.. .+ .++|+++|
T Consensus 82 ~~~~~~~~~l~~~~~~~~~~~~~lVaHna-~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~-~~---~~~L~~l~ 156 (189)
T cd06134 82 EALKEIFKPIRKALKAQGCTRAILVGHNA-HFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLA-YG---QTVLAKAC 156 (189)
T ss_pred HHHHHHHHHHHHHHhhcccCCCeEEEecc-hhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHH-hC---CCcHHHHH
Confidence 77777777663 679999999 99999999999999983 332 23589999998854 33 46899999
Q ss_pred HHhCCC---CCCCChHHHHHHHHHHHHHHHHH
Q 010297 152 TYFGLG---QQTHRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 152 k~fGI~---~~aHRALdDA~aTA~Ll~~ll~~ 180 (513)
++||++ .++|+|++||++|+++|.+++++
T Consensus 157 ~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~ 188 (189)
T cd06134 157 QAAGIEFDNKEAHSALYDTQKTAELFCKIVNR 188 (189)
T ss_pred HHCCCCCCCCCCcChHHHHHHHHHHHHHHHHh
Confidence 999998 37899999999999999998764
No 27
>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=99.97 E-value=2.2e-29 Score=231.71 Aligned_cols=166 Identities=22% Similarity=0.265 Sum_probs=144.8
Q ss_pred EEEEEEecCCCCCC---CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 10 IAFFDVETTVPTRP---GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 10 ~VVfDlETTGLd~~---g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
||+||+||||+++. +..++|||||||+++.+..++++.|+.+|+|.....+++.+.++||||++++++++++.+|+.
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 69999999999861 124899999999999987668899999999997557999999999999999999999999999
Q ss_pred HHHHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCC--CCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-C-CC
Q 010297 87 TVFDILHGR--IWAGHNILRFDCARIREAFAEIGRP--APEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-Q-QT 160 (513)
Q Consensus 87 ef~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~--~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~-~a 160 (513)
+|.+|+++. .+++|++ .||..+|.+.+.+.+.. ++....++|+..++++.+ +..+.++|.+++++||++ . ++
T Consensus 81 ~~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~-~~~~~~~L~~l~~~~gi~~~~~~ 158 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFY-GLKKRTGLSKALEYLGLEFEGRH 158 (176)
T ss_pred HHHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHh-CCCCCCCHHHHHHHCCCCCCCCC
Confidence 999999987 6777777 99999999998888764 344457999999988544 445789999999999998 4 79
Q ss_pred CChHHHHHHHHHHHHHH
Q 010297 161 HRSLDDVRMNLEVLKYC 177 (513)
Q Consensus 161 HRALdDA~aTA~Ll~~l 177 (513)
|+|++||++|+++|+++
T Consensus 159 H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 159 HRGLDDARNIARILKRL 175 (176)
T ss_pred cCcHHHHHHHHHHHHHh
Confidence 99999999999999886
No 28
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=6.6e-29 Score=281.45 Aligned_cols=169 Identities=20% Similarity=0.354 Sum_probs=154.7
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 3 ~t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
|+....+||+||+||||+++ .++|||||||+++++ +++++|+++|+|.. ++++.++++||||++||+++|+|+
T Consensus 2 ~~~~~~~~vvvD~ETTGl~~---~d~IIeIgaV~v~~g--~i~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ 74 (820)
T PRK07246 2 TQKKLRKYAVVDLEATGAGP---NASIIQVGIVIIEGG--EIIDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFS 74 (820)
T ss_pred ccccCCCEEEEEEecCCcCC---CCeEEEEEEEEEECC--EEEEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHH
Confidence 34566889999999999975 489999999999987 67899999999998 899999999999999999999999
Q ss_pred HHHHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCC
Q 010297 83 DIADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTH 161 (513)
Q Consensus 83 EVl~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aH 161 (513)
+|+.+|.+|+++.++||||+ .||++||++++.+.|.+.+ .+++||+.+++ .++|..++|+|.+||++||++ .++|
T Consensus 75 ev~~~~~~~l~~~~lVaHN~-~FD~~fL~~~~~~~g~~~~--~~~iDT~~la~-~~~p~~~~~~L~~L~~~lgl~~~~~H 150 (820)
T PRK07246 75 QVARHIYDLIEDCIFVAHNV-KFDANLLAEALFLEGYELR--TPRVDTVELAQ-VFFPTLEKYSLSHLSRELNIDLADAH 150 (820)
T ss_pred HHHHHHHHHhCCCEEEEECc-HHHHHHHHHHHHHcCCCCC--CCceeHHHHHH-HHhCCCCCCCHHHHHHHcCCCCCCCC
Confidence 99999999999999999999 9999999999988888755 35899999987 566778899999999999999 6899
Q ss_pred ChHHHHHHHHHHHHHHHHHhh
Q 010297 162 RSLDDVRMNLEVLKYCATVLF 182 (513)
Q Consensus 162 RALdDA~aTA~Ll~~ll~~L~ 182 (513)
||++||++|+++|.++++++.
T Consensus 151 ~Al~DA~ata~L~~~l~~~l~ 171 (820)
T PRK07246 151 TAIADARATAELFLKLLQKIE 171 (820)
T ss_pred CHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999998774
No 29
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.96 E-value=6.2e-29 Score=234.80 Aligned_cols=160 Identities=23% Similarity=0.282 Sum_probs=136.2
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcC-CCCHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTFADIADTVF 89 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~-Apsf~EVl~ef~ 89 (513)
+|||+||||+++ ..++|||||||+++++.. +++.|+.+|+|.....+++.+.++||||++||++ ++++.+++.+|.
T Consensus 1 ~~~D~ETTGl~~--~~d~Iieig~v~v~~~~~-~~~~~~~~v~p~~~~~~~~~a~~ihGIt~e~l~~~~~~~~~~l~~~~ 77 (183)
T cd06138 1 LFYDYETFGLNP--SFDQILQFAAIRTDENFN-EIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIH 77 (183)
T ss_pred CEEEeecCCCCC--CCCceEEEEEEEECCCCC-CccceeEEEeCCCCCCCCHHHHHHhCCCHHHHHhcCCCHHHHHHHHH
Confidence 589999999998 689999999999987643 4489999999875336788999999999999999 899999999999
Q ss_pred HHHc--CCeEEEeC-cchHHHHHHHHHHHHcCCCCCC-----CCcceeHHHHHHHHh--cC----------CCCCCCHHH
Q 010297 90 DILH--GRIWAGHN-ILRFDCARIREAFAEIGRPAPE-----PKGTIDSLALLTQRF--GR----------RAGDMKMAS 149 (513)
Q Consensus 90 efL~--g~vLVAHN-a~~FD~~FL~~~f~r~Gi~~p~-----~~~~IDTL~Lar~~l--~p----------rl~s~kL~~ 149 (513)
+|++ +.++|||| + .||+.||++++.+++..++. ...++||+.+++..+ .+ ..++++|++
T Consensus 78 ~~~~~~~~~lVahn~~-~FD~~fL~~~~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~ 156 (183)
T cd06138 78 RLFNTPGTCIVGYNNI-RFDDEFLRFAFYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLED 156 (183)
T ss_pred HHHccCCCcEEeeCch-hhHHHHHHHHHHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHH
Confidence 9995 57899997 6 99999999999999886432 224689999887432 12 246899999
Q ss_pred HHHHhCCC-CCCCChHHHHHHHHHHH
Q 010297 150 LATYFGLG-QQTHRSLDDVRMNLEVL 174 (513)
Q Consensus 150 LAk~fGI~-~~aHRALdDA~aTA~Ll 174 (513)
|+++||++ .++|||++||++|++|+
T Consensus 157 l~~~~gi~~~~~H~Al~Da~~ta~l~ 182 (183)
T cd06138 157 LAQANGIEHSNAHDALSDVEATIALA 182 (183)
T ss_pred HHHHCCCCccccccHHHHHHHHHHHh
Confidence 99999999 68999999999999886
No 30
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.8e-28 Score=281.11 Aligned_cols=168 Identities=24% Similarity=0.377 Sum_probs=154.7
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
.++||+||+||||+++. ..++|||||||+++++ +++++|+.+|+|.. ++++++.++||||++||+++|+|.+++.
T Consensus 2 ~~~~vvvD~ETTG~~p~-~~d~IIeigav~v~~~--~i~~~f~~~v~P~~--~i~~~~~~ltGIt~~~l~~ap~f~ev~~ 76 (928)
T PRK08074 2 SKRFVVVDLETTGNSPK-KGDKIIQIAAVVVEDG--EILERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDVAP 76 (928)
T ss_pred CCCEEEEEEeCCCCCCC-CCCcEEEEEEEEEECC--EEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHhcCCCHHHHHH
Confidence 46799999999999762 3589999999999877 67899999999998 8999999999999999999999999999
Q ss_pred HHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHH
Q 010297 87 TVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSLD 165 (513)
Q Consensus 87 ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHRALd 165 (513)
+|.+|+++.++||||+ .||++||+++|.+.|++.+.. +++||+.+++ .+.|...+|+|.+|+++||++ .++|||++
T Consensus 77 ~l~~~l~~~~~VaHN~-~FD~~fL~~~~~~~g~~~~~~-~~iDt~~la~-~~~p~~~~~~L~~l~~~l~i~~~~~H~Al~ 153 (928)
T PRK08074 77 EIVELLEGAYFVAHNV-HFDLNFLNEELERAGYTEIHC-PKLDTVELAR-ILLPTAESYKLRDLSEELGLEHDQPHRADS 153 (928)
T ss_pred HHHHHhCCCeEEEECh-HHHHHHHHHHHHHcCCCCCCC-CeeeHHHHHH-HhcCCCCCCCHHHHHHhCCCCCCCCCChHH
Confidence 9999999999999999 999999999999999986643 6999999987 566778899999999999999 68999999
Q ss_pred HHHHHHHHHHHHHHHhh
Q 010297 166 DVRMNLEVLKYCATVLF 182 (513)
Q Consensus 166 DA~aTA~Ll~~ll~~L~ 182 (513)
||++|+++|.+++.++.
T Consensus 154 DA~ata~l~~~l~~~~~ 170 (928)
T PRK08074 154 DAEVTAELFLQLLNKLE 170 (928)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999998875
No 31
>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=99.96 E-value=3.9e-28 Score=215.05 Aligned_cols=157 Identities=28% Similarity=0.458 Sum_probs=141.4
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~e 90 (513)
|++|+||||+++ ..++|||||+|.++.+ +++++.|+.+|+|.. .+++.+.++||||++++++++++.+++.+|.+
T Consensus 1 v~~D~Ettg~~~--~~~~iiei~~v~~~~~-~~~~~~~~~~i~p~~--~~~~~~~~~~gi~~~~~~~~~~~~~~~~~~~~ 75 (159)
T cd06127 1 VVFDTETTGLDP--KKDRIIEIGAVKVDGG-IEIVERFETLVNPGR--PIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75 (159)
T ss_pred CeEEeeCCCcCC--CCCeEEEEEEEEEECC-cChhhhhheeeCcCC--cCCHhheeccCCCHHHHhcCCCHHHHHHHHHH
Confidence 689999999987 6899999999999987 567899999999998 78999999999999999999999999999999
Q ss_pred HHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHH-HHHhCCC-CCCCChHHHHH
Q 010297 91 ILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASL-ATYFGLG-QQTHRSLDDVR 168 (513)
Q Consensus 91 fL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~L-Ak~fGI~-~~aHRALdDA~ 168 (513)
|+.+.++||||+ .||..||++.+.++|... ....++||+.+++. +.+....+++..+ ++++|++ ..+|+|++||+
T Consensus 76 ~l~~~~~v~~n~-~fD~~~l~~~~~~~~~~~-~~~~~iDt~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~H~Al~Da~ 152 (159)
T cd06127 76 FLGGRVLVAHNA-SFDLRFLNRELRRLGGPP-LPNPWIDTLRLARR-LLPGLRSHRLGLLLAERYGIPLEGAHRALADAL 152 (159)
T ss_pred HHCCCEEEEeCc-HhhHHHHHHHHHHhCCCC-CCCCeeEHHHHHHH-HcCCCCcCchHHHHHHHcCCCCCCCCCcHHHHH
Confidence 999999999999 999999999999998443 34579999999874 4555677899998 8899998 68999999999
Q ss_pred HHHHHHH
Q 010297 169 MNLEVLK 175 (513)
Q Consensus 169 aTA~Ll~ 175 (513)
+|+++|.
T Consensus 153 ~t~~l~~ 159 (159)
T cd06127 153 ATAELLL 159 (159)
T ss_pred HHHHHhC
Confidence 9999873
No 32
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.96 E-value=6.3e-28 Score=274.33 Aligned_cols=165 Identities=24% Similarity=0.382 Sum_probs=152.4
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHH
Q 010297 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (513)
Q Consensus 9 ~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef 88 (513)
+||+||+||||+++ ..++|||||||+++++ +++++|+++|+|.. ++++.++++||||++||+++|.|.+++.+|
T Consensus 1 ~~vvvD~ETTG~~~--~~~~IIeig~v~v~~~--~i~~~f~~~v~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l 74 (850)
T TIGR01407 1 RYAVVDLETTGTQL--SFDKIIQIGIVVVEDG--EIVDTFHTDVNPNE--PIPPFIQELTGISDNMLQQAPYFSQVAQEI 74 (850)
T ss_pred CEEEEEEECCCCCC--CCCeEEEEEEEEEECC--EEEEEEEEEeCCCC--CCChhhhhhcCcCHHHHhCCCCHHHHHHHH
Confidence 48999999999987 6799999999999876 67799999999998 899999999999999999999999999999
Q ss_pred HHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCChHHHH
Q 010297 89 FDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRSLDDV 167 (513)
Q Consensus 89 ~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHRALdDA 167 (513)
.+|+++.++||||+ .||+.||+++|+++|+++.. .+++||+.+++ .+.|..++++|.+|+++||++ .++|||++||
T Consensus 75 ~~~l~~~~~VahN~-~fD~~fL~~~~~~~g~~~~~-~~~iDt~~l~~-~~~p~~~~~~L~~l~~~~gi~~~~~H~Al~DA 151 (850)
T TIGR01407 75 YDLLEDGIFVAHNV-HFDLNFLAKALKDCGYEPLP-KPRIDTVELAQ-IFFPTEESYQLSELSEALGLTHENPHRADSDA 151 (850)
T ss_pred HHHhCCCEEEEeCc-HHHHHHHHHHHHHcCCCCCC-CCeEeHHHHHH-HhcCCCCCCCHHHHHHHCCCCCCCCCChHHHH
Confidence 99999999999999 99999999999999987543 36999999987 566777899999999999999 6899999999
Q ss_pred HHHHHHHHHHHHHhh
Q 010297 168 RMNLEVLKYCATVLF 182 (513)
Q Consensus 168 ~aTA~Ll~~ll~~L~ 182 (513)
++|+++|.++++++.
T Consensus 152 ~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 152 QATAELLLLLFEKME 166 (850)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999988764
No 33
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=99.96 E-value=1.1e-27 Score=248.69 Aligned_cols=164 Identities=16% Similarity=0.270 Sum_probs=140.3
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
+.+..||+||+||||+++ ..++|||||||++..++ .+++.|+++|+|.. ...+ ..+||||++||+++|+|.++
T Consensus 43 ~~~~~fVvlDiETTGLdp--~~drIIeIgAV~i~~~g-~ive~f~tLVnP~~--~~~p--~~LHGIT~e~La~AP~f~eV 115 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHP--STSRLITIDAVTLTADG-EEVEHFHAVLNPGE--DPGP--FHLHGLSAEEFAQGKRFSQI 115 (377)
T ss_pred CCCCCEEEEEEECCCCCC--CCCeEEEEEEEEEEcCC-EEEEEEEEEECcCC--CCCC--ccccCCCHHHHhcCCCHHHH
Confidence 456789999999999998 78999999999998553 67899999999987 3333 37999999999999999999
Q ss_pred HHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCC--------------------------CCCCCCcceeHHHHHHHHh
Q 010297 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGR--------------------------PAPEPKGTIDSLALLTQRF 138 (513)
Q Consensus 85 l~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi--------------------------~~p~~~~~IDTL~Lar~~l 138 (513)
+.+|.+|+++++|||||+ .||++||++++++++. ..+....++||+.++| .+
T Consensus 116 l~el~~fL~g~vLVaHNA-~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~p~p~~~iDTL~LAR-rl 193 (377)
T PRK05601 116 LKPLDRLIDGRTLILHNA-PRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKPVVIVDTLATAR-RQ 193 (377)
T ss_pred HHHHHHHhCCCEEEEECc-HHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCCCCCCCEEEhHHHHH-HH
Confidence 999999999999999999 9999999999877522 1122336999999998 46
Q ss_pred cCCCCCCCHHHHHHHhCCCC-----------CCCChH--HHHHHHHHHHHHH
Q 010297 139 GRRAGDMKMASLATYFGLGQ-----------QTHRSL--DDVRMNLEVLKYC 177 (513)
Q Consensus 139 ~prl~s~kL~~LAk~fGI~~-----------~aHRAL--dDA~aTA~Ll~~l 177 (513)
++.+++|+|.+||++||++. ..|+|+ +||+.++++|.++
T Consensus 194 ~p~l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~ 245 (377)
T PRK05601 194 GVALDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFAL 245 (377)
T ss_pred cCCCCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHh
Confidence 67889999999999999963 357778 5999999999886
No 34
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.95 E-value=2.8e-27 Score=231.24 Aligned_cols=147 Identities=22% Similarity=0.235 Sum_probs=129.2
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHH
Q 010297 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVF 89 (513)
Q Consensus 10 ~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~ 89 (513)
++|||+||||+++ .|||||+|.+.++ .+.+.|+.+|+|.. +|++.++++||||++||+++|++.+++.+
T Consensus 2 ~~vlD~ETTGl~~-----~IieIg~v~v~~~--~i~~~~~~lv~P~~--~i~~~~~~ihgIt~e~v~~ap~~~ev~~~-- 70 (219)
T PRK07983 2 LRVIDTETCGLQG-----GIVEIASVDVIDG--KIVNPMSHLVRPDR--PISPQAMAIHRITEAMVADKPWIEDVIPH-- 70 (219)
T ss_pred eEEEEEECCCCCC-----CCEEEEEEEEECC--EEEEEEEEEECcCC--CCCHHHhhcCCCCHHHHcCCCCHHHHHHH--
Confidence 7999999999964 3999999999876 56789999999998 89999999999999999999999999887
Q ss_pred HHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC------CCCCCh
Q 010297 90 DILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG------QQTHRS 163 (513)
Q Consensus 90 efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~------~~aHRA 163 (513)
|+++.++||||+ .||++||.. . ...|+||++++|+ ++|+.+ ++|..|+++||++ ..+|||
T Consensus 71 -~~~~~~lVaHNa-~FD~~~L~~---------~-~~~~idTl~lar~-l~p~~~-~~l~~L~~~~~l~~~~~~~~~aHrA 136 (219)
T PRK07983 71 -YYGSEWYVAHNA-SFDRRVLPE---------M-PGEWICTMKLARR-LWPGIK-YSNMALYKSRKLNVQTPPGLHHHRA 136 (219)
T ss_pred -HcCCCEEEEeCc-HhhHHHHhC---------c-CCCcEeHHHHHHH-HccCCC-CCHHHHHHHcCCCCCCCCCCCCCcH
Confidence 468899999999 999999952 1 1369999999985 566665 8999999999985 369999
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010297 164 LDDVRMNLEVLKYCATVL 181 (513)
Q Consensus 164 LdDA~aTA~Ll~~ll~~L 181 (513)
++||.+|+++|.++++..
T Consensus 137 l~Da~ata~ll~~l~~~~ 154 (219)
T PRK07983 137 LYDCYITAALLIDIMNTS 154 (219)
T ss_pred HHHHHHHHHHHHHHHHHc
Confidence 999999999999998654
No 35
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=99.95 E-value=4.4e-28 Score=285.30 Aligned_cols=217 Identities=22% Similarity=0.287 Sum_probs=191.2
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
..+.++|+||+||||+++ ..++|||||||+++.+ .+++.|+.+|+|.. ++++.++++||||++|+.+++++.+|
T Consensus 416 L~~~~~VVfDLETTGL~~--~~deIIEIgAV~V~~G--~iie~F~~~V~P~~--~I~~~~~~LTGIT~e~L~~aps~~Ea 489 (1437)
T PRK00448 416 LKDATYVVFDVETTGLSA--VYDEIIEIGAVKIKNG--EIIDKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEV 489 (1437)
T ss_pred hccCcEEEEEhhhcCCCC--chhhhheeeeEEEeCC--eEeeeEEEEECCCC--CCCHHHHHHhCCCHHHHcCCCCHHHH
Confidence 345689999999999987 7899999999999977 56799999999998 89999999999999999999999999
Q ss_pred HHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC-CCCCCh
Q 010297 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG-QQTHRS 163 (513)
Q Consensus 85 l~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~-~~aHRA 163 (513)
+.+|.+|+++.++||||+ .||++||++.++++|++.+.. .++||+.+++ .+.+...+++|.+||++||++ ..+|||
T Consensus 490 L~~f~~figg~vLVAHNa-~FD~~fL~~~l~rlgl~~l~~-~~IDTLelar-~l~p~~k~~kL~~LAk~lGL~~~~~HrA 566 (1437)
T PRK00448 490 LPKFKEFCGDSILVAHNA-SFDVGFINTNYEKLGLEKIKN-PVIDTLELSR-FLYPELKSHRLNTLAKKFGVELEHHHRA 566 (1437)
T ss_pred HHHHHHHhCCCEEEEeCc-cccHHHHHHHHHHcCCccccc-cceeHHHHHH-HHcCccccccHHHHHHHcCCCCCCCcCh
Confidence 999999999999999999 999999999999999976544 6999999987 466777899999999999999 689999
Q ss_pred HHHHHHHHHHHHHHHHHhhcccCCCCcccccccc-CCCccccccCCccccC---CCCCCC---CCCCCCcccccc
Q 010297 164 LDDVRMNLEVLKYCATVLFLESSLPDIFTVNSWV-SPNATTRSRSNAKSSP---EGTSQN---LSTPSSKFKFEN 231 (513)
Q Consensus 164 LdDA~aTA~Ll~~ll~~L~~~~~~P~v~~~~~l~-~~~~~~r~r~~h~~~~---~~~~~~---~~s~~~~~~~~~ 231 (513)
++||.+|+++|.++++.+.. .++..+.+++.+. ....+++.|++|.+++ +.|.+| ++|-+...+|.+
T Consensus 567 l~DA~aTa~lf~~ll~~l~~-~gi~~~~~L~~~~~~~~~~~~~~~~h~~llAkn~~G~knL~kLvS~s~~~~f~~ 640 (1437)
T PRK00448 567 DYDAEATAYLLIKFLKDLKE-KGITNLDELNKKLGSEDAYKKARPKHATILVKNQVGLKNLFKLVSLSNTKYFYR 640 (1437)
T ss_pred HHHHHHHHHHHHHHHHHHHH-cCCCCHHHHHHHhccccchhccCcccceEEeCCHHHHHHHHHHHHHHHHhcCCC
Confidence 99999999999999999875 4777777787766 3466789999998777 677777 677777666654
No 36
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=99.95 E-value=4e-28 Score=225.25 Aligned_cols=144 Identities=21% Similarity=0.324 Sum_probs=124.4
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCC-------HHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPT-------FAD 83 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Aps-------f~E 83 (513)
|+|||||||+++ ..++|||||||.+.++ +++ |+.+|+|.. +++++++++||||++||+++++ +++
T Consensus 1 v~lD~EttGl~~--~~d~ii~Ig~V~v~~g--~i~--~~~~v~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~~~~~~~~ 72 (161)
T cd06137 1 VALDCEMVGLAD--GDSEVVRISAVDVLTG--EVL--IDSLVRPSV--RVTDWRTRFSGVTPADLEEAAKAGKTIFGWEA 72 (161)
T ss_pred CEEEeeeeeEcC--CCCEEEEEEEEEcCCC--eEE--EeccccCCC--CCCccceeccCCCHHHHhhhhhcCCccccHHH
Confidence 689999999998 6899999999999766 333 889999987 8999999999999999999875 458
Q ss_pred HHHHHHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCC---CCCCHHHHHHH-hCCC-
Q 010297 84 IADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRA---GDMKMASLATY-FGLG- 157 (513)
Q Consensus 84 Vl~ef~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl---~s~kL~~LAk~-fGI~- 157 (513)
++++|.+|+++ .++||||+ .||+.||+.. ..+++||+.++++ +.+.. .+++|.+||++ ||++
T Consensus 73 ~~~~~~~~i~~~~vlVgHn~-~fD~~fL~~~----------~~~~iDT~~l~~~-~~~~~~~~~~~~L~~L~~~~~~~~~ 140 (161)
T cd06137 73 ARAALWKFIDPDTILVGHSL-QNDLDALRMI----------HTRVVDTAILTRE-AVKGPLAKRQWSLRTLCRDFLGLKI 140 (161)
T ss_pred HHHHHHHhcCCCcEEEeccH-HHHHHHHhCc----------CCCeeEehhhhhh-ccCCCcCCCCccHHHHHHHHCCchh
Confidence 99999999998 89999999 9999999742 1258999999985 44544 68999999986 6876
Q ss_pred ---CCCCChHHHHHHHHHHH
Q 010297 158 ---QQTHRSLDDVRMNLEVL 174 (513)
Q Consensus 158 ---~~aHRALdDA~aTA~Ll 174 (513)
..+|+|+.||++|+++|
T Consensus 141 ~~~~~~H~A~~DA~at~~l~ 160 (161)
T cd06137 141 QGGGEGHDSLEDALAAREVV 160 (161)
T ss_pred cCCCCCCCcHHHHHHHHHHh
Confidence 25899999999999987
No 37
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=99.95 E-value=2.9e-26 Score=223.48 Aligned_cols=164 Identities=26% Similarity=0.389 Sum_probs=149.9
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEe-eeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEEL-HNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eiv-dsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
.++++||+||||+++ ..++|||||||.+.++ .++ .+|+.+|+|.. ++++.+.++||||.+||.++|.|.+++.
T Consensus 13 ~~~vv~D~ETtg~~~--~~~~iieIgav~~~~~--~i~~~~~~~~v~P~~--~i~~~~~~i~git~e~l~~~p~~~~v~~ 86 (243)
T COG0847 13 TRFVVIDLETTGLNP--KKDRIIEIGAVTLEDG--RIVERSFHTLVNPER--PIPPEIFKIHGITDEMLADAPKFAEVLP 86 (243)
T ss_pred CcEEEEecccCCCCC--CCCceEEEEeEEEECC--eeecceeEEEECCCC--CCChhhhhhcCCCHHHHhcCCCHHHHHH
Confidence 578999999999987 6899999999999998 445 44999999976 8999999999999999999999999999
Q ss_pred HHHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC---CCCCC
Q 010297 87 TVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG---QQTHR 162 (513)
Q Consensus 87 ef~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~---~~aHR 162 (513)
+|.+|+++ +++||||+ .||+.||+.++.+++.+.+ ...++||+.+++ ...+....++|+.||.++|++ ...|+
T Consensus 87 ~~~~~i~~~~~~Vahna-~fD~~fl~~~~~~~~~~~~-~~~~~~t~~~~r-~~~~~~~~~~L~~l~~~~gi~~~~~~~H~ 163 (243)
T COG0847 87 EFLDFIGGLRLLVAHNA-AFDVGFLRVESERLGIEIP-GDPVLDTLALAR-RHFPGFDRSSLDALAERLGIDRNPFHPHR 163 (243)
T ss_pred HHHHHHCCCCeEEEEch-hhcHHHHHHHHHHcCCCcc-cCceehHHHHHH-HHcCCCccchHHHHHHHcCCCcCCcCCcc
Confidence 99999999 99999999 9999999999999999877 346999999988 455667899999999999999 47799
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 010297 163 SLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 163 ALdDA~aTA~Ll~~ll~~ 180 (513)
|+.||.++++++..+.+.
T Consensus 164 Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 164 ALFDALALAELFLLLQTG 181 (243)
T ss_pred hHHHHHHHHHHHHHHHhc
Confidence 999999999999998885
No 38
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=99.94 E-value=6e-27 Score=217.13 Aligned_cols=149 Identities=22% Similarity=0.347 Sum_probs=124.5
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~e 90 (513)
|+|||||||+++.+..++|++||+|.+++. ++ |+++|+|.. +++++++++||||++||++|+++++++.+|.+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~---~~--~~~lv~P~~--~i~~~~~~i~GIt~~~l~~a~~~~~v~~~l~~ 73 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGD---VL--YDKYIRPEG--PVTDYRTRWSGIRRQHLVNATPFAVAQKEILK 73 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCC---EE--EEEeECCCC--ccCccceECCCCCHHHHhcCCCHHHHHHHHHH
Confidence 689999999997333588999999987432 33 899999998 89999999999999999999999999999999
Q ss_pred HHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHH--HHHH-hcCCCCCCCHHHHHHHh---CCC--CCCCC
Q 010297 91 ILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLAL--LTQR-FGRRAGDMKMASLATYF---GLG--QQTHR 162 (513)
Q Consensus 91 fL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~L--ar~~-l~prl~s~kL~~LAk~f---GI~--~~aHR 162 (513)
|++++++||||+ .||++||+.. .+.. .++||..+ +++. ..|..++++|..|+++| +++ .+.||
T Consensus 74 ~l~~~vlV~Hn~-~~D~~~l~~~-------~~~~-~~~Dt~~l~~~~~~~~~p~~~~~~L~~L~~~~~~~~i~~~~~~H~ 144 (157)
T cd06149 74 ILKGKVVVGHAI-HNDFKALKYF-------HPKH-MTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHS 144 (157)
T ss_pred HcCCCEEEEeCc-HHHHHHhccc-------CCCc-CEEECcccccchhhcCCcccCChhHHHHHHHHcChhhcCCCCCcC
Confidence 999999999999 9999999733 2222 47888764 4433 25666789999999999 565 35799
Q ss_pred hHHHHHHHHHHHH
Q 010297 163 SLDDVRMNLEVLK 175 (513)
Q Consensus 163 ALdDA~aTA~Ll~ 175 (513)
|++||++|+++|+
T Consensus 145 Al~DA~at~~l~~ 157 (157)
T cd06149 145 SVEDARATMELYK 157 (157)
T ss_pred cHHHHHHHHHHhC
Confidence 9999999999884
No 39
>PRK05359 oligoribonuclease; Provisional
Probab=99.94 E-value=2.8e-26 Score=217.78 Aligned_cols=162 Identities=20% Similarity=0.256 Sum_probs=136.7
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCC--CCCCChhhHHhh---CCCHHHHcCCCCH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPAD--PELISSLSVRCN---GITPDAVVSSPTF 81 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~--~~~I~~~~teIh---GIT~EmLa~Apsf 81 (513)
..+|||||+|||||++ ..|+|||||||+++++...+.+.|+.+|+|.. ...+++++..+| |||++++++++++
T Consensus 2 ~~~~vvlD~ETTGLdp--~~d~IieIgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~ 79 (181)
T PRK05359 2 EDNLIWIDLEMTGLDP--ERDRIIEIATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSE 79 (181)
T ss_pred CCcEEEEEeecCCCCC--CCCeEEEEEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCH
Confidence 5789999999999998 78999999999998875444577999999986 124688899998 8999999999999
Q ss_pred HHHHHHHHHHHc------CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCccee--HH-HHHHHHhcCCCCCCCHHHHHH
Q 010297 82 ADIADTVFDILH------GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTID--SL-ALLTQRFGRRAGDMKMASLAT 152 (513)
Q Consensus 82 ~EVl~ef~efL~------g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~ID--TL-~Lar~~l~prl~s~kL~~LAk 152 (513)
.+|+.+|.+|++ +.+++|||+ .||+.||++.+++++..... +++| |+ ++++ .+.|+.
T Consensus 80 ~e~~~~~l~fl~~~~~~~~~~l~g~~v-~FD~~FL~~~~~~~~~~l~~--~~~Dv~tl~~l~r-~~~P~~---------- 145 (181)
T PRK05359 80 AEAEAQTLEFLKQWVPAGKSPLCGNSI-GQDRRFLARYMPELEAYFHY--RNLDVSTLKELAR-RWKPEI---------- 145 (181)
T ss_pred HHHHHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHhcccCCC--cccchhHHHHHHH-HhChhh----------
Confidence 999999999995 578999999 99999999999988876443 4666 77 5666 566643
Q ss_pred HhCCC-CCCCChHHHHHHHHHHHHHHHHHhhcc
Q 010297 153 YFGLG-QQTHRSLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 153 ~fGI~-~~aHRALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
+++++ ...|||++||+++.+.++++.+.++..
T Consensus 146 ~~~~~~~~~HRal~D~~~s~~~~~~~~~~~~~~ 178 (181)
T PRK05359 146 LNGFKKQGTHRALADIRESIAELKYYREHFFKL 178 (181)
T ss_pred hhCCCCcCCcccHHHHHHHHHHHHHHHHHhccC
Confidence 46777 678999999999999999999887653
No 40
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.94 E-value=1.3e-26 Score=217.75 Aligned_cols=156 Identities=19% Similarity=0.227 Sum_probs=129.8
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCC--CCCChhhHHhh---CCCHHHHcCCCCHHHH
Q 010297 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADP--ELISSLSVRCN---GITPDAVVSSPTFADI 84 (513)
Q Consensus 10 ~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~--~~I~~~~teIh---GIT~EmLa~Apsf~EV 84 (513)
++|||+||||+++ ..++|||||||+++++.+++.++|+.+|+|... ..+++++.++| |||++|+++++++.++
T Consensus 1 lv~iD~ETTGl~p--~~d~IieIgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~v 78 (173)
T cd06135 1 LVWIDLEMTGLDP--EKDRILEIACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQA 78 (173)
T ss_pred CEEEEEecCCCCC--CCCeeEEEEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHH
Confidence 5899999999998 689999999999998777788999999999861 13456777775 9999999999999999
Q ss_pred HHHHHHHHcC------CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeH---HHHHHHHhcCCCCCCCHHHHHHHhC
Q 010297 85 ADTVFDILHG------RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDS---LALLTQRFGRRAGDMKMASLATYFG 155 (513)
Q Consensus 85 l~ef~efL~g------~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDT---L~Lar~~l~prl~s~kL~~LAk~fG 155 (513)
+.+|.+|+++ .+++|||+ .||+.||+++++++|.. ...+.+|+ +.+++ .+.|...+ ++
T Consensus 79 l~~~~~f~~~~~~~~~~~lvgh~~-~FD~~fL~~~~~~~~~~--~~~~~~D~~~l~~l~~-~l~p~~~~---------~~ 145 (173)
T cd06135 79 EAELLEFIKKYVPKGKSPLAGNSV-HQDRRFLDKYMPELEEY--LHYRILDVSSIKELAR-RWYPEIYR---------KA 145 (173)
T ss_pred HHHHHHHHHHhcCCCCCceeecch-hhCHHHHHHHHHHHhcc--CCcchhhHHHHHHHHH-HhCcHhhh---------cC
Confidence 9999999974 58999999 99999999999999843 22357887 55665 56664422 56
Q ss_pred CC-CCCCChHHHHHHHHHHHHHHHHH
Q 010297 156 LG-QQTHRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 156 I~-~~aHRALdDA~aTA~Ll~~ll~~ 180 (513)
+. ..+|||++||++++.+|+++++.
T Consensus 146 ~~~~~~HrAl~Da~~~~~~~~~~~~~ 171 (173)
T cd06135 146 PKKKGTHRALDDIRESIAELKYYREN 171 (173)
T ss_pred CCCCCCcchHHHHHHHHHHHHHHHHH
Confidence 66 68899999999999999998764
No 41
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=99.94 E-value=8e-27 Score=214.41 Aligned_cols=148 Identities=20% Similarity=0.337 Sum_probs=119.8
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~e 90 (513)
|+|||||||+++ . ++++||++|.+....+.+ .|+.+|+|.. +++++++++||||++||+++|++.+++.+|.+
T Consensus 1 v~lD~EttGl~~--~-~~~~~i~~v~~v~~~~~~--~~~~~v~P~~--~i~~~~~~ihGIt~~~v~~a~~~~~~~~~l~~ 73 (152)
T cd06144 1 VALDCEMVGVGP--D-GSESALARVSIVNEDGNV--VYDTYVKPQE--PVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAE 73 (152)
T ss_pred CEEEEEeecccC--C-CCEEEEEEEEEEeCCCCE--EEEEEECCCC--CCCcccccCCCCCHHHHcCCCCHHHHHHHHHH
Confidence 689999999986 2 367777766554432233 3999999988 89999999999999999999999999999999
Q ss_pred HHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCC-CCCCCHHHHHHH-hCCC--CCCCChHHH
Q 010297 91 ILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRR-AGDMKMASLATY-FGLG--QQTHRSLDD 166 (513)
Q Consensus 91 fL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~pr-l~s~kL~~LAk~-fGI~--~~aHRALdD 166 (513)
|+++.++||||+ .||+.||+ ...+.+ .++||+.+.. ...+. ..+++|.+||++ +|++ ..+|||++|
T Consensus 74 ~l~~~vlVgHn~-~fD~~~L~-------~~~~~~-~~~dt~~l~~-~~~~~~~~~~sL~~l~~~~lgi~~~~~~H~Al~D 143 (152)
T cd06144 74 LLKGRILVGHAL-KNDLKVLK-------LDHPKK-LIRDTSKYKP-LRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVED 143 (152)
T ss_pred HhCCCEEEEcCc-HHHHHHhc-------CcCCCc-cEEEeEEeec-cccccCCCChhHHHHHHHHcCcccCCCCcCcHHH
Confidence 999999999999 99999996 233332 5788877532 22221 478999999997 5997 369999999
Q ss_pred HHHHHHHHH
Q 010297 167 VRMNLEVLK 175 (513)
Q Consensus 167 A~aTA~Ll~ 175 (513)
|++|+++|+
T Consensus 144 A~at~~l~~ 152 (152)
T cd06144 144 ARAAMRLYR 152 (152)
T ss_pred HHHHHHHhC
Confidence 999999874
No 42
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.94 E-value=6.6e-26 Score=230.42 Aligned_cols=160 Identities=22% Similarity=0.215 Sum_probs=131.8
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeC---Cce-eEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCP---KKL-EELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~---g~~-eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
...+||||+||||+++ ..|+|||||+|+++. |.+ .+.+.|+.+++|.. +|++.++++||||++||++++...
T Consensus 36 ~~~~vvlD~ETTGLd~--~~d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~--~I~~~~t~IhGIt~e~v~~~~~~~ 111 (294)
T PRK09182 36 VRLGVILDTETTGLDP--RKDEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSR--PIPPEITRLTGITDEMVAGQTIDP 111 (294)
T ss_pred CCeEEEEEeeCCCCCC--CCCeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCC--CCCHHHHHhcCCCHHHHhcCCCcH
Confidence 3579999999999998 789999999999983 322 45789999999998 899999999999999999988765
Q ss_pred HHHHHHHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCCCCC
Q 010297 83 DIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQQTH 161 (513)
Q Consensus 83 EVl~ef~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~~aH 161 (513)
++ |.+|++. .++||||+ .||++||++.+..+. ...|.|++..+. ...+..++++|.+|+.+||....+|
T Consensus 112 ~~---l~~fl~~~~vlVAHNA-~FD~~fL~~~~~~~~-----~~~~~ct~~~i~-~~~~~~~~~kL~~La~~~g~~~~aH 181 (294)
T PRK09182 112 AA---VDALIAPADLIIAHNA-GFDRPFLERFSPVFA-----TKPWACSVSEID-WSARGFEGTKLGYLAGQAGFFHEGH 181 (294)
T ss_pred HH---HHHHhcCCCEEEEeCH-HHHHHHHHHHHHhcc-----CCcccccHHHHh-hccccCCCCCHHHHHHHcCCCCCCc
Confidence 44 5555654 59999999 999999998775542 225788887554 2234568999999999999557899
Q ss_pred ChHHHHHHHHHHHHHHHHH
Q 010297 162 RSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 162 RALdDA~aTA~Ll~~ll~~ 180 (513)
||++||++|++||..++..
T Consensus 182 rAl~Da~Ata~ll~~~l~~ 200 (294)
T PRK09182 182 RAVDDCQALLELLARPLPE 200 (294)
T ss_pred ChHHHHHHHHHHHHHHHhh
Confidence 9999999999999987654
No 43
>PTZ00315 2'-phosphotransferase; Provisional
Probab=99.94 E-value=9e-26 Score=245.22 Aligned_cols=171 Identities=18% Similarity=0.217 Sum_probs=143.1
Q ss_pred CcEEEEEEecCCCCCC-CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 8 SEIAFFDVETTVPTRP-GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~-g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
..|+|||+||||+++. ...++|||||||+++...++++++|+.||+|.....++++++++||||++||++|++|.+|+.
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~Ii~~F~~yVkP~~~p~Ls~fct~LTGITqe~V~~Ap~F~eVl~ 135 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATPVAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVYC 135 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEEEEEEEEEECCCCCCCCChhHhhhcCcCHHHHhcCCCHHHHHH
Confidence 7899999999999762 135899999999998544578899999999987557999999999999999999999999999
Q ss_pred HHHHHHcCC----------eEEEeCcchHHH-HHHHHHHH---HcCCCCCCCCcceeHHHHHHHHhcC-----------C
Q 010297 87 TVFDILHGR----------IWAGHNILRFDC-ARIREAFA---EIGRPAPEPKGTIDSLALLTQRFGR-----------R 141 (513)
Q Consensus 87 ef~efL~g~----------vLVAHNa~~FD~-~FL~~~f~---r~Gi~~p~~~~~IDTL~Lar~~l~p-----------r 141 (513)
+|.+|+++. .+++||+ +||+ .||..+|+ +.|++..+ ..|+|+...+.+.+.+ .
T Consensus 136 ef~~fL~~~~~~e~~~~~~~~vah~g-~fDl~~fL~~e~~~~~~~g~p~~f-~~widLk~~lar~l~p~~~~~~~~~~~~ 213 (582)
T PTZ00315 136 EALQFLAEAGLGDAPPLRSYCVVTCG-DWDLKTMLPSQMRVSGQQGTPLSF-QRWCNLKKYMSQLGFGNGSGCGGGATPP 213 (582)
T ss_pred HHHHHHhccccccccccCceEEEecc-HHHHHHHHHHHHHHhhhcCCCccc-ceEEEhHHHHHHHhCccccccccccccc
Confidence 999999754 5899999 9999 59999887 45665544 3577764333334443 3
Q ss_pred CCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHH
Q 010297 142 AGDMKMASLATYFGLG--QQTHRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 142 l~s~kL~~LAk~fGI~--~~aHRALdDA~aTA~Ll~~ll~~ 180 (513)
.+.++|.++++++|++ ..+|||++||++||+||.+++++
T Consensus 214 ~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~ 254 (582)
T PTZ00315 214 LGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRR 254 (582)
T ss_pred cCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHc
Confidence 4678999999999998 47899999999999999999876
No 44
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=99.94 E-value=2.5e-26 Score=211.36 Aligned_cols=143 Identities=22% Similarity=0.321 Sum_probs=121.9
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCC-CHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSP-TFADIADTVF 89 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Ap-sf~EVl~ef~ 89 (513)
+++||||||+.. .++|++||+|.+++. + .|++||+|.. +++++++++||||++||+++| ++.+++.+|.
T Consensus 1 ~~iD~E~~g~~~---g~ei~~i~~v~~~~~---~--~f~~lv~P~~--~i~~~~t~itGIt~~~l~~a~~~~~~v~~~~~ 70 (150)
T cd06145 1 FALDCEMCYTTD---GLELTRVTVVDENGK---V--VLDELVKPDG--EIVDYNTRFSGITEEMLENVTTTLEDVQKKLL 70 (150)
T ss_pred CEEeeeeeeecC---CCEEEEEEEEeCCCC---E--EEEEeECCCC--ccchhccCcCCCCHHHhccCCCCHHHHHHHHH
Confidence 589999999975 399999999987432 2 4999999998 899999999999999999995 9999999999
Q ss_pred HHHc-CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC----CCCCCh
Q 010297 90 DILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG----QQTHRS 163 (513)
Q Consensus 90 efL~-g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~----~~aHRA 163 (513)
+|++ +.++||||+ .||+.||+.. . .+++||+.++++ +.+...+++|+.||++| +.. ..+|||
T Consensus 71 ~fl~~~~vlVgHn~-~fD~~fL~~~---------~-~~~iDT~~l~r~-~~~~~~~~~L~~L~~~~~~~~i~~~~~~H~A 138 (150)
T cd06145 71 SLISPDTILVGHSL-ENDLKALKLI---------H-PRVIDTAILFPH-PRGPPYKPSLKNLAKKYLGRDIQQGEGGHDS 138 (150)
T ss_pred HHhCCCCEEEEcCh-HHHHHHhhcc---------C-CCEEEcHHhccc-cCCCCCChhHHHHHHHHCCcceeCCCCCCCc
Confidence 9997 799999999 9999999741 1 258999999874 33444589999999987 533 378999
Q ss_pred HHHHHHHHHHHH
Q 010297 164 LDDVRMNLEVLK 175 (513)
Q Consensus 164 LdDA~aTA~Ll~ 175 (513)
++||++|+++|+
T Consensus 139 l~DA~~t~~l~~ 150 (150)
T cd06145 139 VEDARAALELVK 150 (150)
T ss_pred HHHHHHHHHHhC
Confidence 999999999873
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=99.94 E-value=4e-28 Score=214.98 Aligned_cols=160 Identities=32% Similarity=0.540 Sum_probs=135.4
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~e 90 (513)
||||+||||+++ ..++|||||+|+++.+...+...|+.+|+|.....++++++++||||+++|++++++.+++.+|.+
T Consensus 1 v~~D~Ettg~~~--~~~~iieig~v~~~~~~~~~~~~~~~~i~p~~~~~i~~~~~~~~gIt~~~l~~~~~~~~~~~~~~~ 78 (164)
T PF00929_consen 1 VVFDTETTGLDP--RQDEIIEIGAVKVDDDENEEVESFNSLIRPEEPPKISPWATKVHGITQEDLEDAPSFEEALDEFEE 78 (164)
T ss_dssp EEEEEEESSSTT--TTCTEEEEEEEEEETTTTEEEEEEEEEBEHSSHCSSEHHHHHHHHHCHHHHHCHCEHHHHHHHHHH
T ss_pred cEEEeEcCCCCC--CCCeEEEEEEEEeeCCccccceeeeecccccccccCCHHHeeecCCcccccccCCcHHHHHHhhhh
Confidence 799999999987 679999999999999865578899999999984459999999999999999999999999999999
Q ss_pred HHc-CCeEEEeCcchHHHHHHHHHHHHcC-CCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC-C-CCChHHH
Q 010297 91 ILH-GRIWAGHNILRFDCARIREAFAEIG-RPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ-Q-THRSLDD 166 (513)
Q Consensus 91 fL~-g~vLVAHNa~~FD~~FL~~~f~r~G-i~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~-~-aHRALdD 166 (513)
|+. +.++||||+ .||.+++...+.+.+ ...+....++|++.+.+..+. ....++|..++++||++. . +|+|++|
T Consensus 79 ~~~~~~~~v~~n~-~fd~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~l~~~~~~~~~~~~H~Al~D 156 (164)
T PF00929_consen 79 FLKKNDILVGHNA-SFDIGFLRREDKRFLGKPIPKPNPFIDTLELARALFP-NRKKYSLDDLAEYFGIPFDGTAHDALDD 156 (164)
T ss_dssp HHHHHTEEEETTC-CHEEESSHHHHHHHHHHHHHHHHHECEEEEEHHHHHH-HHHHHSHHHHHHHTTSSSTSTTTSHHHH
T ss_pred hhhcccccccccc-cchhhHHHHhhhhcccccccccchhhhhhHHHHHHhh-ccccCCHHHHHHHcCCCCCCCCcChHHH
Confidence 999 789999998 999999999998873 333311247777776654332 223379999999999993 3 6999999
Q ss_pred HHHHHHHH
Q 010297 167 VRMNLEVL 174 (513)
Q Consensus 167 A~aTA~Ll 174 (513)
|++|+++|
T Consensus 157 a~~t~~l~ 164 (164)
T PF00929_consen 157 ARATAELF 164 (164)
T ss_dssp HHHHHHHH
T ss_pred HHHHhCcC
Confidence 99999986
No 46
>PRK11779 sbcB exonuclease I; Provisional
Probab=99.93 E-value=1.1e-24 Score=233.89 Aligned_cols=174 Identities=20% Similarity=0.181 Sum_probs=141.7
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcC-CCCHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTFAD 83 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~-Apsf~E 83 (513)
.+..+|||||+||||+++ ..|+|||||||+++.+.+.+.+.|..+|+|.....+++.+..+||||++|+.+ +.+..+
T Consensus 3 ~~~~~fvv~D~ETTGLdP--~~DrIIeiAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~a~~IhGIT~e~l~~~g~~e~e 80 (476)
T PRK11779 3 KMQPTFLWHDYETFGANP--ALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLITGITPQEALEKGLPEAE 80 (476)
T ss_pred CCCCcEEEEEEECCCCCC--CCCeeEEEEEEEEeCCCceecceeEEEEcCCcCcCCCHHHHHHhCCCHHHHHhcCCCHHH
Confidence 456789999999999998 78999999999999876566678999999986324578899999999999955 567999
Q ss_pred HHHHHHHHHc--CCeEEEeCcchHHHHHHHHHHHHcCCCC-----CCCCcceeHHHHHHHHhc--------C----CCCC
Q 010297 84 IADTVFDILH--GRIWAGHNILRFDCARIREAFAEIGRPA-----PEPKGTIDSLALLTQRFG--------R----RAGD 144 (513)
Q Consensus 84 Vl~ef~efL~--g~vLVAHNa~~FD~~FL~~~f~r~Gi~~-----p~~~~~IDTL~Lar~~l~--------p----rl~s 144 (513)
++.+|.+|+. +.++||||..+||..||+..+.+..+.+ ......+|++.+++..+. | ..++
T Consensus 81 ~~~~i~~~l~~~~~~lVGhNni~FD~eflr~~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s 160 (476)
T PRK11779 81 FAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPS 160 (476)
T ss_pred HHHHHHHHHhcCCCEEEEeCchhhcHHHHHHHHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCC
Confidence 9999999995 7899999843899999999987654431 122234577776653321 2 2368
Q ss_pred CCHHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHH
Q 010297 145 MKMASLATYFGLG-QQTHRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 145 ~kL~~LAk~fGI~-~~aHRALdDA~aTA~Ll~~ll~~ 180 (513)
++|..|++++|++ .++|||++||.+|+++++.+.++
T Consensus 161 ~rLe~L~~~~gI~~~~AHdALsDa~aT~~la~~l~~~ 197 (476)
T PRK11779 161 FKLEHLTKANGIEHENAHDAMSDVYATIAMAKLIKQK 197 (476)
T ss_pred CcHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHh
Confidence 9999999999999 68999999999999999999876
No 47
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=99.73 E-value=1.7e-17 Score=164.04 Aligned_cols=170 Identities=18% Similarity=0.259 Sum_probs=140.6
Q ss_pred CcEEEEEEecCCCCCC--CCCCcEEEEEEEEEeCCceeEee-eEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 8 SEIAFFDVETTVPTRP--GQRFAILEFGAILVCPKKLEELH-NYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~--g~~deIIEIGAV~Vd~g~~eivd-sFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
..++++|+|+|+-+.. ....+|||+.||.++.-...+++ +|+.||+|..+..++.+|+.+|||.+++|..|++|.+|
T Consensus 56 dYLliiDFEaTC~e~~~~~~~~EIIEfP~V~l~~~~~~~Ie~eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~v 135 (280)
T KOG0542|consen 56 DYLLILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQV 135 (280)
T ss_pred ceEEEEeeeeeccccCCCCcchheeecceeEeeccchhhHHHHHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHH
Confidence 5688999999996541 24578999999977764444555 99999999998899999999999999999999999999
Q ss_pred HHHHHHHHcC--------C-eEEEeCcchHHH-HHHHHHHHHcCCCCCC-CCcceeHHHHHHHHhcCCCCCCCHHHHHHH
Q 010297 85 ADTVFDILHG--------R-IWAGHNILRFDC-ARIREAFAEIGRPAPE-PKGTIDSLALLTQRFGRRAGDMKMASLATY 153 (513)
Q Consensus 85 l~ef~efL~g--------~-vLVAHNa~~FD~-~FL~~~f~r~Gi~~p~-~~~~IDTL~Lar~~l~prl~s~kL~~LAk~ 153 (513)
+.+|..|+.. . -+|. .. +.|+ .||..+|+.-++..|. .++|||+.+..+ .++.+...-++..+.++
T Consensus 136 l~~f~~Wlr~~~~~~k~~~~Afvt-dg-~wDl~~~l~~qck~~~i~~P~~f~qwInirk~yk-~~y~~~~~t~it~mLe~ 212 (280)
T KOG0542|consen 136 LSEFDSWLRKDSLGDKNGKFAFVT-DG-DWDLWVFLQYQCKLKNIRIPAFFNQWINIRKIYK-NFYNRPAPTNITGMLEH 212 (280)
T ss_pred HHHHHHHHHHhhcccccCceEEEe-Cc-hhhHHHHHHHHHHHhcCCCcHHHHHHhHHHHHHH-HHhcCccccCHHHHHHH
Confidence 9999999961 1 2332 33 7888 5889999999988773 348999999887 45554456789999999
Q ss_pred hCCC--CCCCChHHHHHHHHHHHHHHHHH
Q 010297 154 FGLG--QQTHRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 154 fGI~--~~aHRALdDA~aTA~Ll~~ll~~ 180 (513)
+|++ +..|++++||++++.++.++.+.
T Consensus 213 ~gL~f~Gr~HsGiDDa~Nia~I~~kM~~d 241 (280)
T KOG0542|consen 213 YGLQFEGRAHSGIDDARNIARIAQKMIRD 241 (280)
T ss_pred hCCcccCCcccCchhHHHHHHHHHHHHhC
Confidence 9998 69999999999999999998874
No 48
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=99.69 E-value=4.6e-17 Score=153.15 Aligned_cols=171 Identities=21% Similarity=0.256 Sum_probs=139.3
Q ss_pred CCcEEEEEEecCCCCCC--CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 7 RSEIAFFDVETTVPTRP--GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~--g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
...++++|+|+|..+.- .+..+||||+|-.++.-.-++++.|+.||+|..+..++.+|..+|||++..|.+||-|..+
T Consensus 3 ~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v 82 (210)
T COG5018 3 TNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMV 82 (210)
T ss_pred CceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHH
Confidence 35789999999986541 2677899999999886545689999999999998889999999999999999999999999
Q ss_pred HHHHHHHHc------CCeEEEeCcchHHHHHHHHHHHHcCCCCCC-CCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 010297 85 ADTVFDILH------GRIWAGHNILRFDCARIREAFAEIGRPAPE-PKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG 157 (513)
Q Consensus 85 l~ef~efL~------g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~-~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~ 157 (513)
+++|..||. +..|+.+ +++|+..|.+.+..+++.+.+ -.+++|...-.+..+ ..-.--.|+.+++.+|..
T Consensus 83 ~E~f~r~L~~h~Pr~~~~wa~w--G~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~-~~pr~tgln~ale~~G~s 159 (210)
T COG5018 83 FEDFIRKLNEHDPRKNSTWATW--GNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVF-GDPRLTGLNKALEEYGDS 159 (210)
T ss_pred HHHHHHHHHhcCcccCCccccc--cchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHh-cCCccccHHHHHHHhccc
Confidence 999999997 2345533 389999999999999988433 337888766555333 222225799999999998
Q ss_pred --CCCCChHHHHHHHHHHHHHHHHH
Q 010297 158 --QQTHRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 158 --~~aHRALdDA~aTA~Ll~~ll~~ 180 (513)
+++|||++||++++++++.+...
T Consensus 160 f~G~~HraldDArn~~rl~klv~~~ 184 (210)
T COG5018 160 FTGTHHRALDDARNAYRLFKLVEQD 184 (210)
T ss_pred cCCchhhhHHHHHHHHHHHHHHcch
Confidence 69999999999999999887543
No 49
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=99.68 E-value=2.1e-16 Score=147.86 Aligned_cols=166 Identities=19% Similarity=0.243 Sum_probs=134.5
Q ss_pred CCCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCC--CCCCChhhHHhh---CCCHHHHcC
Q 010297 3 PTQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPAD--PELISSLSVRCN---GITPDAVVS 77 (513)
Q Consensus 3 ~t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~--~~~I~~~~teIh---GIT~EmLa~ 77 (513)
|+.+.+++|++|||+|||++ ..|+||||++++.|.+...+.+.+...|.-.. +..+++++++.| |++....++
T Consensus 1 m~~~~~nLiWIDlEMTGLd~--~~drIIEiA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S 78 (184)
T COG1949 1 MSANKNNLIWIDLEMTGLDP--ERDRIIEIATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKAS 78 (184)
T ss_pred CCCcCCceEEEeeeeccCCc--CcceEEEEEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHh
Confidence 46678999999999999999 89999999999999987777777777776443 457889999998 688877788
Q ss_pred CCCHHHHHHHHHHHHc------CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCccee--HHHHHHHHhcCCCCCCCHHH
Q 010297 78 SPTFADIADTVFDILH------GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTID--SLALLTQRFGRRAGDMKMAS 149 (513)
Q Consensus 78 Apsf~EVl~ef~efL~------g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~ID--TL~Lar~~l~prl~s~kL~~ 149 (513)
..+.++|-.+.++|++ .++++|..+ .-|+.||.+.|.++---+.+ +.+| |++-+.++|.|+.
T Consensus 79 ~~t~~~aE~~~l~flkkwvp~~~spicGNSI-~qDRrFl~r~MP~Le~yfHY--R~lDVSTlKELa~RW~P~i------- 148 (184)
T COG1949 79 TVTEAEAEAQTLDFLKKWVPKGVSPICGNSI-AQDRRFLFRYMPKLEAYFHY--RYLDVSTLKELARRWNPEI------- 148 (184)
T ss_pred hccHHHHHHHHHHHHHHhCCCCCCCCccchh-hHHHHHHHHHhhhHHHHhhh--HhhhHHHHHHHHHhhCcHh-------
Confidence 8999999999999996 468999999 99999999999877433332 3555 5544445787765
Q ss_pred HHHHhCCC-CCCCChHHHHHHHHHHHHHHHHHhhc
Q 010297 150 LATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFL 183 (513)
Q Consensus 150 LAk~fGI~-~~aHRALdDA~aTA~Ll~~ll~~L~~ 183 (513)
+.|.. ...|+|++|++..+.-|+++.+.++.
T Consensus 149 ---~~~~~K~~~H~Al~DI~ESI~EL~~YR~~f~~ 180 (184)
T COG1949 149 ---LAGFKKGGTHRALDDIRESIAELRYYREHFLK 180 (184)
T ss_pred ---hhccccccchhHHHHHHHHHHHHHHHHHHhcc
Confidence 44554 68999999999999999999887664
No 50
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=99.60 E-value=3e-15 Score=141.45 Aligned_cols=164 Identities=18% Similarity=0.260 Sum_probs=132.4
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCC--CCCCChhhHHhh---CCCHHHHcCCCC
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPAD--PELISSLSVRCN---GITPDAVVSSPT 80 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~--~~~I~~~~teIh---GIT~EmLa~Aps 80 (513)
..+++||+|||+|||+- +.|+|+||+++..+++...+.+.+...|+-+. ...++++|.+.| |+|..-+++..+
T Consensus 24 l~q~lVWiD~EMTGLdv--ekd~i~EiacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~t 101 (208)
T KOG3242|consen 24 LKQPLVWIDCEMTGLDV--EKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKIT 101 (208)
T ss_pred ccCceEEEeeecccccc--ccceeEEEEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhcc
Confidence 45789999999999998 89999999999999987777888888887443 457899999998 589888899999
Q ss_pred HHHHHHHHHHHHc------CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeH--H-HHHHHHhcCCCCCCCHHHHH
Q 010297 81 FADIADTVFDILH------GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDS--L-ALLTQRFGRRAGDMKMASLA 151 (513)
Q Consensus 81 f~EVl~ef~efL~------g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDT--L-~Lar~~l~prl~s~kL~~LA 151 (513)
+++|-.++++|++ ..++.|..+ ..|..||...|.++--..++ +.||+ . +|++ +|+|...
T Consensus 102 l~~aEnevl~yikk~ip~~~~~laGNSV-~~DrlFl~k~mPk~~~~lhy--rivDVStIkeL~~-Rw~P~~~-------- 169 (208)
T KOG3242|consen 102 LADAENEVLEYIKKHIPKGKCPLAGNSV-YMDRLFLKKYMPKLIKHLHY--RIVDVSTIKELAR-RWYPDIK-------- 169 (208)
T ss_pred HHHHHHHHHHHHHHhCCCCCCCccCcch-hhHHHHHHHHhHHHHHhcce--eeeeHHHHHHHHH-HhCchhh--------
Confidence 9999999999996 357777777 99999999999887444443 46664 3 3444 6777541
Q ss_pred HHhCC-CCCCCChHHHHHHHHHHHHHHHHHhhcc
Q 010297 152 TYFGL-GQQTHRSLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 152 k~fGI-~~~aHRALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
.+.- ....|||++|.+..++-|+++...+|..
T Consensus 170 -~~aPkK~~~HrAldDI~ESI~ELq~Yr~nifkk 202 (208)
T KOG3242|consen 170 -ARAPKKKATHRALDDIRESIKELQYYRENIFKK 202 (208)
T ss_pred -ccCcccccccchHHHHHHHHHHHHHHHHHhccC
Confidence 1111 2578999999999999999999988764
No 51
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=99.53 E-value=6.8e-14 Score=139.59 Aligned_cols=156 Identities=19% Similarity=0.314 Sum_probs=123.7
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHH
Q 010297 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (513)
Q Consensus 9 ~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef 88 (513)
++|++|||+.|..+.|..+.+.-++.|-..++ + -|+.||+|.. +++++.++.+||+++.+.+|.+|+.|..++
T Consensus 106 r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~---V--vyDkyVkP~~--~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev 178 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGRESLLARVSIVNYHGH---V--VYDKYVKPTE--PVTDYRTRVSGIRPEHMRDAMPFKVAQKEV 178 (280)
T ss_pred eEEEEeeeEeccCCCccceeeeEEEEeeccCc---E--eeeeecCCCc--ccccceeeecccCHHHhccCccHHHHHHHH
Confidence 69999999999987566677777777766554 3 3888999999 999999999999999999999999999999
Q ss_pred HHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHH--HHHHhcCCCCCCCHHHHHH-HhCCC--CCCCCh
Q 010297 89 FDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLAL--LTQRFGRRAGDMKMASLAT-YFGLG--QQTHRS 163 (513)
Q Consensus 89 ~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~L--ar~~l~prl~s~kL~~LAk-~fGI~--~~aHRA 163 (513)
.++|.|+|||||.. .-|+..|. +..|.. .+-||-.. +++. ...-...+|..|++ ++|.+ ...|..
T Consensus 179 ~klL~gRIlVGHaL-hnDl~~L~-------l~hp~s-~iRDTs~~~pl~k~-~~~~~tpSLK~Lt~~~Lg~~IQ~GeHsS 248 (280)
T KOG2249|consen 179 LKLLKGRILVGHAL-HNDLQALK-------LEHPRS-MIRDTSKYPPLMKL-LSKKATPSLKKLTEALLGKDIQVGEHSS 248 (280)
T ss_pred HHHHhCCEEecccc-ccHHHHHh-------hhCchh-hhcccccCchHHHH-hhccCCccHHHHHHHHhchhhhccccCc
Confidence 99999999999999 77777765 444433 25566542 2222 23345779999997 55776 456999
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 010297 164 LDDVRMNLEVLKYCATVL 181 (513)
Q Consensus 164 LdDA~aTA~Ll~~ll~~L 181 (513)
..||++|+++|+......
T Consensus 249 vEDA~AtM~LY~~vk~qw 266 (280)
T KOG2249|consen 249 VEDARATMELYKRVKVQW 266 (280)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999876543
No 52
>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=99.46 E-value=1.1e-12 Score=124.63 Aligned_cols=156 Identities=17% Similarity=0.108 Sum_probs=112.9
Q ss_pred EEEEEecCCC----CCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 11 AFFDVETTVP----TRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 11 VVfDlETTGL----d~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
++||+||||+ ++ ..++|++||++....|... .+.....+.. ...+ ||+..++...++..+++.
T Consensus 2 ~~~DIEt~~~~~~p~~--~~d~Ii~I~~~~~~~g~~~---~~~~~~~~~~--~~~~------~i~~~~v~~~~~E~~lL~ 68 (199)
T cd05160 2 LSFDIETTPPVGGPEP--DRDPIICITYADSFDGVKV---VFLLKTSTVG--DDIE------FIDGIEVEYFADEKELLK 68 (199)
T ss_pred ccEEEeecCCCCCcCC--CCCCEEEEEEEEeeCCcee---eEEEeecccC--CcCC------CCCCceEEEeCCHHHHHH
Confidence 6899999998 65 6899999999988555322 2222222222 1111 888889999999999999
Q ss_pred HHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCC---------------------CCCcceeHHHHHHHHhcCCC
Q 010297 87 TVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAP---------------------EPKGTIDSLALLTQRFGRRA 142 (513)
Q Consensus 87 ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p---------------------~~~~~IDTL~Lar~~l~prl 142 (513)
+|.++++. .+++|||+..||+++|.+.+.++|++.. ....++|++.++++.+ + .
T Consensus 69 ~f~~~i~~~dpdiivg~N~~~FD~~~L~~R~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~gr~~~D~~~~~r~~~-~-l 146 (199)
T cd05160 69 RFFDIIREYDPDILTGYNIDDFDLPYLLKRAEALGIKLTDGIYRRSGGEKSSGSTERIAVKGRVVFDLLAAYKRDF-K-L 146 (199)
T ss_pred HHHHHHHhcCCCEEEEeccCCCcHHHHHHHHHHhCCCcccccccccCCCccCCcccceeeeccEeeehHHHHHHhc-C-c
Confidence 99999985 5999999999999999999999998762 0224799999987543 4 7
Q ss_pred CCCCHHHHHHHhCCC-CCCCCh--HH---HHHHHHHHHHHHHHHh
Q 010297 143 GDMKMASLATYFGLG-QQTHRS--LD---DVRMNLEVLKYCATVL 181 (513)
Q Consensus 143 ~s~kL~~LAk~fGI~-~~aHRA--Ld---DA~aTA~Ll~~ll~~L 181 (513)
.+|+|+++|+.++.. ...+.. +. +.....+++.++++..
T Consensus 147 ~sy~L~~v~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~~Y~~~D~ 191 (199)
T cd05160 147 KSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPERLIEYNLKDA 191 (199)
T ss_pred ccCCHHHHHHHHhCCCCCcCCHHHHhhccCcchHHHHHHHHHHHH
Confidence 899999999988665 333322 21 2234455666666543
No 53
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=99.45 E-value=6.6e-13 Score=137.96 Aligned_cols=173 Identities=20% Similarity=0.162 Sum_probs=142.6
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHH-cCCCCHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAV-VSSPTFAD 83 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmL-a~Apsf~E 83 (513)
.....|.|+|.||.|.+| ..|++.||++|+.+.+-+.+.+-...|++|.+-.--.|.++-|||||++.. +.|.+.++
T Consensus 6 ~~~~tF~~yDYETfG~~P--a~DRPaQFAgiRTD~~~NiIgeP~~fyCkpsdDyLP~P~a~LITGITPQ~~~~~G~~E~~ 83 (475)
T COG2925 6 TKQPTFLFYDYETFGVHP--ALDRPAQFAGIRTDIEFNIIGEPIVFYCKPADDYLPQPGAVLITGITPQEAREKGINEAA 83 (475)
T ss_pred CCCCcEEEEehhhcCCCc--ccccchhhheeeccccccccCCCeEEEecCccccCCCCCceeeecCCHHHHHhcCCChHH
Confidence 345789999999999998 789999999999999888888889999999872222378899999999998 66888888
Q ss_pred HHHHHHHHHc--CCeEEEeCcchHHHHHHHHHHHHcCCC-----CCCCCcceeHHHHHHHHhc--CC----------CCC
Q 010297 84 IADTVFDILH--GRIWAGHNILRFDCARIREAFAEIGRP-----APEPKGTIDSLALLTQRFG--RR----------AGD 144 (513)
Q Consensus 84 Vl~ef~efL~--g~vLVAHNa~~FD~~FL~~~f~r~Gi~-----~p~~~~~IDTL~Lar~~l~--pr----------l~s 144 (513)
...++..-+. +.+++|+|-.+||-.+.+..|.|.-++ +.....-+|.+.+.|..+. |. +.+
T Consensus 84 F~~~I~~~ls~P~Tcv~GYNniRFDDEvtRy~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pS 163 (475)
T COG2925 84 FAARIHAELTQPNTCVLGYNNIRFDDEVTRYIFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPS 163 (475)
T ss_pred HHHHHHHHhCCCCeeeecccccccchHHHHHHHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcc
Confidence 8888888886 678999998899999998888776554 2233356788888876542 21 468
Q ss_pred CCHHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHH
Q 010297 145 MKMASLATYFGLG-QQTHRSLDDVRMNLEVLKYCAT 179 (513)
Q Consensus 145 ~kL~~LAk~fGI~-~~aHRALdDA~aTA~Ll~~ll~ 179 (513)
+||..|.+.-|++ .++|+|++|+.+|+.+.+.+.+
T Consensus 164 FkLEhLt~ANgieH~nAHdAmsDVyATIamAklvk~ 199 (475)
T COG2925 164 FKLEHLTKANGIEHSNAHDAMSDVYATIAMAKLVKT 199 (475)
T ss_pred hhhHHHhhccccccchhhHHHHHHHHHHHHHHHHHh
Confidence 9999999999999 7999999999999988776655
No 54
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=99.36 E-value=1.1e-11 Score=118.15 Aligned_cols=152 Identities=19% Similarity=0.272 Sum_probs=110.1
Q ss_pred CcEEEEEEecCCCCCCCCC-------CcEEEEEEEEEeC-CceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCC
Q 010297 8 SEIAFFDVETTVPTRPGQR-------FAILEFGAILVCP-KKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSP 79 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g~~-------deIIEIGAV~Vd~-g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Ap 79 (513)
-+||-+|.|++++.+.|.. .++.-|++|-..+ ..+++ -++.||+|.. ++..+.++.+|||+++++++.
T Consensus 5 ~e~v~~~~~~~~~~~~g~~~~~~~~~~~LaRVsiVd~~~~~~g~v--llD~~VkP~~--~V~DYrT~~SGIt~~~L~~a~ 80 (174)
T cd06143 5 AEFVKLKPEETEIRSDGTKSTIRPSQMSLARVSVVRGEGELEGVP--FIDDYISTTE--PVVDYLTRFSGIKPGDLDPKT 80 (174)
T ss_pred eeEEEecchhceecCCCcEeeeccCCceeEEEEEEcCCCCcCCCE--EEeeeECCCC--CccCcCccccccCHHHcCccc
Confidence 4566666666665542222 2455555554210 11233 3778999988 999999999999999998864
Q ss_pred ------CHHHHHHHHHHHHc-CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHH
Q 010297 80 ------TFADIADTVFDILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLAT 152 (513)
Q Consensus 80 ------sf~EVl~ef~efL~-g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk 152 (513)
+++++..++.+++. +.++|||.. ..|+..| ++..|.. .++||..+.+ .+....++|..|++
T Consensus 81 ~~~~~~t~~~v~~~l~~li~~~tILVGHsL-~nDL~aL-------~l~hp~~-~viDTa~l~~---~~~~r~~sLk~La~ 148 (174)
T cd06143 81 SSKNLTTLKSAYLKLRLLVDLGCIFVGHGL-AKDFRVI-------NIQVPKE-QVIDTVELFH---LPGQRKLSLRFLAW 148 (174)
T ss_pred cccccCCHHHHHHHHHHHcCCCCEEEeccc-hhHHHHh-------cCcCCCc-ceEEcHHhcc---CCCCCChhHHHHHH
Confidence 58999999999996 899999999 7777776 4555543 5899987643 23334679999998
Q ss_pred Hh-CCC--CCCCChHHHHHHHHHHHH
Q 010297 153 YF-GLG--QQTHRSLDDVRMNLEVLK 175 (513)
Q Consensus 153 ~f-GI~--~~aHRALdDA~aTA~Ll~ 175 (513)
.| |.. ...|+++.||++++++|+
T Consensus 149 ~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 149 YLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 55 655 569999999999999873
No 55
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=99.13 E-value=6.1e-10 Score=95.70 Aligned_cols=79 Identities=30% Similarity=0.339 Sum_probs=61.9
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~e 90 (513)
++||+||||+++ ..++|++|++.....+. .| +.. |.+
T Consensus 1 ~~~DiEt~~~~~--~~~~i~~i~~~~~~~~~-----~~---~~~---------------------------------f~~ 37 (96)
T cd06125 1 IAIDTEATGLDG--AVHEIIEIALADVNPED-----TA---VID---------------------------------LKD 37 (96)
T ss_pred CEEEEECCCCCC--CCCcEEEEEEEEccCCC-----EE---Eeh---------------------------------HHH
Confidence 479999999987 78999999987643221 11 110 777
Q ss_pred HHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCCC-CCcceeHHHH
Q 010297 91 ILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE-PKGTIDSLAL 133 (513)
Q Consensus 91 fL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~-~~~~IDTL~L 133 (513)
|+++ .++|+||+ .||++||+++++++|.+.|. ..+++||+.+
T Consensus 38 ~l~~~~~~v~V~hn~-~fD~~fL~~~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 38 ILRDKPLAILVGHNG-SFDLPFLNNRCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHhhCCCCEEEEeCc-HHhHHHHHHHHHHcCCCCCCcCCcEEEehHH
Confidence 7764 58999999 99999999999999988763 4579999986
No 56
>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=98.90 E-value=3.2e-08 Score=94.91 Aligned_cols=127 Identities=14% Similarity=0.141 Sum_probs=90.7
Q ss_pred cEEEEEEecC---CC-CCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 9 EIAFFDVETT---VP-TRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 9 ~~VVfDlETT---GL-d~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
++++||+||| |+ ++ ..+.|+.||++....+ .++ . .++.. . ..+..-.+..+.
T Consensus 4 ~i~~fDIEt~~~~g~p~~--~~d~Ii~Is~~~~~~~--~~~----~-~~~~~--~-------------~~v~~~~~E~~l 59 (195)
T cd05780 4 KILSFDIEVLNHEGEPNP--EKDPIIMISFADEGGN--KVI----T-WKKFD--L-------------PFVEVVKTEKEM 59 (195)
T ss_pred eEEEEEEEecCCCCCCCC--CCCcEEEEEEecCCCc--eEE----E-ecCCC--C-------------CeEEEeCCHHHH
Confidence 6889999998 44 33 6899999998652221 211 1 11111 0 023334567889
Q ss_pred HHHHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCCC---------------------CCcceeHHHHHHHHhcC
Q 010297 85 ADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE---------------------PKGTIDSLALLTQRFGR 140 (513)
Q Consensus 85 l~ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~---------------------~~~~IDTL~Lar~~l~p 140 (513)
+.+|.+++.. .+++|||+..||+++|...+.++|++.+. ....+|++.++++. .
T Consensus 60 L~~F~~~i~~~dpdiivgyN~~~FD~pyL~~R~~~~gi~~~~~r~~~~~~~~~~g~~~~~~i~Gr~~lDl~~~~~~~--~ 137 (195)
T cd05780 60 IKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT--L 137 (195)
T ss_pred HHHHHHHHHHcCCCEEEecCCCCCcHHHHHHHHHHhCCCCccccCCCceeEeecceeeeeccCCeEEEeHHHHHHhh--C
Confidence 9999999984 68999999899999999999999987543 12489999998753 3
Q ss_pred CCCCCCHHHHHH-HhCCCCCCC
Q 010297 141 RAGDMKMASLAT-YFGLGQQTH 161 (513)
Q Consensus 141 rl~s~kL~~LAk-~fGI~~~aH 161 (513)
.+.+|+|+++++ ++|.+...+
T Consensus 138 ~l~sy~L~~v~~~~Lg~~k~d~ 159 (195)
T cd05780 138 NLTRYTLERVYEELFGIEKEDV 159 (195)
T ss_pred CCCcCcHHHHHHHHhCCCCCcC
Confidence 578999999987 678774433
No 57
>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=98.89 E-value=4.1e-09 Score=96.77 Aligned_cols=115 Identities=19% Similarity=0.286 Sum_probs=65.3
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHHH
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFD 90 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~e 90 (513)
++||+||||+++ ..+.|.=||++.++.+.... |..+..... ..++++.++.+
T Consensus 1 l~~DIET~Gl~~--~~~~i~liG~~~~~~~~~~~---~~~~~~~~~-----------------------~ee~~~~~~~~ 52 (164)
T PF13482_consen 1 LFFDIETTGLSP--DNDTIYLIGVADFDDDEIIT---FIQWFAEDP-----------------------DEEEIILEFFE 52 (164)
T ss_dssp --EEEEESS-GG---G---EEEEEEE-ETTTTE----EEEE-GGGH-----------------------HHHHHHHH--H
T ss_pred CcEEecCCCCCC--CCCCEEEEEEEEeCCCceEE---eeHhhccCc-----------------------HHHHHHHHHHH
Confidence 689999999987 66789999999988874321 333332221 11223333224
Q ss_pred HHc-CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC
Q 010297 91 ILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ 158 (513)
Q Consensus 91 fL~-g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~ 158 (513)
++. ...+|+||+..||.++|++.+.+++++.+ ...+|++..+++.+. .+++|.++++.+|+..
T Consensus 53 ~l~~~~~iv~yng~~FD~p~L~~~~~~~~~~~~--~~~iDl~~~~~~~~~---~~~~Lk~ve~~lg~~~ 116 (164)
T PF13482_consen 53 LLDEADNIVTYNGKNFDIPFLKRRAKRYGLPPP--FNHIDLLKIIKKHFL---ESYSLKNVEKFLGIER 116 (164)
T ss_dssp HHHTT--EEESSTTTTHHHHHHHHH-HHHH--G--GGEEEHHHHHT-TTS---CCTT--SHHH------
T ss_pred HHhcCCeEEEEeCcccCHHHHHHHHHHcCCCcc--cchhhHHHHHHhccC---CCCCHHHHhhhccccc
Confidence 544 57899999889999999999988887753 369999998865443 7889999999999984
No 58
>KOG2248 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=98.79 E-value=2.5e-08 Score=105.44 Aligned_cols=154 Identities=19% Similarity=0.294 Sum_probs=118.3
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcC-CCCHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVS-SPTFAD 83 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~-Apsf~E 83 (513)
....+++++|||+..... +-++..+++|-++.. . -|+.||+|.. +|.++.+..+|||.+++++ +.++.+
T Consensus 213 ~~~~~i~AlDCEm~~te~---g~el~RVt~VD~~~~--v---i~D~fVkP~~--~VvDy~T~~SGIT~~~~e~~t~tl~d 282 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVTEN---GLELTRVTAVDRDGK--V---ILDTFVKPNK--PVVDYNTRYSGITEEDLENSTITLED 282 (380)
T ss_pred CCCCCeEEEEeeeeeecc---ceeeEEeeeeeccCc--E---EeEEeecCCC--cccccccccccccHHHHhcCccCHHH
Confidence 455789999999998864 367888998877655 2 4778999999 8999999999999999975 578999
Q ss_pred HHHHHHHHHc-CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC----
Q 010297 84 IADTVFDILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG---- 157 (513)
Q Consensus 84 Vl~ef~efL~-g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~---- 157 (513)
+..++..|+. +.+||||.. .-|+.-|+- .. ..+|||.-++....++.....+|..|++.| |..
T Consensus 283 vq~~l~~~~~~~TILVGHSL-enDL~aLKl-------~H---~~ViDTa~lf~~~~g~~~~k~sLk~L~~~~L~~~Iq~~ 351 (380)
T KOG2248|consen 283 VQKELLELISKNTILVGHSL-ENDLKALKL-------DH---PSVIDTAVLFKHPTGPYPFKSSLKNLAKSYLGKLIQEG 351 (380)
T ss_pred HHHHHHhhcCcCcEEEeech-hhHHHHHhh-------hC---CceeeeeEEEecCCCCccchHHHHHHHHHHHHHHHhcc
Confidence 9999999998 679999999 899988874 11 148999754321112101233588888754 433
Q ss_pred CCCCChHHHHHHHHHHHHHHHH
Q 010297 158 QQTHRSLDDVRMNLEVLKYCAT 179 (513)
Q Consensus 158 ~~aHRALdDA~aTA~Ll~~ll~ 179 (513)
...|.+..||.+++++++...+
T Consensus 352 ~~~HdS~eDA~acm~Lv~~k~~ 373 (380)
T KOG2248|consen 352 VGGHDSVEDALACMKLVKLKIK 373 (380)
T ss_pred CCCCccHHHHHHHHHHHHHHHh
Confidence 3569999999999999987655
No 59
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=98.76 E-value=1.7e-07 Score=89.90 Aligned_cols=116 Identities=16% Similarity=0.134 Sum_probs=87.4
Q ss_pred CcEEEEEEecC---CC-CCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHH
Q 010297 8 SEIAFFDVETT---VP-TRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (513)
Q Consensus 8 ~~~VVfDlETT---GL-d~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~E 83 (513)
-+.++||+||+ |+ ++ ..+.|+.||+...++. .++ +. ....+..+
T Consensus 3 l~~l~fDIEt~~~~gfp~~--~~d~Ii~Is~~~~~g~-~~~------~~-----------------------~~~~~E~~ 50 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNP--RRDPIIVISLATSNGD-VEF------IL-----------------------AEGLDDRK 50 (188)
T ss_pred ceEEEEEEEecCCCCCCCC--CCCCEEEEEEEeCCCC-EEE------EE-----------------------ecCCCHHH
Confidence 36789999999 44 33 6799999998764332 111 10 11356788
Q ss_pred HHHHHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCCCC-------------------CcceeHHHHHHHHhcCC
Q 010297 84 IADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPEP-------------------KGTIDSLALLTQRFGRR 141 (513)
Q Consensus 84 Vl~ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~-------------------~~~IDTL~Lar~~l~pr 141 (513)
.+.+|.++++. .+++|||+..||+++|...++++|+..... ...+|++.++++.. .
T Consensus 51 lL~~F~~~i~~~dPd~i~gyN~~~FDlpyl~~Ra~~~gi~~~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~--~ 128 (188)
T cd05781 51 IIREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP--E 128 (188)
T ss_pred HHHHHHHHHHHcCCCEEEecCCCcCcHHHHHHHHHHhCCCcccccCCCcccccCCcceEeeeeEEEEEhHHHHHhhC--C
Confidence 99999999983 589999999999999999999999765311 12899999987543 3
Q ss_pred CCCCCHHHHHHHhCCC
Q 010297 142 AGDMKMASLATYFGLG 157 (513)
Q Consensus 142 l~s~kL~~LAk~fGI~ 157 (513)
+++++|+++|+++|..
T Consensus 129 l~~y~L~~Va~~Lg~~ 144 (188)
T cd05781 129 VKVKTLENVAEYLGVM 144 (188)
T ss_pred CCCCCHHHHHHHHCCC
Confidence 7899999999999974
No 60
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=98.73 E-value=2.1e-07 Score=92.96 Aligned_cols=122 Identities=16% Similarity=0.165 Sum_probs=86.6
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCH-HHH
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF-ADI 84 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf-~EV 84 (513)
..++++|||+|||||++ .++.|+=.|...+.++.. .|+-.. ..+|.. ..+
T Consensus 96 ~~e~~~FFDiETTGL~~--ag~~I~~~g~a~~~~~~~--------~Vrq~~-------------------lp~p~~E~av 146 (278)
T COG3359 96 EAEDVAFFDIETTGLDR--AGNTITLVGGARGVDDTM--------HVRQHF-------------------LPAPEEEVAV 146 (278)
T ss_pred cccceEEEeeeccccCC--CCCeEEEEEEEEccCceE--------EEEeec-------------------CCCcchhhHH
Confidence 45789999999999997 567788888777766532 222111 011111 124
Q ss_pred HHHHHHHHcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 010297 85 ADTVFDILHGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG 157 (513)
Q Consensus 85 l~ef~efL~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~ 157 (513)
++.|.....-..||.+|+.+||.+||++ +.+..++.......+|.+.-+|+.+.-.+.+-+|.++.+.+|+.
T Consensus 147 le~fl~~~~~~~lvsfNGkaFD~PfikR-~v~~~~el~l~~~H~DL~h~~RRlwk~~l~~c~Lk~VEr~LGi~ 218 (278)
T COG3359 147 LENFLHDPDFNMLVSFNGKAFDIPFIKR-MVRDRLELSLEFGHFDLYHPSRRLWKHLLPRCGLKTVERILGIR 218 (278)
T ss_pred HHHHhcCCCcceEEEecCcccCcHHHHH-HHhcccccCccccchhhhhhhhhhhhccCCCCChhhHHHHhCcc
Confidence 4445444444589999999999999995 76776765544578999999997775556777999999999985
No 61
>cd05779 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique
Probab=98.68 E-value=5.6e-07 Score=87.83 Aligned_cols=145 Identities=14% Similarity=0.097 Sum_probs=90.9
Q ss_pred CcEEEEEEecCCCC---CCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCC-hhhHHhhCCCHHHHcCCCCHHH
Q 010297 8 SEIAFFDVETTVPT---RPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELIS-SLSVRCNGITPDAVVSSPTFAD 83 (513)
Q Consensus 8 ~~~VVfDlETTGLd---~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~-~~~teIhGIT~EmLa~Apsf~E 83 (513)
-+++.||+||.+.. |....|.||.|+.+.-..+ ..+..+ ..+.+... .+. ..+..+.|. -.+..-.+..+
T Consensus 2 lrilafDIE~~~~~~~fP~~~~D~Ii~IS~~~~~~g-~~~~~~--~~~~~~~~-~~~~~~~~~~~~~--~~v~~~~~E~~ 75 (204)
T cd05779 2 PRVLAFDIETTKLPLKFPDAETDQIMMISYMIDGQG-YLIVNR--EIVSEDIE-DFEYTPKPEYEGP--FKVFNEPDEKA 75 (204)
T ss_pred ceEEEEEEEecCCCCCCcCCCCCeEEEEEEEEecCC-EEEecc--cccccccc-cccccCCCCCCCc--eEEecCCCHHH
Confidence 36789999998631 1127899999998764333 111100 01100000 000 000001110 11223467889
Q ss_pred HHHHHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCC--C---C----------CcceeHHHHHHHHhcCCCCCC
Q 010297 84 IADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAP--E---P----------KGTIDSLALLTQRFGRRAGDM 145 (513)
Q Consensus 84 Vl~ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p--~---~----------~~~IDTL~Lar~~l~prl~s~ 145 (513)
.+.+|.+++.. .+++|||+..||+++|.+.+.++|+... . . ...+|.+.++++......+++
T Consensus 76 lL~~f~~~i~~~~Pd~i~gyN~~~FD~pyl~~R~~~~~~~~~~~~g~~~~~~~~~~~~gr~~iDl~~~~~~~~~l~~~sy 155 (204)
T cd05779 76 LLQRFFEHIREVKPHIIVTYNGDFFDWPFVEARAAIHGLSMEEEIGFRKDSEGEYKSRYIIHMDCFRWVKRDSYLPQGSQ 155 (204)
T ss_pred HHHHHHHHHHHhCCCEEEecCccccCHHHHHHHHHHhCCCchhhhCeEecCCCeEEeccEEEEEhHHHHHHhhcCCCCCc
Confidence 99999999984 4899999999999999999999987643 0 0 127899998876444344689
Q ss_pred CHHHHHH-HhCCCC
Q 010297 146 KMASLAT-YFGLGQ 158 (513)
Q Consensus 146 kL~~LAk-~fGI~~ 158 (513)
+|+.+|+ ++|.++
T Consensus 156 sLd~Va~~~Lg~~K 169 (204)
T cd05779 156 GLKAVTKAKLGYDP 169 (204)
T ss_pred cHHHHHHHHhCCCc
Confidence 9999999 488864
No 62
>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=98.64 E-value=1.5e-06 Score=80.90 Aligned_cols=144 Identities=14% Similarity=0.166 Sum_probs=99.7
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHH
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl 85 (513)
.+..+++||+||||+++ ..++|+.++...- .+ ..|..-+.+.. . .+++.+.+++
T Consensus 3 ~~~~~~a~d~e~~~~~~--~~~~i~~l~~~~~-~~-----~~~~~~~~~~~---~---------------~~~~~~~~~~ 56 (193)
T cd06139 3 EKAKVFAFDTETTSLDP--MQAELVGISFAVE-PG-----EAYYIPLGHDY---G---------------GEQLPREEVL 56 (193)
T ss_pred ccCCeEEEEeecCCCCc--CCCeEEEEEEEcC-CC-----CEEEEecCCCc---c---------------ccCCCHHHHH
Confidence 46788999999999976 4677887775421 11 12211122211 1 1345678888
Q ss_pred HHHHHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC-----
Q 010297 86 DTVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG----- 157 (513)
Q Consensus 86 ~ef~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~----- 157 (513)
..|.+++.+. .+|+||+ .||+.+|+ +.|+..+. .++||+.+++ .+.|..++++|..+++.| |..
T Consensus 57 ~~l~~~l~~~~~~~v~hn~-k~d~~~l~----~~gi~~~~--~~~Dt~l~a~-ll~p~~~~~~l~~l~~~~l~~~~~~~~ 128 (193)
T cd06139 57 AALKPLLEDPSIKKVGQNL-KFDLHVLA----NHGIELRG--PAFDTMLASY-LLNPGRRRHGLDDLAERYLGHKTISFE 128 (193)
T ss_pred HHHHHHHhCCCCcEEeecc-HHHHHHHH----HCCCCCCC--CcccHHHHHH-HhCCCCCCCCHHHHHHHHhCCCCccHH
Confidence 9999999864 7999999 99999986 35776442 5899999876 566655457999998876 321
Q ss_pred ------------------CCCCChHHHHHHHHHHHHHHHHHhhc
Q 010297 158 ------------------QQTHRSLDDVRMNLEVLKYCATVLFL 183 (513)
Q Consensus 158 ------------------~~aHRALdDA~aTA~Ll~~ll~~L~~ 183 (513)
...|.|..||.++..++..+.+.+..
T Consensus 129 ~~~~k~~~~~~~~~~~~~~~~~ya~~d~~~~~~l~~~l~~~l~~ 172 (193)
T cd06139 129 DLVGKGKKQITFDQVPLEKAAEYAAEDADITLRLYELLKPKLKE 172 (193)
T ss_pred HHcCCCcCcCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 02236888899999999998887754
No 63
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.62 E-value=1.2e-06 Score=85.53 Aligned_cols=126 Identities=22% Similarity=0.273 Sum_probs=90.4
Q ss_pred CCCCCCCcEEEEEEecCCCCC------CCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHH
Q 010297 2 GPTQDRSEIAFFDVETTVPTR------PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAV 75 (513)
Q Consensus 2 ~~t~~~~~~VVfDlETTGLd~------~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmL 75 (513)
+++..+=+++.||+||++... ....+.|+.||.. +.++.+. .+.
T Consensus 3 ~~~~~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~--~~~~~~~------~~~---------------------- 52 (207)
T cd05785 3 GMTFDDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALR--DNRGWEE------VLH---------------------- 52 (207)
T ss_pred CCCCCCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecc--cCCCcee------eec----------------------
Confidence 455566789999999976431 1256889999974 2221111 110
Q ss_pred cCCCCHHHHHHHHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCCC-----------------------------
Q 010297 76 VSSPTFADIADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE----------------------------- 123 (513)
Q Consensus 76 a~Apsf~EVl~ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~----------------------------- 123 (513)
....+..+.+.+|.+++.. .+++|||+..||+++|.+.++++|+...+
T Consensus 53 ~~~~~E~~lL~~f~~~i~~~dPdii~g~N~~~FD~pyl~~R~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~ 132 (207)
T cd05785 53 AEDAAEKELLEELVAIIRERDPDVIEGHNIFRFDLPYLRRRCRRHGVPLAIGRDGSIPRQRPSRFRFAERLIDYPRYDIP 132 (207)
T ss_pred cCCCCHHHHHHHHHHHHHHhCCCEEeccCCcccCHHHHHHHHHHhCCCcccccCCCcceEeeccccccccccccceEEec
Confidence 0146788899999999985 79999999999999999999999987631
Q ss_pred CCcceeHHHHHHHHh--cCCCCCCCHHHHHHHhCCC
Q 010297 124 PKGTIDSLALLTQRF--GRRAGDMKMASLATYFGLG 157 (513)
Q Consensus 124 ~~~~IDTL~Lar~~l--~prl~s~kL~~LAk~fGI~ 157 (513)
....+|++.++++.- ...+.+|+|+++|++||+.
T Consensus 133 Gr~~iDl~~~~~~~~~~~~~l~sysL~~Va~~~g~~ 168 (207)
T cd05785 133 GRHVIDTYFLVQLFDVSSRDLPSYGLKAVAKHFGLA 168 (207)
T ss_pred CEEEEEcHHHHHhhcccccCCCCCCHHHHHHHhccc
Confidence 012389999887421 2356899999999999874
No 64
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=98.56 E-value=1.1e-07 Score=95.74 Aligned_cols=177 Identities=19% Similarity=0.193 Sum_probs=130.2
Q ss_pred CCCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCce------------------eEeeeEEEEEcCCCCCCCChhhH
Q 010297 4 TQDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKL------------------EELHNYSTLVRPADPELISSLSV 65 (513)
Q Consensus 4 t~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~------------------eivdsFs~lIrP~~~~~I~~~~t 65 (513)
.++-..++|+|+|+||+.. ....|.|++...+....+ .++++.+.+..|.. ...+.+.
T Consensus 9 ~pr~~tf~fldleat~lp~--~~~~iteLcLlav~assle~k~~e~dq~~~~tlp~~Rvl~Klsvl~~p~~--v~~p~ae 84 (318)
T KOG4793|consen 9 VPRLRTFSFLDLEATGLPG--WIPNITELCLLAVHASSLEGKAREIDQNVSTTLPGSRVLDKLSVLGGPVP--VTRPIAE 84 (318)
T ss_pred CCceeEEEeeeeccccCCc--ccccchhhhHHHHHHHhhcCCccccccCCCccCCccchhhhhhhccCCcC--CcChhhh
Confidence 4455789999999999965 777899988665542111 24566777788887 7889999
Q ss_pred HhhCCCHHHHcC--CCCHH-HHHHHHHHHHcC----CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHh
Q 010297 66 RCNGITPDAVVS--SPTFA-DIADTVFDILHG----RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRF 138 (513)
Q Consensus 66 eIhGIT~EmLa~--Apsf~-EVl~ef~efL~g----~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l 138 (513)
++||.+++-+.- ..-|+ ++.+-+..|++. ..+|+||..+||.+.|.+++++.|+..+.....+|++...+..-
T Consensus 85 eitgls~~~~~l~rr~~~D~dla~LL~afls~lp~p~CLVaHng~~~dfpil~qela~lg~~lpq~lvcvdslpa~~ald 164 (318)
T KOG4793|consen 85 EITGLSQPFLALQRRLAFDKDLAKLLTAFLSRLPTPGCLVAHNGNEYDFPILAQELAGLGYSLPQDLVCVDSLPALNALD 164 (318)
T ss_pred hhcccccHHHHHHHHhhhhHHHHHHHHHHHhcCCCCceEEeecCCccccHHHHHHHHhcCccchhhhcCcchhHHHHHHh
Confidence 999999866532 23344 355556777763 47899999999999999999999999886656888888765322
Q ss_pred c--------CCCCCCCHHHHHHHh-CC-C-CCCCChHHHHHHHHHHHHHHHHHhhcc
Q 010297 139 G--------RRAGDMKMASLATYF-GL-G-QQTHRSLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 139 ~--------prl~s~kL~~LAk~f-GI-~-~~aHRALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
. +..++|.|..+-..| +- + ...|.|..|.....-+++.....+...
T Consensus 165 ~a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~~e~d~~~l~~~fqf~~~ellR~ 221 (318)
T KOG4793|consen 165 RANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHVAEGDVNGLLFIFQFRINELLRW 221 (318)
T ss_pred hhcCcccCCCCCcccccchHHHhhhcccCCCcceeeecccchhHHHHHHHHHHHHhh
Confidence 1 113577888876644 44 2 578999999998888888877776554
No 65
>PHA02570 dexA exonuclease; Provisional
Probab=98.49 E-value=1.2e-06 Score=86.54 Aligned_cols=166 Identities=16% Similarity=0.159 Sum_probs=100.8
Q ss_pred EEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhh-CC------------CHH---H
Q 010297 11 AFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCN-GI------------TPD---A 74 (513)
Q Consensus 11 VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIh-GI------------T~E---m 74 (513)
+++|+||.|..+ +..|++||||.++...+ ...+|+.+|.....-.+...... . +. ++| .
T Consensus 4 lMIDlETmG~~p---~AaIisIgAV~Fdp~~~-~g~tF~elV~~~~~~k~d~~sq~-g~~~~d~~TI~WW~kQS~EAR~~ 78 (220)
T PHA02570 4 FIIDFETFGNTP---DGAVIDLAVIAFEHDPH-NPPTFEELVSRGRRIKFDLKSQK-GKRLFDKSTIEWWKNQSPEARKN 78 (220)
T ss_pred EEEEeeccCCCC---CceEEEEEEEEecCCCC-ccccHHHHhhcccccccchhhcc-CCCccCchHHHHHHhCCHHHHHh
Confidence 689999999975 67899999999998654 57788877764221111111111 1 11 111 1
Q ss_pred Hc---CCCCHHHHHHHHHHHHc--C-----CeEEEeCcchHHHHHHHHHHHHc----C--CCCCCCC-cceeHHHHHHHH
Q 010297 75 VV---SSPTFADIADTVFDILH--G-----RIWAGHNILRFDCARIREAFAEI----G--RPAPEPK-GTIDSLALLTQR 137 (513)
Q Consensus 75 La---~Apsf~EVl~ef~efL~--g-----~vLVAHNa~~FD~~FL~~~f~r~----G--i~~p~~~-~~IDTL~Lar~~ 137 (513)
|. +..++.+++.+|.+||. + ..+.|... .||...|+.+++++ + ++.|+.. ..-|+-.+....
T Consensus 79 L~~s~~~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~-sFD~~IL~~a~r~~~~~~~~~~~~Pw~fwN~RDVRT~ie~~ 157 (220)
T PHA02570 79 LKPSDEDVSTYEGHKKFFEYLEANGVDPWKSQGWCRGN-SFDFPILVDVIRDIHNTRDTFKLEPVKFWNQRDVRTAIEAT 157 (220)
T ss_pred ccCCCccccHHHHHHHHHHHHHHcCCCccceeEecCCC-ccCHHHHHHHHHHHhcccCcCcCCCeeecCccchHHHHhhh
Confidence 21 23578999999999997 2 13445555 99999999999988 6 4555321 233433333222
Q ss_pred -hcCCC-----CCCCHHHHHHHhCCC-CCCCChHHHHHHHHHHHHHHHHHhhcccCCCCcc
Q 010297 138 -FGRRA-----GDMKMASLATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFLESSLPDIF 191 (513)
Q Consensus 138 -l~prl-----~s~kL~~LAk~fGI~-~~aHRALdDA~aTA~Ll~~ll~~L~~~~~~P~v~ 191 (513)
+.+.+ ..-. ++ -.+|+|+.||..-+..+.+-.+....=...|...
T Consensus 158 ~l~r~~~~cp~~~g~---------l~gfv~H~sihDcakd~lml~y~~rya~~le~~p~~~ 209 (220)
T PHA02570 158 LLTRGMTTCPLPKGT---------LDGFVAHDSIHDCAKDILMLIYAKRYALGLEDLPTEE 209 (220)
T ss_pred hccCCcccCCCcCcc---------ccchhhcccHHHHHHHHHHHHHHHHHhcCCCcCCccC
Confidence 33321 1111 12 3689999999888888877766633223455433
No 66
>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=98.36 E-value=1.7e-05 Score=78.10 Aligned_cols=138 Identities=17% Similarity=0.178 Sum_probs=92.0
Q ss_pred CCCcEEEEEEecCCC---CCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 6 DRSEIAFFDVETTVP---TRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 6 ~~~~~VVfDlETTGL---d~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
-.-+.+.||+||+.. -|....|.|+.||++.-..+......+.-..+.+.. +++ | ..+..-.+..
T Consensus 5 p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~--~~~-------~---~~v~~~~~E~ 72 (230)
T cd05777 5 APLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCA--PIV-------G---AQVFSFETEE 72 (230)
T ss_pred CCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCC--CCC-------C---CEEEEECCHH
Confidence 345689999999853 122267999999998765543222222111223221 111 1 1223346788
Q ss_pred HHHHHHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCC--C-------------------------------CCc
Q 010297 83 DIADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAP--E-------------------------------PKG 126 (513)
Q Consensus 83 EVl~ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p--~-------------------------------~~~ 126 (513)
+.+.+|.+++.. .+++|||+..||+++|.+.++++|+... . ...
T Consensus 73 eLL~~f~~~i~~~DPDii~GyN~~~FDl~yL~~R~~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~ 152 (230)
T cd05777 73 ELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRI 152 (230)
T ss_pred HHHHHHHHHHHhcCCCEEEEecCCCCCHHHHHHHHHHhCCccccccccccCCceeEeCCcccccccccccceEEEEcCEE
Confidence 899999999884 6999999999999999999988876521 0 013
Q ss_pred ceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC
Q 010297 127 TIDSLALLTQRFGRRAGDMKMASLATYF-GLG 157 (513)
Q Consensus 127 ~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~ 157 (513)
.+|++.++++.+ .+.+|+|+++|+++ |..
T Consensus 153 ~iD~~~~~~~~~--kl~sy~L~~Va~~~Lg~~ 182 (230)
T cd05777 153 QFDLLQVIQRDY--KLRSYSLNSVSAHFLGEQ 182 (230)
T ss_pred eeeHHHHHHHhc--CcccCcHHHHHHHHhCCC
Confidence 568898887543 57899999999855 543
No 67
>PRK05755 DNA polymerase I; Provisional
Probab=98.33 E-value=6.5e-06 Score=95.54 Aligned_cols=135 Identities=15% Similarity=0.196 Sum_probs=98.9
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
...+++||+||||+++ ..++|+.|++ ...++. ..+|.+. ++. .+++.
T Consensus 314 ~~~~~a~DtEt~~l~~--~~~~i~~i~l-s~~~g~-------~~~ip~~-------------~i~----------~~~l~ 360 (880)
T PRK05755 314 AAGLFAFDTETTSLDP--MQAELVGLSF-AVEPGE-------AAYIPLD-------------QLD----------REVLA 360 (880)
T ss_pred ccCeEEEEeccCCCCc--ccccEEEEEE-EeCCCc-------EEEEecc-------------ccc----------HHHHH
Confidence 4678999999999987 6788999886 333331 1233321 111 15777
Q ss_pred HHHHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCCC-----
Q 010297 87 TVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLGQ----- 158 (513)
Q Consensus 87 ef~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~~----- 158 (513)
.|.+++.+. +.|+||+ .||+.+|.+ +|+..+ ..++||+-+++ .+.+.. .++|.+|++.| |.+.
T Consensus 361 ~l~~~L~d~~v~kV~HNa-kfDl~~L~~----~gi~~~--~~~~DT~iAa~-Ll~~~~-~~~L~~L~~~ylg~~~~~~~~ 431 (880)
T PRK05755 361 ALKPLLEDPAIKKVGQNL-KYDLHVLAR----YGIELR--GIAFDTMLASY-LLDPGR-RHGLDSLAERYLGHKTISFEE 431 (880)
T ss_pred HHHHHHhCCCCcEEEecc-HhHHHHHHh----CCCCcC--CCcccHHHHHH-HcCCCC-CCCHHHHHHHHhCCCccchHH
Confidence 888999864 4899999 999999984 477654 25899999765 556654 38999999887 4431
Q ss_pred ---------------CCCChHHHHHHHHHHHHHHHHHhhc
Q 010297 159 ---------------QTHRSLDDVRMNLEVLKYCATVLFL 183 (513)
Q Consensus 159 ---------------~aHRALdDA~aTA~Ll~~ll~~L~~ 183 (513)
..|.|..|+..+++++.++.+.+..
T Consensus 432 ~~gk~~~~~~~ple~~~~YAa~Dv~~~~~L~~~L~~~L~~ 471 (880)
T PRK05755 432 VAGKQLTFAQVDLEEAAEYAAEDADVTLRLHEVLKPKLLE 471 (880)
T ss_pred hcCCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3478999999999999999988654
No 68
>cd05782 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=98.23 E-value=2.6e-05 Score=76.20 Aligned_cols=75 Identities=17% Similarity=0.238 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCC---------------CcceeHHHHHHHHhcCCCC
Q 010297 81 FADIADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEP---------------KGTIDSLALLTQRFGRRAG 143 (513)
Q Consensus 81 f~EVl~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~---------------~~~IDTL~Lar~~l~prl~ 143 (513)
..+.+.+|.+++.. .++|+||+..||+++|...+..+|++.|.. .+.+|++.+++. + ....
T Consensus 78 E~elL~~F~~~i~~~~p~lv~yNg~~FDlP~L~~Ra~~~gi~~p~~~~~~~~~~~y~~r~~~~h~DL~~~~~~-~-~~~~ 155 (208)
T cd05782 78 EKELLEDFFQLIEKKNPRLVSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAF-Y-GARA 155 (208)
T ss_pred HHHHHHHHHHHHHHhCCEEEecCCCcCCHHHHHHHHHHhCCCCccccCcccchhhccCcCCCCcccHHHHHhc-c-CccC
Confidence 47788999999884 589999999999999999999999965421 138899998752 3 2357
Q ss_pred CCCHHHHHHHhCCC
Q 010297 144 DMKMASLATYFGLG 157 (513)
Q Consensus 144 s~kL~~LAk~fGI~ 157 (513)
+++|+.+|+.+|++
T Consensus 156 ~~~L~~va~~lG~~ 169 (208)
T cd05782 156 RASLDLLAKLLGIP 169 (208)
T ss_pred CCCHHHHHHHhCCC
Confidence 89999999999996
No 69
>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=98.19 E-value=3.8e-05 Score=74.94 Aligned_cols=161 Identities=17% Similarity=0.279 Sum_probs=95.4
Q ss_pred CcEEEEEEecCCCC----C-C-CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCH
Q 010297 8 SEIAFFDVETTVPT----R-P-GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (513)
Q Consensus 8 ~~~VVfDlETTGLd----~-~-g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf 81 (513)
-+++.||+||++.. | + ...+.||.|+.. ..++. ..+ .++........+.... -+ ..+..-.+.
T Consensus 5 lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~--~~~~~---~~v-~~~~~~~~~~~~~~~~--~~---~~v~~~~~E 73 (204)
T cd05783 5 LKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALA--GSDGL---KRV-LVLKREGVEGLEGLLP--EG---AEVEFFDSE 73 (204)
T ss_pred ceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEc--CCCCC---cEE-EEEecCCcccccccCC--CC---CeEEecCCH
Confidence 46899999998522 1 1 123689999985 21211 122 2222111000000000 01 113334678
Q ss_pred HHHHHHHHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCC---CC----------CCCcceeHHHHHHHH------hcCC
Q 010297 82 ADIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRP---AP----------EPKGTIDSLALLTQR------FGRR 141 (513)
Q Consensus 82 ~EVl~ef~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~---~p----------~~~~~IDTL~Lar~~------l~pr 141 (513)
.+.+.+|.+++.. .+++|||+..||+++|.+.++++|+. .+ .....+|.++.++.. +...
T Consensus 74 ~~lL~~F~~~i~~~~~iig~N~~~FDlpyl~~R~~~~gi~~~~~~~~~~~~~~~~~g~~~iDl~~~~~~~~~~~~~~~~~ 153 (204)
T cd05783 74 KELIREAFKIISEYPIVLTFNGDNFDLPYLYNRALKLGIPKEEIPIYLKRDYATLKHGIHIDLYKFFSNRAIQVYAFGNK 153 (204)
T ss_pred HHHHHHHHHHHhcCCEEEEeCCCCcCHHHHHHHHHHhCCChhhCceeecCCceeccCcEEeECHHHhhccchhhhhhccc
Confidence 8999999999984 58899999999999999999999987 11 122578988865531 2225
Q ss_pred CCCCCHHHHHHHh-CCCC-CCCChHHHHHHHHHHHHHHHHH
Q 010297 142 AGDMKMASLATYF-GLGQ-QTHRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 142 l~s~kL~~LAk~f-GI~~-~aHRALdDA~aTA~Ll~~ll~~ 180 (513)
+.+++|+++|+++ |.+. ..+....+. ...++..++++.
T Consensus 154 ~~~~~L~~Va~~~lg~~K~~~~~~i~~~-~~~~l~~Y~~~D 193 (204)
T cd05783 154 YREYTLDAVAKALLGEGKVELEKNISEL-NLYELAEYNYRD 193 (204)
T ss_pred cccCcHHHHHHHhcCCCcccCCchhhhh-cHHHHHHhhHHH
Confidence 5799999999966 5542 222333333 445555555554
No 70
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=98.11 E-value=7.9e-05 Score=73.43 Aligned_cols=127 Identities=16% Similarity=0.147 Sum_probs=90.3
Q ss_pred CCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHHHHHHc--CCeEEEeCc
Q 010297 25 QRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTVFDILH--GRIWAGHNI 102 (513)
Q Consensus 25 ~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef~efL~--g~vLVAHNa 102 (513)
.-++|+-|+++..+.+.. . +...+-.+. ....+.+++|.++++ ...||+||+
T Consensus 7 ~f~kIV~Is~~~~~~~~~-~--~v~s~~~~~-----------------------~~E~~lL~~F~~~~~~~~p~LVs~NG 60 (209)
T PF10108_consen 7 PFHKIVCISVVYADDDGQ-F--KVKSLGGPD-----------------------DDEKELLQDFFDLVEKYNPQLVSFNG 60 (209)
T ss_pred cCCCeEEEEEEEEecCCc-E--EEEeccCCC-----------------------CCHHHHHHHHHHHHHhCCCeEEecCC
Confidence 457899999997775421 1 222221111 236788999999997 457999999
Q ss_pred chHHHHHHHHHHHHcCCCCCCC----------------CcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCCC--CC----
Q 010297 103 LRFDCARIREAFAEIGRPAPEP----------------KGTIDSLALLTQRFGRRAGDMKMASLATYFGLGQ--QT---- 160 (513)
Q Consensus 103 ~~FD~~FL~~~f~r~Gi~~p~~----------------~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~~--~a---- 160 (513)
..||+++|....-.+|++.|.. ...+|++++.. .+......+|+.||+.+|+|. .-
T Consensus 61 ~~FDlP~L~~Ral~~gi~~p~~~~~~~k~WenY~~Ry~~~H~DLmd~l~--~~g~~~~~sLd~la~~lgiPgK~~idGs~ 138 (209)
T PF10108_consen 61 RGFDLPVLCRRALIHGISAPRYLDIGNKPWENYRNRYSERHLDLMDLLS--FYGAKARTSLDELAALLGIPGKDDIDGSQ 138 (209)
T ss_pred ccCCHHHHHHHHHHhCCCCchhhhcCCCCccccccccCcccccHHHHHh--ccCccccCCHHHHHHHcCCCCCCCCCHHH
Confidence 9999999998888899886531 23688888754 233335779999999999972 11
Q ss_pred --------------CChHHHHHHHHHHHHHHHH
Q 010297 161 --------------HRSLDDVRMNLEVLKYCAT 179 (513)
Q Consensus 161 --------------HRALdDA~aTA~Ll~~ll~ 179 (513)
.--..||++|+.||.++..
T Consensus 139 V~~~y~~g~i~~I~~YCe~DVl~T~~lylR~~~ 171 (209)
T PF10108_consen 139 VAELYQEGDIDEIREYCEKDVLNTYLLYLRFEL 171 (209)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1126799999999988754
No 71
>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=98.05 E-value=9.2e-05 Score=71.72 Aligned_cols=124 Identities=15% Similarity=0.177 Sum_probs=83.9
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHH
Q 010297 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (513)
Q Consensus 9 ~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef 88 (513)
++++||+||+|.. .|+-||..-...+ .+ -.+=.+.. .. |. .+.--.+..+.+.+|
T Consensus 4 ~~~~fDIE~~~~~------~i~~i~~~~~~~~--~i----~~~~~~~~---~~-------~~---~v~~~~~E~~lL~~f 58 (193)
T cd05784 4 KVVSLDIETSMDG------ELYSIGLYGEGQE--RV----LMVGDPED---DA-------PD---NIEWFADEKSLLLAL 58 (193)
T ss_pred cEEEEEeecCCCC------CEEEEEeecCCCC--EE----EEECCCCC---CC-------CC---EEEEECCHHHHHHHH
Confidence 5799999998752 6888887432222 11 11111111 10 11 123345778899999
Q ss_pred HHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCCCC-----------------------CcceeHHHHHHHHhcCCC
Q 010297 89 FDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPEP-----------------------KGTIDSLALLTQRFGRRA 142 (513)
Q Consensus 89 ~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~-----------------------~~~IDTL~Lar~~l~prl 142 (513)
.+++.. .+++|||...||+++|.+.+.++|+..... ...+|++.++++.. ..+
T Consensus 59 ~~~i~~~dPDvi~g~N~~~FD~~yl~~R~~~~~i~~~~gR~~~~~~~~~~g~~~~~~~~i~GR~~~D~~~~~k~~~-~kl 137 (193)
T cd05784 59 IAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTAT-YHF 137 (193)
T ss_pred HHHHHhhCCCEEEECCCcCcCHHHHHHHHHHhCCCcccccCCCccccccCCcCCcceEEEeeEEEEEhHHHHHHcc-CCC
Confidence 999984 589999999999999999999998875211 12789998887422 257
Q ss_pred CCCCHHHHHHHh-CCCC
Q 010297 143 GDMKMASLATYF-GLGQ 158 (513)
Q Consensus 143 ~s~kL~~LAk~f-GI~~ 158 (513)
.+|+|+++|+++ |...
T Consensus 138 ~sy~L~~Va~~~Lg~~K 154 (193)
T cd05784 138 ESFSLENVAQELLGEGK 154 (193)
T ss_pred CcCCHHHHHHHHhCCCc
Confidence 899999999955 4443
No 72
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=98.04 E-value=0.00011 Score=74.02 Aligned_cols=161 Identities=20% Similarity=0.265 Sum_probs=95.0
Q ss_pred CcEEEEEEecCCCCCCC-------------------CCCcEEEEEEEEE-eCCceeE-----eeeEEEEEcCCCCCCCCh
Q 010297 8 SEIAFFDVETTVPTRPG-------------------QRFAILEFGAILV-CPKKLEE-----LHNYSTLVRPADPELISS 62 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g-------------------~~deIIEIGAV~V-d~g~~ei-----vdsFs~lIrP~~~~~I~~ 62 (513)
..||.||+|.||+.... ..-.|||+|...+ +.+. .. +..|..++-|........
T Consensus 22 ~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~-~~~~~~~~~~~nf~~f~~~~~~~~~ 100 (262)
T PF04857_consen 22 ADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDG-NIPSSYNVWPFNFYLFPLDRDFSQA 100 (262)
T ss_dssp SSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTS-EEECCEEEEEEEBSTTSTTTCEEEH
T ss_pred CCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccc-cCCceeEEEEeeeeccccccceecc
Confidence 56999999999986522 3356999999999 3332 32 333444433433211222
Q ss_pred hh---HHhhCCCHHHH-cCCCCHHHHHH-----HHHHHHc--------CCeEEEeCcchHHHHHHHHHHHHcCCCCCCC-
Q 010297 63 LS---VRCNGITPDAV-VSSPTFADIAD-----TVFDILH--------GRIWAGHNILRFDCARIREAFAEIGRPAPEP- 124 (513)
Q Consensus 63 ~~---teIhGIT~EmL-a~Apsf~EVl~-----ef~efL~--------g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~- 124 (513)
.+ ..-||+.-+.+ .+|.++....+ +...+-+ ..+|||||. -+|+.+|-+.|-. +.|..
T Consensus 101 ~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~-~~Dl~~l~~~f~~---~LP~t~ 176 (262)
T PF04857_consen 101 SSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNG-LYDLMYLYKKFIG---PLPETL 176 (262)
T ss_dssp HHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESST-HHHHHHHHHHHTT---S--SSH
T ss_pred hhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeCh-HhHHHHHHHHhcC---CCCCCH
Confidence 22 23457776666 55666543321 2222211 379999999 9999999887633 33311
Q ss_pred -----------CcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC--------------------------CCCCChHHHH
Q 010297 125 -----------KGTIDSLALLTQRFGRRAGDMKMASLATYFGLG--------------------------QQTHRSLDDV 167 (513)
Q Consensus 125 -----------~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~--------------------------~~aHRALdDA 167 (513)
..++||.-+++. .. ....+|..+++.++.. ...|.|-.||
T Consensus 177 ~eF~~~~~~~FP~i~DtK~la~~-~~--~~~~~L~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HeAGyDA 253 (262)
T PF04857_consen 177 EEFKELLRELFPRIYDTKYLAEE-CP--GKSTSLQELAEELGIRRNPSSISSPEGFPSYDEEKNNFPMFGEKAHEAGYDA 253 (262)
T ss_dssp HHHHHHHHHHSSSEEEHHHHHTS-TT--TS-SSHHHHHHHTTSTT----EEE-TTS-------------SS-TTSHHHHH
T ss_pred HHHHHHHHHHCcccccHHHHHHh-cc--ccccCHHHHHHHhCCCccccccccccccccccccccccccCCCCCCCcchHH
Confidence 147788776641 11 3467899999999753 2389999999
Q ss_pred HHHHHHHHH
Q 010297 168 RMNLEVLKY 176 (513)
Q Consensus 168 ~aTA~Ll~~ 176 (513)
.+|+.+|.+
T Consensus 254 ~mTg~~F~~ 262 (262)
T PF04857_consen 254 YMTGCVFIK 262 (262)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHcC
Confidence 999999864
No 73
>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=98.01 E-value=0.00017 Score=71.47 Aligned_cols=172 Identities=13% Similarity=0.057 Sum_probs=108.6
Q ss_pred CcEEEEEEecCC---CCCCCCCCcEEEEEEEEEeCCceeEe---eeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCH
Q 010297 8 SEIAFFDVETTV---PTRPGQRFAILEFGAILVCPKKLEEL---HNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTF 81 (513)
Q Consensus 8 ~~~VVfDlETTG---Ld~~g~~deIIEIGAV~Vd~g~~eiv---dsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf 81 (513)
-+++.||+|+.+ +-|....|.|+.|+++.-........ .....++.+... ..... .....+....+.--.+.
T Consensus 4 l~~ls~dI~~~s~~~~~Pdp~~D~I~~I~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~-~~~~~~~~~~v~~~~~E 81 (231)
T cd05778 4 LTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDDVSPFILDANKVGVIIVDELKS-NASNG-RIRSGLSGIPVEVVESE 81 (231)
T ss_pred eEEEEEEEEECCCCCCCcCCCCCCeeEEEEEEecCCCcccccccceeEEEEcCccc-hhhhh-ccccCCCCCeEEEeCCH
Confidence 467899999875 11223789999999986554422111 111233443330 00000 00112222334445677
Q ss_pred HHHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCCC---------------------C-----------CCc
Q 010297 82 ADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAP---------------------E-----------PKG 126 (513)
Q Consensus 82 ~EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p---------------------~-----------~~~ 126 (513)
.+.+.+|.+++. -.+++|||+..||+++|.+.++.+++... + ...
T Consensus 82 ~~LL~~f~~~i~~~DPDii~GyNi~~fd~~YL~~Ra~~l~~~~~~~~lgR~~~~~~~~~~~~~~~~g~~~~~~~~i~GRi 161 (231)
T cd05778 82 LELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDDEWGYTHTSGIKIVGRH 161 (231)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeccccCcHHHHHHHHHHhCCcchhhhccCCCCCCcccccccccccccccCCceEEeeEE
Confidence 888888888887 47999999999999999888877665421 0 013
Q ss_pred ceeHHHHHHHHhcCCCCCCCHHHHHH-HhCCC--CCCCChHHHHH------HHHHHHHHHHHHhhc
Q 010297 127 TIDSLALLTQRFGRRAGDMKMASLAT-YFGLG--QQTHRSLDDVR------MNLEVLKYCATVLFL 183 (513)
Q Consensus 127 ~IDTL~Lar~~l~prl~s~kL~~LAk-~fGI~--~~aHRALdDA~------aTA~Ll~~ll~~L~~ 183 (513)
.+|++.++++.+ .+.+|+|++++. .+|.. .-+|..+.+.. ...+++.+|+++...
T Consensus 162 ~lD~~~~~r~~~--kl~sYsL~~V~~~~L~~~k~~~~~~~i~~~~~~~~~~~r~~v~~Y~l~d~~l 225 (231)
T cd05778 162 ILNVWRLMRSEL--ALTNYTLENVVYHVLHQRIPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRL 225 (231)
T ss_pred EeEhHHHHHHHc--CcccCCHHHHHHHHhCCCCCCCCHHHHHHHHHcCCHhHhHHHHHHHHHHHHH
Confidence 568888887543 678999999998 45654 35566677653 567788888877543
No 74
>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=97.90 E-value=0.00064 Score=62.00 Aligned_cols=135 Identities=19% Similarity=0.264 Sum_probs=85.1
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
...++.||+||+|+..... -..+..+-+..+ ....++.|..... . . +..
T Consensus 19 ~~~~~a~D~E~~~~~~~~~---~~~~~~iq~~~~------~~~~i~~~~~~~~-~-~--------------------~~~ 67 (176)
T PF01612_consen 19 NAKVLAFDTETTGLDPYSY---NPKIALIQLATG------EGCYIIDPIDLGD-N-W--------------------ILD 67 (176)
T ss_dssp TTSEEEEEEEEETSTSTTS---SEEEEEEEEEES------CEEEEECGTTSTT-T-T--------------------HHH
T ss_pred CCCeEEEEEEECCCCcccc---CCeEEEEEEecC------CCceeeeeccccc-c-c--------------------hHH
Confidence 3569999999999976222 233444444433 1223334433100 0 0 566
Q ss_pred HHHHHHc--CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-C-CC----C
Q 010297 87 TVFDILH--GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-G-LG----Q 158 (513)
Q Consensus 87 ef~efL~--g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-G-I~----~ 158 (513)
.+.+++. +...||||+ .||+.+|.+. +|+... .++|| .++...+.+... ++|++|+..+ | +. .
T Consensus 68 ~l~~ll~~~~i~kv~~n~-~~D~~~L~~~---~~i~~~---~~~D~-~l~~~~l~~~~~-~~L~~L~~~~l~~~~~~~~~ 138 (176)
T PF01612_consen 68 ALKELLEDPNIIKVGHNA-KFDLKWLYRS---FGIDLK---NVFDT-MLAAYLLDPTRS-YSLKDLAEEYLGNIDLDKKE 138 (176)
T ss_dssp HHHHHHTTTTSEEEESSH-HHHHHHHHHH---HTS--S---SEEEH-HHHHHHTTTSTT-SSHHHHHHHHHSEEE-GHCC
T ss_pred HHHHHHhCCCccEEEEEE-echHHHHHHH---hccccC---Cccch-hhhhhccccccc-ccHHHHHHHHhhhccCcHHH
Confidence 7778887 458999999 9999999876 477543 48999 555545544433 9999998755 6 32 1
Q ss_pred ---CCC--C---------hHHHHHHHHHHHHHHHHHh
Q 010297 159 ---QTH--R---------SLDDVRMNLEVLKYCATVL 181 (513)
Q Consensus 159 ---~aH--R---------ALdDA~aTA~Ll~~ll~~L 181 (513)
... + |..||..+.+++..+..++
T Consensus 139 ~~~~~~~~~~l~~~~~~YAa~D~~~~~~l~~~l~~~l 175 (176)
T PF01612_consen 139 QMSDWRKARPLSEEQIEYAAQDAVVTFRLYEKLKPQL 175 (176)
T ss_dssp TTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH
T ss_pred hhccCCcCCCChHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 111 2 5669999999998887765
No 75
>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=97.81 E-value=0.00021 Score=72.10 Aligned_cols=131 Identities=17% Similarity=0.186 Sum_probs=86.3
Q ss_pred CCcEEEEEEecCCCCC---CCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHH
Q 010297 7 RSEIAFFDVETTVPTR---PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFAD 83 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~---~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~E 83 (513)
.-.++.||+||..... ....++|+.|+++....+...........+.+.. .... ...+.-..+..+
T Consensus 156 ~l~i~s~DIe~~~~~~~~P~~~~d~I~~Is~~~~~~~~~~~~~~~~~~~~~~~--~~~~---------~~~v~~~~~E~~ 224 (325)
T PF03104_consen 156 PLRILSFDIETYSNDGKFPDPEKDEIIMISYVVYRNGSSEPYRRKVFTLGSCD--SIED---------NVEVIYFDSEKE 224 (325)
T ss_dssp GSEEEEEEEEECSSSSSS-TTTTSEEEEEEEEEEETTEEETTEEEEEECSCSC--CTTC---------TTEEEEESSHHH
T ss_pred ccceeEEEEEEccccCCCCCCCCCeEEEEEEEEEeccccCCCceEEEEecCCC--CCCC---------CcEEEEECCHHH
Confidence 4578999999998652 2368999999998876542111222222233332 1111 223344567888
Q ss_pred HHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCC-------C--------------------------CCCcc
Q 010297 84 IADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPA-------P--------------------------EPKGT 127 (513)
Q Consensus 84 Vl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~-------p--------------------------~~~~~ 127 (513)
.+.+|.+++. -.+++|||+..||+++|.+.++.+|+.. . .....
T Consensus 225 lL~~f~~~i~~~dPDii~GyN~~~fD~~yl~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gr~~ 304 (325)
T PF03104_consen 225 LLEAFLDIIQEYDPDIITGYNIDGFDLPYLIERAKKLGIDMFDLNGRRWSRFGRLKRKKWPSSANGSRKFSRIDIPGRLV 304 (325)
T ss_dssp HHHHHHHHHHHHS-SEEEESSTTTTHHHHHHHHHHHTTTCTHHSTTSTTTEEEEEEEEESEECTCCCTTEEEEEETTSEE
T ss_pred HHHHHHHHHHhcCCcEEEEecccCCCHHHHHHHHHHhCccccccccccccceeEEeecccccccCCCcceeEEEECCChH
Confidence 9999999987 4699999999999999999999885431 0 11257
Q ss_pred eeHHHHHHHHhcCCCCCCCHHHH
Q 010297 128 IDSLALLTQRFGRRAGDMKMASL 150 (513)
Q Consensus 128 IDTL~Lar~~l~prl~s~kL~~L 150 (513)
+|++.++++.+ ++.+|+|+++
T Consensus 305 ~D~~~~~~~~~--~l~sY~L~~V 325 (325)
T PF03104_consen 305 LDLYRLARKDY--KLDSYSLDNV 325 (325)
T ss_dssp EEHHHHHHHHS----SS-SHHHH
T ss_pred hHHHHHHHhhC--CCCCCCCCCC
Confidence 89999988655 7789999864
No 76
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional
Probab=97.80 E-value=0.00037 Score=82.66 Aligned_cols=135 Identities=13% Similarity=0.152 Sum_probs=89.1
Q ss_pred CcEEEEEEecCCCC----CCCCCCcEEEEEEEEEeCCceeEeeeEEE-EEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 8 SEIAFFDVETTVPT----RPGQRFAILEFGAILVCPKKLEELHNYST-LVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 8 ~~~VVfDlETTGLd----~~g~~deIIEIGAV~Vd~g~~eivdsFs~-lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
-+++.||+||++.. |....|.||+|+.+....|... +.+.. ++-+.. +..+.| ..+..-.+..
T Consensus 264 lrilSfDIE~~~~~g~~FP~~~~D~IIqIs~~~~~~g~~~--~~~~r~vftl~~-------c~~i~g---~~V~~f~sE~ 331 (1054)
T PTZ00166 264 LRILSFDIECIKLKGLGFPEAENDPVIQISSVVTNQGDEE--EPLTKFIFTLKE-------CASIAG---ANVLSFETEK 331 (1054)
T ss_pred cEEEEEEEEECCCCCCCCCCCCCCcEEEEEEEEeeCCCcc--CCcceEEEecCc-------cccCCC---ceEEEeCCHH
Confidence 45899999998642 1126799999999876654211 11111 111111 111222 2233346788
Q ss_pred HHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCC----------C------------C-----------CCc
Q 010297 83 DIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPA----------P------------E-----------PKG 126 (513)
Q Consensus 83 EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~----------p------------~-----------~~~ 126 (513)
+.+.+|.+++. -.+++|||+..||+++|.+.++.+|+.. + + ...
T Consensus 332 eLL~~f~~~I~~~DPDII~GYNi~~FDlpYL~~Ra~~l~i~~~~~lgR~~~~~~~~~~~~~~~~~~g~~~~~~~~i~GR~ 411 (1054)
T PTZ00166 332 ELLLAWAEFVIAVDPDFLTGYNIINFDLPYLLNRAKALKLNDFKYLGRIKSTRSVIKDSKFSSKQMGTRESKEINIEGRI 411 (1054)
T ss_pred HHHHHHHHHHHhcCCCEEEecCCcCCcHHHHHHHHHHhCCCchhhcCcccCCCccccccccccccccccccceeEeeeEE
Confidence 88899988887 4799999999999999998888776541 0 0 014
Q ss_pred ceeHHHHHHHHhcCCCCCCCHHHHHHHh-CC
Q 010297 127 TIDSLALLTQRFGRRAGDMKMASLATYF-GL 156 (513)
Q Consensus 127 ~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI 156 (513)
.+|++.++++. ..+.+|+|++++.+| |.
T Consensus 412 ~iDl~~~~~~~--~kl~sYsL~~Vs~~~Lg~ 440 (1054)
T PTZ00166 412 QFDVMDLIRRD--YKLKSYSLNYVSFEFLKE 440 (1054)
T ss_pred EEEHHHHHHHh--cCcCcCCHHHHHHHHhCC
Confidence 68899988754 357899999999965 43
No 77
>smart00486 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Probab=97.56 E-value=0.0013 Score=69.27 Aligned_cols=135 Identities=17% Similarity=0.191 Sum_probs=90.4
Q ss_pred CcEEEEEEecCCCC---CC--CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 8 SEIAFFDVETTVPT---RP--GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 8 ~~~VVfDlETTGLd---~~--g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
-.++.||+||+... |. +..+.|+.|+.+.-+.+.............+.. . +.|+. +..-....
T Consensus 3 ~~~~~~DIEt~~~~~~~p~~~~~~~~ii~i~~~~~~~~~~~~~~~~~~~~~~~~--~-------~~~~~---~~~~~~E~ 70 (471)
T smart00486 3 LKILSFDIETYTDGGLFPDPLIFEDEIIQISLVINDGDKKGPEERICFTLGTCK--E-------IDGVE---VYEFNNEK 70 (471)
T ss_pred ceEEEEEEEECCCCCCCCCCCCCCCeEEEEEEEEEECCCCCCceeEEEEecCcC--C-------CCCCe---EEecCCHH
Confidence 46899999998753 11 126899999998887664222222222233332 2 22322 22223677
Q ss_pred HHHHHHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCCC--------------------------------CCcc
Q 010297 83 DIADTVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAPE--------------------------------PKGT 127 (513)
Q Consensus 83 EVl~ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~--------------------------------~~~~ 127 (513)
+.+.+|.+++.. .+++|||...||+++|...+.++++.... ....
T Consensus 71 ~lL~~f~~~i~~~dpdii~g~N~~~FD~~~i~~R~~~~~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 150 (471)
T smart00486 71 ELLKAFLEFIKKYDPDIIYGHNISNFDLPYIISRLEKLKIKPLSFIGRLKNIIDIKRKKPLFGSKSFGKTIKVKIKGRLV 150 (471)
T ss_pred HHHHHHHHHHHHhCCCEEEeecCCCCCHHHHHHHHHHcCCCCHHHcCcCCCCCCcccccCccccccccccceeEeccEEE
Confidence 888888888873 58999999889999999988877664320 1257
Q ss_pred eeHHHHHHHHhcCCCCCCCHHHHHHHhCC
Q 010297 128 IDSLALLTQRFGRRAGDMKMASLATYFGL 156 (513)
Q Consensus 128 IDTL~Lar~~l~prl~s~kL~~LAk~fGI 156 (513)
+|++.+.++.+ .+.+++|+.+++++..
T Consensus 151 ~Dl~~~~~~~~--kl~~~~L~~va~~~l~ 177 (471)
T smart00486 151 IDLYNLYKNKL--KLPSYKLDTVAEYLLG 177 (471)
T ss_pred EEhHHHHHHHh--CcccCCHHHHHHHHhC
Confidence 89999887544 3789999999987643
No 78
>PRK05762 DNA polymerase II; Reviewed
Probab=97.51 E-value=0.0018 Score=74.76 Aligned_cols=144 Identities=12% Similarity=0.128 Sum_probs=98.0
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
.-+++.||+||++. +.|+.||..-...+ .-..|.+.. ... .+.+..-++..+.+.
T Consensus 154 ~lrvlsfDIE~~~~------~~i~sI~~~~~~~~-------~vi~ig~~~--~~~----------~~~v~~~~sE~~LL~ 208 (786)
T PRK05762 154 PLKVVSLDIETSNK------GELYSIGLEGCGQR-------PVIMLGPPN--GEA----------LDFLEYVADEKALLE 208 (786)
T ss_pred CCeEEEEEEEEcCC------CceEEeeecCCCCC-------eEEEEECCC--CCC----------cceEEEcCCHHHHHH
Confidence 44789999999864 25888887521111 112233322 110 011444678889999
Q ss_pred HHHHHHcC---CeEEEeCcchHHHHHHHHHHHHcCCCCC--------------CC----------CcceeHHHHHHHHhc
Q 010297 87 TVFDILHG---RIWAGHNILRFDCARIREAFAEIGRPAP--------------EP----------KGTIDSLALLTQRFG 139 (513)
Q Consensus 87 ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r~Gi~~p--------------~~----------~~~IDTL~Lar~~l~ 139 (513)
+|.+++.. .+++|||+..||+++|.+.++.+|+... .. ...+|++.++++.+
T Consensus 209 ~F~~~i~~~DPDIIvGyNi~~FDlpyL~~Ra~~lgi~~~~GR~~~~~~~~~~~~~~~~~~~~i~GRv~lDl~~~~k~~~- 287 (786)
T PRK05762 209 KFNAWFAEHDPDVIIGWNVVQFDLRLLQERAERYGIPLRLGRDGSELEWREHPFRSGYGFASVPGRLVLDGIDALKSAT- 287 (786)
T ss_pred HHHHHHHhcCCCEEEEeCCCCCcHHHHHHHHHHhCCCcccCcCCCccccccCCCCCCcceEEEeeEEEEEHHHHHHHhh-
Confidence 99999984 6999999999999999999999988631 00 13789999988544
Q ss_pred CCCCCCCHHHHHHHhCCC-CCCCC----------------------hHHHHHHHHHHHHH
Q 010297 140 RRAGDMKMASLATYFGLG-QQTHR----------------------SLDDVRMNLEVLKY 176 (513)
Q Consensus 140 prl~s~kL~~LAk~fGI~-~~aHR----------------------ALdDA~aTA~Ll~~ 176 (513)
..+.+|+|+++|+++... ...|+ .+.||..+.+++.+
T Consensus 288 ~~l~sysL~~Va~~~Lg~~K~~~d~~~~~~eI~~~~~~~~~~l~~Y~l~Da~lt~~L~~k 347 (786)
T PRK05762 288 WVFDSFSLEYVSQRLLGEGKAIDDPYDRMDEIDRRFAEDKPALARYNLKDCELVTRIFEK 347 (786)
T ss_pred ccCCCCCHHHHHHHHhCCCeeccCccccHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 357899999999987554 22111 36788888888874
No 79
>PHA02528 43 DNA polymerase; Provisional
Probab=97.31 E-value=0.005 Score=72.03 Aligned_cols=163 Identities=15% Similarity=0.137 Sum_probs=97.7
Q ss_pred CCcEEEEEEecCC----CCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChh--hHHhhCCCHHHHcCCCC
Q 010297 7 RSEIAFFDVETTV----PTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSL--SVRCNGITPDAVVSSPT 80 (513)
Q Consensus 7 ~~~~VVfDlETTG----Ld~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~--~teIhGIT~EmLa~Aps 80 (513)
.-+++.||+||+. .++....+.||.||.. +.+ .+++..+.-+.. .+.... .....-...-.+..-.+
T Consensus 105 ~lrv~s~DIE~~~~~gfP~p~~~~d~IisIsl~--~~~----~~~~~v~~~~~~-~~~~~~~~~~~~~~~~~v~~~~~~s 177 (881)
T PHA02528 105 KIRIANLDIEVTAEDGFPDPEEAKYEIDAITHY--DSI----DDRFYVFDLGSV-EEWDAKGDEVPQEILDKVVYMPFDT 177 (881)
T ss_pred CccEEEEEEEECCCCCCCCcccCCCcEEEEEEe--cCC----CCEEEEEEecCc-ccccccCCcccccccCCeeEEEcCC
Confidence 4578999999976 2221126789999972 222 123333322110 000000 00000000011122457
Q ss_pred HHHHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHH-cCCCC-----C----------------------CCCccee
Q 010297 81 FADIADTVFDILH---GRIWAGHNILRFDCARIREAFAE-IGRPA-----P----------------------EPKGTID 129 (513)
Q Consensus 81 f~EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r-~Gi~~-----p----------------------~~~~~ID 129 (513)
..+.+.+|.+|+. -.+++|||+..||+++|.+.+++ +|+.. + .....+|
T Consensus 178 E~eLL~~F~~~i~~~DPDII~GyNi~~FDlpYL~~Ra~~~lg~~~~~~l~~~~~~~~~~~~~~~g~~~~~~~i~GRv~lD 257 (881)
T PHA02528 178 EREMLLEYINFWEENTPVIFTGWNVELFDVPYIINRIKNILGEKTAKRLSPWGKVKERTIENMYGREEIAYDISGISILD 257 (881)
T ss_pred HHHHHHHHHHHHHHhCCcEEEecCCccCCHHHHHHHHHHHcCcccccccccccccccccccccccccceeEEEcceEEEe
Confidence 8889999999996 36999999999999999888874 45331 0 0012577
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHH-hCCCCCCC------------------ChHHHHHHHHHHHHH
Q 010297 130 SLALLTQRFGRRAGDMKMASLATY-FGLGQQTH------------------RSLDDVRMNLEVLKY 176 (513)
Q Consensus 130 TL~Lar~~l~prl~s~kL~~LAk~-fGI~~~aH------------------RALdDA~aTA~Ll~~ 176 (513)
.+.+++......+.+|+|+++|++ ||.....| =.+.||..+.+|+.+
T Consensus 258 ~~dl~k~~~~~~l~SYsLe~VA~~~LG~~K~d~~~~eI~~l~~~d~~~l~~Ynl~Da~Lv~~L~~k 323 (881)
T PHA02528 258 YLDLYKKFTFTNQPSYRLDYIAEVELGKKKLDYSDGPFKKFRETDHQKYIEYNIIDVELVDRLDDK 323 (881)
T ss_pred HHHHHHHhhhcccccCCHHHHHHHHhCCCCccCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence 888877533456789999999994 78763222 126788888888877
No 80
>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=97.23 E-value=0.0025 Score=63.18 Aligned_cols=145 Identities=14% Similarity=0.147 Sum_probs=93.1
Q ss_pred EEEEEEecCCCCCCCCCCcEEEEEEEEEeCCce-------eEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 10 IAFFDVETTVPTRPGQRFAILEFGAILVCPKKL-------EELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 10 ~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~-------eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
++.|-+-|.--.. ....+|+-|+++...+-.. .....+..+++|......+......-.-....+.--.+..
T Consensus 5 v~sls~~T~~n~k-~~~~EI~~iS~~~~~~~~~d~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~v~~~~~E~ 83 (234)
T cd05776 5 VMSLSIKTVLNSK-TNKNEIVMISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENER 83 (234)
T ss_pred EEEEEeEEEecCc-CCcchhheehHHHhcCCCCCCCCCCcccccceEEEEeCCCCCCCCchHHHHHHhcCCcEEEeCCHH
Confidence 4455555543222 2468899999987663211 1123556677887621222222222222222345566788
Q ss_pred HHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCCCC--------------------------CCcceeHHHH
Q 010297 83 DIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAPE--------------------------PKGTIDSLAL 133 (513)
Q Consensus 83 EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~--------------------------~~~~IDTL~L 133 (513)
+.+..|.+++. -.+++|||...||+.+|.+.+..+|++... ....+|++..
T Consensus 84 ~LL~~f~~~i~~~DPDiivG~Ni~~fdl~~L~~R~~~l~i~~ws~iGR~~~~~~~~~~~~~~~~~~~~~~GRl~~D~~~~ 163 (234)
T cd05776 84 ALLNFFLAKLQKIDPDVLVGHDLEGFDLDVLLSRIQELKVPHWSRIGRLKRSVWPKKKGGGKFGERELTAGRLLCDTYLS 163 (234)
T ss_pred HHHHHHHHHHhhcCCCEEEeeccCCCCHHHHHHHHHHhCCCccccccccccccCccccccccccccccccCchhhccHHH
Confidence 89999999987 479999999999999999998887775210 1136788888
Q ss_pred HHHHhcCCCCCCCHHHHHH-HhCCC
Q 010297 134 LTQRFGRRAGDMKMASLAT-YFGLG 157 (513)
Q Consensus 134 ar~~l~prl~s~kL~~LAk-~fGI~ 157 (513)
++.. . ...+|+|+++|+ .+|..
T Consensus 164 ~k~~-~-~~~sY~L~~va~~~Lg~~ 186 (234)
T cd05776 164 AKEL-I-RCKSYDLTELSQQVLGIE 186 (234)
T ss_pred HHHH-h-CCCCCChHHHHHHHhCcC
Confidence 8644 3 378999999999 66765
No 81
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=97.17 E-value=0.0039 Score=67.67 Aligned_cols=120 Identities=14% Similarity=0.154 Sum_probs=86.3
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
....++||+||+. ...-...+|++..+++. ..+.|..|..... ....+++.
T Consensus 283 ~~~~~ffDiEt~P-----~~~~~yL~G~~~~~~~~--~~~~~~~fla~~~----------------------~~E~~~~~ 333 (457)
T TIGR03491 283 APGELIFDIESDP-----DENLDYLHGFLVVDKGQ--ENEKYRPFLAEDP----------------------NTEELAWQ 333 (457)
T ss_pred CCccEEEEecCCC-----CCCCceEEEEEEecCCC--CCcceeeeecCCc----------------------hHHHHHHH
Confidence 3567899999993 23557899997766542 2234655554332 12456788
Q ss_pred HHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCCC----CCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC
Q 010297 87 TVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAP----EPKGTIDSLALLTQRFGRRAGDMKMASLATYFGLG 157 (513)
Q Consensus 87 ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p----~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~ 157 (513)
+|.+|+. +.+++.|| .|....|++...++|.+.. ....++|.....++.+.-..++|+|..++..+|.+
T Consensus 334 ~f~~~l~~~~~~~i~hY~--~~e~~~l~rla~~~~~~~~~~~~l~~~~vDL~~~vr~~~~~p~~sysLK~v~~~lg~~ 409 (457)
T TIGR03491 334 QFLQLLQSYPDAPIYHYG--ETEKDSLRRLAKRYGTPEAEIEELLKRFVDIHTIVRRSWILPIESYSLKSIARWLGFE 409 (457)
T ss_pred HHHHHHHHCCCCeEEeeC--HHHHHHHHHHHHHcCCCHHHHHHHHHHheehHHHHHhhEECCCCCCCHHHHHHHhCcc
Confidence 8888886 45788888 6899999999999987621 11168999998887664445899999999999997
No 82
>PHA02524 43A DNA polymerase subunit A; Provisional
Probab=96.64 E-value=0.01 Score=65.46 Aligned_cols=143 Identities=15% Similarity=0.125 Sum_probs=83.1
Q ss_pred CcEEEEEEecCCCCCCC---CCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhh-CC-CHHHHcCCCCHH
Q 010297 8 SEIAFFDVETTVPTRPG---QRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCN-GI-TPDAVVSSPTFA 82 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g---~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIh-GI-T~EmLa~Apsf~ 82 (513)
-+++.||+|+|+..-|. ...+|.-|....... .-++|..+.-....+++.+....++ ++ ..-.+-.-++..
T Consensus 106 i~~~~~DIEv~~~~fp~~~~a~~~i~~i~~~d~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~f~sE~ 181 (498)
T PHA02524 106 VVIDVVDIEVTAPEFPEPKYAKYEIDMISHVRLHN----GKKTYYIFDLVKDVGHWDPKKSVLEKYILDNVVYMPFEDEV 181 (498)
T ss_pred ceEEEEEEEecCCCCCChhhcCCceEEEEeeeccc----CCccEEEEeccccccCCCcccccccccccCCeEEEEeCCHH
Confidence 46899999998743221 223344444333221 1234544432111112221111110 11 111123356788
Q ss_pred HHHHHHHHHHcC---CeEEEeCcchHHHHHHHHHHHH-cCCCC-----CC---------------------CCcceeHHH
Q 010297 83 DIADTVFDILHG---RIWAGHNILRFDCARIREAFAE-IGRPA-----PE---------------------PKGTIDSLA 132 (513)
Q Consensus 83 EVl~ef~efL~g---~vLVAHNa~~FD~~FL~~~f~r-~Gi~~-----p~---------------------~~~~IDTL~ 132 (513)
+.+.+|.+|+.. .+++|||+..||+++|.+.+++ +|+.. ++ ....+|.+.
T Consensus 182 eLL~~F~~~i~~~DPDIItGYNi~nFDlPYL~~Ra~~~lGi~~~~~~~~~Gr~~~~~s~~~~G~~~~~~I~GRv~iDl~~ 261 (498)
T PHA02524 182 DLLLNYIQLWKANTPDLVFGWNSEGFDIPYIITRITNILGEKAANQLSPYGKITSKTITNLYGEKIIYKIHGIALMDYMD 261 (498)
T ss_pred HHHHHHHHHHHHhCCCEEEeCCCcccCHHHHHHHHHHHhCCccccccccccccccccceeecCceeEEEEeeEEEeEHHH
Confidence 999999999984 7999999999999999887753 66531 00 113578899
Q ss_pred HHHHHhcCCCCCCCHHHHHHHh
Q 010297 133 LLTQRFGRRAGDMKMASLATYF 154 (513)
Q Consensus 133 Lar~~l~prl~s~kL~~LAk~f 154 (513)
++++.-...+.+|+|++++..+
T Consensus 262 l~kk~s~~~l~sYsL~~Vs~~~ 283 (498)
T PHA02524 262 VFKKFSFTPMPDYKLGNVGYRE 283 (498)
T ss_pred HHHHhhhccCCCCCHHHHHHHh
Confidence 8874314578999999998743
No 83
>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=96.58 E-value=0.023 Score=54.74 Aligned_cols=143 Identities=14% Similarity=0.113 Sum_probs=86.8
Q ss_pred CCCCcEEEEEEecCCCCCC--CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 5 QDRSEIAFFDVETTVPTRP--GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~--g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
.....++.||+|+++.... ...-.+|||+. .+. ..+|++.. +. +- .-.
T Consensus 19 l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat----~~~-------~~lid~~~---~~-------~~---------~~~ 68 (193)
T cd06146 19 LEAGRVVGIDSEWKPSFLGDSDPRVAILQLAT----EDE-------VFLLDLLA---LE-------NL---------ESE 68 (193)
T ss_pred hccCCEEEEECccCCCccCCCCCCceEEEEec----CCC-------EEEEEchh---cc-------cc---------chH
Confidence 4567899999999865431 13457888883 221 12444332 00 00 011
Q ss_pred HHHHHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCC---------CCCCCHHHHH
Q 010297 83 DIADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRR---------AGDMKMASLA 151 (513)
Q Consensus 83 EVl~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~pr---------l~s~kL~~LA 151 (513)
.....+..++.+ -+-|||++ .+|..+|.+.+...+........++||..+++...... ...++|..|+
T Consensus 69 ~~~~~L~~ll~d~~i~KVg~~~-~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~~~~~~~~~~~~~~~~sL~~l~ 147 (193)
T cd06146 69 DWDRLLKRLFEDPDVLKLGFGF-KQDLKALSASYPALKCMFERVQNVLDLQNLAKELQKSDMGRLKGNLPSKTKGLADLV 147 (193)
T ss_pred HHHHHHHHHhCCCCeeEEEech-HHHHHHHHHhcCccccccccCCceEEHHHHHHHHhhccccccccccCcccCCHHHHH
Confidence 122345666664 34599999 99999998766332110011236999998876433211 2467999999
Q ss_pred HHh-CCC-----------------CCCCChHHHHHHHHHHHHHHH
Q 010297 152 TYF-GLG-----------------QQTHRSLDDVRMNLEVLKYCA 178 (513)
Q Consensus 152 k~f-GI~-----------------~~aHRALdDA~aTA~Ll~~ll 178 (513)
+.+ |.+ .+-+-|..||..+..++.++.
T Consensus 148 ~~~lg~~l~K~~q~SdW~~rpLs~~Qi~YAA~Da~~l~~l~~~L~ 192 (193)
T cd06146 148 QEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLL 192 (193)
T ss_pred HHHhCCCcCcccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 865 432 134568889999999988865
No 84
>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]
Probab=96.23 E-value=0.0044 Score=71.44 Aligned_cols=161 Identities=19% Similarity=0.271 Sum_probs=103.7
Q ss_pred CCCCCcEEEEEEecCCCCC-------CC-------CCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhC
Q 010297 4 TQDRSEIAFFDVETTVPTR-------PG-------QRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNG 69 (513)
Q Consensus 4 t~~~~~~VVfDlETTGLd~-------~g-------~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhG 69 (513)
.++..++|.+|-|..-|.. .| ..-.+.-|.+|+-.+ -++-+-=-.-||--.+ .+-++-++..|
T Consensus 906 mPk~g~LVgiDAEFVtLq~Ee~Eir~DG~~stIkP~~msvARiScvRGeG-p~eGiPFiDDYv~T~d--~VvDYLTqySG 982 (1118)
T KOG1275|consen 906 MPKSGDLVGIDAEFVTLQTEELEIRSDGKTSTIKPSRMSVARISCVRGEG-PNEGIPFIDDYVSTDD--KVVDYLTQYSG 982 (1118)
T ss_pred cCCCCceeeeehhheecchHHhccccCCceeEeccccceeEEEEEEcccC-CCCCCccccceecchh--HHHHHHHHhcC
Confidence 3456789999999887654 01 111233344443331 0111111122444344 67788999999
Q ss_pred CCHHHHcCCC------CHHHHHHHHHHHHc-CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCC
Q 010297 70 ITPDAVVSSP------TFADIADTVFDILH-GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRA 142 (513)
Q Consensus 70 IT~EmLa~Ap------sf~EVl~ef~efL~-g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl 142 (513)
|-+-+|.-.. ++.-+..++.-.+. |.++|||.. . ..|+-+++..|.. +.+||..+.+ .+..
T Consensus 983 I~PGDLDp~~S~K~Lt~lK~~Y~Kl~~Li~~GviFVGHGL-~-------nDFrvINi~Vp~~-QiiDTv~lf~---~~s~ 1050 (1118)
T KOG1275|consen 983 IKPGDLDPTTSEKRLTTLKVLYLKLRLLIQRGVIFVGHGL-Q-------NDFRVINIHVPEE-QIIDTVTLFR---LGSQ 1050 (1118)
T ss_pred CCccccCCccCcceehhHHHHHHHHHHHHHcCcEEEcccc-c-------ccceEEEEecChh-hheeeeEEEe---cccc
Confidence 9999995533 34445566655555 789999998 4 4455556666654 5899988743 2333
Q ss_pred CCCCHHHHHHHh-CCC--CCCCChHHHHHHHHHHHHHHHH
Q 010297 143 GDMKMASLATYF-GLG--QQTHRSLDDVRMNLEVLKYCAT 179 (513)
Q Consensus 143 ~s~kL~~LAk~f-GI~--~~aHRALdDA~aTA~Ll~~ll~ 179 (513)
.-.+|..||.++ |-. ..+|+.+.||+.+.++|+++++
T Consensus 1051 R~LSLrfLa~~lLg~~IQ~~~HDSIeDA~taLkLYk~Yl~ 1090 (1118)
T KOG1275|consen 1051 RMLSLRFLAWELLGETIQMEAHDSIEDARTALKLYKKYLK 1090 (1118)
T ss_pred cEEEHHHHHHHHhcchhhccccccHHHHHHHHHHHHHHHH
Confidence 345899999877 333 6899999999999999999876
No 85
>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=96.21 E-value=0.085 Score=48.85 Aligned_cols=129 Identities=21% Similarity=0.294 Sum_probs=83.1
Q ss_pred CCcEEEEEEecCCCCC--CCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 7 RSEIAFFDVETTVPTR--PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~--~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
....+.||+|+++... ....-.+|+|+. .+ ...++++.. + ...
T Consensus 17 ~~~~ig~D~E~~~~~~~~~~~~~~liQl~~----~~-------~~~l~~~~~---~---------------------~~~ 61 (170)
T cd06141 17 KEKVVGFDTEWRPSFRKGKRNKVALLQLAT----ES-------RCLLFQLAH---M---------------------DKL 61 (170)
T ss_pred CCCEEEEeCccCCccCCCCCCCceEEEEec----CC-------cEEEEEhhh---h---------------------hcc
Confidence 6789999999998753 123456888872 22 123455443 0 111
Q ss_pred HHHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC----
Q 010297 85 ADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG---- 157 (513)
Q Consensus 85 l~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~---- 157 (513)
...|.+++.+ ...|+|++ .+|+.+|.+. +|+... ..+|+..++. .+.+.....+|..+++.+ |..
T Consensus 62 ~~~l~~ll~~~~i~kv~~~~-k~D~~~L~~~---~g~~~~---~~~Dl~~aa~-ll~~~~~~~~l~~l~~~~l~~~~~k~ 133 (170)
T cd06141 62 PPSLKQLLEDPSILKVGVGI-KGDARKLARD---FGIEVR---GVVDLSHLAK-RVGPRRKLVSLARLVEEVLGLPLSKP 133 (170)
T ss_pred cHHHHHHhcCCCeeEEEeee-HHHHHHHHhH---cCCCCC---CeeeHHHHHH-HhCCCcCCccHHHHHHHHcCcccCCC
Confidence 1345566664 45699999 9999998653 466532 3699998775 455543346999999876 542
Q ss_pred ---------------CCCCChHHHHHHHHHHHHHHH
Q 010297 158 ---------------QQTHRSLDDVRMNLEVLKYCA 178 (513)
Q Consensus 158 ---------------~~aHRALdDA~aTA~Ll~~ll 178 (513)
.+-|-|..||..+.+++..+.
T Consensus 134 k~~~~s~W~~rpLt~~qi~YAa~Da~~~~~l~~~l~ 169 (170)
T cd06141 134 KKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169 (170)
T ss_pred CCcccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 123557888888888887754
No 86
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=96.02 E-value=0.096 Score=52.34 Aligned_cols=171 Identities=15% Similarity=0.106 Sum_probs=103.1
Q ss_pred CCcEEEEEEecCCCCC--CC-----------------CCCcEEEEEEEEEeCCceeE---eeeEEEEEc----CCCC-CC
Q 010297 7 RSEIAFFDVETTVPTR--PG-----------------QRFAILEFGAILVCPKKLEE---LHNYSTLVR----PADP-EL 59 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~--~g-----------------~~deIIEIGAV~Vd~g~~ei---vdsFs~lIr----P~~~-~~ 59 (513)
+-.||.+|+|.-|.=. .+ ..-.+||+|.-..+..+... .+.|+.--+ +.+. ..
T Consensus 23 ~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWqfNF~dF~~~~D~~a~ 102 (239)
T KOG0304|consen 23 DYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQFNFSDFNLEKDMYAQ 102 (239)
T ss_pred hCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCCCCCceeEEecccCCchhhccch
Confidence 3468999999887211 11 22359999999998643211 123333222 2220 11
Q ss_pred CChhhHHhhCCCHHHHc-CCCCHHHHHHHHH---HHHc-CCeEEEeCcchHHHHHHHHHHHHcCCCCC----------CC
Q 010297 60 ISSLSVRCNGITPDAVV-SSPTFADIADTVF---DILH-GRIWAGHNILRFDCARIREAFAEIGRPAP----------EP 124 (513)
Q Consensus 60 I~~~~teIhGIT~EmLa-~Apsf~EVl~ef~---efL~-g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p----------~~ 124 (513)
-+-.-.+-+||.-+-.+ .+....+-.+.+. -.+. +-.||.+.. .||.+.|-..+-.-.++.. ..
T Consensus 103 ~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs-~YDfgYLlK~Lt~~~LP~~~~eF~~~v~~~f 181 (239)
T KOG0304|consen 103 DSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHS-GYDFGYLLKILTGKPLPETEEEFFEIVRQLF 181 (239)
T ss_pred hhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeec-cchHHHHHHHHcCCCCcchHHHHHHHHHHHc
Confidence 22233345688877763 3554443222222 1222 347999888 9999999877654333211 00
Q ss_pred CcceeHHHHHHHHhcCCCCCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHH
Q 010297 125 KGTIDSLALLTQRFGRRAGDMKMASLATYFGLG--QQTHRSLDDVRMNLEVLKYCAT 179 (513)
Q Consensus 125 ~~~IDTL~Lar~~l~prl~s~kL~~LAk~fGI~--~~aHRALdDA~aTA~Ll~~ll~ 179 (513)
..+.|+..+++..-. ..-...|..+|+.++++ ...|.|-+|++.|+.+|.++.+
T Consensus 182 p~vYDiK~l~~~c~~-~~l~~GL~~lA~~L~~~RvG~~HqAGSDSlLT~~~F~kl~~ 237 (239)
T KOG0304|consen 182 PFVYDVKYLMKFCEG-LSLKGGLQRLADLLGLKRVGIAHQAGSDSLLTARVFFKLKE 237 (239)
T ss_pred chhhhHHHHHHhhhh-hhhhcCHHHHHHHhCCCeeecccccCcHHHHHHHHHHHHHh
Confidence 146676666542211 11356899999999999 6899999999999999999865
No 87
>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=95.85 E-value=0.093 Score=46.30 Aligned_cols=66 Identities=17% Similarity=0.297 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHhC
Q 010297 82 ADIADTVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYFG 155 (513)
Q Consensus 82 ~EVl~ef~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~fG 155 (513)
..+...|.+++.+. ..|+||+ .||+.+|.+. +...+. .++||+-+++ .+.|...+++|..+++.|.
T Consensus 40 ~~~~~~l~~~l~~~~~~~v~~~~-k~d~~~L~~~----~~~~~~--~~~D~~~~ay-ll~~~~~~~~l~~l~~~~l 107 (155)
T cd00007 40 EEDLEALKELLEDEDITKVGHDA-KFDLVVLARD----GIELPG--NIFDTMLAAY-LLNPGEGSHSLDDLAKEYL 107 (155)
T ss_pred HHHHHHHHHHHcCCCCcEEeccH-HHHHHHHHHC----CCCCCC--CcccHHHHHH-HhCCCCCcCCHHHHHHHHc
Confidence 45666788888753 5899999 9999998643 443332 4799988765 5666553569999999873
No 88
>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=95.81 E-value=0.098 Score=48.60 Aligned_cols=129 Identities=20% Similarity=0.150 Sum_probs=82.7
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
...++.||+|+.........-.+|||+. ..+. ..++++... .. ...
T Consensus 12 ~~~~ig~D~E~~~~~~~~~~~~liQl~~---~~~~-------~~l~d~~~~---~~---------------------~~~ 57 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYYGEVALIQLCV---SEEK-------CYLFDPLSL---SV---------------------DWQ 57 (161)
T ss_pred CCCEEEEECCccCCCCCCCceEEEEEEE---CCCC-------EEEEecccC---cc---------------------CHH
Confidence 5789999999998754223456777774 1121 134454431 00 123
Q ss_pred HHHHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC------
Q 010297 87 TVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG------ 157 (513)
Q Consensus 87 ef~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~------ 157 (513)
.+.+++.+. +.|+|++ ..|+..|.+. +|+... ..+||...++ .+.+. .+.+|..+++.| |..
T Consensus 58 ~L~~lL~d~~i~Kvg~~~-k~D~~~L~~~---~gi~~~---~~~D~~~aa~-ll~~~-~~~~L~~l~~~~lg~~l~K~~~ 128 (161)
T cd06129 58 GLKMLLENPSIVKALHGI-EGDLWKLLRD---FGEKLQ---RLFDTTIAAN-LKGLP-ERWSLASLVEHFLGKTLDKSIS 128 (161)
T ss_pred HHHHHhCCCCEEEEEecc-HHHHHHHHHH---cCCCcc---cHhHHHHHHH-HhCCC-CCchHHHHHHHHhCCCCCccce
Confidence 345566643 5699999 9999998643 466532 3689988765 45543 356999999875 652
Q ss_pred -----------CCCCChHHHHHHHHHHHHHHH
Q 010297 158 -----------QQTHRSLDDVRMNLEVLKYCA 178 (513)
Q Consensus 158 -----------~~aHRALdDA~aTA~Ll~~ll 178 (513)
.+-|-|..||..+.+++.++.
T Consensus 129 ~s~W~~rpLt~~qi~YAa~Da~~l~~l~~~l~ 160 (161)
T cd06129 129 CADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160 (161)
T ss_pred eccCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 134668889998888887753
No 89
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=95.61 E-value=0.15 Score=54.43 Aligned_cols=141 Identities=19% Similarity=0.164 Sum_probs=91.2
Q ss_pred CCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHH
Q 010297 7 RSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIAD 86 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ 86 (513)
...++.+|+||.|... ..++ .|.|-+..+. . ..+|+|.. |+. +.++
T Consensus 16 ~~~~iAiDTEf~r~~t--~~p~---LcLIQi~~~e-----~-~~lIdpl~------------~~~-----d~~~------ 61 (361)
T COG0349 16 GSKAIAIDTEFMRLRT--YYPR---LCLIQISDGE-----G-ASLIDPLA------------GIL-----DLPP------ 61 (361)
T ss_pred CCCceEEecccccccc--cCCc---eEEEEEecCC-----C-ceEecccc------------ccc-----ccch------
Confidence 4679999999999987 3443 3344444442 2 46788765 111 1222
Q ss_pred HHHHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--CC--
Q 010297 87 TVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--QQ-- 159 (513)
Q Consensus 87 ef~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~--~~-- 159 (513)
|...+.+. +=|=|++ +||+.+|.+.| |+.+. +.+||.-.++ ..+. ..+++|++|++.+ |+. +.
T Consensus 62 -l~~Ll~d~~v~KIfHaa-~~DL~~l~~~~---g~~p~---plfdTqiAa~-l~g~-~~~~gl~~Lv~~ll~v~ldK~~q 131 (361)
T COG0349 62 -LVALLADPNVVKIFHAA-RFDLEVLLNLF---GLLPT---PLFDTQIAAK-LAGF-GTSHGLADLVEELLGVELDKSEQ 131 (361)
T ss_pred -HHHHhcCCceeeeeccc-cccHHHHHHhc---CCCCC---chhHHHHHHH-HhCC-cccccHHHHHHHHhCCccccccc
Confidence 33344432 2267999 99999998876 55432 5899988765 3332 2389999998754 664 11
Q ss_pred ----CC---------ChHHHHHHHHHHHHHHHHHhhcccCCCCcc
Q 010297 160 ----TH---------RSLDDVRMNLEVLKYCATVLFLESSLPDIF 191 (513)
Q Consensus 160 ----aH---------RALdDA~aTA~Ll~~ll~~L~~~~~~P~v~ 191 (513)
.+ -|..|+..+..++.++.+.+..+...+...
T Consensus 132 ~SDW~~RPLs~~Ql~YAa~DV~yL~~l~~~L~~~L~~~~r~~~a~ 176 (361)
T COG0349 132 RSDWLARPLSEAQLEYAAADVEYLLPLYDKLTEELAREGRLEWAE 176 (361)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHH
Confidence 12 268999999999999999888765544333
No 90
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair]
Probab=95.30 E-value=0.2 Score=58.42 Aligned_cols=131 Identities=15% Similarity=0.138 Sum_probs=88.7
Q ss_pred CCCcEEEEEEecCCCCC---CCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHH
Q 010297 6 DRSEIAFFDVETTVPTR---PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFA 82 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~---~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~ 82 (513)
..-+++.||+||.+... ++..+.++.|+...-..+... ..+.. ....|.. +....+..
T Consensus 152 p~l~~la~DiE~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~--------~~~~~--------~~~~~~~---v~~~~~e~ 212 (792)
T COG0417 152 PPLRVLAFDIETLSEPGKFPDGEKDPIIMISYAIEAEGGLI--------EVFIY--------TSGEGFS---VEVVISEA 212 (792)
T ss_pred CCceEEEEEEEEecCCCCCCCccCCceEEEEEEeccCCCcc--------ccccc--------cCCCCce---eEEecCHH
Confidence 34578999999998543 235677888887665554221 11111 0001111 44556778
Q ss_pred HHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCCC---------------C---CCcceeHHHHHHHHhcCC
Q 010297 83 DIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAP---------------E---PKGTIDSLALLTQRFGRR 141 (513)
Q Consensus 83 EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p---------------~---~~~~IDTL~Lar~~l~pr 141 (513)
+.+.+|.+++. ..+++|||...||+++|.+.+.++|++.. . ....+|++..++. =...
T Consensus 213 e~l~~~~~~i~~~dPdVIvgyn~~~fd~pyl~~Ra~~lgi~~~~gr~~~~~~~~~~~~~~~~Gr~~iDl~~~~~~-~~~~ 291 (792)
T COG0417 213 ELLERFVELIREYDPDVIVGYNGDNFDWPYLAERAERLGIPLRLGRDGSELRVRKSGFSSQVGRLHIDLYPALRR-RPLN 291 (792)
T ss_pred HHHHHHHHHHHhcCCCEEEeccCCcCChHHHHHHHHHhCCCccccccccccceeecccccccceEEEecHHHHhh-hhcc
Confidence 89999999986 46999999977999999999999998755 1 1257888887762 1234
Q ss_pred CCCCCHHHHHHHhCC
Q 010297 142 AGDMKMASLATYFGL 156 (513)
Q Consensus 142 l~s~kL~~LAk~fGI 156 (513)
+.+++|...+..+..
T Consensus 292 ~~~ysl~~v~~~~l~ 306 (792)
T COG0417 292 LKSYSLEAVSEALLG 306 (792)
T ss_pred cccccHHHHHHHhcc
Confidence 578999999776644
No 91
>PRK10829 ribonuclease D; Provisional
Probab=95.24 E-value=0.54 Score=50.33 Aligned_cols=137 Identities=18% Similarity=0.093 Sum_probs=89.7
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
......+.||+|+.+.......-.+|||+. ++ -..+|.|.. + ++
T Consensus 19 l~~~~~lalDtEf~~~~ty~~~l~LiQl~~----~~-------~~~LiD~l~---~----------~d------------ 62 (373)
T PRK10829 19 ARAFPAIALDTEFVRTRTYYPQLGLIQLYD----GE-------QLSLIDPLG---I----------TD------------ 62 (373)
T ss_pred HhcCCeEEEecccccCccCCCceeEEEEec----CC-------ceEEEecCC---c----------cc------------
Confidence 345788999999998764222345677761 22 124677654 1 10
Q ss_pred HHHHHHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHH-HhCCC--C-
Q 010297 85 ADTVFDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLAT-YFGLG--Q- 158 (513)
Q Consensus 85 l~ef~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk-~fGI~--~- 158 (513)
+..|.+++.+. +-|.|++ .+|+.+|.+. +|+.+ .+++||.-.++ .++.. .+++|..|++ ++|+. +
T Consensus 63 ~~~L~~ll~~~~ivKV~H~~-~~Dl~~l~~~---~g~~p---~~~fDTqiaa~-~lg~~-~~~gl~~Lv~~~lgv~ldK~ 133 (373)
T PRK10829 63 WSPFKALLRDPQVTKFLHAG-SEDLEVFLNA---FGELP---QPLIDTQILAA-FCGRP-LSCGFASMVEEYTGVTLDKS 133 (373)
T ss_pred hHHHHHHHcCCCeEEEEeCh-HhHHHHHHHH---cCCCc---CCeeeHHHHHH-HcCCC-ccccHHHHHHHHhCCccCcc
Confidence 23466677754 3379999 9999999654 47643 25899977654 44321 3578999886 55763 1
Q ss_pred --------------CCCChHHHHHHHHHHHHHHHHHhhcccC
Q 010297 159 --------------QTHRSLDDVRMNLEVLKYCATVLFLESS 186 (513)
Q Consensus 159 --------------~aHRALdDA~aTA~Ll~~ll~~L~~~~~ 186 (513)
+-+-|..|+..+..++.++...+.....
T Consensus 134 ~~~sDW~~RPLs~~ql~YAa~Dv~~L~~l~~~L~~~L~~~g~ 175 (373)
T PRK10829 134 ESRTDWLARPLSERQCEYAAADVFYLLPIAAKLMAETEAAGW 175 (373)
T ss_pred cccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 2345789999999999999888775433
No 92
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.14 E-value=0.44 Score=57.85 Aligned_cols=143 Identities=13% Similarity=0.061 Sum_probs=95.0
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCce-------eEeeeEEEEEcCCCCCCCCh-hhHHhhCCCHHHHcCCCC
Q 010297 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKL-------EELHNYSTLVRPADPELISS-LSVRCNGITPDAVVSSPT 80 (513)
Q Consensus 9 ~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~-------eivdsFs~lIrP~~~~~I~~-~~teIhGIT~EmLa~Aps 80 (513)
.++++|+-.-.+.|.....++|.|+++....... .....+...++|.. ..+|. +.....|+.+..|..-.+
T Consensus 505 Pl~vLdFsi~SlyPsi~~~~nl~iS~~v~~~~~~d~~~~~~~~~~~~~~~~~~~~-~~~p~~~~~~~~~~~~~~L~~~~s 583 (1172)
T TIGR00592 505 PLVVLDFSMKSLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKD-CSFPLDLKGEFPGKKPSLVEDLAT 583 (1172)
T ss_pred CeEEEEeeeEEecCccccCceEEEEEEEeecccccCCCCCCccceEEEEEEccCC-CCCCchhhhhhhccCCcEEEEecC
Confidence 4666554411343322567899999887765211 11123445556632 12232 223455777777777778
Q ss_pred HHHHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCCC--------------------CCCcceeHHHHHHHH
Q 010297 81 FADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAP--------------------EPKGTIDSLALLTQR 137 (513)
Q Consensus 81 f~EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p--------------------~~~~~IDTL~Lar~~ 137 (513)
..+.+..|++++. ..+++|||+..||+..|.+.+.+++++.. .....+|++..++..
T Consensus 584 Er~lL~~fl~~~~~~DPDii~g~n~~qfdlkvl~nR~~~l~i~~~~~~Gr~~~~~~~~~~~~~~~~Grl~~D~~~~~k~~ 663 (1172)
T TIGR00592 584 ERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANRINDLKIPTWSKIGRLRRSPKFGRRFGERTCGRMICDVEISAKEL 663 (1172)
T ss_pred HHHHHHHHHHHHHhcCCCEEEEEcccCccHHHHHHHHHHcCCCcccccCccccCCCccccccceECCEEEEEHHHHHHHH
Confidence 8889999999987 46999999999999999998888877631 112468888888755
Q ss_pred hcCCCCCCCHHHHHHHh
Q 010297 138 FGRRAGDMKMASLATYF 154 (513)
Q Consensus 138 l~prl~s~kL~~LAk~f 154 (513)
+ ...+|+|+++++++
T Consensus 664 ~--~~~sy~L~~v~~~~ 678 (1172)
T TIGR00592 664 I--RCKSYDLSELVQQI 678 (1172)
T ss_pred h--CcCCCCHHHHHHHH
Confidence 4 37899999999865
No 93
>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=94.64 E-value=1.4 Score=46.84 Aligned_cols=134 Identities=16% Similarity=0.119 Sum_probs=84.9
Q ss_pred CCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHH
Q 010297 6 DRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIA 85 (513)
Q Consensus 6 ~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl 85 (513)
....++.||+|+.........-.+|||+. ++ -..+|.|.. . . .+
T Consensus 16 ~~~~~ia~DtE~~~~~~y~~~l~LiQia~----~~-------~~~liD~~~--~-~----------------------~~ 59 (367)
T TIGR01388 16 RTFPFVALDTEFVRERTFWPQLGLIQVAD----GE-------QLALIDPLV--I-I----------------------DW 59 (367)
T ss_pred hcCCEEEEeccccCCCCCCCcceEEEEee----CC-------eEEEEeCCC--c-c----------------------cH
Confidence 34679999999988754222335677763 22 124666643 0 0 02
Q ss_pred HHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--CC-
Q 010297 86 DTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--QQ- 159 (513)
Q Consensus 86 ~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~--~~- 159 (513)
..|.+++.+ .+.|+|++ .+|+.+|.+.+ |. .+. ..+||.-.+. .+.+.. +++|..|++.| |+. ..
T Consensus 60 ~~L~~lL~d~~i~KV~h~~-k~Dl~~L~~~~---~~-~~~--~~fDtqlAa~-lL~~~~-~~~l~~Lv~~~Lg~~l~K~~ 130 (367)
T TIGR01388 60 SPLKELLRDESVVKVLHAA-SEDLEVFLNLF---GE-LPQ--PLFDTQIAAA-FCGFGM-SMGYAKLVQEVLGVELDKSE 130 (367)
T ss_pred HHHHHHHCCCCceEEEeec-HHHHHHHHHHh---CC-CCC--CcccHHHHHH-HhCCCC-CccHHHHHHHHcCCCCCccc
Confidence 235556653 45699999 99999986542 32 332 4799987654 555532 46999998765 654 11
Q ss_pred -----CCC---------hHHHHHHHHHHHHHHHHHhhcc
Q 010297 160 -----THR---------SLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 160 -----aHR---------ALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
..| |..||..+..++..+.+++...
T Consensus 131 ~~sdW~~rPL~~~q~~YAa~Dv~~L~~L~~~L~~~L~~~ 169 (367)
T TIGR01388 131 SRTDWLARPLTDAQLEYAAADVTYLLPLYAKLMERLEES 169 (367)
T ss_pred ccccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 133 7788988999999888877654
No 94
>KOG1798 consensus DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair]
Probab=94.56 E-value=0.47 Score=57.97 Aligned_cols=162 Identities=14% Similarity=0.107 Sum_probs=97.0
Q ss_pred CCcEEEEEEecCCCCC--C-CCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCH-------HHHc
Q 010297 7 RSEIAFFDVETTVPTR--P-GQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITP-------DAVV 76 (513)
Q Consensus 7 ~~~~VVfDlETTGLd~--~-g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~-------EmLa 76 (513)
+..+++||+|||-+.- | ...|+|.=|+. .++ |++-.+ ++-+ -+++.+...+ -|+ =-+-
T Consensus 245 dp~VlAFDIETtKlPLKFPDae~DqIMMISY-MiD-GqGfLI------tNRE---iVs~DIedfE-YTPKpE~eG~F~v~ 312 (2173)
T KOG1798|consen 245 DPRVLAFDIETTKLPLKFPDAESDQIMMISY-MID-GQGFLI------TNRE---IVSEDIEDFE-YTPKPEYEGPFCVF 312 (2173)
T ss_pred CceEEEEeeecccCCCCCCCcccceEEEEEE-Eec-CceEEE------echh---hhccchhhcc-cCCccccccceEEe
Confidence 4678999999998632 1 36788887775 333 322211 1111 1111111110 111 0123
Q ss_pred CCCCHHHHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCCCCC------------CcceeHHH---HHHHHh
Q 010297 77 SSPTFADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPAPEP------------KGTIDSLA---LLTQRF 138 (513)
Q Consensus 77 ~Apsf~EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~------------~~~IDTL~---Lar~~l 138 (513)
+-+.....+++|.+-+. ..++|.+|+-=||++|+.+....+|+.+..- .++++-+. +.++--
T Consensus 313 Ne~dEv~Ll~RfFeHiq~~kP~iivTyNGDFFDWPFve~Ra~~hGi~m~eEiGF~~D~~gEyks~~c~HmDcfrWVKRDS 392 (2173)
T KOG1798|consen 313 NEPDEVGLLQRFFEHIQEVKPTIIVTYNGDFFDWPFVEARAKIHGISMNEEIGFRRDSQGEYKSPFCIHMDCFRWVKRDS 392 (2173)
T ss_pred cCCcHHHHHHHHHHHHHhcCCcEEEEecCccccchhhHHHHHhcCCCcchhcCceecccccccccceeehhhhhhhhhcc
Confidence 45566778888888876 4699999997789999999998888864311 12333343 333211
Q ss_pred cCCCCCCCHHHHHH-HhCCC---------------CC---CCChHHHHHHHHHHHHHHHHH
Q 010297 139 GRRAGDMKMASLAT-YFGLG---------------QQ---THRSLDDVRMNLEVLKYCATV 180 (513)
Q Consensus 139 ~prl~s~kL~~LAk-~fGI~---------------~~---aHRALdDA~aTA~Ll~~ll~~ 180 (513)
+--.++..|....+ .+|.. .. +--..+||.+|..++.++..-
T Consensus 393 YLPqGSqgLKAVTkaKLGYdPvEvdPEdM~~~A~EkPQ~lasYSVSDAVATYyLYMkYVhP 453 (2173)
T KOG1798|consen 393 YLPQGSQGLKAVTKAKLGYDPVEVDPEDMVRMAMEKPQTLASYSVSDAVATYYLYMKYVHP 453 (2173)
T ss_pred cCCCcccchhHHHHHhhCCCcccCCHHHhhhhhhhCchhhhhcchHHHHHHHHHHHHHhhh
Confidence 22247888888776 56642 11 334589999999999888765
No 95
>PHA03036 DNA polymerase; Provisional
Probab=93.56 E-value=0.84 Score=54.45 Aligned_cols=140 Identities=10% Similarity=-0.042 Sum_probs=83.2
Q ss_pred CcEEEEEEecCCCC--CCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCC------C---HHHHc
Q 010297 8 SEIAFFDVETTVPT--RPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGI------T---PDAVV 76 (513)
Q Consensus 8 ~~~VVfDlETTGLd--~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGI------T---~EmLa 76 (513)
-.|++||+|+-... |....+.|+.|++..++..+. +.--++++........+.-...-|. . ....-
T Consensus 160 ~~~lsfDIEC~~~g~FPs~~~~pvshIs~~~~~~~~~---~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (1004)
T PHA03036 160 RSYLFLDIECHFDKKFPSVFINPVSHISCCYIDLSGK---EKRFTLINEDMLSEDEIEEAVKRGYYEIESLLDMDYSKEL 236 (1004)
T ss_pred ceeEEEEEEeccCCCCCCcccCcceEEEEEEEecCCC---eeEEEEeccccccccccccceeeeeeccccccccCCceee
Confidence 46999999987521 113668899999866665532 2233566653311111111111121 1 01111
Q ss_pred CCCCHHHHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCCC--------------------------------
Q 010297 77 SSPTFADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRPA-------------------------------- 121 (513)
Q Consensus 77 ~Apsf~EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~~-------------------------------- 121 (513)
--++..+ +-+|.+++. -.+++|+|+..||++.|...+..+..+.
T Consensus 237 ~~~sE~~-ml~~~~~i~~~d~D~i~~yNg~nFD~~Yi~~R~~~L~~~~~~~~~~~~~~~~~~~v~~r~~~s~~~~gg~~~ 315 (1004)
T PHA03036 237 ILCSEIV-LLRIAKKLLELEFDYVVTFNGHNFDLRYISNRLELLTGEKIIFRSPDGKETVHLCIYERNLSSHKGVGGVAN 315 (1004)
T ss_pred ecCCHHH-HHHHHHHHHhcCCCEEEeccCCCcchHHHHHHHHHhccCceeeccCCCcccccceeeccccccccccCcccc
Confidence 1234455 446666665 4699999999999999987777652200
Q ss_pred -----C--CCCcceeHHHHHHHHhcCCCCCCCHHHHHHH
Q 010297 122 -----P--EPKGTIDSLALLTQRFGRRAGDMKMASLATY 153 (513)
Q Consensus 122 -----p--~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~ 153 (513)
. .....+|.+.+.++.+ .+.+|+|+++++.
T Consensus 316 ~t~~i~~~~G~i~fDLy~~i~k~~--~L~sYkL~~Vsk~ 352 (1004)
T PHA03036 316 TTYHINNNNGTIFFDLYTFIQKTE--KLDSYKLDSISKN 352 (1004)
T ss_pred ceEEecccCCeEEEEhHHHHhhhc--CcccccHHHHHHH
Confidence 0 1124788888887543 5689999999998
No 96
>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=93.32 E-value=3.1 Score=38.56 Aligned_cols=104 Identities=11% Similarity=0.067 Sum_probs=66.2
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHH
Q 010297 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADT 87 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~e 87 (513)
.+.+.+|+|++|.++ ....++-|+ +..+. . ..+|.+.. . + .+...
T Consensus 3 ~~~~~~~~~~~~~~~--~~~~l~~i~---l~~~~----~--~~~i~~~~--~----------~------------~~~~~ 47 (178)
T cd06140 3 ADEVALYVELLGENY--HTADIIGLA---LANGG----G--AYYIPLEL--A----------L------------LDLAA 47 (178)
T ss_pred CCceEEEEEEcCCCc--ceeeEEEEE---EEeCC----c--EEEEeccc--h----------H------------HHHHH
Confidence 467899999999875 344444333 22221 1 13444332 1 0 13445
Q ss_pred HHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh
Q 010297 88 VFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF 154 (513)
Q Consensus 88 f~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f 154 (513)
|.+++.+ ...++||+ .+|+.+|. ++|+..+. ...||+-.+. .+.|...++++.++++.|
T Consensus 48 l~~~l~~~~~~ki~~d~-K~~~~~l~----~~gi~~~~--~~fDt~laaY-LL~p~~~~~~l~~l~~~y 108 (178)
T cd06140 48 LKEWLEDEKIPKVGHDA-KRAYVALK----RHGIELAG--VAFDTMLAAY-LLDPTRSSYDLADLAKRY 108 (178)
T ss_pred HHHHHhCCCCceeccch-hHHHHHHH----HCCCcCCC--cchhHHHHHH-HcCCCCCCCCHHHHHHHH
Confidence 6667764 46899999 99998875 46777553 3689988664 667765557999998865
No 97
>PRK05761 DNA polymerase I; Reviewed
Probab=92.91 E-value=0.48 Score=55.28 Aligned_cols=96 Identities=15% Similarity=0.265 Sum_probs=67.3
Q ss_pred CCHHHHHHHHHHHHcC-CeEEEeCcchHHHHHHHHHHHHcCCCCCCCC-------cceeHHHHHHHH----h--cCCC--
Q 010297 79 PTFADIADTVFDILHG-RIWAGHNILRFDCARIREAFAEIGRPAPEPK-------GTIDSLALLTQR----F--GRRA-- 142 (513)
Q Consensus 79 psf~EVl~ef~efL~g-~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~-------~~IDTL~Lar~~----l--~prl-- 142 (513)
.+..+.+.+|.+|+.. .+.|.+|+..||+++|...+.++|+...... ..+|....++.. + ..+.
T Consensus 208 ~~E~eLL~~f~~~i~~~dPdi~yN~~~FDlPYL~~Ra~~lgi~~~~~~~~~~~~~~~iDl~~~~~~~~~~~y~~~~~~~~ 287 (787)
T PRK05761 208 DSEKELLAELFDIILEYPPVVTFNGDNFDLPYLYNRALKLGIPKEEIPIEPGRAGIHIDLYKFFQNKAVRSYAFYGKYRH 287 (787)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEcCCcchHHHHHHHHHHhCCCchhcccccCCCceEEechhheeecceeeeeccceeec
Confidence 6778899999999984 5777799999999999999999998744111 126665554311 1 1222
Q ss_pred CCCCHHHHHH-HhCCCC-CC-------------CChHHHHHHHHHHH
Q 010297 143 GDMKMASLAT-YFGLGQ-QT-------------HRSLDDVRMNLEVL 174 (513)
Q Consensus 143 ~s~kL~~LAk-~fGI~~-~a-------------HRALdDA~aTA~Ll 174 (513)
.+++|+..++ ++|.+. .. .=.+.||..+.+++
T Consensus 288 ~~ysL~~Va~~~Lg~~K~~~~~~i~~~~~~~l~~Y~l~Da~l~~~L~ 334 (787)
T PRK05761 288 REARLDAVGRALLGISKVELETNISELDLEELAEYNFRDAEITLKLT 334 (787)
T ss_pred ccCChHHHHHHHhCCCcccccccccccCHHHHHHHHHHHHHHHHHHH
Confidence 3789999999 667653 11 12478999998874
No 98
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=92.87 E-value=0.15 Score=52.55 Aligned_cols=151 Identities=16% Similarity=0.069 Sum_probs=95.2
Q ss_pred CCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCC--CHHHHHHHHHHHHcC-------C
Q 010297 25 QRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSP--TFADIADTVFDILHG-------R 95 (513)
Q Consensus 25 ~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Ap--sf~EVl~ef~efL~g-------~ 95 (513)
+++.+++|.+--+...+ ...+..++++.. ++....-.+ +++|...++ ...+...-|..+.+. .
T Consensus 128 g~~~dfpil~qela~lg---~~lpq~lvcvds---lpa~~ald~--a~s~~tr~~~~~~~~l~~If~ry~~q~eppa~~~ 199 (318)
T KOG4793|consen 128 GNEYDFPILAQELAGLG---YSLPQDLVCVDS---LPALNALDR--ANSMVTRPEVRRMYSLGSIFLRYVEQREPPAGHV 199 (318)
T ss_pred CCccccHHHHHHHHhcC---ccchhhhcCcch---hHHHHHHhh--hcCcccCCCCCcccccchHHHhhhcccCCCccee
Confidence 44555666555444442 234556777764 332222222 445554432 222222224444442 2
Q ss_pred eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHh---cCC-CCCCCHHHHHHHhCCC--CCCCChHHHHHH
Q 010297 96 IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRF---GRR-AGDMKMASLATYFGLG--QQTHRSLDDVRM 169 (513)
Q Consensus 96 vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l---~pr-l~s~kL~~LAk~fGI~--~~aHRALdDA~a 169 (513)
..+.||+..|+..|..+++-|.+-+.+.++..++-|-+++... .|+ ...++|..|+.|+... ..+|||+.|+.+
T Consensus 200 ~e~d~~~l~~~fqf~~~ellR~~deqa~pw~~ir~l~~~~~~a~~~~P~p~~vs~le~Lat~~~~~p~l~ahra~~Dv~~ 279 (318)
T KOG4793|consen 200 AEGDVNGLLFIFQFRINELLRWSDEQARPWLLIRPLYLARENAKSVEPTPKLVSSLEALATYYSLTPELDAHRALSDVLL 279 (318)
T ss_pred eecccchhHHHHHHHHHHHHhhHhhcCCCcccccchhhhhhhccccCCCCccchhHHHHHHHhhcCcccchhhhccccch
Confidence 4456888899999999999888766555556777777655433 232 2477899999999876 589999999999
Q ss_pred HHHHHHHHHHHhhc
Q 010297 170 NLEVLKYCATVLFL 183 (513)
Q Consensus 170 TA~Ll~~ll~~L~~ 183 (513)
+-++++++-..++.
T Consensus 280 ~~k~~q~~~idlla 293 (318)
T KOG4793|consen 280 LSKVFQKLTIDLLA 293 (318)
T ss_pred hhhHHHHhhhhhhh
Confidence 99999998776654
No 99
>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=92.83 E-value=1.5 Score=42.39 Aligned_cols=139 Identities=13% Similarity=0.139 Sum_probs=83.9
Q ss_pred CCCCcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 5 QDRSEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 5 ~~~~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
.+...++.||+|++++... ..-.+|+|+.- .+.. .++.+.. +. . ..+
T Consensus 7 l~~~~~i~~D~E~~~~~~~-~~~~LiQia~~---~~~v-------~l~D~~~---~~-------~---------~~~--- 53 (197)
T cd06148 7 LKKQKVIGLDCEGVNLGRK-GKLCLVQIATR---TGQI-------YLFDILK---LG-------S---------IVF--- 53 (197)
T ss_pred hhhCCEEEEEcccccCCCC-CCEEEEEEeeC---CCcE-------EEEEhhh---cc-------c---------hhH---
Confidence 4568899999999988652 24455666532 1211 3444432 00 0 011
Q ss_pred HHHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCC-------CCCCHHHHHHHh-
Q 010297 85 ADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRA-------GDMKMASLATYF- 154 (513)
Q Consensus 85 l~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl-------~s~kL~~LAk~f- 154 (513)
...+.+++.+ ...|+|++ .+|..+|.+ .+|+... .++||.-.+. .+.+.. ...+|..+++.|
T Consensus 54 ~~~L~~iLe~~~i~Kv~h~~-k~D~~~L~~---~~gi~~~---~~fDt~iA~~-lL~~~~~~~~~~~~~~~L~~l~~~~l 125 (197)
T cd06148 54 INGLKDILESKKILKVIHDC-RRDSDALYH---QYGIKLN---NVFDTQVADA-LLQEQETGGFNPDRVISLVQLLDKYL 125 (197)
T ss_pred HHHHHHHhcCCCccEEEEec-hhHHHHHHH---hcCcccc---ceeeHHHHHH-HHHHHhcCCccccccccHHHHHHHhh
Confidence 2345555653 35699999 999998743 4476532 3589876543 333211 134788887764
Q ss_pred CCC-------------------------CCCCChHHHHHHHHHHHHHHHHHhhcc
Q 010297 155 GLG-------------------------QQTHRSLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 155 GI~-------------------------~~aHRALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
|++ .+-+=|..||..+..++..+...+...
T Consensus 126 ~~~~~k~~~~~~~~~~~~s~W~~RPLt~~ql~YAa~Dv~~Ll~l~~~l~~~l~~~ 180 (197)
T cd06148 126 YISISLKEDVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLDALISK 180 (197)
T ss_pred CCChHHHHHHHHHHhcCchhhhcCCCCHHHHHHHHHHHHhHHHHHHHHHHHhhhh
Confidence 432 123457889999999999998887654
No 100
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=92.04 E-value=2.2 Score=38.29 Aligned_cols=88 Identities=17% Similarity=0.245 Sum_probs=56.1
Q ss_pred HHHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC-CC-
Q 010297 85 ADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG-QQ- 159 (513)
Q Consensus 85 l~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~-~~- 159 (513)
...+.+++.+ ...|+||+ .+|+.+|+ ++|+... .++||+-.+. .+.|....++|..+++.| |.. ..
T Consensus 64 ~~~l~~~l~~~~~~kv~~d~-k~~~~~L~----~~gi~~~---~~~D~~laay-ll~p~~~~~~l~~l~~~~l~~~~~~~ 134 (172)
T smart00474 64 LEILKDLLEDETITKVGHNA-KFDLHVLA----RFGIELE---NIFDTMLAAY-LLLGGPSKHGLATLLKEYLGVELDKE 134 (172)
T ss_pred HHHHHHHhcCCCceEEEech-HHHHHHHH----HCCCccc---chhHHHHHHH-HHcCCCCcCCHHHHHHHHhCCCCCcc
Confidence 3446666663 46899999 99999986 3677654 2489987665 455654446999998876 443 11
Q ss_pred -----------CC----ChHHHHHHHHHHHHHHHHHh
Q 010297 160 -----------TH----RSLDDVRMNLEVLKYCATVL 181 (513)
Q Consensus 160 -----------aH----RALdDA~aTA~Ll~~ll~~L 181 (513)
.. -|..||..+.+++..+.+++
T Consensus 135 ~~~~~~~~~~l~~~~~~ya~~~a~~~~~L~~~l~~~l 171 (172)
T smart00474 135 EQKSDWGARPLSEEQLQYAAEDADALLRLYEKLEKEL 171 (172)
T ss_pred cCccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 00 14555666666666655543
No 101
>KOG0969 consensus DNA polymerase delta, catalytic subunit [Replication, recombination and repair]
Probab=89.98 E-value=0.073 Score=61.05 Aligned_cols=145 Identities=14% Similarity=0.187 Sum_probs=85.7
Q ss_pred CcEEEEEEecCCCCC---CCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHH
Q 010297 8 SEIAFFDVETTVPTR---PGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADI 84 (513)
Q Consensus 8 ~~~VVfDlETTGLd~---~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EV 84 (513)
-++.-||+|+.|-.+ ....|.||+||-+..--|..+. |...|---. ...+|.--+|-......++
T Consensus 274 lrvlSfDIECagrkg~FPe~~~DPvIQIan~v~~~Ge~~p---f~rnvf~l~---------~capI~G~~V~~~~~e~el 341 (1066)
T KOG0969|consen 274 LRVLSFDIECAGRKGVFPEAKIDPVIQIANLVTLQGENEP---FVRNVFTLK---------TCAPIVGSNVHSYETEKEL 341 (1066)
T ss_pred ccccceeEEeccCCCCCCccccChHHHHHHHHHHhcCCch---HHHhhhccc---------CcCCCCCceeEEeccHHHH
Confidence 356789999998432 1267889999977665552221 211111000 1235555555444455555
Q ss_pred HHHHHHH---HcCCeEEEeCcchHHHHHHHHHHHHcCCCCCCC---------------------------------Ccce
Q 010297 85 ADTVFDI---LHGRIWAGHNILRFDCARIREAFAEIGRPAPEP---------------------------------KGTI 128 (513)
Q Consensus 85 l~ef~ef---L~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~---------------------------------~~~I 128 (513)
+.....| +.-.+++|+|+..||++.|-...+.+|++.... .-.+
T Consensus 342 L~~W~~firevDPDvI~GYNi~nFDiPYll~RA~~L~Ie~Fp~LGRikn~~s~irDttfSSkq~GtRetK~v~I~GRlqf 421 (1066)
T KOG0969|consen 342 LESWRKFIREVDPDVIIGYNICNFDIPYLLNRAKTLGIENFPYLGRIKNSRSVIRDSTFSSKQYGTRETKEVNIDGRLQF 421 (1066)
T ss_pred HHHHHHHHHhcCCCeEecccccccccceecChHhhcCcccccccceecccceeeeccccchhhcCcccceEEeecceeee
Confidence 5544444 557899999999999998876666666652211 1234
Q ss_pred eHHHHHHHHhcCCCCCCCHHHHHHHhCCC---CCCCChHHH
Q 010297 129 DSLALLTQRFGRRAGDMKMASLATYFGLG---QQTHRSLDD 166 (513)
Q Consensus 129 DTL~Lar~~l~prl~s~kL~~LAk~fGI~---~~aHRALdD 166 (513)
|.+....+-+ .+.+|+|+....+|=-+ ..||.-+.|
T Consensus 422 Dllqvi~Rd~--KLrSytLNaVs~hFL~EQKEDV~~siItd 460 (1066)
T KOG0969|consen 422 DLLQVILRDY--KLRSYTLNAVSAHFLGEQKEDVHHSIITD 460 (1066)
T ss_pred hHHHHHHHhh--hhhhcchhhhHHHhhhhhcccccccchhh
Confidence 5555443322 35789999998877332 367766544
No 102
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=87.57 E-value=5.1 Score=45.55 Aligned_cols=134 Identities=17% Similarity=0.248 Sum_probs=85.9
Q ss_pred cEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCCCChhhHHhhCCCHHHHcCCCCHHHHHHHH
Q 010297 9 EIAFFDVETTVPTRPGQRFAILEFGAILVCPKKLEELHNYSTLVRPADPELISSLSVRCNGITPDAVVSSPTFADIADTV 88 (513)
Q Consensus 9 ~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~I~~~~teIhGIT~EmLa~Apsf~EVl~ef 88 (513)
..+.+|+||+|+++ ....++-+++..-. ...+|.-.. + ++. -++...+
T Consensus 23 ~~~a~~~et~~l~~--~~~~lvg~s~~~~~---------~~~yi~~~~------------~--~~~-------~~~~~~l 70 (593)
T COG0749 23 ANIAFDTETDGLDP--HGADLVGLSVASEE---------EAAYIPLLH------------G--PEQ-------LNVLAAL 70 (593)
T ss_pred ccceeeccccccCc--ccCCeeEEEeeccc---------cceeEeecc------------c--hhh-------hhhHHHH
Confidence 34899999999998 34556655553222 112222111 1 111 1177788
Q ss_pred HHHHcCC--eEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCCCC------
Q 010297 89 FDILHGR--IWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLGQQ------ 159 (513)
Q Consensus 89 ~efL~g~--vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~~~------ 159 (513)
..|+... ..++||. .||+.+|.+ +|+. .....||+-... .+.+..+.+.|++|+++| +....
T Consensus 71 ~~~l~~~~~~kv~~~~-K~d~~~l~~----~Gi~---~~~~~DtmlasY-ll~~~~~~~~~~~l~~r~l~~~~~~~~~i~ 141 (593)
T COG0749 71 KPLLEDEGIKKVGQNL-KYDYKVLAN----LGIE---PGVAFDTMLASY-LLNPGAGAHNLDDLAKRYLGLETITFEDIA 141 (593)
T ss_pred HHHhhCcccchhcccc-chhHHHHHH----cCCc---ccchHHHHHHHh-ccCcCcCcCCHHHHHHHhcCCccchhHHhh
Confidence 9999854 5899999 999998864 4644 224788887543 456677789999999988 32210
Q ss_pred -----------------CCChHHHHHHHHHHHHHHHHHhhc
Q 010297 160 -----------------THRSLDDVRMNLEVLKYCATVLFL 183 (513)
Q Consensus 160 -----------------aHRALdDA~aTA~Ll~~ll~~L~~ 183 (513)
.-.+..||..+.++..++...+..
T Consensus 142 ~kg~~~~~~~~~~~~~~~~y~a~~a~~~~~L~~~l~~~l~~ 182 (593)
T COG0749 142 GKGKKQLTFADVKLEKATEYAAEDADATLRLESILEPELLK 182 (593)
T ss_pred ccccccCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 223567888888888887765443
No 103
>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=86.39 E-value=9.5 Score=34.96 Aligned_cols=90 Identities=20% Similarity=0.232 Sum_probs=59.2
Q ss_pred HHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC---CC
Q 010297 86 DTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG---QQ 159 (513)
Q Consensus 86 ~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~---~~ 159 (513)
..|.+++.+ ...|+||+ .+|+..|.+.+ |+. .. .++||+-.+ ..+.|... ++|.++++.| |.. ..
T Consensus 54 ~~l~~ll~~~~i~kv~~d~-K~~~~~L~~~~---gi~-~~--~~~D~~laa-yLl~p~~~-~~l~~l~~~~l~~~~~~~~ 124 (178)
T cd06142 54 SPLKELLADPNIVKVFHAA-REDLELLKRDF---GIL-PQ--NLFDTQIAA-RLLGLGDS-VGLAALVEELLGVELDKGE 124 (178)
T ss_pred HHHHHHHcCCCceEEEecc-HHHHHHHHHHc---CCC-CC--CcccHHHHH-HHhCCCcc-ccHHHHHHHHhCCCCCccc
Confidence 345566664 46899999 99999886433 776 32 478997554 36666544 5999998864 553 10
Q ss_pred -----C---------CChHHHHHHHHHHHHHHHHHhhcc
Q 010297 160 -----T---------HRSLDDVRMNLEVLKYCATVLFLE 184 (513)
Q Consensus 160 -----a---------HRALdDA~aTA~Ll~~ll~~L~~~ 184 (513)
. +-|..||.++.+++..+.+++...
T Consensus 125 ~~~~w~~~~l~~~~~~yaa~~a~~l~~L~~~l~~~L~e~ 163 (178)
T cd06142 125 QRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELEEE 163 (178)
T ss_pred ccccCCCCCCCHHHHHHHHHhHHHHHHHHHHHHHHHHHc
Confidence 0 125666777888888877776553
No 104
>PHA02563 DNA polymerase; Provisional
Probab=82.29 E-value=9.4 Score=43.86 Aligned_cols=34 Identities=24% Similarity=0.223 Sum_probs=27.4
Q ss_pred HHHHHHHHc-------CCeEEEeCcchHHHHHHHHHHHHcCC
Q 010297 85 ADTVFDILH-------GRIWAGHNILRFDCARIREAFAEIGR 119 (513)
Q Consensus 85 l~ef~efL~-------g~vLVAHNa~~FD~~FL~~~f~r~Gi 119 (513)
+++|++|+. +.++..||. .||..||...+-+.+.
T Consensus 50 ~~~f~~~i~~~~~k~~~~~vYfHN~-~FD~~Fil~~L~~~~~ 90 (630)
T PHA02563 50 FDEFLQWIEDTTYKETECIIYFHNL-KFDGSFILKWLLRNGF 90 (630)
T ss_pred HHHHHHHHhhccccccceEEEEecC-CccHHHHHHHHHhhcc
Confidence 346777776 568889996 9999999999888764
No 105
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.25 E-value=9.1 Score=45.60 Aligned_cols=93 Identities=12% Similarity=-0.013 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC
Q 010297 81 FADIADTVFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG 157 (513)
Q Consensus 81 f~EVl~ef~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~ 157 (513)
...+...|..++.+ ...++||+ .||+.+|. ++|+.... .+.||+-.+. .+.+... ++|++++..| +..
T Consensus 363 ~~~~~~~l~~~l~~~~~~~v~~n~-K~d~~~l~----~~gi~~~~--~~~Dt~la~y-ll~~~~~-~~l~~la~~yl~~~ 433 (887)
T TIGR00593 363 TILTDDKFARWLLNEQIKKIGHDA-KFLMHLLK----REGIELGG--VIFDTMLAAY-LLDPAQV-STLDTLARRYLVEE 433 (887)
T ss_pred hHHHHHHHHHHHhCCCCcEEEeeH-HHHHHHHH----hCCCCCCC--cchhHHHHHH-HcCCCCC-CCHHHHHHHHcCcc
Confidence 34566778888875 35899999 99999986 56877543 4789998765 5666544 5999998876 321
Q ss_pred --------CC------------CCChHHHHHHHHHHHHHHHHHhh
Q 010297 158 --------QQ------------THRSLDDVRMNLEVLKYCATVLF 182 (513)
Q Consensus 158 --------~~------------aHRALdDA~aTA~Ll~~ll~~L~ 182 (513)
.. ...|..||..+.+++..+..++.
T Consensus 434 ~~~~~~~~~~~~~~~~~~~~~~~~ya~~d~~~~~~L~~~l~~~l~ 478 (887)
T TIGR00593 434 LILDEKIGGKLAKFAFPPLEEATEYLARRAAATKRLAEELLKELD 478 (887)
T ss_pred cccHHHhccCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 00 01367788899999988877764
No 106
>PF13017 Maelstrom: piRNA pathway germ-plasm component
Probab=75.18 E-value=2.4 Score=41.95 Aligned_cols=95 Identities=9% Similarity=0.088 Sum_probs=60.9
Q ss_pred CCcEEEEEEEEEeCCceeEeeeEEEEEcCCCCCC-----CChhhHHhhCCCHHHHcCCC-CHHHHHHHHHHHHcC-----
Q 010297 26 RFAILEFGAILVCPKKLEELHNYSTLVRPADPEL-----ISSLSVRCNGITPDAVVSSP-TFADIADTVFDILHG----- 94 (513)
Q Consensus 26 ~deIIEIGAV~Vd~g~~eivdsFs~lIrP~~~~~-----I~~~~teIhGIT~EmLa~Ap-sf~EVl~ef~efL~g----- 94 (513)
..-.+|||++.+.-..+ +++.|+.+|+|..... .-..+...|+|..+-.+.+. .+..++.++.+||+.
T Consensus 7 ~y~PaEiai~~fSL~~G-I~~~~H~~I~Pg~~p~G~~~~a~~hs~~tH~ip~~~~~~~~~d~~~l~~~l~~fl~~~~~~~ 85 (213)
T PF13017_consen 7 EYVPAEIAICKFSLKEG-IIDSFHTFINPGQIPLGYRYDAQHHSDETHQIPIPPNALGESDYSELYNELLNFLKPNKGGE 85 (213)
T ss_pred cEEeEEEEEEEEecCCc-cchhhhcccCCCCCCcHHHHHHHHhhhhhcCCCCCCcccccCCHHHHHHHHHHHhhhcCCCC
Confidence 45689999999987765 7899999999986211 11223445677766555554 699999999999972
Q ss_pred --CeEEEeCc-chHHHHHHHHHHHHcCCCC
Q 010297 95 --RIWAGHNI-LRFDCARIREAFAEIGRPA 121 (513)
Q Consensus 95 --~vLVAHNa-~~FD~~FL~~~f~r~Gi~~ 121 (513)
.+++.-.- .......|+......+...
T Consensus 86 ~~~~i~~~~~~~~~V~~cl~~La~~a~~~~ 115 (213)
T PF13017_consen 86 KMPPIFTKRDQIPRVQSCLKWLAKKAGEDN 115 (213)
T ss_pred CcceEEEeHhHHHHHHHHHHHHHHhcCCCc
Confidence 13333222 1333345555555555543
No 107
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=74.84 E-value=11 Score=38.17 Aligned_cols=169 Identities=14% Similarity=0.148 Sum_probs=100.5
Q ss_pred CcEEEEEEecCCCCC-C-C-----------------CCCcEEEEEEEEEeCCceeEee----eEEEEEcCCCCCCCChhh
Q 010297 8 SEIAFFDVETTVPTR-P-G-----------------QRFAILEFGAILVCPKKLEELH----NYSTLVRPADPELISSLS 64 (513)
Q Consensus 8 ~~~VVfDlETTGLd~-~-g-----------------~~deIIEIGAV~Vd~g~~eivd----sFs~lIrP~~~~~I~~~~ 64 (513)
-.+|-+|+|..|.-+ | | ..-.||++|...-+..+..... .|+.-.+|.. .-..++.
T Consensus 42 Yn~vSmdTEFpGvvArPiG~FkSs~dyhYQtlraNVD~LkiIQlGlsLSDe~GN~P~~~sTWQFNF~F~l~~-dmya~ES 120 (299)
T COG5228 42 YNHVSMDTEFPGVVARPIGTFKSSVDYHYQTLRANVDFLKIIQLGLSLSDENGNKPNGPSTWQFNFEFDLKK-DMYATES 120 (299)
T ss_pred CCceeeccccCceeecccccccccchHHHHHHhcccchhhhhheeeeeccccCCCCCCCceeEEEEEecchh-hhcchHH
Confidence 457889999988422 1 1 2235999999988866544322 3444455554 1122233
Q ss_pred HHh---hCCCHHHHcC-CCCHHHHHHHHHHHHc--------CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHH
Q 010297 65 VRC---NGITPDAVVS-SPTFADIADTVFDILH--------GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLA 132 (513)
Q Consensus 65 teI---hGIT~EmLa~-Apsf~EVl~ef~efL~--------g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~ 132 (513)
.++ .||.-+.=++ +.. ..+|-+.+- .-+||.+.. .||.++|-..+-. .+.|.+ .=|-..
T Consensus 121 ieLL~ksgIdFkkHe~~GI~----v~eF~elLm~SGLvm~e~VtWitfHs-aYDfgyLikilt~--~plP~~--~EdFy~ 191 (299)
T COG5228 121 IELLRKSGIDFKKHENLGID----VFEFSELLMDSGLVMDESVTWITFHS-AYDFGYLIKILTN--DPLPNN--KEDFYW 191 (299)
T ss_pred HHHHHHcCCChhhHhhcCCC----HHHHHHHHhccCceeccceEEEEeec-chhHHHHHHHHhc--CCCCcc--HHHHHH
Confidence 322 2555433221 222 123444442 347888888 9999999877643 344432 455555
Q ss_pred HHHHHhcCCC------------CCCCHHHHHHHhCCC--CCCCChHHHHHHHHHHHHHHHHHhhcccCC
Q 010297 133 LLTQRFGRRA------------GDMKMASLATYFGLG--QQTHRSLDDVRMNLEVLKYCATVLFLESSL 187 (513)
Q Consensus 133 Lar~~l~prl------------~s~kL~~LAk~fGI~--~~aHRALdDA~aTA~Ll~~ll~~L~~~~~~ 187 (513)
++.. +.|+. .+-.|.+++.-+++. .+.|.|-.||+.|+..|......++.....
T Consensus 192 ~l~~-yfP~fYDik~v~ks~~~~~KglQei~ndlql~r~g~QhQagsdaLlTa~~ff~~R~~~F~~sig 259 (299)
T COG5228 192 WLHQ-YFPNFYDIKLVYKSVLNNSKGLQEIKNDLQLQRSGQQHQAGSDALLTADEFFLPRFSIFTTSIG 259 (299)
T ss_pred HHHH-HCccccchHHHHHhhhhhhhHHHHhcCcHhhhccchhhhccchhhhhhHHhcchhhheeccccc
Confidence 5543 33421 123466666666775 588999999999999998888777765443
No 108
>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=66.17 E-value=77 Score=30.03 Aligned_cols=88 Identities=10% Similarity=0.080 Sum_probs=57.2
Q ss_pred HHHHHc--CCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC--C----
Q 010297 88 VFDILH--GRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG--Q---- 158 (513)
Q Consensus 88 f~efL~--g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~--~---- 158 (513)
|.+++. +...++||. ..|+..|++ ++|+... + . +|++-.+. .+.|. . +.|..+++.| +.. .
T Consensus 69 L~~~L~~~~i~kv~~d~-K~~~~~L~~---~~gi~~~-~-~-fD~~laaY-LL~p~-~-~~l~~l~~~yl~~~~~k~~~~ 138 (192)
T cd06147 69 LNEVFTDPNILKVFHGA-DSDIIWLQR---DFGLYVV-N-L-FDTGQAAR-VLNLP-R-HSLAYLLQKYCNVDADKKYQL 138 (192)
T ss_pred HHHHhcCCCceEEEech-HHHHHHHHH---HhCCCcC-c-h-HHHHHHHH-HhCCC-c-ccHHHHHHHHhCCCcchhhhc
Confidence 556665 357899999 888888753 4577643 2 3 89988765 67776 4 4999998876 433 0
Q ss_pred ---CCC--------ChHHHHHHHHHHHHHHHHHhhccc
Q 010297 159 ---QTH--------RSLDDVRMNLEVLKYCATVLFLES 185 (513)
Q Consensus 159 ---~aH--------RALdDA~aTA~Ll~~ll~~L~~~~ 185 (513)
..+ -+..||.++.+++..+..++..+.
T Consensus 139 ~~~~~~~l~~~~~~y~a~~a~~l~~L~~~L~~~L~e~~ 176 (192)
T cd06147 139 ADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176 (192)
T ss_pred cccccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHhc
Confidence 111 134456666777777777665543
No 109
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=58.21 E-value=45 Score=30.78 Aligned_cols=57 Identities=12% Similarity=0.102 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHc-C-CeEEEeCcchHHHHHHHHHHHHc---C--CCCCCCCcceeHHHHHHHH
Q 010297 79 PTFADIADTVFDILH-G-RIWAGHNILRFDCARIREAFAEI---G--RPAPEPKGTIDSLALLTQR 137 (513)
Q Consensus 79 psf~EVl~ef~efL~-g-~vLVAHNa~~FD~~FL~~~f~r~---G--i~~p~~~~~IDTL~Lar~~ 137 (513)
.+-.+.++.|.+.++ . ..+|++|. .|....|++..+.. . +... ..+.+|.+.+++..
T Consensus 55 DPr~~~~~~L~~~i~~~~g~ivvyN~-sfE~~rL~ela~~~p~~~~~l~~I-~~r~vDL~~~f~~~ 118 (130)
T PF11074_consen 55 DPRRELIEALIKAIGSIYGSIVVYNK-SFEKTRLKELAELFPDYAEKLNSI-IERTVDLLDPFKNH 118 (130)
T ss_pred CchHHHHHHHHHHhhhhcCeEEEech-HHHHHHHHHHHHHhHHHHHHHHHH-HHHHHHHHHHHhhC
Confidence 455667778888887 4 68999999 99999998755432 0 0000 11477777777653
No 110
>KOG3657 consensus Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair]
Probab=57.37 E-value=8.7 Score=45.25 Aligned_cols=37 Identities=32% Similarity=0.576 Sum_probs=28.6
Q ss_pred cCCeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHH
Q 010297 93 HGRIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALL 134 (513)
Q Consensus 93 ~g~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~La 134 (513)
++.++||||+ .||+..+++++. +.-.. ..++||+.|.
T Consensus 240 ke~liVGHNV-sfDRaRirEeY~---i~~Sk-~rFlDTMSlH 276 (1075)
T KOG3657|consen 240 KEQLIVGHNV-SFDRARIREEYN---INGSK-IRFLDTMSLH 276 (1075)
T ss_pred CCceEEeccc-cchHHHHHHHHh---ccccc-eeeeechhhh
Confidence 4679999999 999999998874 43332 2689998874
No 111
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=53.07 E-value=63 Score=28.48 Aligned_cols=62 Identities=18% Similarity=0.201 Sum_probs=42.1
Q ss_pred HHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh-CCC
Q 010297 88 VFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF-GLG 157 (513)
Q Consensus 88 f~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f-GI~ 157 (513)
+.+++.+ ...++||+ .+|+.+|. +.|+.... ..+||+-.+. .+.|..++.+|..+++.| +..
T Consensus 45 l~~~l~~~~~~kv~~d~-K~~~~~L~----~~~~~~~~--~~~D~~laay-Ll~p~~~~~~l~~l~~~~l~~~ 109 (150)
T cd09018 45 LKPLLEDEKALKVGQNL-KYDRGILL----NYFIELRG--IAFDTMLEAY-ILNSVAGRWDMDSLVERWLGHK 109 (150)
T ss_pred HHHHhcCCCCceeeecH-HHHHHHHH----HcCCccCC--cchhHHHHHH-HhCCCCCCCCHHHHHHHHhCCC
Confidence 5556653 56799999 99999875 34655443 4689988764 566654235999998876 543
No 112
>KOG0970 consensus DNA polymerase alpha, catalytic subunit [Replication, recombination and repair]
Probab=40.47 E-value=1.6e+02 Score=36.60 Aligned_cols=142 Identities=13% Similarity=0.184 Sum_probs=81.8
Q ss_pred CcEEEEEEecCCCCCCCCCCcEEEEEEEEEeCCce-------eEeeeEEEEEcCCCCCCCChhhHHhh--CCCHHHHcCC
Q 010297 8 SEIAFFDVETTVPTRPGQRFAILEFGAILVCPKKL-------EELHNYSTLVRPADPELISSLSVRCN--GITPDAVVSS 78 (513)
Q Consensus 8 ~~~VVfDlETTGLd~~g~~deIIEIGAV~Vd~g~~-------eivdsFs~lIrP~~~~~I~~~~teIh--GIT~EmLa~A 78 (513)
-....|-++|+--.. ....+|+-|++.....-.+ .....|..+++|... .+|-...++- ..+. +.-.
T Consensus 529 l~llsL~i~T~~N~k-~~~~Eiv~is~l~~~~~~id~p~p~~~~~~~~c~l~rP~~~-~fP~g~~ela~~k~~~--v~~~ 604 (1429)
T KOG0970|consen 529 LTLLSLNIRTSMNPK-QNKNEIVMISMLCFHNFSIDKPAPAPAFPRHFCVLTRPPGT-SFPLGLKELAKQKLSK--VVLH 604 (1429)
T ss_pred eeEEEeeeeehhccc-cchhhhhhhhhhhcccccccCCCCCCcccCcceeEecCCCC-cCCchHHHHHHhccCc--eEEe
Confidence 456677788775433 2446788887765553221 124468888899861 2332111211 1111 3333
Q ss_pred CCHHHHHHHHHHHHc---CCeEEEeCcchHHHHHHHHHHHHcCCC-----------CCC--C------------CcceeH
Q 010297 79 PTFADIADTVFDILH---GRIWAGHNILRFDCARIREAFAEIGRP-----------APE--P------------KGTIDS 130 (513)
Q Consensus 79 psf~EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~~f~r~Gi~-----------~p~--~------------~~~IDT 130 (513)
.+....+..|+.-++ -.++||||+..|++..|-..+..+.++ ++. . .+.+|-
T Consensus 605 ~sErALLs~fla~~~~~dpD~iVgHn~~~~~l~VLl~R~~~~Kip~WS~IgRLrrS~~~kfg~~s~~~e~~~~aGRl~CD 684 (1429)
T KOG0970|consen 605 NSERALLSHFLAMLNKEDPDVIVGHNIQGFYLDVLLSRLHALKIPNWSSIGRLRRSWPPKFGRSSSFGEFFIIAGRLMCD 684 (1429)
T ss_pred cCHHHHHHHHHHHhhccCCCEEEEeccccchHHHHHHHHHHhcCcchhhhhhhhhccccccCCcccccccccccceEEee
Confidence 455556667777766 479999997799999997666555544 110 0 123444
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHh
Q 010297 131 LALLTQRFGRRAGDMKMASLATYF 154 (513)
Q Consensus 131 L~Lar~~l~prl~s~kL~~LAk~f 154 (513)
+.++.+-+-+ ..+|.|.+|++..
T Consensus 685 ~~~~a~~lik-~~S~~LseL~q~~ 707 (1429)
T KOG0970|consen 685 LNLAARELIK-AQSYSLSELSQQI 707 (1429)
T ss_pred hHHHHHhhhc-cccccHHHHHHHH
Confidence 4655544433 4689999998754
No 113
>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=29.41 E-value=2.2e+02 Score=25.47 Aligned_cols=59 Identities=22% Similarity=0.288 Sum_probs=40.4
Q ss_pred HHHHHcC--CeEEEeCcchHHHHHHHHHHHHcCCCCCCCCcceeHHHHHHHHhcCCCCCCCHHHHHHHh
Q 010297 88 VFDILHG--RIWAGHNILRFDCARIREAFAEIGRPAPEPKGTIDSLALLTQRFGRRAGDMKMASLATYF 154 (513)
Q Consensus 88 f~efL~g--~vLVAHNa~~FD~~FL~~~f~r~Gi~~p~~~~~IDTL~Lar~~l~prl~s~kL~~LAk~f 154 (513)
|.+|+.+ ...++||. .+++.+| .++|+.... ...|++-.+. .+.|...+..|.++++.|
T Consensus 45 l~~~l~~~~~~ki~~d~-K~~~~~l----~~~gi~l~~--~~fD~~LAaY-LL~p~~~~~~l~~la~~y 105 (151)
T cd06128 45 LKPLLEDEKALKVGQNL-KYDRVIL----ANYGIELRG--IAFDTMLEAY-LLDPVAGRHDMDSLAERW 105 (151)
T ss_pred HHHHHcCCCCCEEeeeh-HHHHHHH----HHCCCCCCC--cchhHHHHHH-HcCCCCCCCCHHHHHHHH
Confidence 5566763 45788998 7777775 466877543 3689886544 567755423999998876
No 114
>TIGR00592 pol2 DNA polymerase (pol2). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.69 E-value=31 Score=42.46 Aligned_cols=38 Identities=16% Similarity=0.160 Sum_probs=29.1
Q ss_pred HcCCCCHHHHHHHHHHHHc---CCeEEEeCcchHHHHHHHH
Q 010297 75 VVSSPTFADIADTVFDILH---GRIWAGHNILRFDCARIRE 112 (513)
Q Consensus 75 La~Apsf~EVl~ef~efL~---g~vLVAHNa~~FD~~FL~~ 112 (513)
+..-++..+.+..|.+++. ..+++|+|+..||++.|..
T Consensus 264 v~~~~~E~~~L~~f~~~i~~~dpdii~gYNi~~FD~pyl~~ 304 (1172)
T TIGR00592 264 VESVSEEISMIKRFWDVIDQEDTDVEITVNGDNFDLVYLAD 304 (1172)
T ss_pred ceeccchHHHHhhHHHHHhhcCcchhcccccccCccceecC
Confidence 3334666777888888876 3589999999999987765
Done!